PeakID (cmd=annotatePeaks.pl ESKM_unique_ESKMvsOSKM-D3_Manorm_summits_w1000.bed mm10 -m MORE+1_VM_v2.0.mot MORE_VM_v2.0.mot soxoct_VM_2.mot -size -100,100)	Chr	Start	End	Strand	Peak Score	Focus Ratio/Region Size	Annotation	Detailed Annotation	Distance to TSS	Nearest PromoterID	Entrez ID	Nearest Unigene	Nearest Refseq	Nearest Ensembl	Gene Name	Gene Alias	Gene Description	Gene Type	CpG%	GC%	MORE+1_VM_v2 Distance From Peak(sequence,strand,conservation)	MORE_VM_v2 Distance From Peak(sequence,strand,conservation)	soxoct_Marson_VM_soxpartStringent Distance From Peak(sequence,strand,conservation)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7575	chr9	28644421	28644621	+	5.28978	NA	intron (NM_177906, intron 1 of 6)	intron (NM_177906, intron 1 of 6)	240193	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1799	chr12	88340004	88340204	+	4.38958	NA	Intergenic	Intergenic	-18342	NR_003647	266459	Mm.312138	NR_003647		Gm5039	EG266459	eukaryotic translation initiation factor 1A pseudogene	pseudo	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-286	chr1	97004690	97004890	+	4.30474	NA	Intergenic	L2c|LINE|L2	-7230	NR_120500	67854	Mm.263706	NM_026413	ENSMUSG00000045463	Slco6b1	1700022M03Rik	solute carrier organic anion transporter family, member 6b1	ncRNA	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5557	chr4	79110724	79110924	+	4.18563	NA	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	516777	NR_131142	623726		NR_131142		A430085M09Rik	EG623726	RIKEN cDNA A430085M09 gene	ncRNA	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6733	chr6	137262141	137262341	+	4.09630	NA	intron (NM_001164401, intron 1 of 25)	intron (NM_001164401, intron 1 of 25)	9942	NM_001164401	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-388	chr1	134901086	134901286	+	3.96205	NA	intron (NM_001368829, intron 1 of 22)	intron (NM_001368829, intron 1 of 22)	45113	NR_162775	114482779		NR_162775		Mir5104b	mmu-mir-5104b	microRNA mir-5104b	ncRNA	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6682	chr6	116068087	116068287	+	3.96157	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	-11176	NM_001364577	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8077	chrX	129975982	129976182	+	3.96157	NA	intron (NM_172493, intron 17 of 26)	intron (NM_172493, intron 17 of 26)	226340	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding	0.015000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-595	chr1	182575155	182575355	+	3.91430	NA	intron (NM_130890, intron 2 of 20)	intron (NM_130890, intron 2 of 20)	10248	NM_001145806	170725	Mm.189201	NM_130890	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding	0.015000	0.393035			12(GAATTCTTATGATAAT,+,0.00),41(ATTTAAAAAACAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4118	chr19	50244423	50244623	+	3.90274	NA	intron (NM_001360457, intron 9 of 26)	intron (NM_001360457, intron 9 of 26)	434123	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1080	chr10	118306133	118306333	+	3.88449	NA	Intergenic	Intergenic	-11195	NM_054079	116849	Mm.213193	NM_054079	ENSMUSG00000090461	Iltifb	IL-22b|IL-TIFb|Il22b	interleukin 10-related T cell-derived inducible factor beta	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6651	chr6	107356196	107356396	+	3.88449	NA	Intergenic	Intergenic	-173430	NM_008516	16979	Mm.428543	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	leucine rich repeat protein 1, neuronal	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-285	chr1	97004468	97004668	+	3.85054	NA	Intergenic	Intergenic	-7008	NR_120500	67854	Mm.263706	NM_026413	ENSMUSG00000045463	Slco6b1	1700022M03Rik	solute carrier organic anion transporter family, member 6b1	ncRNA	0.005000	0.323383			-50(ACATTGGCATGTACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1079	chr10	118305867	118306067	+	3.85054	NA	Intergenic	Intergenic	-10929	NM_054079	116849	Mm.213193	NM_054079	ENSMUSG00000090461	Iltifb	IL-22b|IL-TIFb|Il22b	interleukin 10-related T cell-derived inducible factor beta	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7496	chr8	127535943	127536143	+	3.82938	NA	intron (NM_001363431, intron 22 of 24)	intron (NM_001363431, intron 22 of 24)	236431	NM_001013581	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7495	chr8	127535569	127535769	+	3.80881	NA	intron (NM_001363431, intron 22 of 24)	intron (NM_001363431, intron 22 of 24)	236057	NM_001013581	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1052	chr10	115198952	115199152	+	3.78731	NA	3' UTR (NM_025706, exon 17 of 17)	3' UTR (NM_025706, exon 17 of 17)	-14030	NM_173391	216343	Mm.31597	NM_173391	ENSMUSG00000006764	Tph2	AU043594|Ntph	tryptophan hydroxylase 2	protein-coding	0.010000	0.308458			69(AATTTGTATTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6344	chr6	19919883	19920083	+	3.74351	NA	Intergenic	Intergenic	364641	NR_105789	102465192		NR_105789	ENSMUSG00000099149	Mir6370	Gm27480|mmu-mir-6370	microRNA 6370	ncRNA	0.005000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2570	chr14	77584087	77584287	+	3.74351	NA	intron (NM_172813, intron 10 of 18)	intron (NM_172813, intron 10 of 18)	-77319	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3499	chr17	46988824	46989024	+	3.72342	NA	intron (NM_146078, intron 4 of 46)	intron (NM_146078, intron 4 of 46)	21608	NM_146078	224826	Mm.28234	NM_146078	ENSMUSG00000023977	Ubr2	9930021A08Rik|AI462103|AW540746|E130209G04Rik|mKIAA0349	ubiquitin protein ligase E3 component n-recognin 2	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6726	chr6	135543945	135544145	+	3.70595	NA	Intergenic	Intergenic	-114868	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6414	chr6	40024076	40024276	+	3.70124	NA	intron (NM_001360978, intron 2 of 3)	Tigger19a|DNA|TcMar-Tigger	-86077	NM_001004182	434008	Mm.53915	NM_001004182	ENSMUSG00000057716	Tmem178b	A930009E05Rik|EG434008|Gm5567	transmembrane protein 178B	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6541	chr6	79454234	79454434	+	3.65579	NA	Intergenic	Intergenic	-363697	NM_001190732	100463512	Mm.461086	NM_001190732	ENSMUSG00000096887	Gm20594	Mtrnr2l	predicted gene, 20594	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4483	chr2	103118333	103118533	+	3.63950	NA	Intergenic	Intergenic	44758	NM_001355473	56369	Mm.24772	NM_019735	ENSMUSG00000010911	Apip	APIP2|CGI-29|Mmrp19	APAF1 interacting protein	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5881	chr5	28340734	28340934	+	3.63506	NA	intron (NM_028234, intron 5 of 18)	intron (NM_028234, intron 5 of 18)	23645	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding	0.000000	0.263682			72(ATTTAAAAAAAAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-239	chr1	84557267	84557467	+	3.63101	NA	intron (NM_152915, intron 4 of 12)	intron (NM_152915, intron 4 of 12)	-138472	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4466	chr2	96426290	96426490	+	3.62767	NA	intron (NM_001363047, intron 1 of 8)	MLT1B|LTR|ERVL-MaLR	108221	NM_001289743	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4465	chr2	96426077	96426277	+	3.62767	NA	intron (NM_001363047, intron 1 of 8)	intron (NM_001363047, intron 1 of 8)	108008	NM_001289743	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.005000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3389	chr16	94207548	94207748	+	3.62767	NA	intron (NM_139145, intron 6 of 10)	intron (NM_139145, intron 6 of 10)	82643	NM_001360045	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1540	chr12	12289815	12290015	+	3.54479	NA	intron (NM_029758, intron 2 of 12)	intron (NM_029758, intron 2 of 12)	27738	NM_001364432	76820	Mm.440802	NM_029758	ENSMUSG00000020589	Fam49a	2410157M17Rik|9630047E15|D12Ertd553e	family with sequence similarity 49, member A	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6141	chr5	107541700	107541900	+	3.54479	NA	intron (NM_175241, intron 2 of 6)	intron (NM_175241, intron 2 of 6)	7080	NM_182745	76421	Mm.67037	NM_175241	ENSMUSG00000089798	1700028K03Rik	-	RIKEN cDNA 1700028K03 gene	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4532	chr2	115417718	115417918	+	3.54479	NA	Intergenic	Intergenic	-73538	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	ncRNA	0.010000	0.417910			-2(ATTTCCAGGACAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-353	chr1	126083811	126084011	+	3.51869	NA	intron (NM_172484, intron 8 of 14)	intron (NM_172484, intron 8 of 14)	-170983	NM_001311089	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding	0.015000	0.383085			28(ATTTACAAAACCAGGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8098	chrX	139703962	139704162	+	3.50692	NA	intron (NM_001081499, intron 2 of 20)	intron (NM_001081499, intron 2 of 20)	19066	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding	0.010000	0.343284			85(ATTTGCACAGCAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8082	chrX	132170970	132171170	+	3.50692	NA	Intergenic	Intergenic	-1516710	NR_153117	102632590	Mm.403836	NR_153117	ENSMUSG00000096978	Gm26851	-	predicted gene, 26851	ncRNA	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6314	chr6	13827724	13827924	+	3.50692	NA	Intergenic	Intergenic	12118	NM_145066	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding	0.000000	0.358209	72(CATGAATTATTTATA,+,0.00),72(CATGAATTATTTATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5512	chr4	64253614	64253814	+	3.50145	NA	TTS (NR_151546)	TTS (NR_151546)	22889	NR_151546	102633436	Mm.411637	NR_151546		Gm11217	-	predicted gene 11217	ncRNA	0.005000	0.308458	64(TATAAATTATTAATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-422	chr1	141365812	141366012	+	3.49278	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-709510	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7958	chrX	46669617	46669817	+	3.48547	NA	Intergenic	LTRIS2|LTR|ERV1	340710	NM_028514	73360	Mm.60929	NM_028514	ENSMUSG00000046615	Actrt1	1700061J02Rik|Arp-T1	actin-related protein T1	protein-coding	0.000000	0.363184			-23(ATATTTTCATTGAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7224	chr8	41404759	41404959	+	3.48410	NA	intron (NM_013522, intron 5 of 8)	Lx6|LINE|L1	12259	NM_013522	14300	Mm.217312	NM_013522	ENSMUSG00000031590	Frg1	-	FSHD region gene 1	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3115	chr16	22895615	22895815	+	3.46267	NA	intron (NM_001276450, intron 4 of 6)	intron (NM_001276450, intron 4 of 6)	-1329	NR_110508	102632430	Mm.474375	NR_110508	ENSMUSG00000116831	Gm30505	-	predicted gene, 30505	ncRNA	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5420	chr4	34752951	34753151	+	3.45777	NA	intron (NM_001033255, intron 1 of 4)	intron (NM_001033255, intron 1 of 4)	3208	NM_001033255	214568	Mm.297405	NM_001033255	ENSMUSG00000071015	Gm136	-	predicted gene 136	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6609	chr6	98497613	98497813	+	3.45672	NA	Intergenic	Intergenic	-154959	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding	0.010000	0.323383			-41(AATTGCAAAATAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5513	chr4	64253859	64254059	+	3.45672	NA	TTS (NR_151546)	TTS (NR_151546)	22644	NR_151546	102633436	Mm.411637	NR_151546		Gm11217	-	predicted gene 11217	ncRNA	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2661	chr14	102343843	102344043	+	3.43819	NA	Intergenic	Intergenic	503320	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding	0.015000	0.303483			-71(ATTTGCAAGATAAGTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4169	chr2	10723886	10724086	+	3.43819	NA	Intergenic	Intergenic	205831	NR_035418	100316831		NR_035418	ENSMUSG00000080594	Mir669h	Mirn669h|mir-669h|mmu-mir-669h	microRNA 669h	ncRNA	0.015000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3691	chr18	6636286	6636486	+	3.42080	NA	intron (NM_027598, intron 9 of 9)	intron (NM_027598, intron 9 of 9)	32757	NM_001362874	70901	Mm.158484	NM_027598	ENSMUSG00000039540	4921524L21Rik	-	RIKEN cDNA 4921524L21 gene	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6498	chr6	65469841	65470041	+	3.41054	NA	Intergenic	MTD|LTR|ERVL-MaLR	88647	NM_175524	243407	Mm.389758	NM_175524	ENSMUSG00000029917	Qrfprl	C130060K24Rik	pyroglutamylated RFamide peptide receptor like	protein-coding	0.005000	0.432836			78(AGTTGAAAAACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1452	chr11	108185670	108185870	+	3.40945	NA	intron (NM_011101, intron 3 of 16)	intron (NM_011101, intron 3 of 16)	158118	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7529	chr9	14485773	14485973	+	3.39091	NA	intron (NM_173433, intron 1 of 1)	L1M5|LINE|L1	14609	NM_173433	244694	Mm.240457	NM_173433	ENSMUSG00000053914	Kdm4d	4932416A15|Jmjd2d	lysine (K)-specific demethylase 4D	protein-coding	0.005000	0.288557			-4(ATATCAATGACAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7163	chr8	16402518	16402718	+	3.39091	NA	intron (NM_053171, intron 7 of 69)	intron (NM_053171, intron 7 of 69)	-233780	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA	0.005000	0.343284			-46(ATTTAAATGGTAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-829	chr10	54602123	54602323	+	3.39091	NA	Intergenic	Intergenic	526301	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7382	chr8	95122030	95122230	+	3.38366	NA	intron (NM_010631, intron 3 of 19)	intron (NM_010631, intron 3 of 19)	-8788	NM_001145832	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6539	chr6	77047785	77047985	+	3.36594	NA	intron (NM_145732, intron 10 of 18)	intron (NM_145732, intron 10 of 18)	-194592	NR_155299	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7621	chr9	42400061	42400261	+	3.36594	NA	promoter-TSS (NM_001324548)	promoter-TSS (NM_001324548)	-232	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2988	chr15	71101796	71101996	+	3.36594	NA	Intergenic	Intergenic	625942	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2509	chr14	61614718	61614918	+	3.35525	NA	intron (NR_028264, intron 5 of 6)	intron (NR_028264, intron 5 of 6)	7361	NM_001039105	328424	Mm.224464	NM_206974	ENSMUSG00000046168	Kcnrg	Clld4|E030012H22Rik|Gm745	potassium channel regulator	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7417	chr8	102335328	102335528	+	3.35525	NA	Intergenic	Intergenic	449683	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2740	chr14	122158371	122158571	+	3.34724	NA	intron (NM_080556, intron 16 of 16)	intron (NM_080556, intron 16 of 16)	-23223	NM_029556	69634	Mm.34608	NM_029556	ENSMUSG00000025545	Clybl	0610033J05Rik|2310014M14Rik|AI256068|Clb	citrate lyase beta like	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5078	chr3	99593292	99593492	+	3.31866	NA	Intergenic	Intergenic	-292025	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding	0.010000	0.343284			-86(ATTTAAATGACACACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-314	chr1	108295221	108295421	+	3.31866	NA	Intergenic	Intergenic	378062	NR_102307	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1250	chr11	39941465	39941665	+	3.31551	NA	Intergenic	Intergenic	-551340	NR_126439	75315	Mm.461295	NR_126439		4930553C11Rik	-	RIKEN cDNA 4930553C11 gene	ncRNA	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-421	chr1	141365366	141365566	+	3.31551	NA	Intergenic	L1MEc|LINE|L1	-709064	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA	0.000000	0.318408	70(CATTAATATTTCATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5702	chr4	115415936	115416136	+	3.31335	NA	intron (NM_172306, intron 4 of 11)	intron (NM_172306, intron 4 of 11)	4412	NM_172306	13118	Mm.448292	NM_172306	ENSMUSG00000078597	Cyp4a12b	BC060945|Cyp4a12	cytochrome P450, family 4, subfamily a, polypeptide 12B	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5554	chr4	77514628	77514828	+	3.31335	NA	intron (NR_160919, intron 4 of 39)	intron (NR_160919, intron 4 of 39)	697014	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.000000	0.243781		62(CAGGAATATGCATC,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6499	chr6	65470418	65470618	+	3.31335	NA	Intergenic	Intergenic	89224	NM_175524	243407	Mm.389758	NM_175524	ENSMUSG00000029917	Qrfprl	C130060K24Rik	pyroglutamylated RFamide peptide receptor like	protein-coding	0.010000	0.383085		-6(ACTTAATATGCATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7825	chr9	94608885	94609085	+	3.30395	NA	Intergenic	RLTR11A|LTR|ERVK	-60907	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2163	chr13	79458884	79459084	+	3.28978	NA	Intergenic	Intergenic	-1260111	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding	0.000000	0.263682		-44(AATGCAAATGCATC,+,0.00),-44(AATGCAAATGCATC,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-430	chr1	143694175	143694375	+	3.28978	NA	intron (NM_145991, intron 3 of 16)	MTD|LTR|ERVL-MaLR	8618	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-573	chr1	177498246	177498446	+	3.28978	NA	Intergenic	Intergenic	52525	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238.|zfp-238	zinc finger and BTB domain containing 18	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5715	chr4	120137826	120138026	+	3.28110	NA	Intergenic	Intergenic	-23280	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding	0.015000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-712	chr10	17395820	17396020	+	3.28110	NA	Intergenic	Intergenic	-300138	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA	0.010000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5647	chr4	100953436	100953636	+	3.26213	NA	intron (NM_198037, intron 7 of 26)	intron (NM_198037, intron 7 of 26)	-115502	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding	0.015000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3795	chr18	37874141	37874341	+	3.26213	NA	intron (NM_001305980, intron 17 of 27)	intron (NM_001305980, intron 17 of 27)	-19581	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4223	chr2	26226106	26226306	+	3.24250	NA	intron (NM_153559, intron 3 of 12)	intron (NM_153559, intron 3 of 12)	11193	NM_001302956	227638	Mm.116769	NM_153559	ENSMUSG00000036327	Qsox2	BC030934|Qscn6l1|Soxn	quiescin Q6 sulfhydryl oxidase 2	protein-coding	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2420	chr14	30470879	30471079	+	3.24250	NA	intron (NM_028981, intron 1 of 46)	intron (NM_028981, intron 1 of 46)	-8586	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	decapping mRNA 1A	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7217	chr8	39951485	39951685	+	3.24250	NA	Intergenic	Lx8b|LINE|L1	-308907	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6444	chr6	52096346	52096546	+	3.22728	NA	Intergenic	Intergenic	-6503	NR_110440	102635415	Mm.333063	NR_110440	ENSMUSG00000085412	Halr1	Gm15055|Haunt|Linchoxa1|linc-Evx1|linc-Hoxa1|linc1547	Hoxa adjacent long noncoding RNA 1	ncRNA	0.000000	0.348259			13(CTTTGCAAGACTAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3004	chr15	80855520	80855720	+	3.20927	NA	intron (NM_177124, intron 1 of 21)	intron (NM_177124, intron 1 of 21)	57010	NM_177124	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4401	chr2	75907460	75907660	+	3.20897	NA	intron (NM_172666, intron 17 of 19)	intron (NM_172666, intron 17 of 19)	30902	NM_028235	72421	Mm.275109	NM_028235	ENSMUSG00000075273	Ttc30b	2510042P03Rik|Tcc30b	tetratricopeptide repeat domain 30B	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2133	chr13	71375544	71375744	+	3.20282	NA	Intergenic	Intergenic	268555	NR_130325	100316804		NR_130325	ENSMUSG00000080580	Mir466f-4	Mirn466f-4|mmu-mir-466f-4	microRNA 466f-4	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-420	chr1	140858330	140858530	+	3.20282	NA	Intergenic	Intergenic	-202028	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4018	chr19	15975844	15976044	+	3.19563	NA	intron (NM_198019, intron 6 of 14)	intron (NM_198019, intron 6 of 14)	9045	NM_198019	208518	Mm.105652	NM_198019	ENSMUSG00000041491	Cep78	5730599I05Rik|D030027P05	centrosomal protein 78	protein-coding	0.005000	0.393035			33(ATTAGCAAACAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4181	chr2	15075591	15075791	+	3.18180	NA	intron (NM_029466, intron 5 of 5)	intron (NM_029466, intron 5 of 5)	20371	NM_029466	75869	Mm.174068	NM_029466	ENSMUSG00000017418	Arl5b	4930587A11Rik|AW146430|Arl8	ADP-ribosylation factor-like 5B	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6619	chr6	101394448	101394648	+	3.17553	NA	Intergenic	Intergenic	-16651	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2576	chr14	78727512	78727712	+	3.16199	NA	intron (NM_001081336, intron 1 of 29)	intron (NM_001081336, intron 1 of 29)	5117	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7083	chr7	129496126	129496326	+	3.16199	NA	Intergenic	Intergenic	-95637	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding	0.020000	0.422886			42(AAATTATCTTTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7304	chr8	68725998	68726198	+	3.15555	NA	intron (NM_001364256, intron 1 of 10)	intron (NM_001364256, intron 1 of 10)	8987	NM_001364256	234356	Mm.334569	NM_172753	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.010000	0.477612			73(GTTTGCATAAGAAACC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2759	chr15	6007002	6007202	+	3.15372	NA	Intergenic	L1_Mus4|LINE|L1	37602	NR_155428	105245876	Mm.128197	NR_155428		Gm41259	-	predicted gene, 41259	ncRNA	0.000000	0.338308			16(TTTTTGCTATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4659	chr2	137509831	137510031	+	3.15372	NA	Intergenic	Intergenic	-393411	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0.020000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7817	chr9	93149141	93149341	+	3.15372	NA	Intergenic	MER5A|DNA|hAT-Charlie	-143508	NR_040756	78349	Mm.52612	NR_040756	ENSMUSG00000100294	1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	ncRNA	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5583	chr4	86786388	86786588	+	3.14835	NA	intron (NM_184088, intron 6 of 31)	intron (NM_184088, intron 6 of 31)	37933	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7792	chr9	86187198	86187398	+	3.14124	NA	Intergenic	L3|LINE|CR1	277618	NM_027394	70348	Mm.53469	NM_027394	ENSMUSG00000032415	Ube2cbp	2610018I03Rik|Ube3d	ubiquitin-conjugating enzyme E2C binding protein	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1472	chr11	112191116	112191316	+	3.13010	NA	Intergenic	Intergenic	520140	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4027	chr19	17210476	17210676	+	3.12387	NA	intron (NM_181348, intron 16 of 19)	intron (NM_181348, intron 16 of 19)	128929	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1045	chr10	114110980	114111180	+	3.11994	NA	Intergenic	Intergenic	690290	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1150	chr11	7739702	7739902	+	3.11994	NA	Intergenic	MER58A|DNA|hAT-Charlie	-525879	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1453	chr11	108185812	108186012	+	3.11193	NA	intron (NM_011101, intron 3 of 16)	intron (NM_011101, intron 3 of 16)	157976	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-811	chr10	49702432	49702632	+	3.10644	NA	intron (NM_001358866, intron 2 of 16)	Lx8b|LINE|L1	85405	NM_001358866	14806	Mm.185993	NM_010349	ENSMUSG00000056073	Grik2	AW124492|C130030K03Rik|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-49	chr1	17892288	17892488	+	3.10644	NA	Intergenic	Intergenic	-164742	NR_130314	102634913	Mm.319094	NR_130314	ENSMUSG00000085125	Gm16070	-	predicted gene 16070	ncRNA	0.010000	0.338308			27(CTCCTGTCATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-124	chr1	43251289	43251489	+	3.09949	NA	Intergenic	Intergenic	-54628	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-125	chr1	43251640	43251840	+	3.09949	NA	Intergenic	Intergenic	-54979	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-199	chr1	69823983	69824183	+	3.09622	NA	Intergenic	Intergenic	-2887	NM_029160	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding	0.020000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4989	chr3	66812309	66812509	+	3.09622	NA	Intergenic	Intergenic	166402	NM_001302358	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding	0.000000	0.278607			-48(GCATTTTTATACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3898	chr18	62985743	62985943	+	3.09385	NA	intron (NM_028017, intron 5 of 11)	MER102c|DNA|hAT-Charlie	7927	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3065	chr15	103396197	103396397	+	3.08786	NA	Intergenic	Intergenic	-29506	NM_010577	16402	Mm.16234	NM_010577	ENSMUSG00000000555	Itga5	Cd49e|Fnra|VLA5	integrin alpha 5 (fibronectin receptor alpha)	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-934	chr10	90906251	90906451	+	3.07660	NA	intron (NM_001359242, intron 5 of 10)	intron (NM_001359242, intron 5 of 10)	76508	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1|AIDA-1b|C030032C09Rik|E530015N03Rik|EB-1|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-34	chr1	13074658	13074858	+	3.04894	NA	Intergenic	Intergenic	52405	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5576	chr4	84671780	84671980	+	3.04894	NA	intron (NM_001369083, intron 1 of 6)	intron (NM_001369083, intron 1 of 6)	3523	NM_001369084	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4515	chr2	109975851	109976051	+	3.03843	NA	intron (NM_172671, intron 2 of 17)	intron (NM_172671, intron 2 of 17)	-41866	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2930	chr15	54105769	54105969	+	3.03627	NA	Intergenic	Intergenic	172615	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5072	chr3	95789200	95789400	+	3.03627	NA	intron (NM_028328, intron 2 of 8)	(CAAAA)n|Simple_repeat|Simple_repeat	29653	NM_001368180	75137	Mm.196275	NM_028328	ENSMUSG00000028106	Rprd2	2810036A19Rik|4930535B03Rik|6720469I21Rik|AL022841|AL022940|AU021304|BB077382|mKIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2599	chr14	85853018	85853218	+	3.03627	NA	Intergenic	Intergenic	-392852	NR_040457	75155	Mm.399239	NR_040457	ENSMUSG00000115271	4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA	0.010000	0.383085	62(CATGATTTATGTATG,+,0.00),62(CATGATTTATGTATG,-,0.00)		-2(TTTTTTTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1241	chr11	37109992	37110192	+	3.03627	NA	Intergenic	Intergenic	-165851	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding	0.000000	0.368159			17(TTTTTGTATTGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2144	chr13	74335503	74335703	+	3.03627	NA	intron (NM_023281, intron 6 of 14)	intron (NM_023281, intron 6 of 14)	14637	NM_023281	66945	Mm.158231	NM_023281	ENSMUSG00000021577	Sdha	1500032O14Rik|2310034D06Rik|4921513A11|C81073|FP|SDH2|SDHF	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5357	chr4	14672730	14672930	+	3.03627	NA	intron (NM_028499, intron 7 of 7)	intron (NM_028499, intron 7 of 7)	-51052	NM_145947	208890	Mm.483839	NM_145947	ENSMUSG00000040569	Slc26a7	-	solute carrier family 26, member 7	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4871	chr3	22108219	22108419	+	3.03627	NA	intron (NM_030732, intron 1 of 15)	intron (NM_030732, intron 1 of 15)	31667	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2700	chr14	115177337	115177537	+	3.03627	NA	intron (NM_175500, intron 2 of 7)	intron (NM_175500, intron 2 of 7)	85222	NM_175500	103978	Mm.320791	NM_175500	ENSMUSG00000022112	Gpc5	A230034F01Rik	glypican 5	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5907	chr5	36662323	36662523	+	3.03188	NA	intron (NM_001081232, intron 2 of 8)	intron (NM_001081232, intron 2 of 8)	33598	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3741	chr18	22478155	22478355	+	3.03188	NA	intron (NM_001167777, intron 9 of 12)	intron (NM_001167777, intron 9 of 12)	133166	NM_001167777	211961	Mm.392310	NM_001167777	ENSMUSG00000045215	Asxl3	C230079D11Rik|D430002O22Rik|D930044O18Rik|Gm329|Gm945	additional sex combs like 3, transcriptional regulator	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3915	chr18	68266005	68266205	+	3.02932	NA	3' UTR (NM_153794, exon 4 of 4)	3' UTR (NM_153794, exon 4 of 4)	-5132	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3009	chr15	86295569	86295769	+	3.02571	NA	intron (NM_001358062, intron 2 of 9)	intron (NM_001358062, intron 2 of 9)	17994	NM_001358062	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6230	chr5	141408975	141409175	+	3.02571	NA	intron (NM_177879, intron 1 of 44)	intron (NM_177879, intron 1 of 44)	167541	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding	0.000000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1344	chr11	72176350	72176550	+	3.02351	NA	intron (NM_001361564, intron 10 of 18)	intron (NM_001361564, intron 10 of 18)	27321	NM_028963	74477	Mm.289697	NM_028963	ENSMUSG00000020807	4933427D14Rik	C85113|Kiaa0753|MNR	RIKEN cDNA 4933427D14 gene	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4182	chr2	15075885	15076085	+	3.02129	NA	intron (NM_029466, intron 5 of 5)	ID_B1|SINE|B4	20665	NM_029466	75869	Mm.174068	NM_029466	ENSMUSG00000017418	Arl5b	4930587A11Rik|AW146430|Arl8	ADP-ribosylation factor-like 5B	protein-coding	0.010000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4191	chr2	17436824	17437024	+	3.01929	NA	intron (NM_001362722, intron 6 of 25)	intron (NM_001362722, intron 6 of 25)	25932	NM_001362722	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6389	chr6	34220207	34220407	+	3.01929	NA	Intergenic	Intergenic	-43253	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1669	chr12	54823035	54823235	+	3.01929	NA	Intergenic	Intergenic	-27473	NM_026998	72183	Mm.28240	NM_026998	ENSMUSG00000005656	Snx6	2010006G21Rik|2610032J07Rik|2810425K19Rik|AU018928|C85963	sorting nexin 6	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-528	chr1	168067214	168067414	+	3.01929	NA	Intergenic	Intergenic	364855	NM_183355	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7216	chr8	39951266	39951466	+	2.98913	NA	Intergenic	Intergenic	-308688	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2245	chr13	99886212	99886412	+	2.98913	NA	Intergenic	MLTR18_MM|LTR|ERVK	14371	NM_013732	27220	Mm.75498	NM_013732	ENSMUSG00000021647	Cartpt	Cart	CART prepropeptide	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2867	chr15	37616793	37616993	+	2.98913	NA	intron (NM_001359844, intron 3 of 7)	intron (NM_001359844, intron 3 of 7)	63681	NM_001359839	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding	0.010000	0.388060			82(GTTAGCATAACAAGGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-406	chr1	138506646	138506846	+	2.98899	NA	intron (NM_021605, intron 7 of 9)	intron (NM_021605, intron 7 of 9)	113011	NM_001311148	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-48	chr1	17891797	17891997	+	2.98899	NA	Intergenic	MIR|SINE|MIR	-164251	NR_130314	102634913	Mm.319094	NR_130314	ENSMUSG00000085125	Gm16070	-	predicted gene 16070	ncRNA	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-527	chr1	168067061	168067261	+	2.98899	NA	Intergenic	Intergenic	365008	NM_183355	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6083	chr5	90280267	90280467	+	2.98569	NA	intron (NM_198010, intron 14 of 32)	intron (NM_198010, intron 14 of 32)	-56371	NR_028088	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding	0.005000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5452	chr4	49283622	49283822	+	2.98569	NA	intron (NM_178756, intron 3 of 7)	intron (NM_178756, intron 3 of 7)	122036	NM_001356289	209186	Mm.35071	NM_145368	ENSMUSG00000060317	Acnat2	C730036D15Rik	acyl-coenzyme A amino acid N-acyltransferase 2	protein-coding	0.020000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6881	chr7	65373559	65373759	+	2.98160	NA	Intergenic	Intergenic	-2415	NM_001163574	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding	0.025000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-180	chr1	61921235	61921435	+	2.97366	NA	intron (NM_001081050, intron 2 of 22)	intron (NM_001081050, intron 2 of 22)	214774	NR_151537	105243940		NR_151537		Pard3bos2	Gm12747	par-3 family cell polarity regulator beta, opposite strand 2	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3916	chr18	68266298	68266498	+	2.96169	NA	3' UTR (NM_153794, exon 4 of 4)	3' UTR (NM_153794, exon 4 of 4)	-5425	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5778	chr4	143127717	143127917	+	2.96134	NA	3' UTR (NM_001256380, exon 8 of 8)	3' UTR (NM_001256380, exon 8 of 8)	8345	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA	0.010000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5616	chr4	94715822	94716022	+	2.96087	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-23367	NM_001290549	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	TEK receptor tyrosine kinase	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-944	chr10	93130116	93130316	+	2.96087	NA	Intergenic	Intergenic	-30660	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding	0.020000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-812	chr10	49702638	49702838	+	2.96087	NA	intron (NM_001358866, intron 2 of 16)	intron (NM_001358866, intron 2 of 16)	85199	NM_001358866	14806	Mm.185993	NM_010349	ENSMUSG00000056073	Grik2	AW124492|C130030K03Rik|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding	0.010000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3845	chr18	50425355	50425555	+	2.96087	NA	Intergenic	Intergenic	143244	NM_026108	67365	Mm.158150	NM_026108	ENSMUSG00000048875	Pudp	1700121L12Rik|GS1|Hdhd1|Hdhd1a	pseudouridine 5-phosphatase	protein-coding	0.000000	0.368159			-85(ATTTGCATGGCAGACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6388	chr6	34219966	34220166	+	2.95803	NA	Intergenic	Intergenic	-43012	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding	0.035000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2268	chr13	106391075	106391275	+	2.95156	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	545783	NM_001360897	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3186	chr16	42178658	42178858	+	2.95156	NA	3' UTR (NM_001347236, exon 7 of 7)	3' UTR (NM_001347236, exon 7 of 7)	124711	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA	0.020000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3432	chr17	15752497	15752697	+	2.95156	NA	intron (NM_007690, intron 23 of 35)	intron (NM_007690, intron 23 of 35)	47630	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding	0.005000	0.318408	-24(TATAAATAATTCATA,+,0.00),-24(TATAAATAATTCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-143	chr1	47864512	47864712	+	2.95156	NA	Intergenic	Intergenic	-397487	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6014	chr5	69600288	69600488	+	2.95156	NA	Intergenic	Intergenic	-8084	NM_001359239	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding	0.010000	0.343284		18(TATCCATATTCATA,+,0.00),18(TATCCATATTCATA,-,0.00)	-99(ATTTAAATCTCAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1345	chr11	72176676	72176876	+	2.94185	NA	exon (NM_028963, exon 10 of 19)	exon (NM_028963, exon 10 of 19)	26995	NM_028963	74477	Mm.289697	NM_028963	ENSMUSG00000020807	4933427D14Rik	C85113|Kiaa0753|MNR	RIKEN cDNA 4933427D14 gene	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3309	chr16	72261713	72261913	+	2.94185	NA	Intergenic	Intergenic	-27486	NR_131115	319533	Mm.373754	NR_131115	ENSMUSG00000116769	8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA	0.020000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4210	chr2	22351129	22351329	+	2.93841	NA	intron (NM_148413, intron 14 of 19)	B4|SINE|B4	123726	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0.005000	0.343284		-60(AATGAACATGCATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-594	chr1	182574782	182574982	+	2.93841	NA	intron (NM_130890, intron 2 of 20)	intron (NM_130890, intron 2 of 20)	9875	NM_001145806	170725	Mm.189201	NM_130890	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2346	chr14	10671945	10672145	+	2.93841	NA	intron (NM_001308285, intron 4 of 9)	intron (NM_001308285, intron 4 of 9)	-66508	NR_131139	547334	Mm.434606	NR_131139	ENSMUSG00000089833	Fhitos	Gm16542	fragile histidine triad gene, opposite strand	ncRNA	0.000000	0.388060			71(ATTAGAATTGCAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4031	chr19	17738475	17738675	+	2.93793	NA	intron (NM_001190483, intron 3 of 37)	RLTR11A|LTR|ERVK	99057	NM_001163144	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding	0.005000	0.383085			-100(GTTTTTTTTTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4238	chr2	29486547	29486747	+	2.93793	NA	intron (NM_001290489, intron 3 of 6)	intron (NM_001290489, intron 3 of 6)	-11353	NR_105753	102465170		NR_105753	ENSMUSG00000098539	Mir133c	Gm27865|mmu-mir-133c	microRNA 133c	ncRNA	0.015000	0.353234			-71(TCATTCTCATTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1830	chr12	96309817	96310017	+	2.93793	NA	Intergenic	Intergenic	-262695	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo	0.025000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6474	chr6	59367300	59367500	+	2.93793	NA	intron (NM_183183, intron 1 of 1)	intron (NM_183183, intron 1 of 1)	58906	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3726	chr18	18580212	18580412	+	2.93578	NA	Intergenic	Intergenic	-999322	NR_045374	75162	Mm.60874	NR_045374	ENSMUSG00000117615	4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	ncRNA	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1800	chr12	88340546	88340746	+	2.93578	NA	Intergenic	Intergenic	-18884	NR_003647	266459	Mm.312138	NR_003647		Gm5039	EG266459	eukaryotic translation initiation factor 1A pseudogene	pseudo	0.020000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7648	chr9	50274659	50274859	+	2.93578	NA	Intergenic	Intergenic	-41577	NR_131161	71873		NR_131161	ENSMUSG00000110916	2310003N18Rik	-	RIKEN cDNA 2310003N18 gene	ncRNA	0.005000	0.338308		46(AATGCAAATTCAAG,-,0.00)	-85(ATTTCCATCATAAAAG,-,0.00),77(TCTGTGTCTTTTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3360	chr16	85812027	85812227	+	2.93404	NA	Intergenic	Lx8b|LINE|L1	-7084	NR_040506	75310	Mm.108627	NR_040506	ENSMUSG00000116586	4930556C24Rik	-	RIKEN cDNA 4930556C24 gene	ncRNA	0.000000	0.328358			41(TCTTTGCTATGCAGAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1343	chr11	72176035	72176235	+	2.91990	NA	intron (NM_001361564, intron 10 of 18)	intron (NM_001361564, intron 10 of 18)	27636	NM_028963	74477	Mm.289697	NM_028963	ENSMUSG00000020807	4933427D14Rik	C85113|Kiaa0753|MNR	RIKEN cDNA 4933427D14 gene	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7349	chr8	80527404	80527604	+	2.91474	NA	Intergenic	RLTR20B5_MM|LTR|ERVK	33459	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding	0.015000	0.398010	33(TATGCCTTATGCATC,+,0.00),33(TATGCCTTATGCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6669	chr6	112651742	112651942	+	2.91075	NA	intron (NM_021385, intron 9 of 11)	B3|SINE|B2	44828	NM_021385	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-733	chr10	23448486	23448686	+	2.90813	NA	Intergenic	Intergenic	-98643	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7836	chr9	96240886	96241086	+	2.90813	NA	intron (NM_178667, intron 3 of 13)	MTC|LTR|ERVL-MaLR	-17719	NM_001184709	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-148	chr1	51651279	51651479	+	2.90813	NA	Intergenic	Intergenic	-54661	NR_151621	100045066	Mm.404734	NR_151621		Gm17767	-	predicted gene, 17767	ncRNA	0.005000	0.313433			23(ATTTGCATTACATTGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6639	chr6	104613967	104614167	+	2.90669	NA	intron (NM_017383, intron 2 of 22)	intron (NM_017383, intron 2 of 22)	121023	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-352	chr1	126083409	126083609	+	2.90428	NA	intron (NM_172484, intron 8 of 14)	intron (NM_172484, intron 8 of 14)	-170581	NM_001311089	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3812	chr18	41352432	41352632	+	2.89872	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	598662	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6445	chr6	52096526	52096726	+	2.89399	NA	Intergenic	Intergenic	-6323	NR_110440	102635415	Mm.333063	NR_110440	ENSMUSG00000085412	Halr1	Gm15055|Haunt|Linchoxa1|linc-Evx1|linc-Hoxa1|linc1547	Hoxa adjacent long noncoding RNA 1	ncRNA	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3093	chr16	13786041	13786241	+	2.89399	NA	intron (NM_001039521, intron 3 of 17)	MIR|SINE|MIR	5442	NM_001039521	106298	Mm.288606	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2303	chr13	111656062	111656262	+	2.88851	NA	Intergenic	Intergenic	-30016	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding	0.000000	0.398010			-15(ATTTGCATGGCTAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5414	chr4	33481849	33482049	+	2.88851	NA	intron (NM_001305273, intron 14 of 15)	intron (NM_001305273, intron 14 of 15)	43868	NR_106198	102465904		NR_106198	ENSMUSG00000098310	Mir8118	Gm27954|mmu-mir-8118	microRNA 8118	ncRNA	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3825	chr18	44647761	44647961	+	2.87910	NA	intron (NM_001085373, intron 3 of 18)	B4A|SINE|B4	-13804	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4013	chr19	14765597	14765797	+	2.86616	NA	Intergenic	Intergenic	-167514	NM_001302950	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding	0.015000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5073	chr3	96139000	96139200	+	2.86085	NA	intron (NM_001025613, intron 3 of 12)	intron (NM_001025613, intron 3 of 12)	-22870	NM_181409	194126	Mm.268536	NM_181409	ENSMUSG00000045934	Mtmr11	AI035306|BC051083|Cra	myotubularin related protein 11	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1192	chr11	22374723	22374923	+	2.86085	NA	Intergenic	Intergenic	-88028	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3398	chr16	96778957	96779157	+	2.85538	NA	intron (NM_031174, intron 10 of 32)	intron (NM_031174, intron 10 of 32)	311451	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding	0.000000	0.388060			-18(ATTTGAATAACATTAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1580	chr12	30477030	30477230	+	2.85102	NA	Intergenic	Intergenic	-9772	NR_045491	69566	Mm.396405	NR_045491	ENSMUSG00000102098	2310016D03Rik	-	RIKEN cDNA 2310016D03 gene	ncRNA	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6275	chr5	151212584	151212784	+	2.85034	NA	Intergenic	Intergenic	-22491	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5427	chr4	35954682	35954882	+	2.85034	NA	intron (NM_001166000, intron 7 of 8)	intron (NM_001166000, intron 7 of 8)	-109578	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4852	chr3	13568594	13568794	+	2.85034	NA	intron (NM_001357034, intron 1 of 7)	intron (NM_001357034, intron 1 of 7)	84171	NR_040598	75203	Mm.490940	NR_040598		4930539N22Rik	-	RIKEN cDNA 4930539N22 gene	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2154	chr13	77048642	77048842	+	2.84599	NA	intron (NM_134071, intron 18 of 20)	LFSINE_Vert|SINE|tRNA	86726	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-681	chr10	6539713	6539913	+	2.84123	NA	Intergenic	Intergenic	-218780	NM_001302794	18390	Mm.438000	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	opioid receptor, mu 1	protein-coding	0.000000	0.313433			-34(TATTTTTAATGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3268	chr16	62232338	62232538	+	2.83940	NA	Intergenic	Intergenic	554278	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2093	chr13	59490728	59490928	+	2.83940	NA	intron (NM_001284219, intron 16 of 24)	intron (NM_001284219, intron 16 of 24)	53623	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7730	chr9	74460943	74461143	+	2.83940	NA	Intergenic	Intergenic	350709	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3549	chr17	62545459	62545659	+	2.83940	NA	Intergenic	Intergenic	335758	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0.040000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6416	chr6	41699655	41699855	+	2.83940	NA	intron (NM_032540, intron 6 of 18)	intron (NM_032540, intron 6 of 18)	4570	NM_032540	23925	Mm.19958	NM_032540	ENSMUSG00000029866	Kel	CD238|Ece3	Kell blood group	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2424	chr14	30562333	30562533	+	2.83803	NA	intron (NM_009388, intron 4 of 13)	MER99|DNA|hAT?	-9716	NR_037237	100526475		NR_037237	ENSMUSG00000093156	Mir3076	mir-3076|mmu-mir-3076	microRNA 3076	ncRNA	0.000000	0.368159			-93(ATTTGCATAGCTAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2855	chr15	32729191	32729391	+	2.83728	NA	Intergenic	Intergenic	43861	NR_155440	105245909	Mm.229263	NR_155440	ENSMUSG00000115749	Gm41289	-	predicted gene, 41289	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5626	chr4	97617744	97617944	+	2.83728	NA	intron (NM_001122952, intron 1 of 10)	intron (NM_001122952, intron 1 of 10)	-33253	NR_015513	319865	Mm.373807	NM_177023		E130114P18Rik	-	RIKEN cDNA E130114P18 gene	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-618	chr1	187457357	187457557	+	2.83728	NA	Intergenic	Intergenic	-151549	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5648	chr4	100953580	100953780	+	2.83728	NA	intron (NM_198037, intron 7 of 26)	intron (NM_198037, intron 7 of 26)	-115358	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7880	chr9	111382506	111382706	+	2.83728	NA	intron (NM_001164659, intron 15 of 21)	intron (NM_001164659, intron 15 of 21)	-56475	NM_172928	245038	Mm.26361	NM_172928	ENSMUSG00000032500	Dclk3	BC056929|C730036H08|Dcamkl3	doublecortin-like kinase 3	protein-coding	0.010000	0.437811			-77(ATTTAAAAGGCAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-992	chr10	105761331	105761531	+	2.83319	NA	Intergenic	Intergenic	79949	NM_001359640	216292	Mm.250875	NM_207522	ENSMUSG00000036009	Mettl25	-	methyltransferase like 25	protein-coding	0.005000	0.333333		-2(AATACATATGAATT,-,0.00)	3(ATATGAATTACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2584	chr14	79596649	79596849	+	2.83245	NA	exon (NM_026474, exon 4 of 13)	exon (NM_026474, exon 4 of 13)	9089	NM_026474	67955	Mm.18972	NM_026474	ENSMUSG00000022024	Sugt1	2410174K12Rik|SGT1	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3156	chr16	33091277	33091477	+	2.83245	NA	intron (NM_172823, intron 11 of 16)	intron (NM_172823, intron 11 of 16)	-13984	NR_035469	100316698		NR_035469	ENSMUSG00000088860	Mir1947	mir-1947|mmu-mir-1947	microRNA 1947	ncRNA	0.020000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-436	chr1	145363084	145363284	+	2.83245	NA	Intergenic	Intergenic	-587757	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0.005000	0.298507	14(GGTGAATTATTCATG,+,0.00),14(GGTGAATTATTCATG,-,0.00)		-34(ATTAAAATCACAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4164	chr2	8526401	8526601	+	2.83245	NA	Intergenic	Intergenic	-663014	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA	0.005000	0.248756			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6662	chr6	109906545	109906745	+	2.83140	NA	Intergenic	HAL1M8|LINE|L1	-738867	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding	0.005000	0.338308			-65(ATATGCATGACAACTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6745	chr6	138401649	138401849	+	2.83140	NA	intron (NM_207222, intron 3 of 4)	intron (NM_207222, intron 3 of 4)	19765	NM_001356307	109593	Mm.490545	NM_207222	ENSMUSG00000030226	Lmo3	AI854781|BB106490|Lmo-3|Rbtn-3|Rbtn3	LIM domain only 3	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2326	chr13	118471975	118472175	+	2.83140	NA	Intergenic	Intergenic	-84093	NR_045982	75890	Mm.141235	NR_045982	ENSMUSG00000100727	1700003P14Rik	1700030O10Rik|4930584L06Rik	RIKEN cDNA 1700003P14 gene	ncRNA	0.000000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7463	chr8	116138903	116139103	+	2.83140	NA	Intergenic	Intergenic	-366012	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3632	chr17	82830796	82830996	+	2.82129	NA	Intergenic	Intergenic	247329	NR_045094	100503434	Mm.187281	NR_045094	ENSMUSG00000117399	Gm19689	-	predicted gene, 19689	ncRNA	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1878	chr12	107356348	107356548	+	2.82129	NA	Intergenic	Intergenic	379040	NR_045973	74968	Mm.359821	NR_045973	ENSMUSG00000085641	4930465M20Rik	4930431H15Rik	RIKEN cDNA 4930465M20 gene	ncRNA	0.030000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4851	chr3	13568402	13568602	+	2.82129	NA	intron (NM_001357034, intron 1 of 7)	intron (NM_001357034, intron 1 of 7)	84363	NR_040598	75203	Mm.490940	NR_040598		4930539N22Rik	-	RIKEN cDNA 4930539N22 gene	ncRNA	0.000000	0.363184			-51(CCTTTGTCATTTTACT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4655	chr2	136978752	136978952	+	2.81951	NA	intron (NR_149746, intron 4 of 8)	intron (NR_149746, intron 4 of 8)	79501	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-682	chr10	6539875	6540075	+	2.81585	NA	Intergenic	LTR10_RN|LTR|ERVK	-218618	NM_001302794	18390	Mm.438000	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	opioid receptor, mu 1	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7867	chr9	105885136	105885336	+	2.81585	NA	intron (NM_001167923, intron 33 of 40)	intron (NM_001167923, intron 33 of 40)	-57151	NM_001102607	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7576	chr9	28681446	28681646	+	2.81066	NA	intron (NM_177906, intron 2 of 6)	intron (NM_177906, intron 2 of 6)	277218	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-537	chr1	170716413	170716613	+	2.80574	NA	intron (NM_001081304, intron 15 of 15)	intron (NM_001081304, intron 15 of 15)	71981	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding	0.020000	0.383085			2(TTTTTGGTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1581	chr12	30477229	30477429	+	2.79835	NA	Intergenic	Intergenic	-9971	NR_045491	69566	Mm.396405	NR_045491	ENSMUSG00000102098	2310016D03Rik	-	RIKEN cDNA 2310016D03 gene	ncRNA	0.000000	0.427861	47(TATGAATAAATCATT,+,0.00),47(TATGAATAAATCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2893	chr15	43865414	43865614	+	2.79212	NA	Intergenic	Intergenic	4515	NM_175502	239408	Mm.41219	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1048	chr10	114747327	114747527	+	2.79212	NA	intron (NM_146241, intron 2 of 18)	L1MA6|LINE|L1	53943	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0.005000	0.412935			58(ATATTGTGTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7783	chr9	84580644	84580844	+	2.79212	NA	Intergenic	Intergenic	-193654	NR_040739	75253	Mm.401984	NR_040739	ENSMUSG00000099724	4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	ncRNA	0.000000	0.353234			-49(TAATTCTGTTGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4396	chr2	74153973	74154173	+	2.79212	NA	Intergenic	Intergenic	153644	NR_040501	73962	Mm.50289	NR_040501	ENSMUSG00000085405	4930441J16Rik	Astx1a|Astx1b|Astx1c	RIKEN cDNA 4930441J16 gene	ncRNA	0.020000	0.383085			81(GCATTGTCATGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6029	chr5	74019370	74019570	+	2.79164	NA	intron (NM_177561, intron 4 of 8)	intron (NM_177561, intron 4 of 8)	48941	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2416	chr14	29627503	29627703	+	2.79164	NA	intron (NM_009785, intron 2 of 37)	Lx9|LINE|L1	94261	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2409	chr14	27668704	27668904	+	2.79040	NA	intron (NM_177814, intron 2 of 15)	intron (NM_177814, intron 2 of 15)	46397	NM_001347497	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2498	chr14	59799524	59799724	+	2.79040	NA	intron (NM_015803, intron 27 of 35)	intron (NM_015803, intron 27 of 35)	174343	NM_145463	219134	Mm.275409	NM_145463	ENSMUSG00000044461	Shisa2	9430059P22Rik|MAd2|Tmem46|mShisa|shisa	shisa family member 2	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3387	chr16	93285271	93285471	+	2.79040	NA	Intergenic	Intergenic	67818	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1222	chr11	29572761	29572961	+	2.79040	NA	intron (NM_028504, intron 10 of 11)	intron (NM_028504, intron 10 of 11)	-24821	NM_024277	78294	Mm.180003	NM_024277	ENSMUSG00000020460	Rps27a	0610006J14Rik|Uba52|Ubb|Ubc	ribosomal protein S27A	protein-coding	0.005000	0.343284			42(AATTTGTTAAGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2412	chr14	28456441	28456641	+	2.79040	NA	intron (NM_001347497, intron 19 of 19)	intron (NM_001347497, intron 19 of 19)	-48932	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5184	chr3	128755608	128755808	+	2.78775	NA	Intergenic	L1MCa|LINE|L1	-444170	NM_011098	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6770	chr6	146799402	146799602	+	2.78518	NA	Intergenic	Intergenic	-6028	NM_001289679	272322	Mm.333500	NM_172309	ENSMUSG00000040187	Arntl2	4632430A05Rik|BMAL2|CLIF|MOP9|bHLHe6	aryl hydrocarbon receptor nuclear translocator-like 2	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3643	chr17	85829513	85829713	+	2.78412	NA	Intergenic	L1MEf|LINE|L1	-141359	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-390	chr1	135247921	135248121	+	2.78412	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	10451	NM_007921	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7111	chr7	136640339	136640539	+	2.77963	NA	Intergenic	Intergenic	70165	NR_046021	621677	Mm.207290	NR_046021	ENSMUSG00000110101	Gm6249	EG621677	predicted gene 6249	ncRNA	0.025000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1375	chr11	81810954	81811154	+	2.77126	NA	intron (NM_001034013, intron 1 of 9)	RMER15|LTR|ERVL	-49623	NR_038010	71388	Mm.158687	NR_038010	ENSMUSG00000020703	5530401A14Rik	-	RIKEN cDNA 5530401A14 gene	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6119	chr5	102968724	102968924	+	2.76857	NA	intron (NM_001310686, intron 7 of 11)	intron (NM_001310686, intron 7 of 11)	89568	NM_001310686	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5959	chr5	53876796	53876996	+	2.76715	NA	intron (NM_144517, intron 15 of 20)	intron (NM_144517, intron 15 of 20)	67269	NM_144517	67249	Mm.28823	NM_144517	ENSMUSG00000039178	Tbc1d19	2810453K03Rik	TBC1 domain family, member 19	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-991	chr10	105760948	105761148	+	2.76447	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	80332	NM_001359640	216292	Mm.250875	NM_207522	ENSMUSG00000036009	Mettl25	-	methyltransferase like 25	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2128	chr13	70149536	70149736	+	2.76367	NA	Intergenic	Intergenic	-83186	NR_036596	75086	Mm.390616	NR_036596	ENSMUSG00000113463	4930520P13Rik	-	RIKEN cDNA 4930520P13 gene	ncRNA	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7138	chr8	8575100	8575300	+	2.76367	NA	Intergenic	Intergenic	86042	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0.030000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6957	chr7	89699999	89700199	+	2.76367	NA	intron (NM_181407, intron 1 of 13)	intron (NM_181407, intron 1 of 13)	67281	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4516	chr2	109976048	109976248	+	2.76367	NA	intron (NM_172671, intron 2 of 17)	intron (NM_172671, intron 2 of 17)	-41669	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7112	chr7	136640504	136640704	+	2.76234	NA	Intergenic	Intergenic	70000	NR_046021	621677	Mm.207290	NR_046021	ENSMUSG00000110101	Gm6249	EG621677	predicted gene 6249	ncRNA	0.010000	0.417910			-33(CTTAGCAAGGCAAAGC,-,0.00),41(GTTTTATAATGTAGAT,+,0.00),65(ATTTGCATGAACATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2005	chr13	29919768	29919968	+	2.76134	NA	intron (NM_001359994, intron 2 of 6)	intron (NM_001359994, intron 2 of 6)	-64195	NM_001308486	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding	0.030000	0.467662		24(AATGCAAATGCATT,+,0.00),24(AATGCAAATGCATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7886	chr9	113163617	113163817	+	2.76134	NA	Intergenic	Intergenic	423435	NR_040760	102688	Mm.394901	NR_040760	ENSMUSG00000109890	AU023762	-	expressed sequence AU023762	ncRNA	0.005000	0.368159		-39(TATAAATATTCATG,+,0.00),-39(TATAAATATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1922	chr12	119671606	119671806	+	2.76089	NA	Intergenic	Intergenic	228296	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4029	chr19	17248518	17248718	+	2.75646	NA	Intergenic	Intergenic	90887	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6859	chr7	55098303	55098503	+	2.74706	NA	intron (NM_178705, intron 5 of 11)	intron (NM_178705, intron 5 of 11)	263158	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2015	chr13	32705238	32705438	+	2.74706	NA	intron (NM_001368880, intron 14 of 14)	intron (NM_001368880, intron 14 of 14)	78626	NM_001368880	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5794	chr4	151518705	151518905	+	2.73684	NA	intron (NM_001081557, intron 4 of 23)	intron (NM_001081557, intron 4 of 23)	342963	NM_001195565	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding	0.025000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6869	chr7	57317476	57317676	+	2.73684	NA	intron (NM_008074, intron 3 of 9)	intron (NM_008074, intron 3 of 9)	69639	NM_008074	14407	Mm.322667	NM_008074	ENSMUSG00000055026	Gabrg3	6330406O05Rik|B230362M20Rik|Gabrg-3	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5966	chr5	55770754	55770954	+	2.73038	NA	Intergenic	Intergenic	1420862	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13	predicted gene 10440	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5801	chr4	153222102	153222302	+	2.73038	NA	Intergenic	Intergenic	260628	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding	0.000000	0.373134			-29(ATTTAAATAAAAAGAT,-,0.00),-15(ATATTCTCTTTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-705	chr10	13283534	13283734	+	2.72887	NA	intron (NM_001359294, intron 2 of 11)	L1MD|LINE|L1	40655	NM_001195096	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3577	chr17	70256649	70256849	+	2.72887	NA	intron (NM_001360665, intron 3 of 14)	intron (NM_001360665, intron 3 of 14)	-168043	NM_177639	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	DLG associated protein 1	protein-coding	0.005000	0.402985		25(CATGCAAATGCATG,+,0.00),25(CATGCAAATGCATG,-,0.00)	18(ATTGTTTCATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-749	chr10	28284226	28284426	+	2.72887	NA	intron (NM_001359355, intron 3 of 33)	intron (NM_001359355, intron 3 of 33)	209506	NM_001359356	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2464	chr14	45140613	45140813	+	2.72887	NA	intron (NM_172597, intron 19 of 20)	intron (NM_172597, intron 19 of 20)	78712	NM_001310534	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding	0.020000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5631	chr4	97849540	97849740	+	2.72887	NA	intron (NM_001122953, intron 2 of 9)	intron (NM_001122953, intron 2 of 9)	72014	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.010000	0.338308			49(CTTTACAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6684	chr6	116876832	116877032	+	2.72887	NA	Intergenic	Intergenic	-160174	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5386	chr4	25676794	25676994	+	2.71987	NA	intron (NM_010243, intron 2 of 2)	intron (NM_010243, intron 2 of 2)	123109	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5068	chr3	95253597	95253797	+	2.71987	NA	TTS (NM_173347)	TTS (NM_173347)	-2504	NM_001168356	171388	Mm.331209	NM_134253	ENSMUSG00000028115	Bnipl	1700128A13Rik|BNIP-S|BNIPL1|BNIPL2|PP73|PP753	BCL2/adenovirus E1B 19kD interacting protein like	protein-coding	0.015000	0.393035			10(AAATGCAAAACAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2510	chr14	61615009	61615209	+	2.71987	NA	intron (NR_028264, intron 5 of 6)	B2_Mm1t|SINE|B2	7652	NM_001039105	328424	Mm.224464	NM_206974	ENSMUSG00000046168	Kcnrg	Clld4|E030012H22Rik|Gm745	potassium channel regulator	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5909	chr5	38729066	38729266	+	2.71987	NA	intron (NM_013748, intron 15 of 18)	intron (NM_013748, intron 15 of 18)	-44340	NM_001081144	100515	Mm.38277	NM_001081144	ENSMUSG00000046572	Zfp518b	6820424L24Rik|AA410078|AI661722|Znf518b	zinc finger protein 518B	protein-coding	0.030000	0.442786	43(CATGAATTTTTCATG,+,0.00),43(CATGAATTTTTCATG,-,0.00)		-94(GGTGTGTTATTTAAAT,+,0.00),-86(ATTTAAATAGCAGTGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6343	chr6	19919641	19919841	+	2.71987	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	364399	NR_105789	102465192		NR_105789	ENSMUSG00000099149	Mir6370	Gm27480|mmu-mir-6370	microRNA 6370	ncRNA	0.005000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6650	chr6	107356009	107356209	+	2.71987	NA	Intergenic	Intergenic	-173617	NM_008516	16979	Mm.428543	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	leucine rich repeat protein 1, neuronal	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6730	chr6	136430991	136431191	+	2.71865	NA	Intergenic	Intergenic	-15522	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1778	chr12	83141700	83141900	+	2.71865	NA	intron (NM_001310478, intron 17 of 17)	L1_Mus3|LINE|L1	-202645	NR_046045	74283	Mm.398247	NR_046045	ENSMUSG00000100890	1700085C21Rik	-	RIKEN cDNA 1700085C21 gene	ncRNA	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4726	chr2	150193130	150193330	+	2.71865	NA	TTS (NM_001145863)	TTS (NM_001145863)	11475	NM_001145863	100271882		NM_001145863	ENSMUSG00000079009	Gm14139	-	predicted gene 14139	protein-coding	0.015000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2573	chr14	77698867	77699067	+	2.71865	NA	intron (NM_172813, intron 16 of 18)	intron (NM_172813, intron 16 of 18)	100001	NR_157389	380920	Mm.297771	NM_001033440		Gm1587	-	predicted gene 1587	ncRNA	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3613	chr17	80625893	80626093	+	2.71672	NA	intron (NM_001360278, intron 14 of 33)	intron (NM_001360278, intron 14 of 33)	-48180	NM_001360144	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5419	chr4	34752611	34752811	+	2.70949	NA	intron (NM_001033255, intron 1 of 4)	intron (NM_001033255, intron 1 of 4)	3548	NM_001033255	214568	Mm.297405	NM_001033255	ENSMUSG00000071015	Gm136	-	predicted gene 136	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7567	chr9	25510671	25510871	+	2.70949	NA	intron (NM_026189, intron 2 of 7)	intron (NM_026189, intron 2 of 7)	29174	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0.030000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1699	chr12	65501476	65501676	+	2.70918	NA	Intergenic	Eulor8|DNA|TcMar?	276059	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20rt	4921538B03Rik|4930427E19Rik|Wdr20|Wdr20b	WD repeat domain 20, retrogene	protein-coding	0.000000	0.333333			-82(GGATTGTCATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2924	chr15	53209235	53209435	+	2.70234	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	136848	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding	0.000000	0.348259	-15(AATGCATAATGAAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5289	chr3	151567448	151567648	+	2.70234	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	129666	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding	0.000000	0.278607			-98(ATTTAAATAATAATAG,-,0.00),-23(GTTTGAAAAAGAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7910	chr9	123774790	123774990	+	2.70234	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	7679	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5172	chr3	126962736	126962936	+	2.69873	NA	intron (NM_001327939, intron 27 of 45)	intron (NM_001327939, intron 27 of 45)	-19450	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding	0.000000	0.407960			-19(TCAGTGTGTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2270	chr13	106816835	106817035	+	2.69585	NA	intron (NM_029665, intron 28 of 29)	intron (NM_029665, intron 28 of 29)	120023	NM_001360897	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6747	chr6	139794363	139794563	+	2.69222	NA	intron (NM_207683, intron 17 of 31)	L1M5|LINE|L1	-46982	NM_011084	18705	Mm.333471	NM_011084	ENSMUSG00000030228	Pik3c2g	C80387|PI3K-C2-gamma	phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 gamma	protein-coding	0.000000	0.353234		73(AATGAATATGCAAA,+,0.00),73(AATGAATATGCAAA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3342	chr16	82250744	82250944	+	2.69101	NA	Intergenic	Intergenic	1050147	NM_001113208	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0.000000	0.303483			29(ATTAGAATGTGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2305	chr13	112304533	112304733	+	2.69101	NA	intron (NM_001168405, intron 1 of 5)	MurERV4-int|LTR|ERVK	16115	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2636	chr14	96304349	96304549	+	2.69099	NA	intron (NM_053105, intron 4 of 10)	Lx7|LINE|L1	214585	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3229	chr16	51960086	51960286	+	2.69099	NA	Intergenic	Intergenic	27101	NR_153657	629091	Mm.364775	NR_153657		Gm29686	-	predicted gene, 29686	ncRNA	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7466	chr8	117951887	117952087	+	2.69099	NA	Intergenic	Intergenic	-150013	NM_001357232	68533	Mm.181836	NM_026758	ENSMUSG00000031843	Mphosph6	1110001M01Rik|AA536809|C86426	M phase phosphoprotein 6	protein-coding	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4078	chr19	35124056	35124256	+	2.68672	NA	Intergenic	Intergenic	158760	NR_035473	100316775		NR_035473	ENSMUSG00000089151	Mir1950	mmu-mir-1950	microRNA 1950	ncRNA	0.035000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6044	chr5	79057464	79057664	+	2.68311	NA	Intergenic	Intergenic	1592076	NR_131050	69370	Mm.426881	NR_131050	ENSMUSG00000107232	1700017L05Rik	-	RIKEN cDNA 1700017L05 gene	ncRNA	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5407	chr4	31563062	31563262	+	2.68231	NA	Intergenic	Intergenic	-400945	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2332	chr13	119369036	119369236	+	2.68159	NA	intron (NM_008710, intron 10 of 16)	intron (NM_008710, intron 10 of 16)	39875	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000116207	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding	0.020000	0.373134			29(TTTTACATCACAAACG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5718	chr4	122999296	122999496	+	2.67260	NA	intron (NM_008506, intron 1 of 1)	intron (NM_008506, intron 1 of 1)	3465	NM_008506	16918	Mm.1055	NM_008506	ENSMUSG00000028654	Mycl	AW536278|L-myc|Lmyc-1|Lmyc1|Mycl1|bHLHe38	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived	protein-coding	0.010000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6490	chr6	63550563	63550763	+	2.67137	NA	intron (NM_001370966, intron 2 of 15)	intron (NM_001370966, intron 2 of 15)	294657	NM_001370966									0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3675	chr17	94727764	94727964	+	2.67137	NA	intron (NM_001357135, intron 8 of 8)	intron (NM_001357135, intron 8 of 8)	22155	NM_001357136	76781	Mm.139146	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2936	chr15	56387774	56387974	+	2.67137	NA	Intergenic	BGLII_Mus|LTR|ERVK	-302070	NR_002874	594843	Mm.484850	NR_002874	ENSMUSG00000086541	Has2os	EG594843|Has2as|Hasnt	hyaluronan synthase 2, opposite strand	ncRNA	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7902	chr9	118816410	118816610	+	2.67137	NA	intron (NM_001113514, intron 4 of 13)	L1MA5A|LINE|L1	104818	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding	0.005000	0.313433			-35(ATTTGCAAGAAACTGG,-,0.00),84(TTATTTTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2500	chr14	60226822	60227022	+	2.66729	NA	intron (NM_170591, intron 12 of 14)	intron (NM_170591, intron 12 of 14)	1993	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA	0.005000	0.368159			-65(ATTTGCAAGGTTAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6181	chr5	127589554	127589754	+	2.65724	NA	Intergenic	BLACKJACK|DNA|hAT-Blackjack	27738	NM_133895	100561	Mm.28506	NM_133895	ENSMUSG00000029416	Slc15a4	AA987064|AW742963|C130069N12Rik|PHT1|PTR4	solute carrier family 15, member 4	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7036	chr7	116407952	116408152	+	2.65615	NA	intron (NM_011083, intron 2 of 32)	B1F1|SINE|Alu	35406	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5627	chr4	97617898	97618098	+	2.65615	NA	intron (NM_001122952, intron 1 of 10)	intron (NM_001122952, intron 1 of 10)	-33407	NR_015513	319865	Mm.373807	NM_177023		E130114P18Rik	-	RIKEN cDNA E130114P18 gene	ncRNA	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-322	chr1	118437749	118437949	+	2.65394	NA	intron (NM_001359341, intron 2 of 37)	MLT2B3|LTR|ERVL	21416	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4200	chr2	20399184	20399384	+	2.65314	NA	intron (NM_001081006, intron 2 of 21)	intron (NM_001081006, intron 2 of 21)	109371	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.015000	0.333333			-66(GTTTAGTGATTCAAAT,+,0.00),26(ATTTTCCCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7599	chr9	32971138	32971338	+	2.65314	NA	Intergenic	Intergenic	-42272	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA	0.010000	0.427861			-98(ATTAGAAAAACAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2125	chr13	70036612	70036812	+	2.65314	NA	intron (NR_131156, intron 2 of 2)	intron (NR_131156, intron 2 of 2)	-8364	NR_045965	74280	Mm.273343	NR_045965	ENSMUSG00000099639	1700084F23Rik	1700003E18Rik|4930589D02Rik	RIKEN cDNA 1700084F23 gene	ncRNA	0.010000	0.427861			-2(ATTTACATGGCAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6461	chr6	55048375	55048575	+	2.65314	NA	intron (NM_180678, intron 3 of 16)	intron (NM_180678, intron 3 of 16)	10474	NM_180678	353172	Mm.250004	NM_180678	ENSMUSG00000029777	Gars	GENA202|Gena201|Nmf249|Sgrp23	glycyl-tRNA synthetase	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5877	chr5	27306721	27306921	+	2.65314	NA	intron (NM_001136060, intron 1 of 25)	intron (NM_001136060, intron 1 of 25)	44886	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0.005000	0.412935			70(TTCTGCATGGCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6022	chr5	72228426	72228626	+	2.64414	NA	intron (NR_003966, intron 2 of 22)	intron (NR_003966, intron 2 of 22)	25183	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2012	chr13	32400629	32400829	+	2.64371	NA	Intergenic	L1M3|LINE|L1	-62185	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	GDP-mannose 4, 6-dehydratase	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6381	chr6	32323420	32323620	+	2.64371	NA	intron (NM_175750, intron 3 of 31)	MIR|SINE|MIR	-187621	NR_040277	319849	Mm.440860	NR_040277	ENSMUSG00000086763	Plxna4os1	B230378P21Rik	plexin A4, opposite strand 1	ncRNA	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-730	chr10	23170286	23170486	+	2.64371	NA	intron (NM_001347372, intron 4 of 18)	MER58B|DNA|hAT-Charlie	179504	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding	0.015000	0.308458			42(ATTTGTAACACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7410	chr8	101018417	101018617	+	2.64191	NA	Intergenic	Intergenic	1601843	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1234	chr11	33560903	33561103	+	2.64191	NA	intron (NM_146017, intron 6 of 9)	intron (NM_146017, intron 6 of 9)	17954	NM_146017	216643	Mm.99989	NM_146017	ENSMUSG00000020159	Gabrp	-	gamma-aminobutyric acid (GABA) A receptor, pi	protein-coding	0.015000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3484	chr17	41136765	41136965	+	2.63503	NA	Intergenic	Intergenic	202180	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mmut	D230010K02Rik|Mcm|Mut	methylmalonyl-Coenzyme A mutase	protein-coding	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4068	chr19	32308456	32308656	+	2.63320	NA	intron (NM_001362423, intron 2 of 9)	intron (NM_001362423, intron 2 of 9)	40760	NM_001168525	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding	0.010000	0.437811			59(CTATTGTAATGCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7024	chr7	112490788	112490988	+	2.63320	NA	intron (NM_020606, intron 1 of 12)	intron (NM_020606, intron 1 of 12)	44795	NR_154466	102636183	Mm.446701	NR_154466		Parvaos	A230071N21Rik	parvin, alpha, opposite strand	ncRNA	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7104	chr7	134954372	134954572	+	2.63320	NA	intron (NM_001033420, intron 27 of 51)	intron (NM_001033420, intron 27 of 51)	-16042	NM_001143802	627214	Mm.323610	NM_001143802	ENSMUSG00000073805	Insyn2a	B830028B13Rik|Fam196a|InSyn2	inhibitory synaptic factor 2A	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4077	chr19	35123714	35123914	+	2.63253	NA	Intergenic	Intergenic	158418	NR_035473	100316775		NR_035473	ENSMUSG00000089151	Mir1950	mmu-mir-1950	microRNA 1950	ncRNA	0.000000	0.318408	56(TTTGAATTATTCATA,+,0.00),56(TTTGAATTATTCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2345	chr14	10671713	10671913	+	2.63216	NA	intron (NM_001308285, intron 4 of 9)	intron (NM_001308285, intron 4 of 9)	-66740	NR_131139	547334	Mm.434606	NR_131139	ENSMUSG00000089833	Fhitos	Gm16542	fragile histidine triad gene, opposite strand	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1381	chr11	83465835	83466035	+	2.63122	NA	Intergenic	Intergenic	-2895	NM_172797	118453	Mm.264648	NM_080453	ENSMUSG00000020682	Mmp28	D130023P12	matrix metallopeptidase 28 (epilysin)	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3992	chr18	86913597	86913797	+	2.62409	NA	Intergenic	Intergenic	201386	NM_001361145	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0.005000	0.353234			-75(ATATTCATAATAATGT,-,0.00),-4(ATTCTGTCTTTGAAAT,+,0.00),16(GCTTTGCTTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3429	chr17	15144596	15144796	+	2.62016	NA	Intergenic	Intergenic	96087	NR_046164	328747	Mm.256835	NR_046164	ENSMUSG00000097624	Gm5091	C330048F19	predicted gene 5091	ncRNA	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7657	chr9	52840271	52840471	+	2.61606	NA	Intergenic	L1M3|LINE|L1	160508	NR_045333	382139	Mm.335162	NR_045333	ENSMUSG00000111020	Gm1715	-	predicted gene 1715	ncRNA	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5779	chr4	143128039	143128239	+	2.61587	NA	3' UTR (NM_001256380, exon 8 of 8)	3' UTR (NM_001256380, exon 8 of 8)	8023	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-347	chr1	124777709	124777909	+	2.61142	NA	Intergenic	Intergenic	657918	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2296	chr13	110634763	110634963	+	2.61142	NA	Intergenic	Intergenic	239819	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo like kinase 2	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4281	chr2	44712335	44712535	+	2.61142	NA	intron (NM_001362986, intron 5 of 10)	intron (NM_001362986, intron 5 of 10)	149187	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding	0.000000	0.263682			-87(TTATACTCTTTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8105	chrX	143378173	143378373	+	2.61142	NA	intron (NM_031258, intron 2 of 8)	L1MC2|LINE|L1	15989	NM_001114385	83453	Mm.157697	NM_031258	ENSMUSG00000031283	Chrdl1	CHL|CHL1|Nrln1|VOPT	chordin-like 1	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7628	chr9	43093055	43093255	+	2.61142	NA	intron (NM_001359232, intron 1 of 40)	intron (NM_001359232, intron 1 of 40)	12563	NM_001359232	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding	0.020000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3998	chr18	90533254	90533454	+	2.61142	NA	intron (NM_198295, intron 12 of 15)	intron (NM_198295, intron 12 of 15)	23200	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7256	chr8	53446354	53446554	+	2.61048	NA	Intergenic	Intergenic	-65248	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6637	chr6	104417418	104417618	+	2.61048	NA	Intergenic	Intergenic	-75526	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0.000000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2878	chr15	40749182	40749382	+	2.61048	NA	intron (NM_001356998, intron 1 of 6)	intron (NM_001356998, intron 1 of 6)	94240	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3243	chr16	55576010	55576210	+	2.61048	NA	Intergenic	Intergenic	81379	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2823	chr15	23781690	23781890	+	2.61048	NA	Intergenic	Intergenic	745327	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l|Tg(GFAP-APOE_i4)1Hol	cadherin 18	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4367	chr2	67687040	67687240	+	2.61048	NA	Intergenic	Intergenic	11683	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA	0.000000	0.328358			-6(AGTTTGTCATTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5166	chr3	126300743	126300943	+	2.61048	NA	Intergenic	Intergenic	-63009	NM_173451	271970	Mm.317021	NM_173451	ENSMUSG00000046561	Arsj	9330196J05Rik|D830047F08	arylsulfatase J	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1801	chr12	88341463	88341663	+	2.61048	NA	Intergenic	RLTR13D6|LTR|ERVK	-18951	NM_001361601	72113	Mm.181387	NM_028105	ENSMUSG00000021044	Adck1	2610005A10Rik	aarF domain containing kinase 1	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4332	chr2	59574268	59574468	+	2.61048	NA	Intergenic	Intergenic	-37674	NM_198294	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6536	chr6	75536714	75536914	+	2.60403	NA	Intergenic	URR1A|DNA|hAT-Charlie	-1705663	NR_155299	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.000000	0.308458			-14(ATTTACATTACAATTT,-,0.00),65(ATCAACATGACAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7478	chr8	122982137	122982337	+	2.59926	NA	intron (NM_001081379, intron 1 of 12)	intron (NM_001081379, intron 1 of 12)	60047	NM_001081379	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding	0.005000	0.393035			-14(ATTTTGGTTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4666	chr2	138697442	138697642	+	2.59926	NA	Intergenic	Lx8b|LINE|L1	-122387	NR_035477	100316816		NR_035477	ENSMUSG00000088983	Mir1952	mmu-mir-1952	microRNA 1952	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6185	chr5	128393200	128393400	+	2.59926	NA	intron (NM_172885, intron 1 of 8)	intron (NM_172885, intron 1 of 8)	39777	NM_172885	243274	Mm.447698	NM_172885	ENSMUSG00000034310	Tmem132d	C630028F04Rik	transmembrane protein 132D	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6640	chr6	104614245	104614445	+	2.59926	NA	intron (NM_017383, intron 2 of 22)	intron (NM_017383, intron 2 of 22)	121301	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5967	chr5	55771060	55771260	+	2.59926	NA	Intergenic	Charlie17b|DNA|hAT-Charlie	1421168	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13	predicted gene 10440	ncRNA	0.005000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5007	chr3	70686460	70686660	+	2.59608	NA	Intergenic	Intergenic	120731	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	ncRNA	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3017	chr15	90597464	90597664	+	2.59463	NA	intron (NM_001357979, intron 5 of 18)	intron (NM_001357979, intron 5 of 18)	81824	NM_001033851	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding	0.010000	0.303483			53(CCATTTTTATTTAAAA,+,0.00),61(ATTTAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1625	chr12	43230393	43230593	+	2.59444	NA	Intergenic	Intergenic	-196276	NR_148724	102636207		NR_148724		Gm33340	Gm40882	predicted gene, 33340	ncRNA	0.000000	0.393035		-28(ACTGAATATTCAGG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-816	chr10	51425876	51426076	+	2.59444	NA	Intergenic	Intergenic	-54636	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000112023	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3705	chr18	10868707	10868907	+	2.59444	NA	Intergenic	Intergenic	-83255	NR_029781	723959		NR_029781	ENSMUSG00000106348	Mir1a-2	Mir1-2|Mirn1-2|mir-1a-2|mmu-mir-1-2|mmu-mir-1a-2	microRNA 1a-2	ncRNA	0.020000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2548	chr14	75947126	75947326	+	2.59444	NA	intron (NM_026816, intron 5 of 7)	intron (NM_026816, intron 5 of 7)	-7777	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6817	chr7	35721839	35722039	+	2.59444	NA	intron (NM_178704, intron 7 of 18)	intron (NM_178704, intron 7 of 18)	32515	NM_178704	233115	Mm.257808	NM_178704	ENSMUSG00000043671	Dpy19l3	6030410G08|9330164H19Rik	dpy-19-like 3 (C. elegans)	protein-coding	0.020000	0.417910			-86(ATATTCTCATATAAAT,+,0.00),19(TTTTGCAGAACAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7869	chr9	106318034	106318234	+	2.59098	NA	intron (NM_027354, intron 9 of 10)	intron (NM_027354, intron 9 of 10)	37073	NM_027354	70235	Mm.23054	NM_027354	ENSMUSG00000023345	Poc1a	2510040D07Rik|Wdr51a|cha	POC1 centriolar protein A	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7672	chr9	59172152	59172352	+	2.58973	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-119320	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding	0.010000	0.417910	-27(TGTGCATTATACATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7411	chr8	101018591	101018791	+	2.58973	NA	Intergenic	Intergenic	1602017	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.005000	0.248756			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4044	chr19	21637099	21637299	+	2.58087	NA	intron (NM_025423, intron 1 of 3)	ORR1E|LTR|ERVL-MaLR	15592	NM_025423	66206	Mm.272430	NM_025423	ENSMUSG00000035171	1110059E24Rik	-	RIKEN cDNA 1110059E24 gene	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2529	chr14	67675880	67676080	+	2.57681	NA	TTS (NM_175384)	TTS (NM_175384)	39630	NM_001110162	108912	Mm.33831	NM_175384	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5383	chr4	24920161	24920361	+	2.56414	NA	Intergenic	Intergenic	22178	NM_026742	68493	Mm.204831	NM_026742	ENSMUSG00000028261	Ndufaf4	1110007M04Rik|3000003G13Rik|AW214064	NADH:ubiquinone oxidoreductase complex assembly factor 4	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7063	chr7	124063230	124063430	+	2.56414	NA	intron (NM_001252072, intron 1 of 1)	intron (NM_001252072, intron 1 of 1)	80502	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4034	chr19	18420788	18420988	+	2.56414	NA	Intergenic	Intergenic	210925	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding	0.015000	0.378109			-1(CTATTATTATCCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4391	chr2	73114143	73114343	+	2.56320	NA	intron (NM_025942, intron 7 of 10)	intron (NM_025942, intron 7 of 10)	100204	NM_030091	67059	Mm.22661	NM_025942	ENSMUSG00000027108	Ola1	2510025G09Rik|2810405J23Rik|2810409H07Rik|Gtpbp9|PTD004	Obg-like ATPase 1	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4823	chr3	4138233	4138433	+	2.56320	NA	Intergenic	RLTR13D6|LTR|ERVK	630303	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3425	chr17	14602388	14602588	+	2.56320	NA	Intergenic	Intergenic	91774	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding	0.000000	0.338308			-70(ACATTGTTGTTGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5079	chr3	99593578	99593778	+	2.56320	NA	Intergenic	Intergenic	-291739	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4688	chr2	142374887	142375087	+	2.56290	NA	intron (NM_001013802, intron 17 of 18)	intron (NM_001013802, intron 17 of 18)	526477	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.000000	0.407960			-36(GGTTTGTGTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6602	chr6	97110287	97110487	+	2.56290	NA	3' UTR (NM_175313, exon 18 of 18)	3' UTR (NM_175313, exon 18 of 18)	38499	NM_175313	101351	Mm.251789	NM_175313	ENSMUSG00000035245	Eogt	A130022J15Rik|AI447490|AW214473|AW259391|Aer61	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	protein-coding	0.020000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3399	chr16	96779285	96779485	+	2.56112	NA	intron (NM_031174, intron 10 of 32)	intron (NM_031174, intron 10 of 32)	311779	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6696	chr6	119464894	119465094	+	2.56112	NA	intron (NM_009525, intron 1 of 4)	intron (NM_009525, intron 1 of 4)	2217	NM_001271758	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1252	chr11	40454186	40454386	+	2.56112	NA	Intergenic	Intergenic	238396	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6761	chr6	144742848	144743048	+	2.55903	NA	Intergenic	Intergenic	70080	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	Sox5os3	4933425H06Rik	SRY (sex determining region Y)-box 5, opposite strand 3	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2825	chr15	24561282	24561482	+	2.55897	NA	Intergenic	Intergenic	852382	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2212	chr13	94110936	94111136	+	2.55897	NA	intron (NM_172589, intron 1 of 3)	intron (NM_172589, intron 1 of 3)	53240	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7965	chrX	51475166	51475366	+	2.55897	NA	intron (NM_001077202, intron 2 of 4)	intron (NM_001077202, intron 2 of 4)	205211	NM_001290468	50786	Mm.252561	NM_015819	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding	0.000000	0.407960			21(ATCTGAATGGAAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1464	chr11	110732033	110732233	+	2.55897	NA	Intergenic	Intergenic	-235900	NM_001252207	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1958	chr13	15346248	15346448	+	2.55897	NA	Intergenic	Intergenic	-117375	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4363	chr2	65958940	65959140	+	2.55897	NA	intron (NM_001290666, intron 3 of 4)	intron (NM_001290666, intron 3 of 4)	27175	NM_001290665	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding	0.005000	0.373134			18(ATTAACATGTGAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1982	chr13	22357012	22357212	+	2.55897	NA	Intergenic	Intergenic	2766	NM_134220	171254	Mm.377208	NM_134220	ENSMUSG00000095125	Vmn1r198	V1ri3	vomeronasal 1 receptor 198	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1201	chr11	25605163	25605363	+	2.55897	NA	Intergenic	Intergenic	279156	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	ncRNA	0.005000	0.373134			74(TTACTATTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2530	chr14	67676471	67676671	+	2.55568	NA	3' UTR (NM_175384, exon 15 of 15)	3' UTR (NM_175384, exon 15 of 15)	39039	NM_001110162	108912	Mm.33831	NM_175384	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding	0.000000	0.348259			68(TTTAACAAAACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4953	chr3	55860019	55860219	+	2.54881	NA	intron (NM_030595, intron 36 of 57)	L1_Mur1|LINE|L1	13014	NR_033592	71182	Mm.195603	NR_033592	ENSMUSG00000106572	4933417G07Rik	-	SEC13 homolog pseudogene	pseudo	0.010000	0.353234			-40(TCATTTTCATTCAATT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2455	chr14	38411159	38411359	+	2.54881	NA	intron (NM_001190187, intron 4 of 9)	RLTR16B_MM|LTR|ERVK	-487043	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8013	chrX	88202218	88202418	+	2.54881	NA	Intergenic	Intergenic	-86370	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|IL1RAPL-1|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1223	chr11	29653563	29653763	+	2.54881	NA	Intergenic	BGLII|LTR|ERVK	-39235	NM_194053	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding	0.005000	0.432836			73(ATTAAAAAGAAAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6904	chr7	72908119	72908319	+	2.54881	NA	Intergenic	Intergenic	193849	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA	0.005000	0.323383			-56(TCTGTTCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2433	chr14	32616979	32617179	+	2.54881	NA	intron (NM_001001796, intron 5 of 6)	L1M5|LINE|L1	17152	NM_001001796	107751	Mm.119274	NM_001001796	ENSMUSG00000041730	Prrxl1	Drg11|Drgx	paired related homeobox protein-like 1	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6263	chr5	150103664	150103864	+	2.54881	NA	Intergenic	Intergenic	85089	NM_080468	140498	Mm.444643	NM_080468	ENSMUSG00000053368	Rxfp2	Gpr106|Great|Lgr8	relaxin/insulin-like family peptide receptor 2	protein-coding	0.020000	0.407960			52(TCCTTGTTGTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5903	chr5	34430170	34430370	+	2.54881	NA	intron (NM_001243123, intron 5 of 20)	intron (NM_001243123, intron 5 of 20)	60337	NM_001243123	231128	Mm.286885	NM_001030306	ENSMUSG00000037210	Fam193a	-	family with sequence homology 193, member A	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7181	chr8	27800368	27800568	+	2.54881	NA	Intergenic	BGLII|LTR|ERVK	284385	NR_033590	666422	Mm.484413	NR_033590	ENSMUSG00000110372	Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo	0.010000	0.343284			-98(TTTTTCTTTTTTACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-275	chr1	93703467	93703667	+	2.54704	NA	Intergenic	Intergenic	17992	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	matador|mtd	BCL2-related ovarian killer	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7141	chr8	8940548	8940748	+	2.54479	NA	Intergenic	Intergenic	191640	NR_045854	71249	Mm.158635	NR_045854	ENSMUSG00000108848	4933430N04Rik	-	RIKEN cDNA 4933430N04 gene	ncRNA	0.020000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5731	chr4	126053387	126053587	+	2.53792	NA	intron (NM_025544, intron 5 of 7)	intron (NM_025544, intron 5 of 7)	-5078	NM_001356446	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding	0.035000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3665	chr17	90587001	90587201	+	2.53684	NA	intron (NM_001346957, intron 12 of 18)	intron (NM_001346957, intron 12 of 18)	-131221	NM_001346960	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.000000	0.412935			20(GTTTGCAAAAGAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1508	chr11	121802477	121802677	+	2.53684	NA	Intergenic	Intergenic	-27641	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1987	chr13	24636895	24637095	+	2.53662	NA	intron (NM_178658, intron 1 of 13)	MLT1E1|LTR|ERVL-MaLR	-1653	NM_029679	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Ripor2	Fam65b	RHO family interacting cell polarization regulator 2	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7283	chr8	62073518	62073718	+	2.53662	NA	intron (NM_011922, intron 5 of 10)	intron (NM_011922, intron 5 of 10)	49575	NM_001136089	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3755	chr18	26506254	26506454	+	2.53555	NA	Intergenic	Intergenic	-752197	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.000000	0.328358			31(CATTTGCTATGTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3108	chr16	21542591	21542791	+	2.53318	NA	intron (NM_001081366, intron 34 of 46)	intron (NM_001081366, intron 34 of 46)	119573	NM_001285894	209018	Mm.235683	NM_145948	ENSMUSG00000033653	Vps8	AI315068|AU040738|mKIAA0804	VPS8 CORVET complex subunit	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3633	chr17	82830975	82831175	+	2.53318	NA	Intergenic	Intergenic	247150	NR_045094	100503434	Mm.187281	NR_045094	ENSMUSG00000117399	Gm19689	-	predicted gene, 19689	ncRNA	0.000000	0.278607			30(ATCTGCATACCAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6443	chr6	49966597	49966797	+	2.53318	NA	Intergenic	Intergenic	-143544	NM_019939	56524	Mm.41288	NM_008016	ENSMUSG00000038388	Mpp6	P55t|Pals2	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3400	chr16	96822587	96822787	+	2.53318	NA	intron (NM_031174, intron 6 of 32)	intron (NM_031174, intron 6 of 32)	348048	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	DS cell adhesion molecule	protein-coding	0.000000	0.338308		-60(TATACTTATTCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2888	chr15	42516531	42516731	+	2.53318	NA	intron (NM_001286062, intron 2 of 8)	intron (NM_001286062, intron 2 of 8)	160346	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5584	chr4	87064576	87064776	+	2.52881	NA	intron (NM_172426, intron 4 of 10)	intron (NM_172426, intron 4 of 10)	163287	NM_001110240	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8102	chrX	142906022	142906222	+	2.52881	NA	intron (NM_019496, intron 2 of 5)	intron (NM_019496, intron 2 of 5)	60604	NM_019496	56068	Mm.143724	NM_019496	ENSMUSG00000042225	Ammecr1	6230420G18Rik	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3606	chr17	78983697	78983897	+	2.52881	NA	intron (NM_001171005, intron 2 of 17)	intron (NM_001171005, intron 2 of 17)	24708	NM_001171005	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding	0.010000	0.298507			-57(ATTTATATGAAAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3843	chr18	50124668	50124868	+	2.52881	NA	Intergenic	Intergenic	-3433	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7368	chr8	90392701	90392901	+	2.52508	NA	Intergenic	Intergenic	-44549	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6179	chr5	126176647	126176847	+	2.52508	NA	Intergenic	Intergenic	-326846	NM_001370875	231736		NM_001370875		Gm4868	EG231736	predicted gene 4868	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6273	chr5	151174807	151175007	+	2.52508	NA	intron (NR_153382, intron 1 of 13)	intron (NR_153382, intron 1 of 13)	15286	NM_001359985	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding	0.000000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4997	chr3	68829075	68829275	+	2.52115	NA	Intergenic	Intergenic	-40411	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding	0.020000	0.402985	-89(TATGCATTATTTATA,+,0.00),-89(TATGCATTATTTATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3421	chr17	13570818	13571018	+	2.52115	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	-16824	NR_045437	72578	Mm.46549	NR_045436	ENSMUSG00000117042	2700054A10Rik	-	RIKEN cDNA 2700054A10 gene	ncRNA	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2330	chr13	119210427	119210627	+	2.52115	NA	Intergenic	Intergenic	198484	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000116207	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding	0.005000	0.283582			-5(AATTTCTCATGCTCAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5286	chr3	149801537	149801737	+	2.52115	NA	Intergenic	L1M4|LINE|L1	526900	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-150	chr1	51835484	51835684	+	2.52115	NA	intron (NM_001161817, intron 3 of 30)	intron (NM_001161817, intron 3 of 30)	80394	NM_001161817	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding	0.005000	0.492537		-31(AATGAATTTGCAAG,-,0.00)	-26(ATTTGCAAGGCAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4791	chr2	170009806	170010006	+	2.51720	NA	intron (NM_001363022, intron 2 of 2)	UCON20|Unknown|Unknown	-46719	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA	0.040000	0.472637	-18(CATGCATAATGGATC,+,0.00),-18(CATGCATAATGGATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-655	chr1	194239582	194239782	+	2.51718	NA	Intergenic	Intergenic	-16923	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.000000	0.353234		49(AATACATATACATA,-,0.00)	34(ATATACATAGAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3428	chr17	15144421	15144621	+	2.51562	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	96262	NR_046164	328747	Mm.256835	NR_046164	ENSMUSG00000097624	Gm5091	C330048F19	predicted gene 5091	ncRNA	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2283	chr13	109671669	109671869	+	2.51431	NA	intron (NM_011056, intron 3 of 16)	ORSL-2b|DNA|hAT-Tip100	-232040	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2228	chr13	96532945	96533145	+	2.51169	NA	intron (NM_012048, intron 1 of 14)	intron (NM_012048, intron 1 of 14)	9534	NM_012048	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding	0.010000	0.328358			-83(AATTTACTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5539	chr4	74291389	74291589	+	2.51169	NA	intron (NM_001356561, intron 3 of 20)	Lx8b|LINE|L1	39610	NM_001356561	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding	0.000000	0.353234			12(TATTTGTTATTCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-863	chr10	67150068	67150268	+	2.50774	NA	intron (NM_207221, intron 1 of 25)	intron (NM_207221, intron 1 of 25)	23080	NM_207221	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding	0.000000	0.258706			-75(ATTAAAAAAAGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7214	chr8	39486058	39486258	+	2.50774	NA	Intergenic	Intergenic	156520	NM_001113326	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2512	chr14	62347279	62347479	+	2.50774	NA	intron (NM_026001, intron 2 of 10)	intron (NM_026001, intron 2 of 10)	15311	NM_026001	67153	Mm.26040	NM_026001	ENSMUSG00000021932	Rnaseh2b	1110019N06Rik|2610207P08Rik|Dleu8	ribonuclease H2, subunit B	protein-coding	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5334	chr4	8787961	8788161	+	2.50774	NA	intron (NM_001277149, intron 3 of 37)	intron (NM_001277149, intron 3 of 37)	36737	NM_001355382	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6178	chr5	126114160	126114360	+	2.50774	NA	Intergenic	RMER16|LTR|ERVK	-264359	NM_001370875	231736		NM_001370875		Gm4868	EG231736	predicted gene 4868	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-29	chr1	9961473	9961673	+	2.50774	NA	3' UTR (NM_001285425, exon 3 of 3)	3' UTR (NM_001285425, exon 3 of 3)	6237	NM_001285425	100039596	Mm.412928	NM_001285425	ENSMUSG00000099032	Tcf24	Gm10567|Gm2330	transcription factor 24	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7528	chr9	14467834	14468034	+	2.50774	NA	intron (NM_173433, intron 1 of 1)	intron (NM_173433, intron 1 of 1)	32548	NM_173433	244694	Mm.240457	NM_173433	ENSMUSG00000053914	Kdm4d	4932416A15|Jmjd2d	lysine (K)-specific demethylase 4D	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4708	chr2	145708174	145708374	+	2.50774	NA	intron (NR_033220, intron 1 of 3)	intron (NR_033220, intron 1 of 3)	7079	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000001768	BC039771	-	cDNA sequence BC039771	ncRNA	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5817	chr5	5534009	5534209	+	2.50774	NA	Intergenic	Intergenic	-19133	NM_022890	64945	Mm.40132	NM_022890	ENSMUSG00000046798	Cldn12	-	claudin 12	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2130	chr13	70835747	70835947	+	2.50765	NA	intron (NR_137640, intron 3 of 22)	intron (NR_137640, intron 3 of 22)	5964	NM_172053	271127	Mm.115970	NM_172053	ENSMUSG00000049538	Adamts16	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5479	chr4	55049203	55049403	+	2.50765	NA	intron (NM_172867, intron 7 of 12)	intron (NM_172867, intron 7 of 12)	101358	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip|Znf462	zinc finger protein 462	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3099	chr16	15720884	15721084	+	2.50765	NA	intron (NM_011159, intron 39 of 85)	L1MA7|LINE|L1	83118	NM_011159	19090	Mm.71	NM_011159	ENSMUSG00000022672	Prkdc	AI326420|AU019811|DNA-PKcs|DNAPDcs|DNAPK|DNPK1|DOXNPH|HYRC1|XRCC7|dxnph|p460|scid|slip	protein kinase, DNA activated, catalytic polypeptide	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3427	chr17	15144236	15144436	+	2.50188	NA	Intergenic	Intergenic	96447	NR_046164	328747	Mm.256835	NR_046164	ENSMUSG00000097624	Gm5091	C330048F19	predicted gene 5091	ncRNA	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6274	chr5	151212337	151212537	+	2.50153	NA	Intergenic	Intergenic	-22244	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7521	chr9	13012229	13012429	+	2.49506	NA	Intergenic	Intergenic	93526	NR_040755	78219	Mm.414868	NR_040755	ENSMUSG00000111830	4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3028	chr15	92702258	92702458	+	2.49222	NA	intron (NM_001164593, intron 5 of 9)	intron (NM_001164593, intron 5 of 9)	105249	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding	0.000000	0.308458			-86(TCACTCTTTTGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-989	chr10	105115578	105115778	+	2.49222	NA	Intergenic	Intergenic	458801	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding	0.020000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-31	chr1	12359168	12359368	+	2.49222	NA	Intergenic	Intergenic	-66718	NR_105759	102465961		NR_105759	ENSMUSG00000098555	Mir6341	Gm27262|mmu-mir-6341	microRNA 6341	ncRNA	0.005000	0.353234			43(ATTTGCATGGCAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7499	chr8	128254951	128255151	+	2.48631	NA	Intergenic	Intergenic	23174	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7543	chr9	16833054	16833254	+	2.48631	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-331100	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding	0.000000	0.353234			-78(CAAGTGTAATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-577	chr1	178221370	178221570	+	2.48631	NA	intron (NM_024282, intron 1 of 4)	L1MB7|LINE|L1	34053	NM_024282	78825	Mm.440132	NM_024282	ENSMUSG00000026502	Desi2	5830417C01Rik|DeSI-2|Fam152a|Pppde1	desumoylating isopeptidase 2	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4662	chr2	138130498	138130698	+	2.48631	NA	Intergenic	Intergenic	-125986	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4886	chr3	28715335	28715535	+	2.48328	NA	intron (NM_031197, intron 4 of 10)	intron (NM_031197, intron 4 of 10)	17532	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding	0.010000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1917	chr12	119033927	119034127	+	2.48328	NA	Intergenic	L1_Rod|LINE|L1	-67606	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8053	chrX	105143907	105144107	+	2.48328	NA	Intergenic	L1M2|LINE|L1	21498	NR_002167	279610	Mm.418157	NR_002167		E530001F21Rik	-	RIKEN cDNA E530001F21 gene	pseudo	0.000000	0.298507		-65(TTTGCCTATGCATA,+,0.00)	50(TATTTTGCATGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3697	chr18	9027518	9027718	+	2.48328	NA	Intergenic	Intergenic	-185238	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled class receptor 8	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1679	chr12	58257267	58257467	+	2.48328	NA	Intergenic	L1M4|LINE|L1	11891	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	C-type lectin domain family 14, member a	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2146	chr13	75124967	75125167	+	2.48328	NA	intron (NM_013628, intron 9 of 13)	intron (NM_013628, intron 9 of 13)	35210	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7348	chr8	80527084	80527284	+	2.47919	NA	Intergenic	Intergenic	33139	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3766	chr18	30163374	30163574	+	2.47919	NA	Intergenic	Intergenic	-109391	NR_151699	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.015000	0.447761		-87(AATGCATTTTCATC,+,0.00),-87(AATGCATTTTCATC,-,0.00)	-17(ATTTGCAACACAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3276	chr16	64248637	64248837	+	2.47919	NA	Intergenic	Intergenic	353594	NM_001368721	224291	Mm.246580	NM_173861	ENSMUSG00000068167	Csnka2ip	Ckt2	casein kinase 2, alpha prime interacting protein	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4626	chr2	133238524	133238724	+	2.47781	NA	Intergenic	Intergenic	-292588	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-419	chr1	140857825	140858025	+	2.47781	NA	Intergenic	Intergenic	-201523	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3818	chr18	43329437	43329637	+	2.47781	NA	intron (NM_009468, intron 11 of 13)	intron (NM_009468, intron 11 of 13)	43735	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4165	chr2	8526557	8526757	+	2.47781	NA	Intergenic	Intergenic	-662858	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5589	chr4	88323315	88323515	+	2.47781	NA	intron (NM_001081184, intron 21 of 43)	intron (NM_001081184, intron 21 of 43)	115511	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-562	chr1	175989575	175989775	+	2.47781	NA	intron (NM_001195816, intron 6 of 9)	L1M5|LINE|L1	69346	NM_001290692	226720	Mm.11282	NM_001290692	ENSMUSG00000104158	Becn2	Beclin-2|Gm104	beclin 2	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2613	chr14	88243260	88243460	+	2.47781	NA	Intergenic	Intergenic	228036	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5338	chr4	9747885	9748085	+	2.47781	NA	Intergenic	Intergenic	-22600	NR_030693	320152	Mm.159946	NR_030693		4930412C18Rik	5730591J02Rik	RIKEN cDNA 4930412C18 gene	ncRNA	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5257	chr3	146995356	146995556	+	2.47387	NA	Intergenic	L1_Mus2|LINE|L1	143089	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2050	chr13	42681384	42681584	+	2.46915	NA	intron (NM_001302635, intron 1 of 13)	intron (NM_001302635, intron 1 of 13)	685	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding	0.025000	0.477612			-12(TTTTACATGGGAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3352	chr16	84424419	84424619	+	2.46915	NA	Intergenic	Lx8b|LINE|L1	53376	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.015000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6638	chr6	104613715	104613915	+	2.46915	NA	intron (NM_017383, intron 2 of 22)	intron (NM_017383, intron 2 of 22)	120771	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5634	chr4	98939875	98940075	+	2.46812	NA	intron (NM_001369285, intron 48 of 48)	intron (NM_001369285, intron 48 of 48)	16165	NM_001301414	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7658	chr9	52840469	52840669	+	2.46812	NA	Intergenic	L1M3|LINE|L1	160706	NR_045333	382139	Mm.335162	NR_045333	ENSMUSG00000111020	Gm1715	-	predicted gene 1715	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2434	chr14	33293543	33293743	+	2.46336	NA	intron (NM_153800, intron 3 of 10)	B4|SINE|B4	76820	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding	0.000000	0.348259			11(CTATTCTGTTTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5699	chr4	114800899	114801099	+	2.46046	NA	Intergenic	Intergenic	-20721	NR_033617	433746	Mm.388908	NR_033617	ENSMUSG00000055198	Gm12830	-	predicted gene 12830	ncRNA	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4282	chr2	44996262	44996462	+	2.46037	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	26815	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA	0.005000	0.353234			78(CATTTGTTTTGGTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-168	chr1	57284415	57284615	+	2.45466	NA	Intergenic	L1M2|LINE|L1	-69519	NR_037990	407809	Mm.134505	NR_037990	ENSMUSG00000101429	BC055402	-	cDNA sequence BC055402	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6048	chr5	80082590	80082790	+	2.45466	NA	Intergenic	Intergenic	-937881	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-574	chr1	177498923	177499123	+	2.45458	NA	Intergenic	Intergenic	53202	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238.|zfp-238	zinc finger and BTB domain containing 18	protein-coding	0.040000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-229	chr1	83318866	83319066	+	2.45458	NA	intron (NM_172430, intron 3 of 10)	ORR1C1|LTR|ERVL-MaLR	89234	NM_172430	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding	0.005000	0.363184		-50(CATGCATAAGAATA,+,0.00)	-8(GTTTGAATAAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-924	chr10	88368447	88368647	+	2.45458	NA	Intergenic	Intergenic	-10721	NM_001364707	432486	Mm.335190	NM_001004164	ENSMUSG00000035311	Gnptab	EG432486	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1218	chr11	29072100	29072300	+	2.45458	NA	Intergenic	Intergenic	-58544	NR_157297	71701	Mm.211131	NM_027869	ENSMUSG00000020464	Pnpt1	1200003F12Rik|Old35|PNPase|Pnptl1	polyribonucleotide nucleotidyltransferase 1	protein-coding	0.000000	0.378109		-60(CATGCATATACATA,+,0.00),-60(CATGCATATACATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2414	chr14	28756231	28756431	+	2.45458	NA	Intergenic	Intergenic	244926	NM_001256224	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7894	chr9	115639764	115639964	+	2.45458	NA	Intergenic	Intergenic	258045	NR_130329	100316675		NR_130329	ENSMUSG00000080409	Mir467h	Mirn467h|mmu-mir-467h	microRNA 467h	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-279	chr1	95070558	95070758	+	2.45458	NA	Intergenic	Intergenic	-242970	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6066	chr5	84025859	84026059	+	2.45458	NA	Intergenic	Intergenic	391423	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-531	chr1	168793392	168793592	+	2.45458	NA	Intergenic	Intergenic	225597	NR_105772	102466632		NR_105772	ENSMUSG00000098829	Mir6354	Gm27282|mmu-mir-6354	microRNA 6354	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1422	chr11	96716392	96716592	+	2.45015	NA	intron (NM_001177898, intron 9 of 10)	intron (NM_001177898, intron 9 of 10)	61063	NM_001163389	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-315	chr1	109094758	109094958	+	2.45015	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	-888042	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding	0.010000	0.437811			62(ATTTGAAAAAAAAAAT,-,0.00),75(AATTACATGACAAGGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7310	chr8	73056345	73056545	+	2.45015	NA	intron (NM_001317391, intron 6 of 15)	intron (NM_001317391, intron 6 of 15)	39933	NR_039551	100628574		NR_039551	ENSMUSG00000093140	Mir28b	mmu-mir-28b	microRNA 28b	ncRNA	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1030	chr10	111487975	111488175	+	2.44495	NA	intron (NR_152558, intron 4 of 14)	intron (NR_152558, intron 4 of 14)	-12713	NR_033603	382421	Mm.245643	NR_033603	ENSMUSG00000111997	Gm5176	EG382421	high mobility group box 2 pseudogene	pseudo	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4956	chr3	56437268	56437468	+	2.44495	NA	Intergenic	Intergenic	-253667	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding	0.010000	0.398010			-13(TAATTGACATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3652	chr17	87362204	87362404	+	2.44444	NA	intron (NM_028639, intron 17 of 19)	intron (NM_028639, intron 17 of 19)	65437	NM_029298	75467	Mm.50108	NM_029298	ENSMUSG00000036557	Stpg4	1700011E24Rik|GSE	sperm tail PG rich repeat containing 4	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5830	chr5	12766258	12766458	+	2.43855	NA	Intergenic	Lx7|LINE|L1	383192	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5922	chr5	44222568	44222768	+	2.43600	NA	intron (NM_173764, intron 1 of 13)	intron (NM_173764, intron 1 of 13)	3938	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7116	chr7	138606105	138606305	+	2.43600	NA	Intergenic	Intergenic	51963	NR_131022	75187	Mm.410810	NR_131022	ENSMUSG00000110037	4930543N07Rik	Gm45685	RIKEN cDNA 4930543N07 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7524	chr9	13536613	13536813	+	2.43600	NA	Intergenic	Intergenic	-83276	NM_001013813	270118	Mm.116898	NM_173776	ENSMUSG00000031925	Maml2	5930431H10|BC032967	mastermind like transcriptional coactivator 2	protein-coding	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4610	chr2	130509389	130509589	+	2.43600	NA	intron (NM_008980, intron 3 of 21)	intron (NM_008980, intron 3 of 21)	54260	NR_040348	321014	Mm.442588	NR_040348	ENSMUSG00000060029	4930473A02Rik	-	RIKEN cDNA 4930473A02 gene	ncRNA	0.005000	0.378109			75(TTTTGCATATCAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3751	chr18	25827774	25827974	+	2.43418	NA	Intergenic	Intergenic	-73717	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.000000	0.338308			-19(CCATTATCATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5442	chr4	44161362	44161562	+	2.43418	NA	intron (NM_001038993, intron 1 of 11)	B3|SINE|B2	6076	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding	0.030000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-988	chr10	104690574	104690774	+	2.43418	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	403405	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5687	chr4	109803820	109804020	+	2.43418	NA	intron (NM_007983, intron 8 of 18)	MTD|LTR|ERVL-MaLR	127293	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3696	chr18	8335821	8336021	+	2.43309	NA	Intergenic	Intergenic	466208	NM_001360956	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6530	chr6	73095717	73095917	+	2.43309	NA	intron (NM_001164669, intron 45 of 76)	ORR1D1|LTR|ERVL-MaLR	125814	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7203	chr8	35714515	35714715	+	2.43309	NA	Intergenic	B3|SINE|B2	-51108	NM_001370844	100502846		NM_001370844	ENSMUSG00000109372	Gm19410	-	predicted gene, 19410	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-195	chr1	67021588	67021788	+	2.43309	NA	intron (NM_001190985, intron 2 of 8)	intron (NM_001190985, intron 2 of 8)	17146	NM_001190984	14768	Mm.20522	NM_021295	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3690	chr18	6485417	6485617	+	2.43309	NA	intron (NM_007935, intron 1 of 13)	intron (NM_007935, intron 1 of 13)	5129	NR_035446	100316773		NR_035446	ENSMUSG00000084514	Mir1893	Mirn1893|mmu-mir-1893	microRNA 1893	ncRNA	0.000000	0.253731			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3803	chr18	39360301	39360501	+	2.43309	NA	intron (NM_175164, intron 21 of 22)	MER53|DNA|hAT	128878	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding	0.000000	0.338308			-49(ATATGCAAAACAAATA,-,0.00),56(ATTTGCATGAAATTCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2402	chr14	24644196	24644396	+	2.43053	NA	Intergenic	Intergenic	153543	NM_001360586	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4748	chr2	157984635	157984835	+	2.43053	NA	intron (NM_029282, intron 7 of 7)	intron (NM_029282, intron 7 of 7)	43699	NM_029282	75425	Mm.29068	NM_029282	ENSMUSG00000027650	Tti1	2610036D13Rik|AI449463	TELO2 interacting protein 1	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3483	chr17	41136428	41136628	+	2.42187	NA	Intergenic	Intergenic	201843	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mmut	D230010K02Rik|Mcm|Mut	methylmalonyl-Coenzyme A mutase	protein-coding	0.005000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6089	chr5	92202759	92202959	+	2.42049	NA	TTS (NM_019490)	TTS (NM_019490)	12549	NR_033483	57425	Mm.2548	NM_020562	ENSMUSG00000029409	U90926	-	cDNA sequence U90926	ncRNA	0.010000	0.353234			-94(GTTTTCATAATAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6840	chr7	48830831	48831031	+	2.42049	NA	intron (NM_001198841, intron 5 of 5)	intron (NM_001198841, intron 5 of 5)	12740	NM_013808	13009	Mm.17235	NM_013808	ENSMUSG00000030470	Csrp3	CRP3|MLP|MMLP	cysteine and glycine-rich protein 3	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6516	chr6	70172180	70172380	+	2.42049	NA	Intergenic	Intergenic	619895	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.000000	0.422886			4(CCTTTCTGATGCAGAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1680	chr12	59049844	59050044	+	2.42049	NA	intron (NM_001306217, intron 3 of 4)	B3A|SINE|B2	11528	NM_001306217	78232	Mm.290070	NM_030057	ENSMUSG00000020993	Trappc6b	5830498C14Rik|C79212	trafficking protein particle complex 6B	protein-coding	0.005000	0.388060			53(AAATTCTAATTTAAAT,+,0.00),61(ATTTAAATAATAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-775	chr10	38906113	38906313	+	2.41828	NA	Intergenic	Intergenic	-59302	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7008	chr7	105506437	105506637	+	2.41747	NA	Intergenic	Intergenic	-24340	NM_028444	109042	Mm.3124	NM_028444	ENSMUSG00000037060	Cavin3	3110015B12Rik|6330514M23Rik|Prkcdbp|SRBC	caveolae associated 3	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4743	chr2	156039412	156039612	+	2.41606	NA	intron (NM_001136556, intron 19 of 44)	intron (NM_001136556, intron 19 of 44)	13481	NM_001136556	74562	Mm.159241	NM_001136556	ENSMUSG00000013338	Fer1l4	9130402C12Rik	fer-1-like 4 (C. elegans)	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3899	chr18	62999349	62999549	+	2.41606	NA	TTS (NM_028017)	TTS (NM_028017)	21533	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding	0.015000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1649	chr12	49945910	49946110	+	2.41606	NA	Intergenic	Intergenic	-465148	NR_045472	69054	Mm.417838	NR_045472	ENSMUSG00000100844	1810007C17Rik	-	RIKEN cDNA 1810007C17 gene	ncRNA	0.010000	0.412935	1(AATGAATAATTCATC,+,0.00),1(AATGAATAATTCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2011	chr13	32400451	32400651	+	2.41606	NA	Intergenic	L1MB4|LINE|L1	-62007	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	GDP-mannose 4, 6-dehydratase	protein-coding	0.015000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-371	chr1	128540395	128540595	+	2.41606	NA	Intergenic	Lx8|LINE|L1	51804	NM_001356509	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|CXC-R4|CXCR-4|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2267	chr13	105910368	105910568	+	2.41606	NA	Intergenic	Intergenic	466775	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-656	chr1	194239681	194239881	+	2.41531	NA	Intergenic	Intergenic	-17022	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.005000	0.298507		-50(AATACATATACATA,-,0.00)	-65(ATATACATAGAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2443	chr14	35058611	35058811	+	2.41455	NA	intron (NM_008166, intron 4 of 15)	BGLII|LTR|ERVK	164102	NR_029774	723847		NR_029774	ENSMUSG00000065481	Mir346	Mirn346|mir-346|mmu-mir-346	microRNA 346	ncRNA	0.005000	0.412935			-26(CCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5920	chr5	43942275	43942475	+	2.41455	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	39424	NM_008009	14181	Mm.46053	NM_008009	ENSMUSG00000048373	Fgfbp1	FGF-BP|FGF-BP1|FGFBP-1	fibroblast growth factor binding protein 1	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4443	chr2	89719220	89719420	+	2.41455	NA	Intergenic	L1M2|LINE|L1	2789	NM_207568	404331	Mm.377275	NM_207568	ENSMUSG00000110819	Olfr1252	GA_x5J8B7W62NC-992588-991951	olfactory receptor 1252	protein-coding	0.000000	0.248756			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5412	chr4	32017365	32017565	+	2.41455	NA	intron (NM_009316, intron 16 of 16)	B3A|SINE|B2	53358	NM_009316	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5233	chr3	140551900	140552100	+	2.41455	NA	Intergenic	Intergenic	523751	NR_105798	102465198		NR_105798	ENSMUSG00000099169	Mir7j	Gm27716|Mirlet7j|mmu-let-7j	microRNA 7j	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1610	chr12	38130298	38130498	+	2.41455	NA	intron (NM_178681, intron 8 of 24)	intron (NM_178681, intron 8 of 24)	249881	NM_001361686	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5056	chr3	86978121	86978321	+	2.41455	NA	Intergenic	L1_Mur3|LINE|L1	-8365	NR_038188	12480	Mm.389465	NM_007640	ENSMUSG00000041750	Cd1d2	CD1.2|Cd1b|Ly-38	CD1d2 antigen	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4967	chr3	60397287	60397487	+	2.41455	NA	Intergenic	Intergenic	-75443	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind like splicing factor 1	protein-coding	0.010000	0.313433			77(CTTTTATTATTTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5476	chr4	53837200	53837400	+	2.41318	NA	intron (NM_028053, intron 1 of 5)	intron (NM_028053, intron 1 of 5)	11255	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7820	chr9	93284530	93284730	+	2.40835	NA	Intergenic	Intergenic	-278897	NR_040756	78349	Mm.52612	NR_040756	ENSMUSG00000100294	1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2460	chr14	40656620	40656820	+	2.40738	NA	Intergenic	Intergenic	236594	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1198	chr11	24699823	24700023	+	2.40730	NA	Intergenic	Intergenic	30799	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	-	predicted gene 10466	ncRNA	0.000000	0.442786			-54(TCTTTGCTTTGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1686	chr12	62216291	62216491	+	2.40730	NA	Intergenic	L1_Mur3|LINE|L1	-471396	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA	0.005000	0.358209			-32(CTATTGTCATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3897	chr18	62898148	62898348	+	2.40730	NA	Intergenic	Intergenic	-24079	NM_133237	494504	Mm.24042	NM_133237	ENSMUSG00000071847	Apcdd1	AB023957|AU041258|Drapc1|EIG180	adenomatosis polyposis coli down-regulated 1	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-91	chr1	29359271	29359471	+	2.40206	NA	Intergenic	MT2B1|LTR|ERVL	-62117	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA	0.005000	0.348259			-77(CTTAGCATTAGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7970	chrX	56431760	56431960	+	2.40206	NA	Intergenic	L1ME2|LINE|L1	-22979	NM_172779	236790	Mm.474772	NM_172779	ENSMUSG00000035967	Ints6l	4930535D10Rik|6330505F04Rik|D130066O12|Ddx26b	integrator complex subunit 6 like	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1816	chr12	92530430	92530630	+	2.40206	NA	Intergenic	Intergenic	-681373	NM_011344	20338	Mm.250605	NM_011344	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0.000000	0.378109			-38(ATTTTAATGACAGTTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-61	chr1	21775936	21776136	+	2.40206	NA	intron (NM_001160139, intron 1 of 14)	intron (NM_001160139, intron 1 of 14)	185906	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.005000	0.358209			11(TTTTTGGTATGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1404	chr11	89248658	89248858	+	2.39933	NA	Intergenic	Intergenic	53801	NM_008711	18121	Mm.135266	NM_008711	ENSMUSG00000048616	Nog	-	noggin	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5847	chr5	18882012	18882212	+	2.39933	NA	Intergenic	Intergenic	344443	NR_102341	70832	Mm.398993	NR_102341	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6047	chr5	80048264	80048464	+	2.39933	NA	Intergenic	Intergenic	-972207	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.248756			-41(ATTTGAAATAAAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-892	chr10	73983976	73984176	+	2.39587	NA	intron (NM_001142739, intron 2 of 31)	intron (NM_001142739, intron 2 of 31)	162209	NM_001142742	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding	0.025000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3952	chr18	80413629	80413829	+	2.39454	NA	intron (NM_026295, intron 12 of 12)	PB1D11|SINE|Alu	-49475	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4213	chr2	22953665	22953865	+	2.39020	NA	intron (NM_145994, intron 6 of 9)	intron (NM_145994, intron 6 of 9)	58243	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1393	chr11	87606101	87606301	+	2.38690	NA	intron (NM_001357901, intron 14 of 17)	intron (NM_001357901, intron 14 of 17)	-10963	NM_001045527	327992	Mm.390371	NM_001045527	ENSMUSG00000070345	Hsf5	Gm739|MLZ-220	heat shock transcription factor family member 5	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5110	chr3	109488500	109488700	+	2.38690	NA	intron (NM_020505, intron 2 of 26)	intron (NM_020505, intron 2 of 26)	-85407	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6370	chr6	28525675	28525875	+	2.38690	NA	intron (NM_019776, intron 4 of 23)	intron (NM_019776, intron 4 of 23)	45427	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7612	chr9	37241074	37241274	+	2.38690	NA	intron (NM_001145960, intron 3 of 18)	intron (NM_001145960, intron 3 of 18)	14564	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding	0.005000	0.497512			-79(ATAAACATGCCAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1027	chr10	110982281	110982481	+	2.38690	NA	intron (NM_001359622, intron 2 of 16)	intron (NM_001359622, intron 2 of 16)	27628	NM_001359622	320150	Mm.339281	NM_172554	ENSMUSG00000035798	Zdhhc17	A230053P19Rik|BB187739|D130071N24Rik|DHHC-17|Hip14	zinc finger, DHHC domain containing 17	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2976	chr15	67802143	67802343	+	2.38690	NA	Intergenic	Intergenic	456613	NM_198644	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding	0.000000	0.313433			-6(ACCTTCACATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7085	chr7	129930226	129930426	+	2.38690	NA	Intergenic	Intergenic	-31839	NR_046077	100043150	Mm.334264	NR_046077	ENSMUSG00000108504	Gm4265	-	predicted gene 4265	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6098	chr5	96685725	96685925	+	2.38690	NA	intron (NM_175473, intron 34 of 73)	intron (NM_175473, intron 34 of 73)	-107560	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3462	chr17	30166821	30167021	+	2.38581	NA	intron (NM_001356265, intron 4 of 5)	intron (NM_001356265, intron 4 of 5)	161882	NR_151442	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1352	chr11	74892063	74892263	+	2.38581	NA	intron (NM_197943, intron 1 of 22)	intron (NM_197943, intron 1 of 22)	4917	NM_197943	97761	Mm.245894	NM_197943	ENSMUSG00000038351	Sgsm2	D630003G22Rik|R74628|Rutbc1|mKIAA0397	small G protein signaling modulator 2	protein-coding	0.005000	0.373134			10(GCATTATTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2531	chr14	67676678	67676878	+	2.38064	NA	3' UTR (NM_175384, exon 15 of 15)	3' UTR (NM_175384, exon 15 of 15)	38832	NM_001110162	108912	Mm.33831	NM_175384	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4710	chr2	146356984	146357184	+	2.37995	NA	intron (NM_001033348, intron 27 of 40)	intron (NM_001033348, intron 27 of 40)	97798	NR_040619	77806	Mm.392819	NR_040619	ENSMUSG00000085958	A930019D19Rik	-	RIKEN cDNA A930019D19 gene	ncRNA	0.010000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2435	chr14	33293736	33293936	+	2.37965	NA	intron (NM_153800, intron 3 of 10)	B4|SINE|B4	77013	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding	0.010000	0.417910			74(CAATTTTTATTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1340	chr11	71902887	71903087	+	2.37685	NA	Intergenic	Intergenic	37135	NR_045942	73816	Mm.390391	NR_045942	ENSMUSG00000085528	4930401O10Rik	-	RIKEN cDNA 4930401O10 gene	ncRNA	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4747	chr2	157984327	157984527	+	2.37685	NA	intron (NM_029282, intron 7 of 7)	intron (NM_029282, intron 7 of 7)	44007	NM_029282	75425	Mm.29068	NM_029282	ENSMUSG00000027650	Tti1	2610036D13Rik|AI449463	TELO2 interacting protein 1	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3884	chr18	58067716	58067916	+	2.37638	NA	intron (NM_010181, intron 31 of 64)	URR1B|DNA|hAT-Charlie	142110	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding	0.020000	0.393035			9(ATTTACATTACAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4957	chr3	56494007	56494207	+	2.37638	NA	Intergenic	Intergenic	-310406	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6813	chr7	34804516	34804716	+	2.37638	NA	intron (NM_175140, intron 1 of 3)	intron (NM_175140, intron 1 of 3)	8095	NM_175140	68947	Mm.29380	NM_175140	ENSMUSG00000060402	Chst8	1500011J21Rik|AI426009	carbohydrate sulfotransferase 8	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2004	chr13	29713666	29713866	+	2.37638	NA	intron (NR_131896, intron 6 of 16)	intron (NR_131896, intron 6 of 16)	141907	NM_144536	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3953	chr18	80413978	80414178	+	2.37322	NA	intron (NM_026295, intron 12 of 12)	intron (NM_026295, intron 12 of 12)	-49824	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-170	chr1	58188626	58188826	+	2.37185	NA	intron (NM_023617, intron 33 of 34)	intron (NM_023617, intron 33 of 34)	-21671	NM_023631	71872	Mm.244525	NM_023631	ENSMUSG00000038242	Aox4	2310003G12Rik|Aoh2	aldehyde oxidase 4	protein-coding	0.005000	0.452736			-42(CTTTGAATAGCAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2770	chr15	7322965	7323165	+	2.36879	NA	intron (NM_178748, intron 1 of 21)	L1MC1|LINE|L1	75325	NM_178748	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding	0.000000	0.353234			-100(CTCTTGTTATTTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6827	chr7	39978093	39978293	+	2.36728	NA	Intergenic	RMER15|LTR|ERVL	460427	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3543	chr17	59384989	59385189	+	2.36728	NA	Intergenic	Intergenic	-371767	NM_001368393	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1637	chr12	45133768	45133968	+	2.36728	NA	Intergenic	Intergenic	-59385	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4665	chr2	138697266	138697466	+	2.36728	NA	Intergenic	Lx8b|LINE|L1	-122563	NR_035477	100316816		NR_035477	ENSMUSG00000088983	Mir1952	mmu-mir-1952	microRNA 1952	ncRNA	0.005000	0.417910			-65(ACATTCCTATGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2520	chr14	63174580	63174780	+	2.36728	NA	intron (NM_001360211, intron 1 of 7)	intron (NM_001360211, intron 1 of 7)	3207	NM_001360211	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7009	chr7	105506546	105506746	+	2.36637	NA	Intergenic	Intergenic	-24449	NM_028444	109042	Mm.3124	NM_028444	ENSMUSG00000037060	Cavin3	3110015B12Rik|6330514M23Rik|Prkcdbp|SRBC	caveolae associated 3	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1729	chr12	71817373	71817573	+	2.36472	NA	Intergenic	Intergenic	-13595	NM_026102	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2248	chr13	100819683	100819883	+	2.36290	NA	intron (NM_022885, intron 5 of 15)	intron (NM_022885, intron 5 of 15)	13644	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	solute carrier family 30 (zinc transporter), member 5	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4055	chr19	26770345	26770545	+	2.36290	NA	intron (NR_045306, intron 3 of 3)	intron (NR_045306, intron 3 of 3)	22042	NM_026003	67155	Mm.491146	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.035000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2250	chr13	101588033	101588233	+	2.35924	NA	Intergenic	Intergenic	104497	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7581	chr9	29733125	29733325	+	2.35924	NA	intron (NM_001357597, intron 1 of 8)	intron (NM_001357597, intron 1 of 8)	230044	NM_001357598	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1896	chr12	116452434	116452634	+	2.35924	NA	intron (NM_133762, intron 28 of 28)	ORR1D1|LTR|ERVL-MaLR	-33186	NM_011215	19276	Mm.206054	NM_011215	ENSMUSG00000056553	Ptprn2	4930425H11Rik|IA2beta|PTP-NP|Phol|mKIAA0387|phogrin	protein tyrosine phosphatase, receptor type, N polypeptide 2	protein-coding	0.015000	0.487562			-55(GTTTGAATGAGAACGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3478	chr17	36982238	36982438	+	2.35567	NA	Intergenic	Intergenic	-1101	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2258	chr13	103065668	103065868	+	2.35478	NA	intron (NM_175171, intron 3 of 28)	intron (NM_175171, intron 3 of 28)	268724	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding	0.025000	0.393035			54(ATTTGCTTCACAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2286	chr13	109691326	109691526	+	2.35207	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-212383	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3375	chr16	88629218	88629418	+	2.35206	NA	Intergenic	Intergenic	-1652	NM_027173	69699	Mm.158296	NM_027173	ENSMUSG00000045331	2310079G19Rik	-	RIKEN cDNA 2310079G19 gene	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6960	chr7	90493189	90493389	+	2.35206	NA	Intergenic	L1MA6|LINE|L1	-17294	NM_026734	68472	Mm.289791	NM_026734	ENSMUSG00000030614	Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3265	chr16	60225517	60225717	+	2.35206	NA	intron (NM_007938, intron 3 of 17)	intron (NM_007938, intron 3 of 17)	379914	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0.005000	0.308458			-83(TTTTACTCATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-657	chr1	194239882	194240082	+	2.34909	NA	Intergenic	Intergenic	-17223	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3756	chr18	26506430	26506630	+	2.34555	NA	Intergenic	Intergenic	-752373	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.010000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7377	chr8	93441697	93441897	+	2.34555	NA	Intergenic	RLTR13D6|LTR|ERVK	-62020	NM_001370830	75704	Mm.480920	NM_001370830	ENSMUSG00000074156	Ces1h	2310039D24Rik	carboxylesterase 1H	protein-coding	0.025000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6795	chr7	16579421	16579621	+	2.34555	NA	intron (NM_172739, intron 1 of 6)	intron (NM_172739, intron 1 of 6)	-34303	NR_136928	102634559	Mm.421602	NR_136928	ENSMUSG00000100583	Gm29443	-	predicted gene 29443	ncRNA	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4800	chr2	173781900	173782100	+	2.34555	NA	3' UTR (NM_019806, exon 6 of 6)	3' UTR (NM_019806, exon 6 of 6)	44429	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding	0.020000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-632	chr1	189664309	189664509	+	2.34341	NA	intron (NM_001081363, intron 10 of 17)	intron (NM_001081363, intron 10 of 17)	23677	NM_001081363	108000	Mm.129746	NM_001081363	ENSMUSG00000026605	Cenpf	6530404A22Rik|AI325968|CENF|Lek1|PRO1779|mitosin	centromere protein F	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8058	chrX	109100862	109101062	+	2.34292	NA	intron (NM_019989, intron 1 of 3)	intron (NM_019989, intron 1 of 3)	5555	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7892	chr9	114706344	114706544	+	2.34230	NA	intron (NM_146229, intron 4 of 12)	intron (NM_146229, intron 4 of 12)	17613	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-894	chr10	75266775	75266975	+	2.34230	NA	intron (NM_153406, intron 9 of 15)	intron (NM_153406, intron 9 of 15)	-50002	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR|ARA2A	adenosine A2a receptor	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4571	chr2	123980799	123980999	+	2.34230	NA	Intergenic	Intergenic	-109070	NM_001290997	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding	0.005000	0.283582		-76(CACGAATATTCATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-927	chr10	88975525	88975725	+	2.34230	NA	intron (NR_102339, intron 21 of 26)	intron (NR_102339, intron 21 of 26)	89633	NM_145423	216225	Mm.77381	NM_145423	ENSMUSG00000020062	Slc5a8	Ait|SMCT	solute carrier family 5 (iodide transporter), member 8	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6428	chr6	45920157	45920357	+	2.34230	NA	intron (NM_001004357, intron 3 of 23)	intron (NM_001004357, intron 3 of 23)	860196	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4301	chr2	51715577	51715777	+	2.34230	NA	intron (NR_040639, intron 1 of 6)	intron (NR_040639, intron 1 of 6)	16332	NR_040639	433426	Mm.244381	NR_040639	ENSMUSG00000085014	Gm13490	-	predicted gene 13490	ncRNA	0.000000	0.417910			16(CTTAGCATCAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8106	chrX	143669969	143670169	+	2.34230	NA	intron (NM_001195049, intron 1 of 17)	intron (NM_001195049, intron 1 of 17)	4324	NM_001195049	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 (RAC1) activated kinase 3	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2458	chr14	40441900	40442100	+	2.34230	NA	Intergenic	Intergenic	451314	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7124	chr7	141926867	141927067	+	2.34230	NA	Intergenic	Intergenic	-22784	NM_001009929	75770	Mm.274868	NM_029426	ENSMUSG00000053046	Brsk2	4833424K13Rik|SAD-A|SADA	BR serine/threonine kinase 2	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1560	chr12	17231126	17231326	+	2.34230	NA	Intergenic	Intergenic	-35363	NM_027959	71853	Mm.222825	NM_027959	ENSMUSG00000020571	Pdia6	1700015E05Rik|AL023058|C77895|CaBP5|P5|Txndc7	protein disulfide isomerase associated 6	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-27	chr1	9592155	9592355	+	2.34183	NA	intron (NR_015470, intron 3 of 4)	MER5A|DNA|hAT-Charlie	-9012	NM_178399	76982	Mm.491098	NM_178399	ENSMUSG00000067879	Vxn	3110035E14Rik|AI415019|AV164974|R75066	vexin	protein-coding	0.010000	0.457711			25(ATTTGCATGTCTAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-391	chr1	135658920	135659120	+	2.34183	NA	Intergenic	Intergenic	-61043	NM_001360782	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding	0.005000	0.393035		-14(TATACATATGAATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7286	chr8	62752712	62752912	+	2.34183	NA	Intergenic	Intergenic	-198420	NM_001252621	72902	Mm.334552	NM_023689	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1689	chr12	63032051	63032251	+	2.34183	NA	Intergenic	ETnERV2-int|LTR|ERVK	344364	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1507	chr11	121802347	121802547	+	2.33962	NA	Intergenic	Intergenic	-27771	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5349	chr4	13259058	13259258	+	2.33914	NA	Intergenic	RLTR31D_MM|LTR|ERVK	352321	NM_001171801	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818	triple QxxK/R motif containing	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3853	chr18	53195596	53195796	+	2.33914	NA	intron (NM_026386, intron 3 of 14)	intron (NM_026386, intron 3 of 14)	19404	NM_001357463	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding	0.020000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5874	chr5	26508088	26508288	+	2.33914	NA	Intergenic	Intergenic	-14874	NR_029445	75942	Mm.50087	NR_029445	ENSMUSG00000029044	4930584F24Rik	1700001J09Rik|4930522C06Rik	RIKEN cDNA 4930584F24 gene	ncRNA	0.000000	0.358209			-18(ATTTTCTTTTATAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5181	chr3	127921107	127921307	+	2.33914	NA	intron (NR_040552, intron 1 of 4)	MER5A|DNA|hAT-Charlie	5036	NR_040552	329753	Mm.119720	NR_040552	ENSMUSG00000104763	9830132P13Rik	9830132P13	RIKEN cDNA 9830132P13 gene	ncRNA	0.010000	0.472637			36(AGATTCTTATGTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4362	chr2	65953527	65953727	+	2.33914	NA	intron (NM_001290666, intron 3 of 4)	intron (NM_001290666, intron 3 of 4)	21762	NM_001290665	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding	0.010000	0.368159			65(TGTTGTTTTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1828	chr12	95874972	95875172	+	2.33914	NA	Intergenic	Intergenic	172150	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7006	chr7	104205859	104206059	+	2.33699	NA	Intergenic	Intergenic	-12836	NM_001013616	94088	Mm.274843	NM_001013616	ENSMUSG00000072244	Trim6	C430046K18Rik|D7Ertd684e	tripartite motif-containing 6	protein-coding	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7451	chr8	113612513	113612713	+	2.33699	NA	Intergenic	(TCTG)n|Simple_repeat|Simple_repeat	-22973	NM_001048143	270096	Mm.74689	NM_173015	ENSMUSG00000078908	Mon1b	5031407H10|5033413H12Rik	MON1 homolog B, secretory traffciking associated	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7229	chr8	43353680	43353880	+	2.33699	NA	Intergenic	BGLII|LTR|ERVK	-46771	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-810	chr10	48774379	48774579	+	2.33699	NA	Intergenic	Lx2|LINE|L1	1013458	NM_001358866	14806	Mm.185993	NM_010349	ENSMUSG00000056073	Grik2	AW124492|C130030K03Rik|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4729	chr2	152489939	152490139	+	2.33699	NA	promoter-TSS (NM_001002791)	promoter-TSS (NM_001002791)	99	NM_001002791	442835	Mm.99065	NM_001002791	ENSMUSG00000027468	Defb22	9230002F21Rik	defensin beta 22	protein-coding	0.015000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1007	chr10	107752010	107752210	+	2.33699	NA	Intergenic	Intergenic	-32169	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	R-PTP-Q	protein tyrosine phosphatase, receptor type, Q	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5573	chr4	83471634	83471834	+	2.33555	NA	intron (NM_133948, intron 6 of 15)	Tigger1|DNA|TcMar-Tigger	14729	NM_001347143	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7045	chr7	119873056	119873256	+	2.33555	NA	intron (NM_001163703, intron 1 of 2)	intron (NM_001163703, intron 1 of 2)	22302	NM_173408	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4872	chr3	22183624	22183824	+	2.33555	NA	intron (NM_030732, intron 3 of 15)	intron (NM_030732, intron 3 of 15)	-67646	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4069	chr19	32723937	32724137	+	2.33555	NA	Intergenic	Intergenic	-11739	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding	0.025000	0.447761			-42(ATAAGAATAACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5214	chr3	136208518	136208718	+	2.33555	NA	intron (NM_001033350, intron 7 of 16)	intron (NM_001033350, intron 7 of 16)	117448	NM_001310749	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4822	chr3	4137983	4138183	+	2.33555	NA	Intergenic	RLTR13D6|LTR|ERVK	630053	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1549	chr12	13984181	13984381	+	2.33416	NA	Intergenic	Intergenic	167757	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Lratd1	2310003N02Rik|4731402F03Rik|AW125753|Fam84a|Nse1	LRAT domain containing 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2271	chr13	106817181	106817381	+	2.33267	NA	intron (NM_029665, intron 28 of 29)	intron (NM_029665, intron 28 of 29)	119677	NM_001360897	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4074	chr19	34455311	34455511	+	2.33161	NA	Intergenic	Intergenic	19737	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2889	chr15	42536159	42536359	+	2.33161	NA	intron (NM_001286062, intron 1 of 8)	intron (NM_001286062, intron 1 of 8)	140718	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3050	chr15	96589169	96589369	+	2.33161	NA	intron (NM_001166458, intron 7 of 15)	intron (NM_001166458, intron 7 of 15)	52693	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2669	chr14	105009993	105010193	+	2.33161	NA	Intergenic	Intergenic	167221	NM_134077	74213	Mm.124957	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-593	chr1	182573588	182573788	+	2.32759	NA	intron (NM_130890, intron 2 of 20)	intron (NM_130890, intron 2 of 20)	8681	NM_001145806	170725	Mm.189201	NM_130890	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4112	chr19	49728879	49729079	+	2.32759	NA	Intergenic	Intergenic	949667	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.005000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-580	chr1	178772588	178772788	+	2.32759	NA	intron (NM_001161665, intron 4 of 14)	tRNA-Ala-GCY_|tRNA|tRNA	243563	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5478	chr4	55049017	55049217	+	2.32360	NA	intron (NM_172867, intron 7 of 12)	intron (NM_172867, intron 7 of 12)	101172	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip|Znf462	zinc finger protein 462	protein-coding	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3266	chr16	60225615	60225815	+	2.32360	NA	intron (NM_007938, intron 3 of 17)	intron (NM_007938, intron 3 of 17)	379816	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7424	chr8	104126555	104126755	+	2.32360	NA	exon (NM_009868, exon 4 of 12)	exon (NM_009868, exon 4 of 12)	-20782	NR_131138	546096	Mm.252264	NR_131138	ENSMUSG00000110053	Gm29682	Gm45664	predicted gene, 29682	ncRNA	0.030000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-276	chr1	93703634	93703834	+	2.32296	NA	Intergenic	Intergenic	18159	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	matador|mtd	BCL2-related ovarian killer	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3896	chr18	62898029	62898229	+	2.31971	NA	Intergenic	Intergenic	-24198	NM_133237	494504	Mm.24042	NM_133237	ENSMUSG00000071847	Apcdd1	AB023957|AU041258|Drapc1|EIG180	adenomatosis polyposis coli down-regulated 1	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2276	chr13	108273382	108273582	+	2.31971	NA	intron (NM_029001, intron 5 of 7)	intron (NM_029001, intron 5 of 7)	-42855	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5048	chr3	84672805	84673005	+	2.31971	NA	intron (NM_177260, intron 1 of 6)	intron (NM_177260, intron 1 of 6)	6713	NM_177260	320782	Mm.107370	NM_177260	ENSMUSG00000056498	Tmem154	9930117H01Rik	transmembrane protein 154	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3161	chr16	33697715	33697915	+	2.31879	NA	intron (NM_175256, intron 1 of 14)	intron (NM_175256, intron 1 of 14)	13349	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629	heart development protein with EGF-like domains 1	protein-coding	0.020000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5800	chr4	153221189	153221389	+	2.31595	NA	Intergenic	RMER1A|Other|Other	261541	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding	0.010000	0.472637			-45(ATTTTCACTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3661	chr17	90384990	90385190	+	2.31595	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	70790	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5732	chr4	126053646	126053846	+	2.31480	NA	intron (NM_025544, intron 6 of 7)	intron (NM_025544, intron 6 of 7)	-4819	NM_001356446	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6703	chr6	120358836	120359036	+	2.31232	NA	intron (NR_045558, intron 1 of 9)	intron (NR_045558, intron 1 of 9)	-1467	NM_026028	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1728	chr12	71817142	71817342	+	2.30478	NA	Intergenic	Intergenic	-13826	NM_026102	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.005000	0.358209			73(ATTATCAAAACAAGGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6616	chr6	100973795	100973995	+	2.30228	NA	Intergenic	Intergenic	140257	NM_182939	232314	Mm.27223	NM_182939	ENSMUSG00000052144	Ppp4r2	BE691708|C230060M08Rik	protein phosphatase 4, regulatory subunit 2	protein-coding	0.005000	0.507463			36(GATTTGCTTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4314	chr2	55182051	55182251	+	2.29520	NA	Intergenic	Intergenic	-253819	NM_001355118	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-937	chr10	91492980	91493180	+	2.29520	NA	Intergenic	Intergenic	-272461	NR_151510	102633753	Mm.416936	NR_151510		4930534H03Rik	-	RIKEN cDNA 4930534H03 gene	ncRNA	0.020000	0.437811			55(TTTAGAATAAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1592	chr12	34166506	34166706	+	2.29520	NA	intron (NM_001271386, intron 24 of 27)	intron (NM_001271386, intron 24 of 27)	208935	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding	0.000000	0.333333			7(CTATAATTATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4719	chr2	149844525	149844725	+	2.29520	NA	intron (NM_001363094, intron 2 of 4)	intron (NM_001363094, intron 2 of 4)	13842	NM_001363094	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|Tmem90b	synapse differentiation inducing 1	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-428	chr1	143567919	143568119	+	2.29502	NA	Intergenic	Intergenic	-72678	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding	0.015000	0.358209			-11(GATTTGTTTTGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7875	chr9	110163550	110163750	+	2.29502	NA	intron (NM_009211, intron 7 of 27)	intron (NM_009211, intron 7 of 27)	31626	NM_009211	20588	Mm.85410	NM_009211	ENSMUSG00000032481	Smarcc1	AI115498|BAF155|Rsc8|SRG3|msp3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2750	chr14	123941385	123941585	+	2.29502	NA	intron (NM_145467, intron 7 of 10)	intron (NM_145467, intron 7 of 10)	-46150	NR_045479	69393	Mm.491348	NR_045479	ENSMUSG00000099994	1700024B18Rik	-	RIKEN cDNA 1700024B18 gene	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4920	chr3	41358750	41358950	+	2.29502	NA	Intergenic	L1_Mur2|LINE|L1	134349	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-851	chr10	63763744	63763944	+	2.29502	NA	intron (NM_177612, intron 5 of 17)	intron (NM_177612, intron 5 of 17)	-57211	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5360	chr4	15069902	15070102	+	2.29502	NA	intron (NM_178617, intron 3 of 12)	intron (NM_178617, intron 3 of 12)	79129	NM_178617	69352	Mm.389031	NM_178617	ENSMUSG00000040536	Necab1	1700003H21Rik|Efcbp1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding	0.005000	0.318408			-1(GTATTTTCTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3939	chr18	74967550	74967750	+	2.29455	NA	Intergenic	L2b|LINE|L2	-6387	NM_010720	16891	Mm.299647	NM_010720	ENSMUSG00000053846	Lipg	3110013K01Rik|EL|lipase|mEDL	lipase, endothelial	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4012	chr19	14543989	14544189	+	2.29455	NA	intron (NM_001302950, intron 5 of 18)	intron (NM_001302950, intron 5 of 18)	53124	NM_001302951	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding	0.005000	0.388060			74(TCTTTGTTATTCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8025	chrX	93687745	93687945	+	2.29455	NA	intron (NM_211138, intron 1 of 7)	ID4_|SINE|ID	12733	NM_211138	236899	Mm.166467	NM_177546	ENSMUSG00000035246	Pcyt1b	AW045697|CTTbeta	phosphate cytidylyltransferase 1, choline, beta isoform	protein-coding	0.000000	0.313433			-8(GGTTTTTCATGTTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5453	chr4	49283963	49284163	+	2.29350	NA	intron (NM_178756, intron 3 of 7)	intron (NM_178756, intron 3 of 7)	121695	NM_001356289	209186	Mm.35071	NM_145368	ENSMUSG00000060317	Acnat2	C730036D15Rik	acyl-coenzyme A amino acid N-acyltransferase 2	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5228	chr3	138449932	138450132	+	2.29350	NA	intron (NM_007410, intron 4 of 8)	intron (NM_007410, intron 4 of 8)	6939	NM_007410	11532	Mm.3874	NM_007410	ENSMUSG00000028138	Adh5	Adh-5|Adh3|GSNOR	alcohol dehydrogenase 5 (class III), chi polypeptide	protein-coding	0.000000	0.388060			19(ATTTGCAAGGAAAGAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2156	chr13	77470108	77470308	+	2.29350	NA	intron (NM_001145676, intron 19 of 19)	intron (NM_001145676, intron 19 of 19)	-238482	NM_001163420	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding	0.015000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2331	chr13	119210643	119210843	+	2.29350	NA	Intergenic	Intergenic	198268	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000116207	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4092	chr19	42805515	42805715	+	2.29350	NA	intron (NM_001081257, intron 11 of 11)	intron (NM_001081257, intron 11 of 11)	-25637	NM_001346703	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Gm21361|Hps|ep	HPS1, biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4370	chr2	67929813	67930013	+	2.29350	NA	Intergenic	Intergenic	148870	NR_105752	102466627		NR_105752	ENSMUSG00000098734	Mir6335	Gm27836|mmu-mir-6335	microRNA 6335	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1752	chr12	77452124	77452324	+	2.29350	NA	intron (NM_016893, intron 10 of 11)	intron (NM_016893, intron 10 of 11)	42083	NM_001252616	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4046	chr19	22076866	22077066	+	2.29350	NA	Intergenic	Intergenic	-62080	NM_001035240	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1737	chr12	73068188	73068388	+	2.29350	NA	Intergenic	Intergenic	-21576	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding	0.000000	0.348259			21(ATTAGCATAACTCTGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4670	chr2	139876013	139876213	+	2.29338	NA	intron (NM_175225, intron 12 of 13)	intron (NM_175225, intron 12 of 13)	190692	NM_001289611	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5496	chr4	59629607	59629807	+	2.29338	NA	intron (NM_001015681, intron 1 of 3)	intron (NM_001015681, intron 1 of 3)	3496	NM_001015681	230259	Mm.45688	NM_153158	ENSMUSG00000045071	E130308A19Rik	-	RIKEN cDNA E130308A19 gene	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-163	chr1	56226660	56226860	+	2.29338	NA	Intergenic	Intergenic	207782	NR_126075	69356	Mm.393775	NR_126075	ENSMUSG00000100372	1700003I22Rik	-	RIKEN cDNA 1700003I22 gene	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-824	chr10	53506185	53506385	+	2.29338	NA	intron (NR_037973, intron 3 of 3)	intron (NR_037973, intron 3 of 3)	12704	NR_037973	100502868	Mm.297722	NR_037973	ENSMUSG00000112739	Gm20597	B230314j19	predicted gene, 20597	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7378	chr8	93442012	93442212	+	2.29187	NA	Intergenic	RLTR13D6|LTR|ERVK	-62335	NM_001370830	75704	Mm.480920	NM_001370830	ENSMUSG00000074156	Ces1h	2310039D24Rik	carboxylesterase 1H	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-316	chr1	109095080	109095280	+	2.29014	NA	Intergenic	Intergenic	-887720	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding	0.000000	0.288557			-91(CTATTTTCATGCAAAA,+,0.00),-89(ATTTTCATGCAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5658	chr4	103458499	103458699	+	2.28972	NA	intron (NR_040673, intron 3 of 3)	intron (NR_040673, intron 3 of 3)	76099	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	-	predicted gene 12718	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4123	chr19	54003041	54003241	+	2.28972	NA	exon (NM_001168505, exon 3 of 9)	exon (NM_001168505, exon 3 of 9)	-42118	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4060	chr19	28441175	28441375	+	2.28972	NA	intron (NM_175459, intron 4 of 10)	URR1A|DNA|hAT-Charlie	-236949	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7980	chrX	68627517	68627717	+	2.28972	NA	Intergenic	RLTR20B5_MM|LTR|ERVK	50782	NR_033481	100038638	Mm.368431	NR_033481	ENSMUSG00000096946	Fmr1os	Asfmr1|Gm10474	fragile X mental retardation 1, opposite strand	ncRNA	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4249	chr2	33279963	33280163	+	2.28972	NA	intron (NM_175211, intron 5 of 19)	L1MC3|LINE|L1	64102	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2662	chr14	102466708	102466908	+	2.28972	NA	Intergenic	Lx2|LINE|L1	515824	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-776	chr10	38906330	38906530	+	2.28434	NA	Intergenic	Intergenic	-59085	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5250	chr3	145465266	145465466	+	2.28434	NA	intron (NM_001317733, intron 37 of 59)	intron (NM_001317733, intron 37 of 59)	-110842	NM_001081094	229937	Mm.24586	NM_001081094	ENSMUSG00000074182	Znhit6	2410019A14Rik	zinc finger, HIT type 6	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3907	chr18	65606698	65606898	+	2.28232	NA	intron (NM_001361052, intron 1 of 8)	intron (NM_001361052, intron 1 of 8)	115	NM_001361052	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7885	chr9	113080562	113080762	+	2.28188	NA	Intergenic	L1M2|LINE|L1	506490	NR_040760	102688	Mm.394901	NR_040760	ENSMUSG00000109890	AU023762	-	expressed sequence AU023762	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3986	chr18	86005926	86006126	+	2.28188	NA	Intergenic	Intergenic	-388926	NM_001360910	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0.000000	0.218905			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7284	chr8	62451431	62451631	+	2.28188	NA	Intergenic	Intergenic	-328338	NM_011922	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6874	chr7	63228721	63228921	+	2.28188	NA	Intergenic	URR1B|DNA|hAT-Charlie	-16295	NM_007390	11441	Mm.113464	NM_007390	ENSMUSG00000030525	Chrna7	Acra7|alpha7|nAchR	cholinergic receptor, nicotinic, alpha polypeptide 7	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3038	chr15	94811979	94812179	+	2.28188	NA	intron (NM_178789, intron 3 of 7)	intron (NM_178789, intron 3 of 7)	182894	NM_178789	320709	Mm.74873	NM_178789	ENSMUSG00000063296	Tmem117	B930062P21Rik	transmembrane protein 117	protein-coding	0.010000	0.398010		-42(AATGCATTTTCATT,+,0.00),-42(AATGCATTTTCATT,-,0.00)	-32(CATTAGCTTTGCAAAT,+,0.00),-4(ATCAAAATAACAATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4259	chr2	37986664	37986864	+	2.28188	NA	intron (NM_001362973, intron 10 of 22)	intron (NM_001362973, intron 10 of 22)	210515	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-672	chr10	4402502	4402702	+	2.28188	NA	TTS (NR_002891)	TTS (NR_002891)	-14494	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4615	chr2	131308279	131308479	+	2.28188	NA	intron (NM_178607, intron 3 of 5)	intron (NM_178607, intron 3 of 5)	20327	NR_029755	723825		NR_029755	ENSMUSG00000065563	Mir103-2	Mirn103-2|mir-103-2	microRNA 103-2	ncRNA	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2232	chr13	97103622	97103822	+	2.28188	NA	intron (NM_001100458, intron 5 of 12)	intron (NM_001100458, intron 5 of 12)	32079	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding	0.020000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7511	chr9	8676595	8676795	+	2.26741	NA	intron (NM_013838, intron 10 of 12)	intron (NM_013838, intron 10 of 12)	64293	NR_110513	102634431	Mm.387913	NR_110513	ENSMUSG00000111602	Gm32014	-	predicted gene, 32014	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1160	chr11	12262705	12262905	+	2.26741	NA	intron (NM_001282993, intron 9 of 13)	intron (NM_001282993, intron 9 of 13)	149335	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding	0.005000	0.383085			65(ATTTGCAGGCCAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7282	chr8	62073318	62073518	+	2.26737	NA	intron (NM_011922, intron 5 of 10)	intron (NM_011922, intron 5 of 10)	49775	NM_001136089	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-671	chr10	4233738	4233938	+	2.26737	NA	Intergenic	Intergenic	-20718	NR_152620	102632515	Mm.416995	NR_152620	ENSMUSG00000111266	Gm30570	-	predicted gene, 30570	ncRNA	0.000000	0.383085			25(ATTTGCAAGTAAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5856	chr5	21466968	21467168	+	2.26690	NA	intron (NM_177869, intron 7 of 7)	intron (NM_177869, intron 7 of 7)	42165	NM_177869	330050	Mm.40655	NM_177869	ENSMUSG00000047221	Fam185a	4631428I10|AI847670	family with sequence similarity 185, member A	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5795	chr4	151519005	151519205	+	2.26655	NA	intron (NM_001081557, intron 4 of 23)	intron (NM_001081557, intron 4 of 23)	342663	NM_001195565	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding	0.020000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3211	chr16	47002386	47002586	+	2.26616	NA	Intergenic	Intergenic	-505519	NM_021495	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-650	chr1	194176983	194177183	+	2.26614	NA	Intergenic	Intergenic	45676	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2069	chr13	51083198	51083398	+	2.26614	NA	Intergenic	RLTR19-int|LTR|ERVK	17429	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA	0.005000	0.407960			6(GGTTTGCCTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7642	chr9	47776045	47776245	+	2.26614	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	42063	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	-	predicted gene 10677	ncRNA	0.005000	0.393035			-28(ATTTGCATCACCAGGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2060	chr13	46686107	46686307	+	2.26614	NA	intron (NM_175749, intron 18 of 21)	intron (NM_175749, intron 18 of 21)	16685	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7949	chrX	38361731	38361931	+	2.26614	NA	Intergenic	Lx5c|LINE|L1	45709	NM_133690	67821	Mm.60134	NM_133690	ENSMUSG00000016327	Atp1b4	1110020B02Rik	ATPase, (Na+)/K+ transporting, beta 4 polypeptide	protein-coding	0.010000	0.442786			-70(CTATACTCATGTAATT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-95	chr1	33878857	33879057	+	2.26614	NA	intron (NM_001310484, intron 1 of 5)	intron (NM_001310484, intron 1 of 5)	28664	NM_177235	320705	Mm.336619	NM_177235	ENSMUSG00000042182	Bend6	B230209C24Rik	BEN domain containing 6	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6984	chr7	97150645	97150845	+	2.26614	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	68994	NM_001162477	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8100	chrX	141613278	141613478	+	2.26614	NA	intron (NM_001163155, intron 24 of 50)	intron (NM_001163155, intron 24 of 50)	111839	NM_010572	16370	Mm.261591	NM_010572	ENSMUSG00000054667	Irs4	IRS-4	insulin receptor substrate 4	protein-coding	0.020000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3015	chr15	90022478	90022678	+	2.26490	NA	Intergenic	Intergenic	-180718	NM_018803	54526	Mm.261601	NM_018803	ENSMUSG00000063260	Syt10	-	synaptotagmin X	protein-coding	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3491	chr17	43647748	43647948	+	2.26490	NA	intron (NM_001357122, intron 6 of 8)	intron (NM_001357122, intron 6 of 8)	-17549	NM_001161367	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7855	chr9	103156727	103156927	+	2.26421	NA	intron (NM_173781, intron 2 of 7)	intron (NM_173781, intron 2 of 7)	44753	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3262	chr16	58638096	58638296	+	2.26308	NA	intron (NM_175011, intron 1 of 3)	intron (NM_175011, intron 1 of 3)	207	NM_175011	224247	Mm.26145	NM_175011	ENSMUSG00000055789	E330017A01Rik	-	RIKEN cDNA E330017A01 gene	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-217	chr1	80135020	80135220	+	2.26206	NA	Intergenic	Intergenic	78824	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-784	chr10	39403993	39404193	+	2.26206	NA	intron (NM_001122892, intron 2 of 12)	intron (NM_001122892, intron 2 of 12)	34294	NM_001122892	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1243	chr11	37368099	37368299	+	2.26206	NA	Intergenic	Intergenic	-290790	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7395	chr8	97533111	97533311	+	2.25746	NA	Intergenic	Intergenic	-1478676	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	-	predicted gene 15679	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7918	chrX	9231053	9231253	+	2.25016	NA	intron (NM_173414, intron 1 of 4)	intron (NM_173414, intron 1 of 4)	31180	NM_173414	236285	Mm.245119	NM_173414	ENSMUSG00000047344	Lancl3	6030463G20Rik	LanC lantibiotic synthetase component C-like 3 (bacterial)	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7699	chr9	65937628	65937828	+	2.25016	NA	intron (NM_173185, intron 1 of 13)	intron (NM_173185, intron 1 of 13)	28718	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	casein kinase 1, gamma 1	protein-coding	0.010000	0.348259			-38(CTAAGCAAGAGAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2448	chr14	38276971	38277171	+	2.25016	NA	Intergenic	Intergenic	-621231	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-197	chr1	67145131	67145331	+	2.25016	NA	intron (NM_001080809, intron 4 of 37)	intron (NM_001080809, intron 4 of 37)	22204	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1084	chr10	119677536	119677736	+	2.25016	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	84063	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	Grip1os2	4930564G21Rik	glutamate receptor interacting protein 1, opposite strand 2	ncRNA	0.005000	0.313433			-59(TTATTATTATTTTAAT,+,0.00),5(TTTTTTTTTTGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-563	chr1	175989792	175989992	+	2.25016	NA	intron (NM_001195816, intron 6 of 9)	L1MB7|LINE|L1	69563	NM_001290692	226720	Mm.11282	NM_001290692	ENSMUSG00000104158	Becn2	Beclin-2|Gm104	beclin 2	protein-coding	0.000000	0.368159			44(ATTTACAATACAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5275	chr3	148848359	148848559	+	2.24470	NA	intron (NM_001081298, intron 9 of 23)	intron (NM_001081298, intron 9 of 23)	106176	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.005000	0.378109			-54(ATTTGAAACACATTGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7819	chr9	93284240	93284440	+	2.24470	NA	Intergenic	Intergenic	-278607	NR_040756	78349	Mm.52612	NR_040756	ENSMUSG00000100294	1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4276	chr2	44180735	44180935	+	2.24244	NA	intron (NM_001364029, intron 10 of 12)	intron (NM_001364029, intron 10 of 12)	-115511	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5845	chr5	17902458	17902658	+	2.23920	NA	Intergenic	Intergenic	-13599	NM_001159558	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 molecule	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-183	chr1	63075445	63075645	+	2.23920	NA	intron (NM_001114609, intron 6 of 11)	intron (NM_001114609, intron 6 of 11)	38722	NM_001081436	227195	Mm.74718	NM_001081436	ENSMUSG00000040865	Ino80d	7330405I11|A430093A21Rik|BC010584	INO80 complex subunit D	protein-coding	0.000000	0.353234			69(ATTTACACAAGAGAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2616	chr14	88508562	88508762	+	2.23849	NA	Intergenic	Intergenic	-37266	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6225	chr5	139136405	139136605	+	2.23849	NA	intron (NM_001359097, intron 1 of 10)	intron (NM_001359097, intron 1 of 10)	-6028	NM_001359099	19085	Mm.306163	NM_008923	ENSMUSG00000025855	Prkar1b	AI385716|RIbeta	protein kinase, cAMP dependent regulatory, type I beta	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1804	chr12	88555651	88555851	+	2.23849	NA	Intergenic	Lx8b|LINE|L1	-178428	NR_045888	71818	Mm.490789	NR_045888	ENSMUSG00000113434	3200001D21Rik	-	RIKEN cDNA 3200001D21 gene	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1789	chr12	86014420	86014620	+	2.23849	NA	intron (NM_001364627, intron 31 of 31)	intron (NM_001364627, intron 31 of 31)	64521	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-76	chr1	24520550	24520750	+	2.23849	NA	intron (NM_007733, intron 9 of 50)	intron (NM_007733, intron 9 of 50)	66787	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3545	chr17	60473955	60474155	+	2.23849	NA	Intergenic	Intergenic	-1460733	NM_001368393	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.000000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4694	chr2	142797339	142797539	+	2.23849	NA	intron (NM_001355123, intron 12 of 26)	intron (NM_001355123, intron 12 of 26)	104025	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6236	chr5	141934784	141934984	+	2.23461	NA	intron (NM_177879, intron 5 of 44)	intron (NM_177879, intron 5 of 44)	-466613	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|Gm10868|Mnf	forkhead box K1	protein-coding	0.005000	0.437811			36(CTTTGGTCATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-86	chr1	28870798	28870998	+	2.23461	NA	Intergenic	Intergenic	-90646	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4844	chr3	11328307	11328507	+	2.23275	NA	Intergenic	Intergenic	515952	NR_040751	100038545	Mm.388494	NR_040751	ENSMUSG00000104015	Gm10745	-	predicted gene 10745	ncRNA	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3511	chr17	50598776	50598976	+	2.23261	NA	intron (NM_013880, intron 1 of 5)	intron (NM_013880, intron 1 of 5)	89329	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4273	chr2	43921483	43921683	+	2.23261	NA	intron (NM_001364029, intron 5 of 12)	intron (NM_001364029, intron 5 of 12)	134228	NM_001364029	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3297	chr16	68233276	68233476	+	2.23261	NA	Intergenic	Lx6|LINE|L1	-612468	NM_001145977	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-951	chr10	95239600	95239800	+	2.23261	NA	intron (NM_001330175, intron 2 of 2)	intron (NM_001330175, intron 2 of 2)	84009	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding	0.005000	0.412935			16(CCTTTGCAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5507	chr4	62843678	62843878	+	2.23261	NA	Intergenic	L1MDa|LINE|L1	-121789	NM_001369118	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5216	chr3	136799946	136800146	+	2.23261	NA	intron (NM_001293622, intron 2 of 12)	MLT1A0|LTR|ERVL-MaLR	129980	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3455	chr17	29016895	29017095	+	2.22909	NA	Intergenic	Intergenic	-9000	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding	0.015000	0.402985			-3(ATTTCCAAAGCAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6339	chr6	18255908	18256108	+	2.22722	NA	intron (NM_021050, intron 12 of 26)	B4|SINE|B4	85321	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding	0.005000	0.368159			61(CATTTGTGATGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4459	chr2	95973407	95973607	+	2.22141	NA	Intergenic	Intergenic	-344662	NM_001363048	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.000000	0.358209			14(ATTTGCATCACTAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5262	chr3	147774244	147774444	+	2.21927	NA	Intergenic	Intergenic	921977	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5559	chr4	80795046	80795246	+	2.21927	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-39067	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1661	chr12	52980640	52980840	+	2.21927	NA	intron (NM_198111, intron 7 of 13)	intron (NM_198111, intron 7 of 13)	-267692	NM_001370964	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.005000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3173	chr16	37857664	37857864	+	2.21927	NA	intron (NM_001370898, intron 3 of 5)	intron (NM_001370898, intron 3 of 5)	3426	NM_001370898	102639802		NM_001370898	ENSMUSG00000108763	Gm36028	-	predicted gene, 36028	protein-coding	0.025000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2482	chr14	48741054	48741254	+	2.21927	NA	intron (NR_029384, intron 4 of 4)	intron (NR_029384, intron 4 of 4)	71866	NR_029384	606497	Mm.165199	NR_029384	ENSMUSG00000098682	Otx2os1	-	orthodenticle homeobox 2 opposite strand 1	ncRNA	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7992	chrX	76174967	76175167	+	2.21927	NA	Intergenic	RLTR13D6|LTR|ERVK	-89239	NM_001013760	238829	Mm.292319	NM_001013760	ENSMUSG00000071738	Cldn34b3	EG238829|Gm4937	claudin 34B3	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2016	chr13	32982796	32982996	+	2.21927	NA	Intergenic	Intergenic	17635	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding	0.010000	0.398010			61(ATATGAAAGGGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6519	chr6	71213120	71213320	+	2.21927	NA	TTS (NM_009762)	TTS (NM_009762)	13341	NM_017399	14080	Mm.22126	NM_017399	ENSMUSG00000054422	Fabp1	Fabpl|L-FABP	fatty acid binding protein 1, liver	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1207	chr11	26230058	26230258	+	2.21927	NA	Intergenic	Intergenic	-19582	NR_027973	70626	Mm.379180	NM_027486		5730522E02Rik	-	RIKEN cDNA 5730522E02 gene	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8016	chrX	92195321	92195521	+	2.21927	NA	intron (NM_173783, intron 3 of 4)	Lx6|LINE|L1	-179088	NM_010759	17145	Mm.377100	NM_010759	ENSMUSG00000062162	Mageb1	MAGE-Xp|Mage-b1|Mage-rs1|Magel1|Smage1|dam1	melanoma antigen, family B, 1	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4524	chr2	112602008	112602208	+	2.21927	NA	intron (NR_149741, intron 1 of 4)	L1M3|LINE|L1	-16309	NM_001355631	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7940	chrX	22951037	22951237	+	2.21927	NA	Intergenic	Intergenic	315665	NM_001310466	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding	0.010000	0.427861		5(CATCAATATGCACA,+,0.00)	59(ATTTTCATATCAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5306	chr3	156240636	156240836	+	2.21927	NA	Intergenic	ORR1C2-int|LTR|ERVL-MaLR	264382	NR_040553	329780	Mm.119000	NR_040553	ENSMUSG00000104553	9330178D15Rik	9330178D15	RIKEN cDNA 9330178D15 gene	ncRNA	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6856	chr7	54342802	54343002	+	2.21927	NA	Intergenic	Intergenic	-451013	NR_105746	102466619		NR_105746	ENSMUSG00000099176	Mir6238	Gm27982|mmu-mir-6238	microRNA 6238	ncRNA	0.005000	0.333333			-97(GTTTACATTAGAAAAA,-,0.00),-66(ACTGTGCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8148	chrX	163899464	163899664	+	2.21927	NA	Intergenic	B1_Mus2|SINE|Alu	-9453	NM_026887	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7230	chr8	44366649	44366849	+	2.21927	NA	Intergenic	Intergenic	-583459	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4739	chr2	154977598	154977798	+	2.21927	NA	Intergenic	L1ME3G|LINE|L1	-35872	NM_015770	50518	Mm.315593	NM_015770	ENSMUSG00000027596	a	A<y>|ASIP|ASP|As	nonagouti	protein-coding	0.010000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1572	chr12	26227612	26227812	+	2.21927	NA	intron (NR_046278, intron 2 of 2)	intron (NR_046278, intron 2 of 2)	16445	NR_046278	74930	Mm.398932	NR_046278	ENSMUSG00000113115	4930480M12Rik	-	RIKEN cDNA 4930480M12 gene	ncRNA	0.030000	0.432836		23(CATACATTTGCATC,+,0.00)	-90(TGTCTGCCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7238	chr8	47726790	47726990	+	2.21927	NA	Intergenic	Intergenic	-12959	NM_001359133	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8108	chrX	144307981	144308181	+	2.21887	NA	Intergenic	Lx7|LINE|L1	-9885	NR_037145	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031	asparagine-linked glycosylation 13	protein-coding	0.005000	0.353234			-77(ATTAGTAAGAGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3106	chr16	19466241	19466441	+	2.21887	NA	Intergenic	RLTR28B|LTR|ERVL	-20499	NM_147068	259071	Mm.377822	NM_147068	ENSMUSG00000056822	Olfr166	MOR270-1	olfactory receptor 166	protein-coding	0.000000	0.363184			-21(TTAAGCATGACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3773	chr18	32172520	32172720	+	2.21887	NA	intron (NM_011946, intron 1 of 16)	MLT1I|LTR|ERVL-MaLR	9531	NM_011946	26405	Mm.211762	NM_011946	ENSMUSG00000024383	Map3k2	9630061B06Rik|AI585793|Mekk2|Mekk2b	mitogen-activated protein kinase kinase kinase 2	protein-coding	0.005000	0.368159			-62(ATTAAAATTACAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2131	chr13	70908511	70908711	+	2.21887	NA	Intergenic	Intergenic	25663	NR_157373	77166	Mm.159859	NM_029873		8030423J24Rik	-	RIKEN cDNA 8030423J24 gene	ncRNA	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5001	chr3	69073079	69073279	+	2.21887	NA	3' UTR (NM_008467, exon 17 of 17)	3' UTR (NM_008467, exon 17 of 17)	-28437	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding	0.000000	0.338308			-39(CTATTGTGAGGGAAAT,+,0.00),-17(TTTTTTTCATGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1279	chr11	47559307	47559507	+	2.21887	NA	Intergenic	Intergenic	-180082	NM_011891	24052	Mm.34175	NM_011891	ENSMUSG00000020354	Sgcd	35DAG|A530047J11Rik|AI504364|AW547581|SG-delta|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-990	chr10	105219239	105219439	+	2.21887	NA	intron (NM_177368, intron 11 of 11)	ORR1B2|LTR|ERVL-MaLR	355140	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5125	chr3	113796485	113796685	+	2.21706	NA	Intergenic	Intergenic	-166436	NM_026043	67225	Mm.316928	NM_026043	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	RNA-binding region (RNP1, RRM) containing 3	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4891	chr3	29887824	29888024	+	2.21638	NA	Intergenic	Lx8b|LINE|L1	-3093	NR_110437	102636083		NR_110437	ENSMUSG00000102590	Mannr	Manr	Mecom adjacent non-protein coding RNA	ncRNA	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3738	chr18	21999302	21999502	+	2.21130	NA	intron (NM_027616, intron 20 of 22)	intron (NM_027616, intron 20 of 22)	171994	NM_027616	70950	Mm.235716	NM_027616	ENSMUSG00000024306	Ccdc178	4921528I01Rik	coiled coil domain containing 178	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5950	chr5	51730295	51730495	+	2.21130	NA	Intergenic	MER58B|DNA|hAT-Charlie	-162670	NR_132764	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7376	chr8	93304816	93305016	+	2.21130	NA	intron (NM_021456, intron 13 of 13)	ORR1C2|LTR|ERVL-MaLR	-25180	NM_144930	234564	Mm.29110	NM_144930	ENSMUSG00000031725	Ces1f	AU018778|CesML1|TGH-2	carboxylesterase 1F	protein-coding	0.000000	0.402985			-7(TCATTCTTATTTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4160	chr2	7844947	7845147	+	2.21130	NA	Intergenic	Intergenic	-448849	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5436	chr4	41174949	41175149	+	2.21130	NA	intron (NM_026275, intron 2 of 4)	intron (NM_026275, intron 2 of 4)	39028	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1687	chr12	62216775	62216975	+	2.21018	NA	Intergenic	Lx9|LINE|L1	-470912	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3662	chr17	90385264	90385464	+	2.20695	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	70516	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.010000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2399	chr14	23863488	23863688	+	2.20544	NA	intron (NM_001253368, intron 1 of 28)	intron (NM_001253368, intron 1 of 28)	140617	NM_001253365	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3556	chr17	65018204	65018404	+	2.20544	NA	Intergenic	Intergenic	-182233	NM_030031	78057	Mm.109380	NM_030031	ENSMUSG00000024088	4930583I09Rik	-	RIKEN cDNA 4930583I09 gene	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3784	chr18	34441070	34441270	+	2.20544	NA	intron (NM_016927, intron 14 of 14)	intron (NM_016927, intron 14 of 14)	31747	NM_016927	53871	Mm.445792	NM_016927	ENSMUSG00000014503	Pkd2l2	TRPP5	polycystic kidney disease 2-like 2	protein-coding	0.000000	0.368159	-41(AATACATTATGAATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-610	chr1	185298103	185298303	+	2.20544	NA	intron (NM_198653, intron 14 of 22)	intron (NM_198653, intron 14 of 22)	-15116	NR_029580	387189		NR_029580	ENSMUSG00000065581	Mir194-1	Mirn194|Mirn194-1|miR-194|mir-194-1	microRNA 194-1	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1618	chr12	40334282	40334482	+	2.20544	NA	intron (NM_172575, intron 6 of 12)	intron (NM_172575, intron 6 of 12)	111018	NR_045157	629820	Mm.435540	NR_045157	ENSMUSG00000035983	Gm7008	EG629820	predicted gene 7008	ncRNA	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1522	chr12	5442936	5443136	+	2.20365	NA	Intergenic	Intergenic	67316	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA	0.005000	0.348259			3(GTTTTGCATTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-237	chr1	84041177	84041377	+	2.20365	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	177684	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6462	chr6	55076766	55076966	+	2.20365	NA	intron (NM_180678, intron 14 of 16)	intron (NM_180678, intron 14 of 16)	38865	NM_180678	353172	Mm.250004	NM_180678	ENSMUSG00000029777	Gars	GENA202|Gena201|Nmf249|Sgrp23	glycyl-tRNA synthetase	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-71	chr1	23958239	23958439	+	2.20288	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	-35958	NM_001357395	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding	0.015000	0.407960			-5(ATTTAAAAGAAAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6232	chr5	141567213	141567413	+	2.19791	NA	intron (NM_177879, intron 1 of 44)	L1MD1|LINE|L1	325779	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2298	chr13	111185208	111185408	+	2.19774	NA	Intergenic	Intergenic	44123	NR_045908	73129	Mm.417826	NR_045908	ENSMUSG00000114824	3110015C05Rik	-	RIKEN cDNA 3110015C05 gene	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2701	chr14	115241077	115241277	+	2.19333	NA	intron (NM_175500, intron 2 of 7)	intron (NM_175500, intron 2 of 7)	148962	NM_175500	103978	Mm.320791	NM_175500	ENSMUSG00000022112	Gpc5	A230034F01Rik	glypican 5	protein-coding	0.010000	0.402985	-56(CATGAATAATGTAGA,+,0.00),-56(CATGAATAATGTAGA,-,0.00)		13(ATTTGCAAGGCAATCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3605	chr17	78983523	78983723	+	2.19333	NA	exon (NM_029239, exon 4 of 19)	exon (NM_029239, exon 4 of 19)	24882	NM_001171005	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding	0.015000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5461	chr4	51888743	51888943	+	2.19333	NA	Intergenic	Intergenic	162267	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	ncRNA	0.000000	0.368159			-84(TCTTTGTTATGCTCAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7829	chr9	94959311	94959511	+	2.19333	NA	intron (NM_177909, intron 8 of 15)	intron (NM_177909, intron 8 of 15)	207582	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2368	chr14	15314286	15314486	+	2.19121	NA	Intergenic	Intergenic	-123237	NR_152122	77981	Mm.138039	NM_001033183		B230110C06Rik	-	RIKEN cDNA B230110C06 gene	ncRNA	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4277	chr2	44181002	44181202	+	2.19121	NA	intron (NM_001364029, intron 10 of 12)	intron (NM_001364029, intron 10 of 12)	-115778	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6146	chr5	108286349	108286549	+	2.19121	NA	Intergenic	MYSERV6-int|LTR|ERVK	17552	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding	0.000000	0.437811	27(TCTACATTATTCATT,+,0.00),27(TCTACATTATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-777	chr10	38906549	38906749	+	2.19102	NA	Intergenic	Intergenic	-58866	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding	0.000000	0.313433			-52(TTTTTTTTTTTTAGAT,+,0.00),-8(ATAAGCAACACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3693	chr18	7095159	7095359	+	2.18563	NA	intron (NM_001357492, intron 20 of 20)	intron (NM_001357492, intron 20 of 20)	-90480	NM_177595	210719	Mm.257186	NM_177595	ENSMUSG00000061013	Mkx	9430023B20Rik|Irxl1	mohawk homeobox	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6418	chr6	43318474	43318674	+	2.18563	NA	Intergenic	Intergenic	-9020	NM_130869	18291	Mm.17715	NM_130869	ENSMUSG00000029736	Nobox	OG2|Og2x	NOBOX oogenesis homeobox	protein-coding	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5556	chr4	77724806	77725006	+	2.18563	NA	intron (NR_160919, intron 2 of 39)	intron (NR_160919, intron 2 of 39)	486836	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8141	chrX	162079116	162079316	+	2.18563	NA	intron (NM_001081052, intron 1 of 7)	intron (NM_001081052, intron 1 of 7)	80225	NM_001290526	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	NHS actin remodeling regulator	protein-coding	0.000000	0.368159			-47(TTATACATGATAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6854	chr7	53413738	53413938	+	2.18563	NA	Intergenic	Intergenic	478051	NR_105746	102466619		NR_105746	ENSMUSG00000099176	Mir6238	Gm27982|mmu-mir-6238	microRNA 6238	ncRNA	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7984	chrX	70607125	70607325	+	2.18563	NA	Intergenic	Intergenic	61667	NM_001081476	628053	Mm.439630	NM_001081476		Gm14725	-	predicted gene 14725	protein-coding	0.000000	0.348259			32(TAATTGTTATTGAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2507	chr14	61215133	61215333	+	2.18563	NA	3' UTR (NM_015788, exon 10 of 10)	3' UTR (NM_015788, exon 10 of 10)	43257	NM_011892	24053	Mm.72173	NM_011892	ENSMUSG00000035296	Sgcg	35kDa|5430420E18Rik|AI642964|gamma-SG	sarcoglycan, gamma (dystrophin-associated glycoprotein)	protein-coding	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-83	chr1	27879026	27879226	+	2.18563	NA	Intergenic	Intergenic	-4920	NR_151583	433281	Mm.329306	NR_151583	ENSMUSG00000101514	Gm5524	AI875557|EG433281	predicted gene 5524	ncRNA	0.000000	0.368159			31(GTATTCTTTTGTTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7801	chr9	88252365	88252565	+	2.18563	NA	Intergenic	Intergenic	73337	NR_162813	114482949		NR_162813		Mir12205	mmu-mir-12205	microRNA mir-12205	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3944	chr18	78312886	78313086	+	2.18563	NA	intron (NM_030683, intron 3 of 11)	intron (NM_030683, intron 3 of 11)	-106546	NM_001110274	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-597	chr1	183517328	183517528	+	2.18533	NA	Intergenic	Intergenic	98180	NM_001308052	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding	0.005000	0.402985			2(TCTGTGTCATTGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7545	chr9	17585659	17585859	+	2.18533	NA	Intergenic	Lx2B2|LINE|L1	-706508	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4573	chr2	124286718	124286918	+	2.18533	NA	intron (NM_001290997, intron 2 of 20)	intron (NM_001290997, intron 2 of 20)	-64460	NR_040612	75946	Mm.415059	NR_040612	ENSMUSG00000086954	4930583P06Rik	-	RIKEN cDNA 4930583P06 gene	ncRNA	0.000000	0.303483			-32(ATTTCAATAACACTAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1460	chr11	110106154	110106354	+	2.18533	NA	intron (NM_147220, intron 37 of 38)	MTE-int|LTR|ERVL-MaLR	-10317	NM_153145	217258	Mm.344148	NM_153145	ENSMUSG00000041828	Abca8a	-	ATP-binding cassette, sub-family A (ABC1), member 8a	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-669	chr10	3693929	3694129	+	2.18533	NA	Intergenic	Intergenic	-46348	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding	0.020000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1062	chr10	115958532	115958732	+	2.18533	NA	Intergenic	Intergenic	-59731	NM_011217	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2237	chr13	98166228	98166428	+	2.18533	NA	intron (NM_012026, intron 1 of 35)	intron (NM_012026, intron 1 of 35)	39837	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding	0.025000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1823	chr12	94396487	94396687	+	2.18533	NA	Intergenic	Intergenic	469249	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA	0.005000	0.407960			61(ATTAGCTTAAGAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1225	chr11	29772168	29772368	+	2.18533	NA	intron (NM_146016, intron 28 of 41)	intron (NM_146016, intron 28 of 41)	53400	NM_176829	216622	Mm.443260	NM_176829	ENSMUSG00000078157	4931440F15Rik	Fem1ab	RIKEN cDNA 4931440F15 gene	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3783	chr18	34395655	34395855	+	2.18533	NA	Intergenic	RLTR11B|LTR|ERVK	-13668	NM_001163004	53871	Mm.445792	NM_016927	ENSMUSG00000014503	Pkd2l2	TRPP5	polycystic kidney disease 2-like 2	protein-coding	0.000000	0.358209			76(TTTAGCATTACAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5667	chr4	104561058	104561258	+	2.18284	NA	intron (NM_001369049, intron 5 of 19)	intron (NM_001369049, intron 5 of 19)	193620	NR_104385	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.010000	0.407960			-44(ATTTAAAAGACAAGGA,-,0.00),-13(TGTTTCCCTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7889	chr9	113842863	113843063	+	2.18284	NA	TTS (NM_001286603)	TTS (NM_001286603)	30377	NM_001286601	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding	0.000000	0.383085			-37(CTTTTTTCATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5361	chr4	15727187	15727387	+	2.18084	NA	Intergenic	RMER12|LTR|ERVK	-153977	NM_009788	12307	Mm.277665	NM_009788	ENSMUSG00000028222	Calb1	Brain-2|CB|Calb|Calb-1	calbindin 1	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2516	chr14	62728622	62728822	+	2.17918	NA	intron (NM_008715, intron 4 of 18)	L1MC5a|LINE|L1	-31779	NR_045503	71000	Mm.399410	NR_045503	ENSMUSG00000097775	4931440J10Rik	-	RIKEN cDNA 4931440J10 gene	ncRNA	0.000000	0.323383		-88(TATAAATATGAATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1675	chr12	57104328	57104528	+	2.17918	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	56215	NM_001167976	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding	0.000000	0.238806			-75(ATTTACAAGTCAAACT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2234	chr13	97480695	97480895	+	2.17918	NA	intron (NR_110432, intron 1 of 1)	L1M5|LINE|L1	-1906	NR_110430	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5540	chr4	74360334	74360534	+	2.17918	NA	intron (NM_001356561, intron 16 of 20)	intron (NM_001356561, intron 16 of 20)	108555	NM_001356561	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding	0.005000	0.338308			44(GCATTATCATTGAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1000	chr10	106903389	106903589	+	2.17918	NA	intron (NM_001359678, intron 22 of 30)	intron (NM_001359678, intron 22 of 30)	220148	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding	0.010000	0.363184			-75(AATTTTTGATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7356	chr8	82219634	82219834	+	2.17918	NA	Intergenic	Intergenic	182852	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3522	chr17	52184155	52184355	+	2.17918	NA	Intergenic	Lx8|LINE|L1	34966	NR_155494	100503190	Mm.170588	NR_155494		Gm19585	-	predicted gene, 19585	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6071	chr5	88494318	88494518	+	2.17663	NA	intron (NM_017468, intron 8 of 9)	intron (NM_017468, intron 8 of 9)	6443	NM_017468	13801	Mm.8014	NM_017468	ENSMUSG00000029286	Enam	abte	enamelin	protein-coding	0.005000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5253	chr3	146308438	146308638	+	2.17366	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	70406	NR_033542	100038607	Mm.365888	NR_033542	ENSMUSG00000105602	Gm10636	-	predicted gene 10636	ncRNA	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-345	chr1	124526205	124526405	+	2.17366	NA	Intergenic	Intergenic	-480746	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.000000	0.333333	51(AATGCTTAATTCAGA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6829	chr7	40151568	40151768	+	2.17366	NA	Intergenic	Intergenic	-523069	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7484	chr8	125097097	125097297	+	2.17199	NA	intron (NM_174853, intron 3 of 11)	intron (NM_174853, intron 3 of 11)	43002	NM_174854	244667	Mm.233504	NM_170596	ENSMUSG00000043051	Disc1	-	disrupted in schizophrenia 1	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7550	chr9	22243904	22244104	+	2.17199	NA	TTS (NM_172763)	TTS (NM_172763)	15891	NM_181419	235048	Mm.292381	NM_181419	ENSMUSG00000062794	Zfp599	6720416P20	zinc finger protein 599	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6504	chr6	66263967	66264167	+	2.17199	NA	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-8438	NR_136927	102633773	Mm.272086	NR_136927	ENSMUSG00000107653	Gm31520	-	sterol-C5-desaturase pseudogene	pseudo	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2285	chr13	109691171	109691371	+	2.16710	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-212538	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4103	chr19	48440969	48441169	+	2.16552	NA	intron (NM_025696, intron 2 of 26)	intron (NM_025696, intron 2 of 26)	235044	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6982	chr7	96306071	96306271	+	2.16488	NA	TTS (NR_105818)	TTS (NR_105818)	504	NR_105818	102465210		NR_105818	ENSMUSG00000099030	Mir6394	Gm27929|mmu-mir-6394	microRNA 6394	ncRNA	0.005000	0.437811			-23(CCTTTGGTGTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7347	chr8	79829325	79829525	+	2.16488	NA	Intergenic	Intergenic	117576	NM_001357235	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding	0.010000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6564	chr6	84339695	84339895	+	2.16488	NA	Intergenic	Intergenic	84043	NR_046063	100038556	Mm.387783	NR_046063	ENSMUSG00000107797	Gm10445	-	predicted gene 10445	ncRNA	0.000000	0.462687			-82(AATCTGTTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6352	chr6	22600403	22600603	+	2.16488	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-244422	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4156	chr2	6691748	6691948	+	2.15925	NA	intron (NM_001160293, intron 2 of 13)	intron (NM_001160293, intron 2 of 13)	29814	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5818	chr5	6795542	6795742	+	2.15925	NA	intron (NM_001163223, intron 2 of 3)	RLTR13D6|LTR|ERVK	-508522	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	Tex47	4921511H03Rik	testis expressed 47	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3864	chr18	54580562	54580762	+	2.15925	NA	Intergenic	Intergenic	-31082	NR_045400	328957	Mm.402781	NR_045400	ENSMUSG00000118154	9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7616	chr9	39320994	39321194	+	2.15925	NA	Intergenic	Intergenic	-1482	NM_001011756	257912	Mm.377297	NM_001011756	ENSMUSG00000057349	Olfr948	MOR171-45|MOR171-51	olfactory receptor 948	protein-coding	0.010000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7718	chr9	71659176	71659376	+	2.15925	NA	intron (NM_026599, intron 8 of 18)	intron (NM_026599, intron 8 of 18)	-66916	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm20502|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4467	chr2	97534334	97534534	+	2.15925	NA	intron (NM_001363047, intron 7 of 8)	intron (NM_001363047, intron 7 of 8)	66777	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6376	chr6	31139633	31139833	+	2.15925	NA	non-coding (NR_110471, exon 3 of 4)	non-coding (NR_110471, exon 3 of 4)	-76640	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA	0.015000	0.422886			-43(ATTAACAAGACAAACG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1611	chr12	38149424	38149624	+	2.15925	NA	intron (NM_178681, intron 12 of 24)	intron (NM_178681, intron 12 of 24)	269007	NM_001361686	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4959	chr3	57044636	57044836	+	2.15925	NA	Intergenic	MLT2B2|LTR|ERVL	257252	NM_001355130	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-981	chr10	102758198	102758398	+	2.15925	NA	Intergenic	Intergenic	246076	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1336	chr11	70900742	70900942	+	2.15925	NA	intron (NM_019400, intron 6 of 17)	intron (NM_019400, intron 6 of 17)	56081	NM_001291143	54189	Mm.7087	NM_019400	ENSMUSG00000020817	Rabep1	Rab5ep|rabaptin-5|rabaptin-5alpha	rabaptin, RAB GTPase binding effector protein 1	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1727	chr12	71816829	71817029	+	2.15822	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-14139	NM_026102	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1984	chr13	23816339	23816539	+	2.15816	NA	intron (NM_144836, intron 5 of 11)	intron (NM_144836, intron 5 of 11)	9412	NM_144836	218103	Mm.24030	NM_144836	ENSMUSG00000036110	Slc17a2	C730032N17Rik|NPT3	solute carrier family 17 (sodium phosphate), member 2	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1397	chr11	88411849	88412049	+	2.15816	NA	intron (NM_054043, intron 8 of 13)	intron (NM_054043, intron 8 of 13)	59176	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA	0.005000	0.373134			69(ATTAGCAAGTCAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7443	chr8	109338728	109338928	+	2.15816	NA	TTS (NR_002928)	TTS (NR_002928)	2080	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6949	chr7	87392550	87392750	+	2.15767	NA	intron (NM_001285833, intron 19 of 19)	intron (NM_001285833, intron 19 of 19)	100862	NM_011661	22173	Mm.238127	NM_011661	ENSMUSG00000004651	Tyr	Oca1|albino|c|skc35	tyrosinase	protein-coding	0.005000	0.318408			-7(ACATTCCTATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-945	chr10	93130583	93130783	+	2.15767	NA	Intergenic	Intergenic	-30193	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1039	chr10	112308113	112308313	+	2.15767	NA	intron (NM_001359753, intron 2 of 4)	intron (NM_001359753, intron 2 of 4)	36940	NM_001359753	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3878	chr18	57488286	57488486	+	2.15767	NA	Intergenic	Intergenic	19900	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	-	cortexin 3	protein-coding	0.005000	0.338308			-58(CCTTTCTCATGTTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5474	chr4	53724271	53724471	+	2.15767	NA	intron (NM_001363126, intron 2 of 8)	RLTR11A|LTR|ERVK	10217	NR_156448	246179	Mm.247210	NM_139309	ENSMUSG00000028414	Fktn	D830030O17Rik|Fcmd	fukutin	protein-coding	0.000000	0.343284			85(ACTTTGTAATTCTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2222	chr13	95818999	95819199	+	2.15637	NA	intron (NM_027711, intron 2 of 35)	intron (NM_027711, intron 2 of 35)	72823	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding	0.010000	0.482587		-79(TATGCATATACATG,+,0.00),-79(TATGCATATACATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7131	chr8	3111505	3111705	+	2.15380	NA	Intergenic	Intergenic	168012	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding	0.000000	0.373134			-94(ATTTGCATACAAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6420	chr6	43476790	43476990	+	2.15380	NA	intron (NM_013861, intron 6 of 8)	intron (NM_013861, intron 6 of 8)	34461	NR_045988	319812	Mm.446393	NR_045988		9430018G01Rik	-	RIKEN cDNA 9430018G01 gene	ncRNA	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2775	chr15	8189782	8189982	+	2.15374	NA	intron (NM_001162906, intron 15 of 52)	intron (NM_001162906, intron 15 of 52)	20776	NM_001162906	73692	Mm.164436	NM_001162906	ENSMUSG00000039801	Cplane1	2410089E03Rik|4732468D17Rik|Hug|Jbts17|b2b012Clo	ciliogenesis and planar polarity effector 1	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7120	chr7	139827768	139827968	+	2.15374	NA	Intergenic	Intergenic	-6306	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding	0.030000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8069	chrX	116522166	116522366	+	2.15374	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	73322	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6743	chr6	137957027	137957227	+	2.15374	NA	Intergenic	Intergenic	122789	NM_177787	277898	Mm.269823	NM_177787	ENSMUSG00000044378	Slc15a5	9830102E05Rik	solute carrier family 15, member 5	protein-coding	0.015000	0.462687		-68(AATGCATAATCAAG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3936	chr18	73525674	73525874	+	2.15374	NA	Intergenic	MERVL_2A-int|LTR|ERVL	-46931	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8008	chrX	86409861	86410061	+	2.15374	NA	Intergenic	Intergenic	-54967	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5836	chr5	16033766	16033966	+	2.15374	NA	intron (NM_001110843, intron 3 of 38)	RSINE1|SINE|B4	99175	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2804	chr15	13127953	13128153	+	2.15374	NA	intron (NM_007666, intron 1 of 11)	intron (NM_007666, intron 1 of 11)	45622	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.005000	0.383085			-54(TTTAGCAAAACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1948	chr13	11948311	11948511	+	2.15374	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	158534	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding	0.005000	0.368159	14(AATGTAAAATTCATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-87	chr1	29289618	29289818	+	2.15374	NA	Intergenic	L1_Mus4|LINE|L1	-131770	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA	0.015000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6509	chr6	67766791	67766991	+	2.15374	NA	Intergenic	Intergenic	-201192	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo	0.000000	0.388060			68(ATTAGTAAAACAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7035	chr7	116347651	116347851	+	2.14916	NA	intron (NM_011083, intron 27 of 32)	B1_Mur2|SINE|Alu	-13561	NM_026533	68052	Mm.14798	NM_026533	ENSMUSG00000090862	Rps13	2700063M04Rik	ribosomal protein S13	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6276	chr5	151395962	151396162	+	2.14916	NA	non-coding (NR_045699, exon 4 of 4)	non-coding (NR_045699, exon 4 of 4)	-10442	NR_131166	100042166	Mm.443286	NR_131166	ENSMUSG00000097321	Gm3704	-	predicted gene 3704	ncRNA	0.000000	0.348259		58(TATGTATATGAATG,-,0.00)	-78(CTATACTTATGTAAAT,+,0.00),63(ATATGAATGCCAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7968	chrX	52827936	52828136	+	2.14916	NA	Intergenic	Intergenic	36836	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding	0.005000	0.328358	-56(CTTGAATTATTCATC,+,0.00),-56(CTTGAATTATTCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6613	chr6	99625621	99625821	+	2.14433	NA	3' UTR (NM_025829, exon 7 of 7)	3' UTR (NM_025829, exon 7 of 7)	41050	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4824	chr3	5825659	5825859	+	2.13961	NA	Intergenic	Intergenic	-249511	NM_001267715	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0.000000	0.298507			-30(ATTTAAATGGAAATCA,-,0.00),-12(ATTTACAGAAGAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5547	chr4	76812619	76812819	+	2.13961	NA	intron (NR_160919, intron 8 of 39)	intron (NR_160919, intron 8 of 39)	-468476	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.005000	0.368159		-14(ATTACATATTCATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7710	chr9	69199635	69199835	+	2.13961	NA	intron (NM_013646, intron 2 of 10)	intron (NM_013646, intron 2 of 10)	-90106	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding	0.020000	0.437811			-91(GGTTTGTCATTCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6449	chr6	52769718	52769918	+	2.13961	NA	3' UTR (NM_001168277, exon 5 of 5)	3' UTR (NM_001168277, exon 5 of 5)	55653	NM_001355596	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5525	chr4	69008824	69009024	+	2.13961	NA	Intergenic	Intergenic	-54527	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding	0.010000	0.447761			-51(CTTTACATGAGAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2757	chr15	5394518	5394718	+	2.13961	NA	Intergenic	Intergenic	-101700	NR_045274	71432	Mm.291087	NR_045274	ENSMUSG00000110018	5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1895	chr12	116354140	116354340	+	2.13961	NA	intron (NM_028731, intron 13 of 21)	intron (NM_028731, intron 13 of 21)	50921	NR_028421	319545	Mm.390543	NR_028421	ENSMUSG00000112980	D430020J02Rik	-	RIKEN cDNA D430020J02 gene	ncRNA	0.005000	0.402985			-32(ACATTGTGATTTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3145	chr16	28982893	28983093	+	2.13956	NA	Intergenic	RLTR20A2B_MM|LTR|ERVK	-53295	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding	0.010000	0.467662			-58(ATTAAAAAGGCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4908	chr3	38413565	38413765	+	2.13956	NA	Intergenic	Intergenic	71151	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1031	chr10	111488248	111488448	+	2.13956	NA	intron (NR_152558, intron 4 of 14)	intron (NR_152558, intron 4 of 14)	-12440	NR_033603	382421	Mm.245643	NR_033603	ENSMUSG00000111997	Gm5176	EG382421	high mobility group box 2 pseudogene	pseudo	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7031	chr7	114474224	114474424	+	2.13835	NA	intron (NM_011055, intron 1 of 15)	intron (NM_011055, intron 1 of 15)	59070	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding	0.000000	0.263682			-25(TTTTGAAAGATAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8160	chrX	166673528	166673728	+	2.13835	NA	intron (NR_046015, intron 6 of 8)	intron (NR_046015, intron 6 of 8)	11603	NR_046015	382255	Mm.336320	NR_046015	ENSMUSG00000086860	Gm1720	-	predicted gene 1720	ncRNA	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1388	chr11	86695060	86695260	+	2.13835	NA	3' UTR (NM_001356393, exon 33 of 33)	3' UTR (NM_001356393, exon 33 of 33)	11086	NM_175004	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147|PTH 2	peptidyl-tRNA hydrolase 2	protein-coding	0.005000	0.318408			-2(CTTTGAATAAAAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-194	chr1	67010533	67010733	+	2.13835	NA	intron (NM_001190985, intron 3 of 8)	intron (NM_001190985, intron 3 of 8)	28201	NM_001190984	14768	Mm.20522	NM_021295	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3521	chr17	52183960	52184160	+	2.13835	NA	Intergenic	Intergenic	34771	NR_155494	100503190	Mm.170588	NR_155494		Gm19585	-	predicted gene, 19585	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5380	chr4	23690591	23690791	+	2.13835	NA	Intergenic	Intergenic	-805760	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6943	chr7	84615222	84615422	+	2.13805	NA	3' UTR (NM_022985, exon 8 of 8)	3' UTR (NM_022985, exon 8 of 8)	-9380	NM_010176	14085	Mm.3798	NM_010176	ENSMUSG00000030630	Fah	swst	fumarylacetoacetate hydrolase	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4177	chr2	12213152	12213352	+	2.13805	NA	intron (NM_001001309, intron 13 of 29)	intron (NM_001001309, intron 13 of 29)	-87994	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3278	chr16	64594913	64595113	+	2.13525	NA	intron (NM_173861, intron 1 of 2)	intron (NM_173861, intron 1 of 2)	7318	NM_001368721	224291	Mm.246580	NM_173861	ENSMUSG00000068167	Csnka2ip	Ckt2	casein kinase 2, alpha prime interacting protein	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5183	chr3	128755373	128755573	+	2.13525	NA	Intergenic	L1MCa|LINE|L1	-444405	NM_011098	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding	0.015000	0.313433			-22(ACAATGTCTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6360	chr6	24405788	24405988	+	2.13191	NA	Intergenic	Intergenic	109179	NM_172535	214704	Mm.61131	NM_172535	ENSMUSG00000046192	Iqub	4932408B21Rik|Trs4	IQ motif and ubiquitin domain containing	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7179	chr8	26763472	26763672	+	2.13008	NA	Intergenic	Intergenic	60851	NR_045904	72316	Mm.490534	NR_045904	ENSMUSG00000100335	2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	ncRNA	0.030000	0.467662	44(GAGGAATTATGCATG,+,0.00),44(GAGGAATTATGCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5609	chr4	94349465	94349665	+	2.13008	NA	Intergenic	Intergenic	207231	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5178	chr3	127512419	127512619	+	2.13008	NA	Intergenic	Intergenic	-13404	NM_001327938	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding	0.005000	0.363184			2(ATTTGAATAGCAAATC,-,0.00),16(TCATTGGTTTGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7307	chr8	71757684	71757884	+	2.13008	NA	Intergenic	Intergenic	-32103	NM_028715	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5480	chr4	55058244	55058444	+	2.13008	NA	intron (NM_172867, intron 9 of 12)	intron (NM_172867, intron 9 of 12)	110399	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip|Znf462	zinc finger protein 462	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4816	chr2	181053730	181053930	+	2.13008	NA	Intergenic	L1MD|LINE|L1	-14653	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4010	chr19	14435844	14436044	+	2.13008	NA	promoter-TSS (NR_152176)	promoter-TSS (NR_152176)	6	NR_152176	667433	Mm.128913	NR_152176		Gm8630	EG667433	predicted gene 8630	ncRNA	0.025000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7768	chr9	81124312	81124512	+	2.13008	NA	Intergenic	L1_Mur3|LINE|L1	-507518	NR_040393	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA	0.000000	0.293532		-16(TATGCTTATGCATA,+,0.00),-16(TATGCTTATGCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4793	chr2	170952318	170952518	+	2.13008	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	220611	NM_029761	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding	0.000000	0.442786			-64(GTTTGAATAAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5566	chr4	82481465	82481665	+	2.13008	NA	intron (NM_001113209, intron 2 of 11)	intron (NM_001113209, intron 2 of 11)	24214	NM_001286131	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding	0.000000	0.308458			-50(TGTTTCTGATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5541	chr4	75528379	75528579	+	2.13008	NA	Intergenic	L1_Mur3|LINE|L1	-250187	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Dmac1	1700027K24Rik|3110001D03Rik|Tmem261	distal membrane arm assembly complex 1	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1621	chr12	42362895	42363095	+	2.13008	NA	Intergenic	L2a|LINE|L2	671222	NR_148724	102636207		NR_148724		Gm33340	Gm40882	predicted gene, 33340	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3739	chr18	22352249	22352449	+	2.13008	NA	intron (NM_001167777, intron 1 of 12)	intron (NM_001167777, intron 1 of 12)	7260	NM_001167777	211961	Mm.392310	NM_001167777	ENSMUSG00000045215	Asxl3	C230079D11Rik|D430002O22Rik|D930044O18Rik|Gm329|Gm945	additional sex combs like 3, transcriptional regulator	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3840	chr18	49870516	49870716	+	2.13008	NA	intron (NM_001081371, intron 15 of 42)	intron (NM_001081371, intron 15 of 42)	37619	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5185	chr3	129151212	129151412	+	2.13008	NA	Intergenic	Intergenic	-48566	NM_011098	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding	0.025000	0.437811			70(CTTTAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1771	chr12	82180868	82181068	+	2.13008	NA	intron (NM_001167983, intron 1 of 23)	RLTR12A|LTR|ERVK	10952	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6624	chr6	101732314	101732514	+	2.12423	NA	Intergenic	Intergenic	-41835	NR_027989	207157	Mm.57632	NM_177579	ENSMUSG00000052236	Gm9871	0610005I04|EG207157	predicted gene 9871	ncRNA	0.005000	0.422886			58(TCTTTCTCATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7154	chr8	11963751	11963951	+	2.12414	NA	Intergenic	RLTR42-int|LTR|ERVK	123330	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding	0.000000	0.368159			48(ACTTTGTAAAGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4538	chr2	115903821	115904021	+	2.12414	NA	intron (NM_001136072, intron 9 of 12)	intron (NM_001136072, intron 9 of 12)	160698	NM_001159569	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2221	chr13	95818686	95818886	+	2.12112	NA	intron (NM_027711, intron 2 of 35)	intron (NM_027711, intron 2 of 35)	73136	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7632	chr9	44946435	44946635	+	2.12108	NA	TTS (NM_001361075)	TTS (NM_001361075)	19065	NM_001361075	140630	Mm.215069	NM_145400	ENSMUSG00000059890	Ube4a	4732444G18Rik|9930123J21Rik|UFD2b	ubiquitination factor E4A	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4383	chr2	70795698	70795898	+	2.12108	NA	intron (NR_156421, intron 1 of 6)	intron (NR_156421, intron 1 of 6)	29006	NM_001362963	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding	0.010000	0.333333			-6(CTAATGTCATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3157	chr16	33227955	33228155	+	2.12108	NA	intron (NM_176840, intron 9 of 12)	PB1D9|SINE|Alu	-23401	NM_080557	69150	Mm.28196	NM_080557	ENSMUSG00000022808	Snx4	1810036H14Rik|AI037066	sorting nexin 4	protein-coding	0.005000	0.398010			-82(CTATATTTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2692	chr14	111955234	111955434	+	2.12108	NA	Intergenic	Intergenic	280219	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3941	chr18	77078016	77078216	+	2.12108	NA	intron (NM_001164168, intron 1 of 13)	ID_B1|SINE|B4	12436	NM_001164170	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding	0.005000	0.477612	-87(CATGATTTATTTATG,+,0.00),-87(CATGATTTATTTATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1565	chr12	25169645	25169845	+	2.12108	NA	Intergenic	Intergenic	40571	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA	0.010000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5477	chr4	54408030	54408230	+	2.12108	NA	Intergenic	Intergenic	-539815	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip|Znf462	zinc finger protein 462	protein-coding	0.000000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6583	chr6	91547704	91547904	+	2.12108	NA	Intergenic	Intergenic	31769	NM_026309	67678	Mm.246693	NM_026309	ENSMUSG00000034192	Lsm3	1010001J12Rik|2610005D18Rik|6030401D18Rik|SMX4|USS2	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1274	chr11	45444440	45444640	+	2.12108	NA	Intergenic	MER58B|DNA|hAT-Charlie	-327612	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5957	chr5	53597276	53597476	+	2.12108	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	6890	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.015000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5426	chr4	35927770	35927970	+	2.12065	NA	intron (NM_001166000, intron 7 of 8)	intron (NM_001166000, intron 7 of 8)	-82666	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.000000	0.363184	-69(AATGATTAAGTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3303	chr16	70412593	70412793	+	2.12065	NA	intron (NM_028803, intron 3 of 15)	Lx8|LINE|L1	98744	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4772	chr2	164381893	164382093	+	2.11986	NA	Intergenic	B3|SINE|B2	-21201	NM_009036	19668	Mm.473794	NM_009036	ENSMUSG00000017007	Rbpjl	RBP-L|Rbpsuhl	recombination signal binding protein for immunoglobulin kappa J region-like	protein-coding	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7301	chr8	67343441	67343641	+	2.11986	NA	Intergenic	Intergenic	-147427	NM_008673	17960	Mm.14125	NM_008673	ENSMUSG00000025588	Nat1	Nat-1	N-acetyl transferase 1	protein-coding	0.000000	0.293532		80(TTTGAATATTCATG,+,0.00),80(TTTGAATATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4918	chr3	40532316	40532516	+	2.11840	NA	Intergenic	Intergenic	-8351	NM_175515	380614	Mm.105309	NM_175515	ENSMUSG00000060798	Intu	9230116I04Rik|9430087H23Rik|Pdzd6|Pdzk6|mKIAA1284	inturned planar cell polarity protein	protein-coding	0.030000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2100	chr13	62331511	62331711	+	2.11807	NA	Intergenic	Intergenic	51563	NM_001162910	100041979	Mm.445930	NM_001162910	ENSMUSG00000094942	Gm3604	-	predicted gene 3604	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6479	chr6	61286227	61286427	+	2.11527	NA	intron (NM_183310, intron 1 of 10)	intron (NM_183310, intron 1 of 10)	-105517	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3908	chr18	65607057	65607257	+	2.11527	NA	intron (NM_001361052, intron 1 of 8)	intron (NM_001361052, intron 1 of 8)	474	NM_001361052	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5148	chr3	119376374	119376574	+	2.11449	NA	intron (NM_170778, intron 20 of 22)	intron (NM_170778, intron 20 of 22)	406914	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.005000	0.358209			-32(ATTTGGATAAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1961	chr13	15699594	15699794	+	2.11197	NA	intron (NM_008130, intron 10 of 14)	intron (NM_008130, intron 10 of 14)	102936	NR_045507	71071	Mm.380845	NR_045507	ENSMUSG00000113960	4933412O06Rik	-	RIKEN cDNA 4933412O06 gene	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-20	chr1	7497956	7498156	+	2.11197	NA	Intergenic	Intergenic	409136	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.025000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4919	chr3	40533010	40533210	+	2.11164	NA	Intergenic	Intergenic	-7657	NM_175515	380614	Mm.105309	NM_175515	ENSMUSG00000060798	Intu	9230116I04Rik|9430087H23Rik|Pdzd6|Pdzk6|mKIAA1284	inturned planar cell polarity protein	protein-coding	0.010000	0.462687			39(ATCTGAATTACAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5951	chr5	51887110	51887310	+	2.11149	NA	Intergenic	Intergenic	248807	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6568	chr6	84976367	84976567	+	2.11149	NA	intron (NM_177077, intron 6 of 21)	intron (NM_177077, intron 6 of 21)	93046	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5318	chr3	158640684	158640884	+	2.11149	NA	Intergenic	Intergenic	-79023	NM_001081358	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3474	chr17	36109505	36109705	+	2.11149	NA	intron (NM_001271005, intron 5 of 6)	intron (NM_001271005, intron 5 of 6)	2071	NM_001271005	667803	Mm.477808	NM_001271005		H2-T-ps	C920025E04Rik|H2-T11	histocompatibility 2, T region locus, pseudogene	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-738	chr10	24691806	24692006	+	2.11149	NA	intron (NM_001308327, intron 1 of 24)	intron (NM_001308327, intron 1 of 24)	20253	NM_001308327	18605	Mm.27254	NM_008813	ENSMUSG00000037370	Enpp1	4833416E15Rik|AI428932|C76301|CD203c|E-NPP 1|E-NPP1|Ly-41|M6S1|NPP1|Npps|PC-1|Pca|Pca-1|Pdnp1|ttw|twy	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2376	chr14	17667584	17667784	+	2.11149	NA	intron (NM_001113417, intron 1 of 9)	intron (NM_001113417, intron 1 of 9)	6724	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0.000000	0.373134			1(ATTTCCATTACAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3287	chr16	66585894	66586094	+	2.11149	NA	Intergenic	Intergenic	-71124	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA	0.025000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3886	chr18	59199561	59199761	+	2.11149	NA	intron (NM_001081328, intron 2 of 2)	intron (NM_001081328, intron 2 of 2)	24321	NM_001081328	78923	Mm.84007	NM_001081328	ENSMUSG00000058152	Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding	0.010000	0.328358			61(CATTTGTGATGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4303	chr2	52194552	52194752	+	2.11149	NA	intron (NM_010889, intron 113 of 156)	MER44D|DNA|TcMar-Tigger	-96350	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA	0.000000	0.253731			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5611	chr4	94375718	94375918	+	2.11149	NA	Intergenic	Lx5|LINE|L1	180978	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1612	chr12	38149535	38149735	+	2.11149	NA	intron (NM_178681, intron 12 of 24)	intron (NM_178681, intron 12 of 24)	269118	NM_001361686	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1527	chr12	6638040	6638240	+	2.11149	NA	Intergenic	Intergenic	742190	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2763	chr15	6615985	6616185	+	2.11149	NA	intron (NR_155272, intron 4 of 6)	intron (NR_155272, intron 4 of 6)	36238	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Fyb1|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-106	chr1	37131958	37132158	+	2.11149	NA	intron (NM_001370829, intron 14 of 16)	intron (NM_001370829, intron 14 of 16)	-86220	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5757	chr4	134004867	134005067	+	2.11149	NA	3' UTR (NM_145833, exon 4 of 4)	3' UTR (NM_145833, exon 4 of 4)	-4085	NM_001362960	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638|cis-IPTase	dehydrodolichyl diphosphate synthase	protein-coding	0.005000	0.442786		-77(CATAAATTTGCATT,+,0.00)	-72(ATTTGCATTAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4473	chr2	102003355	102003555	+	2.11149	NA	intron (NM_178886, intron 4 of 5)	intron (NM_178886, intron 4 of 5)	117193	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5293	chr3	152434315	152434515	+	2.11070	NA	intron (NM_001080755, intron 4 of 13)	intron (NM_001080755, intron 4 of 13)	37731	NM_001287139	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3098	chr16	15720667	15720867	+	2.11070	NA	intron (NM_011159, intron 39 of 85)	L1MA7|LINE|L1	82901	NM_011159	19090	Mm.71	NM_011159	ENSMUSG00000022672	Prkdc	AI326420|AU019811|DNA-PKcs|DNAPDcs|DNAPK|DNPK1|DOXNPH|HYRC1|XRCC7|dxnph|p460|scid|slip	protein kinase, DNA activated, catalytic polypeptide	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1952	chr13	12456948	12457148	+	2.11070	NA	intron (NM_001291060, intron 1 of 8)	intron (NM_001291060, intron 1 of 8)	2268	NM_001291055	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding	0.020000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2501	chr14	60227081	60227281	+	2.11070	NA	intron (NM_170591, intron 12 of 14)	intron (NM_170591, intron 12 of 14)	1734	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2834	chr15	27548848	27549048	+	2.11039	NA	intron (NM_020332, intron 2 of 11)	intron (NM_020332, intron 2 of 11)	-22546	NR_106065	102466808		NR_106065	ENSMUSG00000098416	Mir7117	Gm27729|mmu-mir-7117	microRNA 7117	ncRNA	0.005000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-216	chr12	117053741	117053941	+	2.10949	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	97428	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.035000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7140	chr8	8940231	8940431	+	2.10861	NA	Intergenic	Intergenic	191957	NR_045854	71249	Mm.158635	NR_045854	ENSMUSG00000108848	4933430N04Rik	-	RIKEN cDNA 4933430N04 gene	ncRNA	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2397	chr14	23397863	23398063	+	2.10652	NA	intron (NM_001253368, intron 19 of 28)	intron (NM_001253368, intron 19 of 28)	-303392	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	-	predicted gene 10248	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-950	chr10	93994404	93994604	+	2.10646	NA	intron (NM_001304575, intron 5 of 11)	intron (NM_001304575, intron 5 of 11)	-30641	NR_029764	723908		NR_029764	ENSMUSG00000065607	Mir331	Mirn331|mmu-mir-331	microRNA 331	ncRNA	0.010000	0.383085			-56(AATAGCAAGACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1485	chr11	114537072	114537272	+	2.10646	NA	Intergenic	Intergenic	-88312	NR_027643	319819	Mm.50754	NM_177008	ENSMUSG00000062391	4932435O22Rik	-	RIKEN cDNA 4932435O22 gene	ncRNA	0.015000	0.437811	-4(CATGCAGAATTCATT,+,0.00),-4(CATGCAGAATTCATT,-,0.00)	35(CTTTAATATTCATG,+,0.00)	38(TAATATTCATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3594	chr17	75305371	75305571	+	2.10646	NA	intron (NM_206958, intron 15 of 29)	intron (NM_206958, intron 15 of 29)	126690	NM_206958	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5961	chr5	54441025	54441225	+	2.10646	NA	Intergenic	Intergenic	91133	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13	predicted gene 10440	ncRNA	0.000000	0.278607			-31(ATTTACATCACAAGAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6698	chr6	119561609	119561809	+	2.10646	NA	Intergenic	L1MB3|LINE|L1	-17362	NM_009525	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding	0.005000	0.388060	70(CATACATAATTCATC,+,0.00),70(CATACATAATTCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3231	chr16	52252432	52252632	+	2.10646	NA	intron (NM_009655, intron 15 of 15)	intron (NM_009655, intron 15 of 15)	200549	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding	0.005000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-576	chr3	119376500	119376700	+	2.10461	NA	intron (NM_170778, intron 20 of 22)	intron (NM_170778, intron 20 of 22)	406788	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1242	chr11	37193805	37194005	+	2.10024	NA	Intergenic	Intergenic	-249664	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1513	chr12	3655869	3656069	+	2.10024	NA	intron (NM_001162465, intron 8 of 17)	intron (NM_001162465, intron 8 of 17)	82985	NM_007886	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5342	chr4	10809742	10809942	+	2.10024	NA	Intergenic	Intergenic	-12040	NR_045185	73624	Mm.67392	NR_045185	ENSMUSG00000086080	1700123O12Rik	-	RIKEN cDNA 1700123O12 gene	ncRNA	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3512	chr17	50773658	50773858	+	2.10024	NA	intron (NM_028162, intron 18 of 21)	intron (NM_028162, intron 18 of 21)	75077	NM_001297747	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4888	chr3	29153086	29153286	+	2.10024	NA	intron (NM_001357198, intron 3 of 13)	intron (NM_001357198, intron 3 of 13)	70655	NM_001357198	75740	Mm.330948	NM_029412	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding	0.005000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7445	chr8	109347216	109347416	+	2.09885	NA	Intergenic	Intergenic	-6408	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-460	chr1	152632670	152632870	+	2.09885	NA	intron (NM_001346118, intron 2 of 18)	intron (NM_001346118, intron 2 of 18)	-7553	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding	0.005000	0.368159			-57(ATTAGCATTACAGATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-683	chr10	6916197	6916397	+	2.09885	NA	intron (NM_001033391, intron 7 of 7)	intron (NM_001033391, intron 7 of 7)	63984	NM_001347225	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5109	chr3	109105746	109105946	+	2.09885	NA	intron (NM_029054, intron 5 of 9)	MLT1B|LTR|ERVL-MaLR	-17303	NM_172685	229731	Mm.33574	NM_172685	ENSMUSG00000040322	Slc25a24	2610016M12Rik	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 24	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1995	chr13	28629236	28629436	+	2.09885	NA	intron (NR_045054, intron 5 of 7)	intron (NR_045054, intron 5 of 7)	81537	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3168	chr16	34623034	34623234	+	2.09630	NA	Intergenic	L1M4|LINE|L1	-28077	NM_030744	76378	Mm.23515	NM_030744	ENSMUSG00000022832	Ropn1	1700008N21Rik|ODF6|RHPNAP1|Rppn|ropporin	ropporin, rhophilin associated protein 1	protein-coding	0.000000	0.268657			19(TCATATTCATTGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5489	chr4	57465484	57465684	+	2.09630	NA	Intergenic	Intergenic	-101292	NR_038178	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6606	chr6	98093622	98093822	+	2.09630	NA	Intergenic	L1MC5|LINE|L1	101939	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	melanogenesis associated transcription factor	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2664	chr14	103378503	103378703	+	2.09630	NA	Intergenic	Intergenic	-31803	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2, E3 ubiquitin protein ligase	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6923	chr7	79850488	79850688	+	2.09630	NA	Intergenic	Intergenic	-2378	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4315	chr2	55282743	55282943	+	2.09630	NA	Intergenic	Intergenic	-153127	NM_001355118	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding	0.000000	0.248756			-37(ATTTAAATATGAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4171	chr2	11050093	11050293	+	2.09630	NA	Intergenic	Intergenic	-122189	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding	0.010000	0.432836			14(ATTTAAAGAAAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5108	chr3	108055724	108055924	+	2.09630	NA	Intergenic	Ricksha_a|DNA|MULE-MuDR	-10965	NM_001160411	14865	Mm.31203	NM_026764	ENSMUSG00000027890	Gstm4	1110004G14Rik|GSTM7-7|Gstb-4|Gstb4	glutathione S-transferase, mu 4	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7818	chr9	93161126	93161326	+	2.09630	NA	Intergenic	Intergenic	-155493	NR_040756	78349	Mm.52612	NR_040756	ENSMUSG00000100294	1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	ncRNA	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1514	chr12	3682578	3682778	+	2.09630	NA	intron (NM_001162465, intron 8 of 17)	intron (NM_001162465, intron 8 of 17)	109694	NM_007886	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2906	chr15	49259465	49259665	+	2.09630	NA	Intergenic	Intergenic	-467576	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4669	chr2	139599535	139599735	+	2.09630	NA	intron (NM_175467, intron 10 of 12)	intron (NM_175467, intron 10 of 12)	-78543	NM_001276489	319909	Mm.41113	NM_001126490	ENSMUSG00000074766	Ism1	5430433G21Rik|Ism	isthmin 1, angiogenesis inhibitor	protein-coding	0.010000	0.467662			20(ATCTGCAATGCAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-582	chr1	178837196	178837396	+	2.09630	NA	intron (NM_001161665, intron 5 of 14)	intron (NM_001161665, intron 5 of 14)	308171	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding	0.005000	0.328358		-22(CATACATATACATG,+,0.00),-22(CATACATATACATG,-,0.00),-12(CATGTATATACATC,+,0.00),15(TATACATTTGCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1968	chr13	19344232	19344432	+	2.09630	NA	Intergenic	Intergenic	51481	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4155	chr2	5745761	5745961	+	2.09630	NA	Intergenic	Intergenic	-31099	NM_001290375	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-696	chr10	12210260	12210460	+	2.09630	NA	Intergenic	Intergenic	601136	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4124	chr19	54299272	54299472	+	2.09385	NA	Intergenic	Intergenic	254113	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding	0.000000	0.358209			17(ATTAACATCAAAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-399	chr1	137903429	137903629	+	2.09385	NA	Intergenic	Intergenic	-62926	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA	0.015000	0.432836			-83(CCTTTCTTATTTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3579	chr17	71313664	71313864	+	2.09385	NA	Intergenic	MER2|DNA|TcMar-Tigger	-2208	NM_001357336	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-374	chr1	128654249	128654449	+	2.09222	NA	Intergenic	Intergenic	-62050	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|CXC-R4|CXCR-4|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3221	chr16	49947545	49947745	+	2.08830	NA	Intergenic	Intergenic	-8185	NR_153658	100503490	Mm.72499	NR_153658		Gm19723	-	predicted gene, 19723	ncRNA	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4834	chr3	9288314	9288514	+	2.08502	NA	Intergenic	Intergenic	37847	NM_177660	229055	Mm.103262	NM_177660	ENSMUSG00000069114	Zbtb10	4832414A18|AU021107|RINZF	zinc finger and BTB domain containing 10	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5026	chr3	77791450	77791650	+	2.08502	NA	Intergenic	Lx8|LINE|L1	1354196	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0.005000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1619	chr12	40480600	40480800	+	2.08502	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	34647	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2392	chr14	21630868	21631068	+	2.08502	NA	intron (NM_017479, intron 9 of 16)	intron (NM_017479, intron 9 of 16)	83608	NM_001013826	435391	Mm.295860	NM_001013826	ENSMUSG00000063821	Dupd1	EG435391	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6882	chr7	65605945	65606145	+	2.08502	NA	intron (NR_131060, intron 1 of 7)	intron (NR_131060, intron 1 of 7)	24014	NR_131060	407810	Mm.249337	NR_131060	ENSMUSG00000086662	BC046251	-	cDNA sequence BC046251	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5343	chr4	10810317	10810517	+	2.08502	NA	Intergenic	Intergenic	-12615	NR_045185	73624	Mm.67392	NR_045185	ENSMUSG00000086080	1700123O12Rik	-	RIKEN cDNA 1700123O12 gene	ncRNA	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5417	chr4	34075054	34075254	+	2.08502	NA	Intergenic	Intergenic	-25087	NM_026293	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6858	chr7	55072886	55073086	+	2.08502	NA	intron (NM_178705, intron 4 of 11)	intron (NM_178705, intron 4 of 11)	237741	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7107	chr7	135906288	135906488	+	2.08502	NA	Intergenic	L1M4|LINE|L1	-190009	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding	0.005000	0.308458			-65(ATTTGTATGACATTAT,-,0.00),-31(CGTTTGTTATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1044	chr10	114075703	114075903	+	2.08502	NA	Intergenic	Intergenic	725567	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4721	chr2	149984149	149984349	+	2.08502	NA	intron (NM_001085521, intron 3 of 3)	intron (NM_001085521, intron 3 of 3)	152429	NM_181266	104348	Mm.485851	NM_023266	ENSMUSG00000068134	Zfp120	AI315103|E030042N05Rik|F80|MZF31|Zfp844	zinc finger protein 120	protein-coding	0.000000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5287	chr3	149822516	149822716	+	2.08502	NA	Intergenic	Intergenic	547879	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7221	chr8	41106464	41106664	+	2.08502	NA	intron (NM_001005863, intron 1 of 13)	intron (NM_001005863, intron 1 of 13)	8103	NM_001286413	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4416	chr2	78649278	78649478	+	2.08502	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-219669	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding	0.000000	0.407960			5(TTATTCTCTTGGTAAG,+,0.00),41(CTGAACATGACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-155	chr1	53302412	53302612	+	2.08502	NA	intron (NM_145517, intron 2 of 3)	Lx9|LINE|L1	5417	NM_145517	227102	Mm.212846	NM_145517	ENSMUSG00000026097	Ormdl1	C730042F17Rik	ORM1-like 1 (S. cerevisiae)	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8028	chrX	94254525	94254725	+	2.08502	NA	3' UTR (NM_153165, exon 5 of 5)	3' UTR (NM_153165, exon 5 of 5)	19695	NM_001039061	236904	Mm.115533	NM_153165	ENSMUSG00000043929	Klhl15	6330500C13Rik	kelch-like 15	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6411	chr6	39801495	39801695	+	2.08502	NA	TTS (NM_010270)	TTS (NM_010270)	9341	NM_001010930	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5560	chr4	81108275	81108475	+	2.08502	NA	Intergenic	Intergenic	197689	NM_026821	52829	Mm.273986	NM_026821	ENSMUSG00000048706	Lurap1l	1110029A09Rik|AV077978|AV175137|D4Bwg0951e|WI-13707|bM350F23.1	leucine rich adaptor protein 1-like	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6607	chr6	98137590	98137790	+	2.08502	NA	Intergenic	Intergenic	145907	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	melanogenesis associated transcription factor	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6803	chr7	26614776	26614976	+	2.08502	NA	Intergenic	Intergenic	-2798	NM_134231	171265	Mm.377217	NM_134231	ENSMUSG00000091924	Vmn1r185	V1re12	vomeronasal 1 receptor 185	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2835	chr15	27549144	27549344	+	2.08371	NA	intron (NM_020332, intron 2 of 11)	intron (NM_020332, intron 2 of 11)	-22250	NR_106065	102466808		NR_106065	ENSMUSG00000098416	Mir7117	Gm27729|mmu-mir-7117	microRNA 7117	ncRNA	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6656	chr6	108545032	108545232	+	2.08371	NA	intron (NM_010585, intron 61 of 61)	intron (NM_010585, intron 61 of 61)	55389	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA	0.015000	0.432836			29(CGTTTGCTATTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6115	chr5	102049809	102050009	+	2.08352	NA	intron (NM_172882, intron 1 of 66)	intron (NM_172882, intron 1 of 66)	20012	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding	0.000000	0.383085			39(TCTTACTTATATAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2939	chr15	58045822	58046022	+	2.08352	NA	Intergenic	L1MB4|LINE|L1	-11628	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2201	chr13	92365358	92365558	+	2.08352	NA	intron (NM_010049, intron 3 of 5)	intron (NM_010049, intron 3 of 5)	-10455	NM_010829	17686	Mm.343101	NM_010829	ENSMUSG00000014850	Msh3	D13Em1|Rep-3|Rep3	mutS homolog 3	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-852	chr10	63764008	63764208	+	2.08352	NA	intron (NM_177612, intron 5 of 17)	intron (NM_177612, intron 5 of 17)	-56947	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6838	chr7	47103217	47103417	+	2.08352	NA	intron (NM_001163565, intron 2 of 13)	intron (NM_001163565, intron 2 of 13)	-20093	NR_106023	102465639		NR_106023	ENSMUSG00000098960	Mir7056	Gm27696|mmu-mir-7056	microRNA 7056	ncRNA	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4718	chr2	149844253	149844453	+	2.08352	NA	intron (NM_001363094, intron 2 of 4)	intron (NM_001363094, intron 2 of 4)	13570	NM_001363094	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|Tmem90b	synapse differentiation inducing 1	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3607	chr17	78999149	78999349	+	2.08352	NA	intron (NM_001171004, intron 2 of 18)	Tigger17a|DNA|TcMar-Tigger	9256	NM_001171005	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6280	chr6	3558497	3558697	+	2.08352	NA	intron (NM_001167751, intron 16 of 26)	L1_Mus3|LINE|L1	60204	NM_001167751	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6601	chr6	96944434	96944634	+	2.08352	NA	intron (NM_177233, intron 3 of 5)	MER20B|DNA|hAT-Charlie	115877	NM_177233	320701	Mm.131700	NM_177233	ENSMUSG00000046500	Tafa4	C130034I18Rik|Fam19a4|Fam19a4 Tafa-4|Tafa-4	TAFA chemokine like family member 4	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4063	chr19	29723099	29723299	+	2.08352	NA	intron (NM_172836, intron 6 of 7)	intron (NM_172836, intron 6 of 7)	25258	NM_029993	77836	Mm.138437	NM_029993	ENSMUSG00000024806	Mlana	A930034P04Rik|Mart1	melan-A	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2054	chr13	44694266	44694466	+	2.08352	NA	Intergenic	Intergenic	-36408	NM_001205044	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8112	chrX	145407303	145407503	+	2.08280	NA	Intergenic	MER2|DNA|TcMar-Tigger	-58464	NM_178358	237091	Mm.135547	NM_178358	ENSMUSG00000041700	Lhfpl1	Lhfp	lipoma HMGIC fusion partner-like 1	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3359	chr16	85811869	85812069	+	2.08280	NA	Intergenic	Lx8b|LINE|L1	-7242	NR_040506	75310	Mm.108627	NR_040506	ENSMUSG00000116586	4930556C24Rik	-	RIKEN cDNA 4930556C24 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6405	chr6	38705732	38705932	+	2.08280	NA	intron (NM_001294144, intron 12 of 14)	Lx7|LINE|L1	42763	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-788	chr10	40083230	40083430	+	2.08280	NA	intron (NM_001114332, intron 1 of 5)	PB1D7|SINE|Alu	-58062	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding	0.000000	0.383085			46(CTTTAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1548	chr12	13809442	13809642	+	2.08280	NA	Intergenic	Intergenic	-181896	NR_136761	102639399	Mm.122052	NR_136761	ENSMUSG00000113666	Gm35725	-	predicted gene, 35725	ncRNA	0.005000	0.422886	-10(GATAACTTATGCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6198	chr5	131680528	131680728	+	2.08280	NA	intron (NM_001363480, intron 5 of 19)	intron (NM_001363480, intron 5 of 19)	-199641	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA	0.025000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4076	chr19	35123287	35123487	+	2.08280	NA	Intergenic	L1MA4A|LINE|L1	157991	NR_035473	100316775		NR_035473	ENSMUSG00000089151	Mir1950	mmu-mir-1950	microRNA 1950	ncRNA	0.020000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7051	chr7	121700118	121700318	+	2.08206	NA	intron (NM_001033173, intron 1 of 15)	L1M3|LINE|L1	7224	NM_001033173	76179	Mm.122538	NM_001033173	ENSMUSG00000063317	Usp31	6330567E21Rik|mKIAA1203	ubiquitin specific peptidase 31	protein-coding	0.000000	0.353234			-81(ATCAACATGACAAAAG,-,0.00),73(ATTTCCAAACCAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3611	chr17	80499346	80499546	+	2.08206	NA	Intergenic	Intergenic	-18993	NM_009231	20662	Mm.60975	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	SOS Ras/Rac guanine nucleotide exchange factor 1	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1139	chr11	4855674	4855874	+	2.07881	NA	Intergenic	Intergenic	-6230	NM_001361675	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6485	chr6	62944694	62944894	+	2.07687	NA	Intergenic	Intergenic	-311212	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding	0.000000	0.318408			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-101	chr10	89481441	89481641	+	2.07687	NA	intron (NM_009108, intron 3 of 8)	intron (NM_009108, intron 3 of 8)	25117	NM_001163700	20186	Mm.3095	NM_009108	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	nuclear receptor subfamily 1, group H, member 4	protein-coding	0.005000	0.318408			-93(AATTTGTGATGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-552	chr1	174600761	174600961	+	2.07586	NA	intron (NM_019445, intron 4 of 17)	MER5A|DNA|hAT-Charlie	99036	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding	0.000000	0.482587			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-52	chr1	174600758	174600958	+	2.07586	NA	intron (NM_019445, intron 4 of 17)	intron (NM_019445, intron 4 of 17)	99033	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding	0.000000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-217	chr12	117054305	117054505	+	2.07563	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	96864	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.020000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5975	chr5	60037847	60038047	+	2.07380	NA	Intergenic	Intergenic	-51945	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA	0.010000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-677	chr5	60037844	60038044	+	2.07380	NA	Intergenic	Intergenic	-51942	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4695	chr2	142817713	142817913	+	2.07300	NA	intron (NM_001355123, intron 12 of 26)	intron (NM_001355123, intron 12 of 26)	83651	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7934	chrX	20380125	20380325	+	2.07300	NA	intron (NR_110967, intron 2 of 8)	intron (NR_110967, intron 2 of 8)	15744	NR_110967	19889	Mm.288141	NM_133669	ENSMUSG00000060090	Rp2	AI662636|Rp2h	retinitis pigmentosa 2 homolog	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4102	chr19	48327234	48327434	+	2.07258	NA	intron (NM_025696, intron 1 of 26)	intron (NM_025696, intron 1 of 26)	121309	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1921	chr12	119624223	119624423	+	2.07258	NA	Intergenic	Intergenic	180913	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1531	chr12	8264477	8264677	+	2.07258	NA	intron (NM_001364260, intron 4 of 6)	intron (NM_001364260, intron 4 of 6)	37377	NM_013527	238057	Mm.271308	NM_013527	ENSMUSG00000037660	Gdf7	BMP12	growth differentiation factor 7	protein-coding	0.005000	0.452736			-60(ATTAGCAAGAGACACA,-,0.00),16(TTTACCATAAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7914	chrX	7454046	7454246	+	2.07258	NA	Intergenic	Intergenic	-31158	NR_027924	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8018	chrX	92515854	92516054	+	2.07258	NA	intron (NM_173783, intron 3 of 4)	intron (NM_173783, intron 3 of 4)	26005	NM_001034103	546347	Mm.380183	NM_001034103	ENSMUSG00000071726	Gm5941	EG546347	predicted gene 5941	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3531	chr17	53793785	53793985	+	2.07258	NA	Intergenic	RLTR17C_Mm|LTR|ERVK	52073	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-44	chr1	15669054	15669254	+	2.07258	NA	intron (NM_001098528, intron 2 of 2)	intron (NM_001098528, intron 2 of 2)	-136492	NM_001286628	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding	0.000000	0.422886			-90(TCTTTGTTTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5405	chr4	30121212	30121412	+	2.07258	NA	Intergenic	BGLII|LTR|ERVK	-543284	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	ncRNA	0.005000	0.363184			-91(CCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6495	chr6	65050056	65050256	+	2.07258	NA	intron (NM_007958, intron 2 of 23)	intron (NM_007958, intron 2 of 23)	6950	NM_001253392	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|etl-1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2771	chr15	7390327	7390527	+	2.07258	NA	intron (NM_178748, intron 1 of 21)	intron (NM_178748, intron 1 of 21)	7963	NM_178748	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5740	chr4	126886683	126886883	+	2.07258	NA	intron (NM_001357201, intron 21 of 27)	L1ME1|LINE|L1	81140	NM_001357201	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-9	chr1	5155461	5155661	+	2.07258	NA	intron (NM_133826, intron 13 of 13)	Lx8b|LINE|L1	72475	NM_133826	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1363	chr11	76416595	76416795	+	2.07258	NA	TTS (NM_001291186)	TTS (NM_001291186)	9552	NM_023355	56322	Mm.18803	NM_019818	ENSMUSG00000020843	Timm22	Tim22	translocase of inner mitochondrial membrane 22	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7601	chr9	33027262	33027462	+	2.07258	NA	Intergenic	L1MD|LINE|L1	-98396	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5582	chr4	86221831	86222031	+	2.07258	NA	intron (NM_029967, intron 7 of 27)	intron (NM_029967, intron 7 of 27)	167956	NM_001368621	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7935	chrX	20529783	20529983	+	2.07252	NA	Intergenic	Intergenic	-19935	NM_009060	19733	Mm.2118	NM_009060	ENSMUSG00000023070	Rgn	AI265316|GNL|SMP30	regucalcin	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3788	chr18	35280195	35280395	+	2.07252	NA	intron (NM_030749, intron 7 of 9)	intron (NM_030749, intron 7 of 9)	-65271	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding	0.015000	0.412935			-59(AATAGCAAGAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5892	chr5	32430606	32430806	+	2.07252	NA	Intergenic	Intergenic	-28264	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1 catalytic subunit beta	protein-coding	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6455	chr6	53530461	53530661	+	2.07252	NA	intron (NM_001327821, intron 5 of 10)	intron (NM_001327821, intron 5 of 10)	-42813	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5599	chr4	91342453	91342653	+	2.07252	NA	intron (NM_001347149, intron 1 of 7)	intron (NM_001347149, intron 1 of 7)	29502	NM_010486	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV like RNA binding protein 1	protein-coding	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7188	chr8	30669553	30669753	+	2.07252	NA	Intergenic	Intergenic	101258	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	ncRNA	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4386	chr2	72122537	72122737	+	2.07021	NA	intron (NM_001355478, intron 1 of 26)	intron (NM_001355478, intron 1 of 26)	68020	NM_001355478	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding	0.030000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3750	chr18	25656242	25656442	+	2.07021	NA	intron (NM_001362325, intron 2 of 12)	intron (NM_001362325, intron 2 of 12)	23406	NM_001362337	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3197	chr16	43710670	43710870	+	2.06422	NA	Intergenic	Intergenic	-46586	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding	0.025000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4709	chr2	146356686	146356886	+	2.06289	NA	intron (NM_001033348, intron 27 of 40)	intron (NM_001033348, intron 27 of 40)	97500	NR_040619	77806	Mm.392819	NR_040619	ENSMUSG00000085958	A930019D19Rik	-	RIKEN cDNA A930019D19 gene	ncRNA	0.010000	0.447761			73(GTTTTCTTATGTAAAA,+,0.00),81(ATGTAAAAGACAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7843	chr9	98721445	98721645	+	2.06289	NA	Intergenic	L1MEf|LINE|L1	98542	NR_045332	331011	Mm.271554	NR_045332	ENSMUSG00000102013	E330023G01Rik	E330023G01	RIKEN cDNA E330023G01 gene	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5962	chr5	54441172	54441372	+	2.06289	NA	Intergenic	Intergenic	91280	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13	predicted gene 10440	ncRNA	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3107	chr16	21449552	21449752	+	2.06289	NA	intron (NM_001081366, intron 7 of 46)	intron (NM_001081366, intron 7 of 46)	26534	NM_001285894	209018	Mm.235683	NM_145948	ENSMUSG00000033653	Vps8	AI315068|AU040738|mKIAA0804	VPS8 CORVET complex subunit	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6009	chr5	68090685	68090885	+	2.06289	NA	intron (NM_001018019, intron 1 of 3)	MTB_Mm|LTR|ERVL-MaLR	58950	NM_001018019	433899	Mm.332422	NM_001018019	ENSMUSG00000068082	Grxcr1	Tg(Eno2-Gabrb3)0370Brll|pi|tde	glutaredoxin, cysteine rich 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6145	chr5	108086885	108087085	+	2.06289	NA	intron (NM_001253879, intron 3 of 14)	intron (NM_001253879, intron 3 of 14)	8820	NM_001253878	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3612	chr17	80499589	80499789	+	2.06236	NA	Intergenic	Intergenic	-19236	NM_009231	20662	Mm.60975	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	SOS Ras/Rac guanine nucleotide exchange factor 1	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2614	chr14	88410904	88411104	+	2.06236	NA	Intergenic	Intergenic	60392	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3216	chr16	49319031	49319231	+	2.06236	NA	Intergenic	Intergenic	261731	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding	0.005000	0.368159	-23(AATGAATAATTCATA,+,0.00),-23(AATGAATAATTCATA,-,0.00)		-44(GTGTCCATGACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-558	chr1	175731381	175731581	+	2.06207	NA	intron (NM_029453, intron 7 of 27)	intron (NM_029453, intron 7 of 27)	32888	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding	0.005000	0.373134			-68(AATAGAAAGAGAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2183	chr13	85886412	85886612	+	2.06207	NA	Intergenic	Intergenic	160283	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit 7C	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4517	chr2	109989640	109989840	+	2.06207	NA	exon (NM_172671, exon 3 of 18)	exon (NM_172671, exon 3 of 18)	-28077	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-710	chr10	15031591	15031791	+	2.06207	NA	Intergenic	L1ME1|LINE|L1	271744	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7258	chr8	54694169	54694369	+	2.06207	NA	intron (NM_001172152, intron 2 of 29)	RMER10A|LTR|ERVL	24409	NM_028220	244484	Mm.95281	NM_028220	ENSMUSG00000039375	Wdr17	3010002I12Rik|B230207L18Rik	WD repeat domain 17	protein-coding	0.005000	0.467662			-69(ATTAGCATACCAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4558	chr2	120298151	120298351	+	2.06207	NA	Intergenic	Intergenic	-9182	NM_001024137	78390	Mm.330507	NM_001024137	ENSMUSG00000070719	Pla2g4d	2610311B01Rik|Pla2delta|cPLA2delta	phospholipase A2, group IVD	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4206	chr2	21710790	21710990	+	2.06207	NA	intron (NM_001004761, intron 5 of 10)	intron (NM_001004761, intron 5 of 10)	343323	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2470	chr14	46480364	46480564	+	2.06207	NA	Intergenic	ERVL-E-int|LTR|ERVL	-89795	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3122	chr16	24815899	24816099	+	2.06207	NA	intron (NM_178665, intron 8 of 12)	intron (NM_178665, intron 8 of 12)	94144	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2197	chr13	91031802	91032002	+	2.06207	NA	intron (NM_025770, intron 4 of 7)	intron (NM_025770, intron 4 of 7)	108780	NM_024175	66475	Mm.306302	NM_024175	ENSMUSG00000049517	Rps23	2410044J15Rik	ribosomal protein S23	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7745	chr9	77732161	77732361	+	2.06207	NA	Intergenic	Intergenic	-22274	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2772	chr15	7400603	7400803	+	2.06207	NA	Intergenic	Intergenic	-2308	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3658	chr17	90251822	90252022	+	2.06207	NA	intron (NM_001346957, intron 15 of 18)	intron (NM_001346957, intron 15 of 18)	-163554	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3248	chr16	55878145	55878345	+	2.06207	NA	intron (NM_001134457, intron 2 of 5)	RLTR12A|LTR|ERVK	17034	NM_001134457	385658	Mm.310635	NM_001134457	ENSMUSG00000075033	Nxpe3	Fam55c|Gm1752|Gm611	neurexophilin and PC-esterase domain family, member 3	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1134	chr10	127693089	127693289	+	2.05435	NA	intron (NM_001113211, intron 5 of 8)	intron (NM_001113211, intron 5 of 8)	-12067	NM_001081219	432516	Mm.90450	NM_001081219	ENSMUSG00000025401	Myo1a	BBM-I|Myhl	myosin IA	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2832	chr15	26598099	26598299	+	2.05435	NA	intron (NM_176959, intron 2 of 3)	intron (NM_176959, intron 2 of 3)	289151	NM_177597	211147	Mm.54257	NM_177597	ENSMUSG00000022269	March11	9630025C22	membrane-associated ring finger (C3HC4) 11	protein-coding	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4161	chr2	7845145	7845345	+	2.05435	NA	Intergenic	Intergenic	-449047	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4461	chr2	96218217	96218417	+	2.05296	NA	Intergenic	Intergenic	-99852	NM_001363048	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7462	chr8	116063703	116063903	+	2.05296	NA	Intergenic	Intergenic	-356909	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1815	chr12	92436400	92436600	+	2.05296	NA	Intergenic	Intergenic	-587343	NM_011344	20338	Mm.250605	NM_011344	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0.000000	0.368159			10(ATTTGAAAGAGAGGGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-711	chr10	16895375	16895575	+	2.05296	NA	Intergenic	Intergenic	200307	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA	0.000000	0.398010			-45(ATGAAAATAACAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6364	chr6	25838954	25839154	+	2.05296	NA	Intergenic	Intergenic	-29836	NM_133931	101185	Mm.274589	NM_133931	ENSMUSG00000029676	Pot1a	1500031H18Rik|AI851169|Pot1	protection of telomeres 1A	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-969	chr10	97288911	97289111	+	2.05296	NA	Intergenic	Intergenic	-134467	NR_039547	100628616		NR_039547	ENSMUSG00000105557	Mir3966	mmu-mir-3966|mu-mir-3966	microRNA 3966	ncRNA	0.000000	0.318408			-42(AAATTGTTTTTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1654	chr12	51607478	51607678	+	2.05296	NA	TTS (NM_052973)	TTS (NM_052973)	14237	NM_001198835	12810	Mm.21325	NM_007728	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	cochlin	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5915	chr5	41476100	41476300	+	2.05296	NA	Intergenic	MIRb|SINE|MIR	231491	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding	0.005000	0.457711		69(CAGGCATATTCATC,+,0.00)	50(ACTTTCCCTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1755	chr12	79426255	79426455	+	2.05296	NA	intron (NM_009014, intron 7 of 10)	L2b|LINE|L2	129004	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding	0.005000	0.393035			74(ATTTTGCTTTGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7837	chr9	97645462	97645662	+	2.05296	NA	intron (NM_022319, intron 2 of 17)	intron (NM_022319, intron 2 of 17)	-275604	NM_030219	78911	Mm.108347	NM_030219	ENSMUSG00000032451	Trim42	4930486B16Rik	tripartite motif-containing 42	protein-coding	0.000000	0.363184			29(TCACTGTAATTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1248	chr11	38106952	38107152	+	2.05296	NA	Intergenic	Lx8|LINE|L1	412993	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	-	predicted gene 12130	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-719	chr10	19836016	19836216	+	2.04667	NA	Intergenic	Intergenic	15343	NM_029529	76157	Mm.74324	NM_029529	ENSMUSG00000050473	Slc35d3	6230421J19Rik|Frcl1	solute carrier family 35, member D3	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3856	chr18	53606391	53606591	+	2.04667	NA	Intergenic	MER77B|LTR|ERVL	-41660	NR_040349	100502945	Mm.376937	NR_040349	ENSMUSG00000118362	Gm19466	-	predicted gene, 19466	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4649	chr2	135793040	135793240	+	2.04667	NA	intron (NM_001355154, intron 1 of 36)	(TG)n|Simple_repeat|Simple_repeat	28302	NM_001355154	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding	0.015000	0.477612			53(CTTTTGCTTTGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7062	chr7	123775343	123775543	+	2.04667	NA	Intergenic	L1ME4a|LINE|L1	-207385	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding	0.015000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3415	chr17	9536063	9536263	+	2.04657	NA	Intergenic	Intergenic	133541	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	poly(A) binding protein, cytoplasmic 6	protein-coding	0.010000	0.343284			-21(ATTTACAAAATTATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4570	chr2	122944684	122944884	+	2.04492	NA	Intergenic	Intergenic	162785	NM_021507	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqor	0610039J17Rik|4930557M22Rik|Sqrdl	sulfide quinone oxidoreductase	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6427	chr6	45373287	45373487	+	2.04492	NA	intron (NM_001004357, intron 1 of 23)	intron (NM_001004357, intron 1 of 23)	313326	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.010000	0.318408			-13(CAATTCTGTTTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6576	chr6	88524112	88524312	+	2.04492	NA	Intergenic	Intergenic	-5412	NM_016906	53421	Mm.28375	NM_016906	ENSMUSG00000030082	Sec61a1	AA408394|AA410007|Sec61a	Sec61 alpha 1 subunit (S. cerevisiae)	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1691	chr12	64521057	64521257	+	2.04492	NA	Intergenic	Intergenic	-46259	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2525	chr14	64459327	64459527	+	2.04492	NA	Intergenic	Intergenic	-3524	NM_026322	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4135	chr19	58527792	58527992	+	2.04492	NA	intron (NM_029372, intron 5 of 8)	intron (NM_029372, intron 5 of 8)	15890	NM_029372	75645	Mm.159542	NM_029372	ENSMUSG00000025090	Ccdc172	1700011F14Rik	coiled-coil domain containing 172	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1863	chr12	103427273	103427473	+	2.04238	NA	Intergenic	L1MA4A|LINE|L1	-1526	NM_001364162	27225	Mm.3935	NM_020494	ENSMUSG00000041645	Ddx24	1700055J08Rik|2510027P10Rik|AI649272	DEAD (Asp-Glu-Ala-Asp) box polypeptide 24	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1484	chr11	114529110	114529310	+	2.04232	NA	Intergenic	Intergenic	-80350	NR_027643	319819	Mm.50754	NM_177008	ENSMUSG00000062391	4932435O22Rik	-	RIKEN cDNA 4932435O22 gene	ncRNA	0.030000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3786	chr18	35187527	35187727	+	2.03972	NA	intron (NM_009818, intron 7 of 17)	intron (NM_009818, intron 7 of 17)	27397	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2297	chr13	111185050	111185250	+	2.03972	NA	Intergenic	Intergenic	44281	NR_045908	73129	Mm.417826	NR_045908	ENSMUSG00000114824	3110015C05Rik	-	RIKEN cDNA 3110015C05 gene	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2453	chr14	38335423	38335623	+	2.03774	NA	Intergenic	Intergenic	-562779	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6627	chr6	101854483	101854683	+	2.03774	NA	Intergenic	Intergenic	80334	NR_027989	207157	Mm.57632	NM_177579	ENSMUSG00000052236	Gm9871	0610005I04|EG207157	predicted gene 9871	ncRNA	0.000000	0.343284			-58(TCATTTTGATTAAAAT,+,0.00),15(TTTATATTTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-554	chr1	175034386	175034586	+	2.03774	NA	Intergenic	Intergenic	-112667	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding	0.010000	0.333333	40(CATAAATAATGCATA,+,0.00),40(CATAAATAATGCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6913	chr7	76235075	76235275	+	2.03656	NA	intron (NM_001199224, intron 1 of 22)	intron (NM_001199224, intron 1 of 22)	5288	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0.000000	0.378109			10(ATTTACATGGCATAAC,-,0.00),66(ATTTGCAATGGAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3279	chr16	64595251	64595451	+	2.03624	NA	intron (NM_173861, intron 1 of 2)	intron (NM_173861, intron 1 of 2)	6980	NM_001368721	224291	Mm.246580	NM_173861	ENSMUSG00000068167	Csnka2ip	Ckt2	casein kinase 2, alpha prime interacting protein	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2086	chr13	58240281	58240481	+	2.03336	NA	intron (NM_019832, intron 8 of 11)	B3A|SINE|B2	-24728	NM_026842	56085	Mm.182053	NM_026842	ENSMUSG00000005312	Ubqln1	1110046H03Rik|1810030E05Rik|AU019746|C77538|D13Ertd372e|Da41|Dsk2|Plic-1|Plic1|Xdrp1	ubiquilin 1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1486	chr11	114692739	114692939	+	2.03336	NA	intron (NM_053273, intron 3 of 13)	MER5A|DNA|hAT-Charlie	17371	NM_053273	117160	Mm.271934	NM_053273	ENSMUSG00000034714	Ttyh2	1110001A03Rik	tweety family member 2	protein-coding	0.025000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-480	chr1	156819226	156819426	+	2.03124	NA	intron (NM_001159965, intron 16 of 19)	intron (NM_001159965, intron 16 of 19)	-19697	NM_028333	72713	Mm.389206	NM_028333	ENSMUSG00000033544	Angptl1	2810039D03Rik|ANG3|ANGPT3|ANGY|ARP1	angiopoietin-like 1	protein-coding	0.000000	0.368159			-19(TTTTACATGACAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4810	chr2	179146257	179146457	+	2.03124	NA	Intergenic	Intergenic	-268579	NM_026596	68175	Mm.158187	NM_026596		4930591A17Rik	-	RIKEN cDNA 4930591A17 gene	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5710	chr4	118030155	118030355	+	2.03124	NA	intron (NM_001285520, intron 4 of 11)	intron (NM_001285520, intron 4 of 11)	-100492	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding	0.025000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6442	chr6	49966254	49966454	+	2.03124	NA	Intergenic	Intergenic	143644	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3749	chr18	25656084	25656284	+	2.02752	NA	intron (NM_001362325, intron 2 of 12)	intron (NM_001362325, intron 2 of 12)	23564	NM_001362337	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.025000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3728	chr18	19785190	19785390	+	2.02530	NA	Intergenic	URR1A|DNA|hAT-Charlie	216807	NM_001291809	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0.005000	0.393035			71(ATTTACATTACAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7081	chr7	129084325	129084525	+	2.02530	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-172669	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding	0.005000	0.388060			42(ATTTGCTCATGTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3782	chr18	34304225	34304425	+	2.02530	NA	intron (NM_001360980, intron 12 of 16)	intron (NM_001360980, intron 12 of 16)	-26820	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5176	chr3	127463860	127464060	+	2.02211	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	35155	NM_001327938	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding	0.030000	0.462687			-27(ATTTTCACATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2161	chr13	78628964	78629164	+	2.02211	NA	Intergenic	Intergenic	-430191	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3649	chr17	86419476	86419676	+	2.01984	NA	intron (NM_011104, intron 2 of 14)	intron (NM_011104, intron 2 of 14)	-132398	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-931	chr10	89481402	89481602	+	2.01561	NA	intron (NM_009108, intron 3 of 8)	intron (NM_009108, intron 3 of 8)	25156	NM_001163700	20186	Mm.3095	NM_009108	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	nuclear receptor subfamily 1, group H, member 4	protein-coding	0.005000	0.343284			-54(AATTTGTGATGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5080	chr3	99913505	99913705	+	2.01479	NA	intron (NM_028892, intron 1 of 48)	intron (NM_028892, intron 1 of 48)	28188	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding	0.005000	0.338308			-15(TATTTCTCATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3326	chr16	76782661	76782861	+	2.01479	NA	Intergenic	Intergenic	-3669	NR_155453	102632814		NR_155453	ENSMUSG00000109333	Gm30790	Gm45028	predicted gene, 30790	ncRNA	0.015000	0.442786			-11(TTTTTGTCCTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1763	chr12	79663190	79663390	+	2.01479	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	261443	NR_131075	77290	Mm.395042	NR_131073	ENSMUSG00000112765	9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA	0.035000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-897	chr10	76823119	76823319	+	2.01479	NA	promoter-TSS (NR_152849)	promoter-TSS (NR_152849)	-407	NR_152849	59093	Mm.272803	NM_021568	ENSMUSG00000001120	Pcbp3	AlphaCP-3	poly(rC) binding protein 3	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3904	chr18	64982119	64982319	+	2.01479	NA	intron (NM_001114386, intron 1 of 30)	intron (NM_001114386, intron 1 of 30)	-41308	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6801	chr7	25647713	25647913	+	2.01276	NA	intron (NM_007533, intron 1 of 8)	intron (NM_007533, intron 1 of 8)	10948	NM_007533	12039	Mm.25848	NM_007533	ENSMUSG00000060376	Bckdha	-	branched chain ketoacid dehydrogenase E1, alpha polypeptide	protein-coding	0.000000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-438	chr1	147134629	147134829	+	2.01276	NA	Intergenic	Intergenic	637042	NM_001145807	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2652	chr14	100544146	100544346	+	2.01276	NA	Intergenic	Intergenic	-394450	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2890	chr15	42638782	42638982	+	2.01276	NA	intron (NM_001286062, intron 1 of 8)	intron (NM_001286062, intron 1 of 8)	38095	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4624	chr2	132938996	132939196	+	2.01276	NA	intron (NM_198029, intron 3 of 14)	intron (NM_198029, intron 3 of 14)	6940	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding	0.035000	0.462687	-15(AATGATTTATGCAAA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3366	chr16	87462661	87462861	+	2.01276	NA	intron (NM_024258, intron 3 of 17)	(TCTA)n|Simple_repeat|Simple_repeat	7776	NM_024258	74112	Mm.152941	NM_024258	ENSMUSG00000025616	Usp16	1200004E02Rik|2810483I07Rik|6330514E22Rik|UBPM	ubiquitin specific peptidase 16	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1678	chr12	58134131	58134331	+	2.01276	NA	Intergenic	Lx2A|LINE|L1	-77573	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding	0.000000	0.343284			59(ATTTGCAGGCCAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3942	chr18	77736814	77737014	+	2.01276	NA	Intergenic	Intergenic	-3444	NR_155289	105246501	Mm.403904	NR_155289	ENSMUSG00000097666	A330094K24Rik	-	RIKEN cDNA A330094K24 gene	ncRNA	0.000000	0.402985	11(AATACATAATGGATT,+,0.00),11(AATACATAATGGATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1277	chr11	47231284	47231484	+	2.01276	NA	intron (NM_011891, intron 2 of 7)	intron (NM_011891, intron 2 of 7)	147941	NM_011891	24052	Mm.34175	NM_011891	ENSMUSG00000020354	Sgcd	35DAG|A530047J11Rik|AI504364|AW547581|SG-delta|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding	0.000000	0.353234		69(TATTCATATTCAGG,-,0.00)	4(AGTCTGTCTTGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5085	chr3	100613435	100613635	+	2.01276	NA	intron (NM_010763, intron 8 of 12)	L1MB4|LINE|L1	71938	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3688	chr18	6231859	6232059	+	2.01276	NA	intron (NM_008448, intron 2 of 25)	ID4|SINE|ID	9565	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding	0.010000	0.333333			-59(CTTTTATTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2721	chr14	119394987	119395187	+	2.01263	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	256822	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding	0.005000	0.293532			-3(ATATGTTCATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1786	chr12	84445274	84445474	+	2.01263	NA	intron (NM_134042, intron 1 of 11)	intron (NM_134042, intron 1 of 11)	2943	NM_001313967	104776	Mm.247510	NM_134042	ENSMUSG00000021238	Aldh6a1	1110038I05Rik|Mmsdh	aldehyde dehydrogenase family 6, subfamily A1	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3272	chr16	63231610	63231810	+	2.01263	NA	Intergenic	MER2|DNA|TcMar-Tigger	377403	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7722	chr9	72465690	72465890	+	2.01263	NA	intron (NM_009359, intron 10 of 11)	intron (NM_009359, intron 10 of 11)	26169	NM_009359	21778	Mm.14485	NM_009359	ENSMUSG00000090626	Tex9	Gm19407|tsec-1	testis expressed gene 9	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1141	chr11	5125735	5125935	+	2.01263	NA	intron (NR_163830, intron 12 of 15)	MTD|LTR|ERVL-MaLR	24239	NM_001371004									0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5033	chr3	81452215	81452415	+	2.01263	NA	Intergenic	Intergenic	-349710	NR_138586	320566	Mm.208417	NR_138586	ENSMUSG00000103695	A830029E22Rik	-	RIKEN cDNA A830029E22 gene	ncRNA	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3472	chr17	33143094	33143294	+	2.01263	NA	intron (NM_001360203, intron 2 of 2)	intron (NM_001360203, intron 2 of 2)	-3511	NM_177719	240069	Mm.157765	NM_177719	ENSMUSG00000048602	Morc2b	4932411A10Rik|Tce6	microrchidia 2B	protein-coding	0.005000	0.323383			4(ATTTGAATAGCAAATT,-,0.00),15(AAATTCTCATTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6365	chr6	26776948	26777148	+	2.01263	NA	Intergenic	RLTR13E|LTR|ERVK	845622	NR_040771	626904	Mm.126787	NR_040771	ENSMUSG00000106799	Gm20756	-	predicted gene, 20756	ncRNA	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3139	chr16	27974717	27974917	+	2.01263	NA	Intergenic	Intergenic	124887	NR_033475	100038623	Mm.387135	NR_033475	ENSMUSG00000116654	Gm10823	-	predicted gene 10823	ncRNA	0.010000	0.328358			-77(CTATACATGAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5045	chr3	84090176	84090376	+	2.01263	NA	intron (NM_029797, intron 7 of 7)	ORR1B1|LTR|ERVL-MaLR	-50115	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	Tmem131l	D930015E06Rik|Kiaa0922|mKIAA0922	transmembrane 131 like	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-707	chr10	14597726	14597926	+	2.01263	NA	Intergenic	L1MA9|LINE|L1	-52790	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3833	chr18	47301521	47301721	+	2.01263	NA	intron (NM_001311097, intron 3 of 17)	intron (NM_001311097, intron 3 of 17)	67247	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding	0.005000	0.338308		-32(GATTAATATGCATT,+,0.00),-32(GATTAATATGCATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4507	chr2	107853588	107853788	+	2.01263	NA	Intergenic	MTD|LTR|ERVL-MaLR	563099	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding	0.000000	0.417910			44(ATTTGCAAGCCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6319	chr6	15354384	15354584	+	2.01263	NA	intron (NM_212435, intron 3 of 16)	L1MC2|LINE|L1	168978	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-441	chr1	148007798	148007998	+	2.01263	NA	Intergenic	Intergenic	1510211	NM_001145807	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2743	chr14	122348890	122349090	+	2.01263	NA	intron (NM_029556, intron 2 of 7)	intron (NM_029556, intron 2 of 7)	102125	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2104	chr13	63504578	63504778	+	2.01263	NA	Intergenic	Intergenic	61057	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes|wig	patched 1	protein-coding	0.025000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2488	chr14	51845070	51845270	+	2.01263	NA	Intergenic	Intergenic	-8598	NM_053111	93719	Mm.221324	NM_053111	ENSMUSG00000062148	Ear6	-	eosinophil-associated, ribonuclease A family, member 6	protein-coding	0.010000	0.447761			-56(ATTTGCATCAGAGTCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1635	chr12	44854992	44855192	+	2.01263	NA	3' UTR (NM_144552, exon 6 of 6)	3' UTR (NM_144552, exon 6 of 6)	219391	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.000000	0.343284			8(ATTAACATGAAAAGAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1357	chr11	75040308	75040508	+	2.01084	NA	intron (NM_001002764, intron 11 of 18)	ID_B1|SINE|B4	25583	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA	0.005000	0.378109			-41(ATTTACAAAACAGTTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2097	chr13	60577999	60578199	+	2.01084	NA	Intergenic	L1MA6|LINE|L1	-23848	NM_029653	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding	0.005000	0.402985		-30(CATACATATGCACA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7029	chr7	113603423	113603623	+	2.01084	NA	Intergenic	MER31A|LTR|ERV1	-38536	NR_126544	69295	Mm.396150	NR_126544	ENSMUSG00000084984	Far1os	1700006P19Rik	fatty acyl CoA reductase 1, opposite strand	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3024	chr15	91640605	91640805	+	2.01084	NA	Intergenic	Intergenic	-32519	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1096	chr10	121814438	121814638	+	2.01084	NA	intron (NM_001081037, intron 15 of 21)	intron (NM_001081037, intron 15 of 21)	74608	NM_173022	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding	0.010000	0.353234		-10(AATGCAAATGTATG,-,0.00)	-44(ATTTAAATCATAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-157	chr1	53644057	53644257	+	2.01084	NA	intron (NM_001252070, intron 9 of 65)	intron (NM_001252070, intron 9 of 65)	62627	NM_001252070	627872	Mm.184692	NM_001252070	ENSMUSG00000096141	Dnah7a	Dnahc7|Dnahc7a|Gm992	dynein, axonemal, heavy chain 7A	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7285	chr8	62451870	62452070	+	2.01084	NA	Intergenic	Intergenic	-328777	NM_011922	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0.005000	0.298507			13(TTATTCTTATGAAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-50	chr1	18948701	18948901	+	2.01084	NA	Intergenic	RSINE1|SINE|B4	-154221	NM_153154	226896	Mm.244858	NM_153154	ENSMUSG00000042596	Tfap2d	Tcfap2d	transcription factor AP-2, delta	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1586	chr12	31841304	31841504	+	2.01084	NA	intron (NM_001163126, intron 14 of 22)	intron (NM_001163126, intron 14 of 22)	108841	NM_177993	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8171	chrX	168196510	168196710	+	2.01084	NA	intron (NM_001033330, intron 3 of 19)	intron (NM_001033330, intron 3 of 19)	-72224	NM_001359072	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8099	chrX	141257770	141257970	+	2.01084	NA	intron (NM_053185, intron 3 of 44)	L1MB3|LINE|L1	216206	NM_053185	94216	Mm.155586	NM_053185	ENSMUSG00000031273	Col4a6	BB116301	collagen, type IV, alpha 6	protein-coding	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7853	chr9	102218405	102218605	+	2.01084	NA	intron (NM_173447, intron 2 of 15)	intron (NM_173447, intron 2 of 15)	86470	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6729	chr6	136424912	136425112	+	2.01084	NA	Intergenic	Intergenic	-9443	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6952	chr7	88394029	88394229	+	2.01084	NA	Intergenic	Intergenic	-36144	NM_028238	72433	Mm.276669	NM_028238	ENSMUSG00000030559	Rab38	2310011F14Rik|AU043391|cht	RAB38, member RAS oncogene family	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1433	chr11	101296989	101297189	+	2.01008	NA	intron (NM_001359819, intron 2 of 10)	intron (NM_001359819, intron 2 of 10)	5197	NM_001359819	56208	Mm.178947	NM_019584	ENSMUSG00000035086	Becn1	Atg6	beclin 1, autophagy related	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6835	chr7	43332369	43332569	+	2.01008	NA	Intergenic	Intergenic	-18872	NM_001271019	233186	Mm.290569	NM_145581	ENSMUSG00000039013	Siglecf	Siglec5|mSiglec-F	sialic acid binding Ig-like lectin F	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1515	chr12	3754801	3755001	+	2.00933	NA	intron (NR_027869, intron 16 of 20)	intron (NR_027869, intron 16 of 20)	-52079	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-47	chr1	17269004	17269204	+	2.00933	NA	Intergenic	L1Md_F2|LINE|L1	123731	NM_010267	14545	Mm.18218	NM_010267	ENSMUSG00000025777	Gdap1	-	ganglioside-induced differentiation-associated-protein 1	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4491	chr2	105786840	105787040	+	2.00933	NA	intron (NM_023876, intron 9 of 9)	intron (NM_023876, intron 9 of 9)	104477	NM_001310146	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding	0.005000	0.268657			-97(ATTTATAAAATAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3692	chr18	6930015	6930215	+	2.00933	NA	Intergenic	Intergenic	74664	NM_177595	210719	Mm.257186	NM_177595	ENSMUSG00000061013	Mkx	9430023B20Rik|Irxl1	mohawk homeobox	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6570	chr6	85130062	85130262	+	2.00933	NA	Intergenic	Intergenic	7602	NM_011467	20751	Mm.28393	NM_011467	ENSMUSG00000033735	Spr	AA409688|Gm10328	sepiapterin reductase	protein-coding	0.010000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8096	chrX	139077390	139077590	+	2.00933	NA	Intergenic	ORR1E-int|LTR|ERVL-MaLR	7746	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7184	chr8	29274685	29274885	+	2.00824	NA	Intergenic	Intergenic	-55149	NM_001347499	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 netrin receptor D	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2213	chr13	94317039	94317239	+	2.00824	NA	Intergenic	Intergenic	-31308	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding	0.015000	0.363184			-20(ACATTGTTGTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4874	chr3	24036790	24036990	+	2.00824	NA	intron (NM_001326288, intron 10 of 13)	intron (NM_001326288, intron 10 of 13)	747116	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding	0.000000	0.293532	-63(TATGCATATTTCAGA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7709	chr9	68985883	68986083	+	2.00824	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	220637	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6778	chr6	148362499	148362699	+	2.00824	NA	intron (NM_198967, intron 5 of 19)	intron (NM_198967, intron 5 of 19)	7943	NR_003634	66184	Mm.391542	NM_025405	ENSMUSG00000063171	Rps4l	1110033J19Rik|AA407494|Rps4y2	ribosomal protein S4-like	pseudo	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-679	chr10	6157163	6157363	+	2.00824	NA	Intergenic	Intergenic	-234863	NM_001161822	56533	Mm.44606	NM_019958	ENSMUSG00000019775	Rgs17	6430507P11Rik|Rgsz2	regulator of G-protein signaling 17	protein-coding	0.020000	0.422886			-95(ATCTGCAAGAAAAGTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4811	chr2	179362802	179363002	+	2.00824	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-52034	NM_026596	68175	Mm.158187	NM_026596		4930591A17Rik	-	RIKEN cDNA 4930591A17 gene	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7673	chr9	59401886	59402086	+	2.00824	NA	intron (NM_019927, intron 11 of 13)	intron (NM_019927, intron 11 of 13)	-48478	NR_153195	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding	0.000000	0.417910		-3(TATGAATATGTATT,+,0.00),-3(TATGAATATGTATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-884	chr10	72563306	72563506	+	2.00824	NA	Intergenic	Intergenic	-91440	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5529	chr4	69831956	69832156	+	2.00824	NA	Intergenic	Intergenic	578379	NM_145990	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8017	chrX	92460476	92460676	+	2.00824	NA	intron (NM_173783, intron 3 of 4)	intron (NM_173783, intron 3 of 4)	-29373	NM_001034103	546347	Mm.380183	NM_001034103	ENSMUSG00000071726	Gm5941	EG546347	predicted gene 5941	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-630	chr1	189207935	189208135	+	2.00824	NA	3' UTR (NM_010607, exon 7 of 7)	3' UTR (NM_010607, exon 7 of 7)	135318	NM_001357119	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding	0.020000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6264	chr5	150687637	150687837	+	2.00824	NA	intron (NM_175310, intron 1 of 34)	intron (NM_175310, intron 1 of 34)	13910	NM_175310	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7696	chr9	65452339	65452539	+	2.00824	NA	3' UTR (NM_027134, exon 9 of 9)	3' UTR (NM_027134, exon 9 of 9)	-8498	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	SPG21, maspardin	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2418	chr14	30015144	30015344	+	2.00824	NA	intron (NM_001136240, intron 1 of 7)	intron (NM_001136240, intron 1 of 7)	-6059	NM_172264	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8022	chrX	93358404	93358604	+	2.00824	NA	intron (NM_008892, intron 36 of 36)	intron (NM_008892, intron 36 of 36)	71997	NM_007492	11878	Mm.275547	NM_007492	ENSMUSG00000035277	Arx	Arx1	aristaless related homeobox	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4126	chr19	55405077	55405277	+	2.00824	NA	intron (NM_001360431, intron 6 of 8)	intron (NM_001360431, intron 6 of 8)	89120	NM_001360432	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding	0.005000	0.338308			42(GTATTAACATGGAAAT,+,0.00),44(ATTAACATGGAAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4660	chr2	137816650	137816850	+	2.00824	NA	Intergenic	Intergenic	-439834	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5994	chr5	65049438	65049638	+	2.00824	NA	Intergenic	B3|SINE|B2	42071	NM_001370814	243025	Mm.297688	NM_001370814	ENSMUSG00000037913	Tmem156	Col28a1|Gm446	transmembrane protein 156	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-187	chr1	65276390	65276590	+	2.00824	NA	3' UTR (NM_001310624, exon 42 of 42)	3' UTR (NM_001310624, exon 42 of 42)	-34767	NM_139270	213527	Mm.294225	NM_139270	ENSMUSG00000025946	Pth2r	Pthr2	parathyroid hormone 2 receptor	protein-coding	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2349	chr14	11248056	11248256	+	2.00824	NA	Intergenic	Intergenic	-34321	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4998	chr3	68881654	68881854	+	2.00824	NA	Intergenic	Intergenic	12168	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3144	chr16	28939595	28939795	+	2.00568	NA	Intergenic	Intergenic	-9997	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1267	chr11	44533887	44534087	+	2.00568	NA	intron (NM_001166553, intron 3 of 5)	intron (NM_001166553, intron 3 of 5)	13698	NM_001363166	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding	0.010000	0.388060			-46(ATTAGAAAGCCAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8041	chrX	102034816	102035016	+	2.00568	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	36391	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rtl5	6430402L03Rik|Mar5|Mart5|Rgag4|mKIAA2001	retrotransposon Gag like 5	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6591	chr6	94001179	94001379	+	2.00568	NA	intron (NM_001029850, intron 1 of 23)	intron (NM_001029850, intron 1 of 23)	-87589	NM_001083321	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2033	chr13	38056467	38056667	+	2.00524	NA	intron (NM_024242, intron 13 of 16)	intron (NM_024242, intron 13 of 16)	19578	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1476	chr11	112570760	112570960	+	2.00524	NA	Intergenic	Intergenic	140496	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA	0.005000	0.402985			4(CCATTGTCATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2752	chr15	3426545	3426745	+	2.00524	NA	intron (NM_001048178, intron 2 of 8)	intron (NM_001048178, intron 2 of 8)	-123119	NM_001357801	100039139	Mm.455610	NM_001166063	ENSMUSG00000091119	Ccdc152	-	coiled-coil domain containing 152	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3461	chr17	30082747	30082947	+	2.00524	NA	intron (NM_001356265, intron 2 of 5)	ORR1C1|LTR|ERVL-MaLR	77808	NR_151442	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5791	chr4	150477225	150477425	+	2.00208	NA	intron (NM_001085492, intron 6 of 22)	intron (NM_001085492, intron 6 of 22)	174849	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4116	chr19	49979644	49979844	+	2.00208	NA	Intergenic	L1_Rod|LINE|L1	698902	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7340	chr8	79366275	79366475	+	2.00208	NA	intron (NM_008539, intron 2 of 6)	intron (NM_008539, intron 2 of 6)	33053	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Mad1|Madh1|Madr1|Mlp1|MusMLP|dwf-A|mMad1	SMAD family member 1	protein-coding	0.025000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6826	chr7	39977926	39978126	+	2.00208	NA	Intergenic	Intergenic	460260	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding	0.000000	0.447761			50(CTCTCCATGACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3443	chr17	24075997	24076197	+	2.00208	NA	3' UTR (NM_011062, exon 14 of 14)	3' UTR (NM_011062, exon 14 of 14)	-2612	NM_027008	69259	Mm.28171	NM_027008	ENSMUSG00000016946	Kctd5	2610030N08Rik|mKIAA0176	potassium channel tetramerisation domain containing 5	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2703	chr14	115875214	115875414	+	2.00208	NA	intron (NM_175500, intron 7 of 7)	intron (NM_175500, intron 7 of 7)	-465762	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2160	chr13	78628792	78628992	+	2.00154	NA	Intergenic	Intergenic	-430019	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding	0.000000	0.328358		-19(CATGCATATCCATA,+,0.00),-19(CATGCATATCCATA,-,0.00)	-14(ATATCCATAACAGAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3217	chr16	49319225	49319425	+	2.00154	NA	Intergenic	Intergenic	261925	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2019	chr13	34631336	34631536	+	2.00154	NA	intron (NM_025831, intron 3 of 4)	intron (NM_025831, intron 3 of 4)	21245	NM_025831	66895	Mm.28943	NM_025831	ENSMUSG00000021411	Pxdc1	1300014I06Rik	PX domain containing 1	protein-coding	0.005000	0.492537			59(AGATTGTGTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4845	chr3	11328482	11328682	+	1.99940	NA	Intergenic	RMER13B|LTR|ERVK	515777	NR_040751	100038545	Mm.388494	NR_040751	ENSMUSG00000104015	Gm10745	-	predicted gene 10745	ncRNA	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6996	chr7	100819791	100819991	+	1.99885	NA	intron (NM_001362169, intron 4 of 8)	URR1B|DNA|hAT-Charlie	43522	NM_001358914	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4946	chr3	53144202	53144402	+	1.99885	NA	intron (NM_175386, intron 2 of 3)	intron (NM_175386, intron 2 of 3)	102755	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968|Lhfpl6	lipoma HMGIC fusion partner	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5034	chr3	81479006	81479206	+	1.99885	NA	Intergenic	Intergenic	-322919	NR_138586	320566	Mm.208417	NR_138586	ENSMUSG00000103695	A830029E22Rik	-	RIKEN cDNA A830029E22 gene	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7115	chr7	138581707	138581907	+	1.99885	NA	Intergenic	Intergenic	27565	NR_131022	75187	Mm.410810	NR_131022	ENSMUSG00000110037	4930543N07Rik	Gm45685	RIKEN cDNA 4930543N07 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-171	chr1	58199501	58199701	+	1.99885	NA	intron (NM_023617, intron 34 of 34)	intron (NM_023617, intron 34 of 34)	-10796	NM_023631	71872	Mm.244525	NM_023631	ENSMUSG00000038242	Aox4	2310003G12Rik|Aoh2	aldehyde oxidase 4	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5544	chr4	76683301	76683501	+	1.99885	NA	intron (NR_160919, intron 9 of 39)	intron (NR_160919, intron 9 of 39)	-339158	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4934	chr3	49769390	49769590	+	1.99765	NA	Intergenic	Intergenic	-12174	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2831	chr15	26075997	26076197	+	1.99565	NA	Intergenic	Intergenic	-13659	NR_155439	105245898	Mm.414064	NR_155439	ENSMUSG00000115335	Gm41279	-	predicted gene, 41279	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8005	chrX	85593354	85593554	+	1.99565	NA	intron (NM_025729, intron 2 of 8)	intron (NM_025729, intron 2 of 8)	19432	NM_025729	66724	Mm.119646	NM_025729	ENSMUSG00000035476	Tab3	4921526G09Rik|Map3k7ip3|mKIAA4135	TGF-beta activated kinase 1/MAP3K7 binding protein 3	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3729	chr18	19785305	19785505	+	1.99565	NA	Intergenic	URR1A|DNA|hAT-Charlie	216692	NM_001291809	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0.005000	0.343284			-44(ATTTACATTACAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7834	chr9	96212890	96213090	+	1.99565	NA	intron (NM_178667, intron 2 of 13)	Lx8b|LINE|L1	16715	NM_178667	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding	0.000000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7659	chr9	52840990	52841190	+	1.99565	NA	Intergenic	Intergenic	161227	NR_045333	382139	Mm.335162	NR_045333	ENSMUSG00000111020	Gm1715	-	predicted gene 1715	ncRNA	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-746	chr10	28084076	28084276	+	1.99565	NA	intron (NM_001359355, intron 1 of 33)	B1_Mur2|SINE|Alu	9356	NM_001359356	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1498	chr11	119550662	119550862	+	1.99565	NA	intron (NR_045099, intron 1 of 3)	intron (NR_045099, intron 1 of 3)	2132	NR_045099	100503830	Mm.428077	NR_045099	ENSMUSG00000087675	Gm11762	-	predicted gene 11762	ncRNA	0.020000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2921	chr15	52611418	52611618	+	1.99396	NA	Intergenic	Intergenic	-100927	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6075	chr5	88802092	88802292	+	1.99249	NA	Intergenic	Intergenic	37179	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5743	chr4	127647203	127647403	+	1.99249	NA	Intergenic	MER97c|DNA|hAT-Tip100	-289139	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding	0.025000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2329	chr13	118981319	118981519	+	1.99249	NA	Intergenic	Intergenic	266720	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3220	chr16	49864727	49864927	+	1.99249	NA	intron (NM_001368415, intron 1 of 8)	LTR37A|LTR|ERV1	9166	NM_001368415	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8088	chrX	133921310	133921510	+	1.99046	NA	intron (NM_001083895, intron 3 of 10)	intron (NM_001083895, intron 3 of 10)	12985	NM_026838	68792	Mm.263553	NM_026838	ENSMUSG00000031253	Srpx2	1110039C07Rik|SRP|SRPUL	sushi-repeat-containing protein, X-linked 2	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6975	chr7	93458210	93458410	+	1.99046	NA	Intergenic	Intergenic	-274134	NM_001358087	100040298	Mm.260904	NM_001358087		Gm15501	EyeLinc5	predicted pseudogene 15501	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1783	chr12	83689979	83690179	+	1.99046	NA	intron (NM_001362271, intron 1 of 11)	intron (NM_001362271, intron 1 of 11)	1927	NM_001362271	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4379	chr2	70105331	70105531	+	1.98941	NA	exon (NM_177376, exon 5 of 35)	exon (NM_177376, exon 5 of 35)	66305	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2679	chr14	105388492	105388692	+	1.98653	NA	Intergenic	MTD|LTR|ERVL-MaLR	-38967	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6657	chr6	108545276	108545476	+	1.98396	NA	intron (NM_010585, intron 61 of 61)	intron (NM_010585, intron 61 of 61)	55633	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA	0.000000	0.353234			-32(TAATTTTCTTGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6295	chr6	7968208	7968408	+	1.98350	NA	Intergenic	Intergenic	123084	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5302	chr3	154691239	154691439	+	1.98093	NA	Intergenic	Intergenic	-19794	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding	0.010000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-460	chr19	49655946	49656146	+	1.98003	NA	Intergenic	Intergenic	1022600	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.005000	0.373134			-54(CTCTTCTCATGCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5381	chr4	23832589	23832789	+	1.97795	NA	Intergenic	X3_LINE|LINE|RTE-BovB	-663762	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1906	chr12	117054499	117054699	+	1.97174	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	96670	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.000000	0.462687	16(CCTGAATTATGTATG,+,0.00),16(CCTGAATTATGTATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1235	chr11	35307023	35307223	+	1.97026	NA	intron (NM_011412, intron 4 of 35)	intron (NM_011412, intron 4 of 35)	185667	NM_011412	20564	Mm.478604	NM_011412	ENSMUSG00000056427	Slit3	Slil2|Slit1|b2b2362.1Clo	slit guidance ligand 3	protein-coding	0.015000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-444	chr18	65607163	65607363	+	1.97026	NA	intron (NM_001361052, intron 1 of 8)	intron (NM_001361052, intron 1 of 8)	580	NM_001361052	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding	0.010000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4110	chr19	49655964	49656164	+	1.96751	NA	Intergenic	Intergenic	1022582	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.010000	0.388060			-72(CTCTTCTCATGCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7798	chr9	87595905	87596105	+	1.96571	NA	Intergenic	Intergenic	135255	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding	0.000000	0.373134	-18(CATGCATTATTCACT,+,0.00),-18(CATGCATTATTCACT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5933	chr5	48145368	48145568	+	1.96571	NA	intron (NR_111900, intron 4 of 35)	intron (NR_111900, intron 4 of 35)	-78474	NR_029798	723822		NR_029798	ENSMUSG00000065603	Mir218-1	Mirn218-1|mir-218-1	microRNA 218-1	ncRNA	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3100	chr16	16007390	16007590	+	1.96571	NA	intron (NM_001355731, intron 7 of 18)	intron (NM_001355731, intron 7 of 18)	120204	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding	0.010000	0.378109		5(AATGAATAAGTATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3102	chr16	17392582	17392782	+	1.96571	NA	intron (NM_001001983, intron 1 of 54)	intron (NM_001001983, intron 1 of 54)	-13318	NM_023348	67474	Mm.271992	NM_023348	ENSMUSG00000022765	Snap29	1300018G05Rik|AI891940|AU020222|BB131856|Gs32	synaptosomal-associated protein 29	protein-coding	0.005000	0.333333			-77(ATCTACATGATAGTAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3473	chr17	33563842	33564042	+	1.96571	NA	intron (NM_053214, intron 1 of 27)	L3b|LINE|CR1	8235	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5983	chr5	62601894	62602094	+	1.96571	NA	TTS (NM_178407)	TTS (NM_178407)	164183	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1318	chr11	63355827	63356027	+	1.96571	NA	Intergenic	Intergenic	223124	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|TRE002|Tr|trembler	peripheral myelin protein 22	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3277	chr16	64589745	64589945	+	1.96571	NA	intron (NM_173861, intron 1 of 2)	intron (NM_173861, intron 1 of 2)	12486	NM_001368721	224291	Mm.246580	NM_173861	ENSMUSG00000068167	Csnka2ip	Ckt2	casein kinase 2, alpha prime interacting protein	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1316	chr11	62514395	62514595	+	1.96571	NA	3' UTR (NM_001039536, exon 7 of 7)	3' UTR (NM_001039536, exon 7 of 7)	24766	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding	0.005000	0.412935			-43(ATCTACATGATAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6759	chr6	143892259	143892459	+	1.96549	NA	intron (NM_001113559, intron 8 of 13)	intron (NM_001113559, intron 8 of 13)	54747	NM_001347506	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding	0.015000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2673	chr14	105229735	105229935	+	1.96549	NA	Intergenic	B1_Mur2|SINE|Alu	-28788	NM_029561	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2266	chr13	105910213	105910413	+	1.96549	NA	Intergenic	Intergenic	466620	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0.005000	0.338308			-42(ATTAAAATCACAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7117	chr7	138728100	138728300	+	1.96549	NA	Intergenic	Intergenic	118067	NM_027115	69546	Mm.31598	NM_027115	ENSMUSG00000041775	Mapk1ip1	2310009E07Rik|AU043776|MISS	mitogen-activated protein kinase 1 interacting protein 1	protein-coding	0.020000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6386	chr6	33907637	33907837	+	1.96549	NA	intron (NM_009148, intron 14 of 17)	intron (NM_009148, intron 14 of 17)	-121711	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding	0.025000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7966	chrX	52348903	52349103	+	1.96549	NA	intron (NM_016697, intron 6 of 7)	intron (NM_016697, intron 6 of 7)	29178	NR_105805	102465202		NR_105805	ENSMUSG00000105738	Mir6384	mmu-mir-6384	microRNA 6384	ncRNA	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4343	chr2	61143781	61143981	+	1.96549	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-168730	NR_045335	100038493	Mm.388076	NR_045335	ENSMUSG00000075325	Gm13582	-	predicted gene 13582	ncRNA	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4720	chr2	149844716	149844916	+	1.96549	NA	intron (NM_001363094, intron 2 of 4)	intron (NM_001363094, intron 2 of 4)	14033	NM_001363094	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|Tmem90b	synapse differentiation inducing 1	protein-coding	0.000000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2247	chr13	100621480	100621680	+	1.96535	NA	intron (NM_011233, intron 15 of 16)	B4|SINE|B4	-4609	NM_001038602	218518	Mm.25300	NM_178410	ENSMUSG00000021636	Marveld2	BC003296|MARVD2|Mrvldc2|Tric|Trica|Tricb|Tricc	MARVEL (membrane-associating) domain containing 2	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6672	chr6	113130966	113131166	+	1.96535	NA	intron (NM_173005, intron 15 of 20)	intron (NM_173005, intron 15 of 20)	26131	NM_173005	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8130	chrX	157487476	157487676	+	1.96535	NA	intron (NM_009214, intron 1 of 10)	intron (NM_009214, intron 1 of 10)	3792	NM_001359185	20603	Mm.18652	NM_009214	ENSMUSG00000071708	Sms	AI427066|Gy|SPMSY|SpmST|gyro	spermine synthase	protein-coding	0.010000	0.432836			25(ATTTGCATGCAAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2374	chr14	16429499	16429699	+	1.96460	NA	intron (NM_009409, intron 35 of 35)	intron (NM_009409, intron 35 of 35)	64393	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding	0.000000	0.313433			-51(TAATTCTTATGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3373	chr16	88555709	88555909	+	1.96460	NA	Intergenic	Intergenic	7374	NM_018778	54420	Mm.25836	NM_018778	ENSMUSG00000050520	Cldn8	AI648025	claudin 8	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1722	chr12	71475094	71475294	+	1.96460	NA	Intergenic	Intergenic	-65413	NR_045941	73815	Mm.416916	NR_045941	ENSMUSG00000113630	4930404H11Rik	-	RIKEN cDNA 4930404H11 gene	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6506	chr6	66937875	66938075	+	1.96460	NA	intron (NM_001177557, intron 2 of 3)	Lx8|LINE|L1	41084	NM_001177558	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2693	chr14	111955566	111955766	+	1.96441	NA	Intergenic	Intergenic	280551	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7399	chr8	98071332	98071532	+	1.96441	NA	Intergenic	Intergenic	-940455	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	-	predicted gene 15679	ncRNA	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5827	chr5	12658704	12658904	+	1.96441	NA	Intergenic	Intergenic	275638	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding	0.005000	0.333333			-56(ATCTGCATTACAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-928	chr10	89156844	89157044	+	1.96441	NA	intron (NR_102339, intron 1 of 26)	intron (NR_102339, intron 1 of 26)	100846	NR_102339	320091	Mm.236464	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding	0.000000	0.407960			-90(GTAGTCCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1797	chr12	87087654	87087854	+	1.96356	NA	intron (NR_155207, intron 25 of 25)	intron (NR_155207, intron 25 of 25)	14785	NM_022414	64242	Mm.41395	NM_022414	ENSMUSG00000021032	Ngb	-	neuroglobin	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4686	chr2	142162273	142162473	+	1.96356	NA	intron (NM_001013802, intron 8 of 18)	intron (NM_001013802, intron 8 of 18)	739091	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5081	chr3	99913754	99913954	+	1.96233	NA	intron (NM_028892, intron 1 of 48)	intron (NM_028892, intron 1 of 48)	28437	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding	0.015000	0.343284			25(ATTTGAATGAGTTTGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4170	chr2	10912393	10912593	+	1.96233	NA	Intergenic	Intergenic	-259889	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding	0.000000	0.402985			47(ATTTGAATAGGAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3378	chr16	90247989	90248189	+	1.96205	NA	intron (NM_001346799, intron 12 of 19)	intron (NM_001346799, intron 12 of 19)	27327	NM_011434	20655	Mm.276325	NM_011434	ENSMUSG00000022982	Sod1	B430204E11Rik|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|SODC|Sod-1	superoxide dismutase 1, soluble	protein-coding	0.005000	0.437811			68(CTATTATGATGTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3676	chr18	3245879	3246079	+	1.96205	NA	Intergenic	RLTR13D4|LTR|ERVK	35153	NM_001311067	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6551	chr6	81584006	81584206	+	1.96205	NA	Intergenic	Intergenic	311557	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4835	chr3	9294553	9294753	+	1.96205	NA	Intergenic	Intergenic	44086	NM_177660	229055	Mm.103262	NM_177660	ENSMUSG00000069114	Zbtb10	4832414A18|AU021107|RINZF	zinc finger and BTB domain containing 10	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5466	chr4	53465952	53466152	+	1.96205	NA	intron (NM_133891, intron 1 of 15)	intron (NM_133891, intron 1 of 15)	25639	NM_133891	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding	0.005000	0.427861			-37(TTTTACATAACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1408	chr11	90477267	90477467	+	1.96205	NA	3' UTR (NM_011505, exon 18 of 18)	3' UTR (NM_011505, exon 18 of 18)	-86450	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7700	chr9	65961804	65962004	+	1.96205	NA	intron (NM_173185, intron 3 of 13)	L2c|LINE|L2	52894	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	casein kinase 1, gamma 1	protein-coding	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6644	chr6	106350144	106350344	+	1.96205	NA	intron (NM_001109749, intron 6 of 25)	intron (NM_001109749, intron 6 of 25)	231302	NM_001364565	269784	Mm.321683	NM_173004	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4827	chr3	7523343	7523543	+	1.96205	NA	intron (NM_173181, intron 3 of 8)	intron (NM_173181, intron 3 of 8)	20017	NM_173181	67306	Mm.332366	NM_173181	ENSMUSG00000043542	Zc2hc1a	3110050N22Rik|AI790358|AU023959|Fam164a	zinc finger, C2HC-type containing 1A	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4338	chr2	60402866	60403066	+	1.96205	NA	Intergenic	BGLII_A|LTR|ERVK	-8559	NR_046065	100039176	Mm.261790	NR_046065	ENSMUSG00000087283	Gm13580	-	predicted gene 13580	ncRNA	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3304	chr16	70412807	70413007	+	1.95796	NA	intron (NM_028803, intron 3 of 15)	intron (NM_028803, intron 3 of 15)	98958	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6213	chr5	136510322	136510522	+	1.95768	NA	intron (NM_001291234, intron 1 of 22)	MER44B|DNA|TcMar-Tigger	55559	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4439	chr2	86060342	86060542	+	1.95768	NA	Intergenic	L1Md_F2|LINE|L1	13998	NM_001011872	258216	Mm.330363	NM_001011872	ENSMUSG00000102091	Olfr1034	MOR227-8P|MOR245-14P|Olfr1533-ps1	olfactory receptor 1034	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2187	chr13	85973689	85973889	+	1.95768	NA	Intergenic	Intergenic	73006	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit 7C	protein-coding	0.000000	0.378109			34(ATTTGAACAACTAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5327	chr4	6538724	6538924	+	1.95768	NA	Intergenic	MTEb-int|LTR|ERVL-MaLR	-84553	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5008	chr3	70835629	70835829	+	1.95768	NA	Intergenic	Intergenic	-28438	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	ncRNA	0.010000	0.313433			77(ATATGAATAGGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1496	chr11	119156263	119156463	+	1.95768	NA	intron (NM_001347625, intron 6 of 11)	intron (NM_001347625, intron 6 of 11)	-2226	NR_105899	102465563		NR_105899	ENSMUSG00000098704	Mir6934	Gm27523|mmu-mir-6934	microRNA 6934	ncRNA	0.045000	0.527363			1(ATTTCAATGTCAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5268	chr3	147975088	147975288	+	1.95689	NA	Intergenic	Intergenic	979447	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.015000	0.348259			28(ATTTATATAAAAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1398	chr11	88412171	88412371	+	1.95639	NA	intron (NM_054043, intron 8 of 13)	intron (NM_054043, intron 8 of 13)	59498	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5829	chr5	12765968	12766168	+	1.95639	NA	Intergenic	Intergenic	382902	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding	0.010000	0.378109	-63(CCTGACTAATGCATA,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2102	chr13	63058461	63058661	+	1.95639	NA	intron (NM_001289926, intron 3 of 15)	intron (NM_001289926, intron 3 of 15)	93668	NM_001289926	72061	Mm.188105	NM_028079	ENSMUSG00000021458	Aopep	2010111I01Rik|2300006M17Rik|AP-O|AW742919|ApO|mir-23b|mir-24-1|mir-27b	aminopeptidase O	protein-coding	0.005000	0.368159			-81(CTTATGTTTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6891	chr7	68548914	68549114	+	1.95480	NA	Intergenic	Intergenic	-69442	NR_003648	384639	Mm.261760	NM_001013781		Gm5334	EG384639	tetraspanin 7 pseudogene	pseudo	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7205	chr8	35974499	35974699	+	1.95319	NA	Intergenic	Intergenic	-91642	NR_046181	330737	Mm.381743	NR_046181	ENSMUSG00000109761	5430403N17Rik	5430403N17	RIKEN cDNA 5430403N17 gene	ncRNA	0.005000	0.398010			-13(CATTTGTTCTGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7510	chr9	7869712	7869912	+	1.95002	NA	intron (NM_007464, intron 1 of 8)	L1MA4A|LINE|L1	3358	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding	0.000000	0.298507			62(TCTTTGTCCTGTTAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4183	chr2	15732815	15733015	+	1.95002	NA	intron (NM_001310455, intron 17 of 38)	intron (NM_001310455, intron 17 of 38)	206436	NM_001310455	102635496		NM_001310455	ENSMUSG00000075520	Malrd1	Diet1|Gm13318|Gm13364	MAM and LDL receptor class A domain containing 1	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5704	chr4	116695815	116696015	+	1.95002	NA	intron (NM_011034, intron 5 of 5)	intron (NM_011034, intron 5 of 5)	-9893	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1826	chr12	94580400	94580600	+	1.95002	NA	Intergenic	Intergenic	653162	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA	0.015000	0.402985			-21(ATAATCAAGAGAATGA,-,0.00),64(ATATGCAAATCAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5400	chr4	29135812	29136012	+	1.95002	NA	Intergenic	Intergenic	67833	NR_151693	102634169		NR_151693		Gm11917	-	predicted gene 11917	ncRNA	0.015000	0.432836			37(ATTTGAATCTGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5844	chr5	17810429	17810629	+	1.95002	NA	intron (NM_001159557, intron 9 of 15)	intron (NM_001159557, intron 9 of 15)	25367	NM_007643	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 molecule	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7915	chrX	7472155	7472355	+	1.95002	NA	Intergenic	B2_Mm2|SINE|B2	-49267	NR_027924	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6432	chr6	46748376	46748576	+	1.95002	NA	intron (NM_001004357, intron 13 of 23)	intron (NM_001004357, intron 13 of 23)	-495920	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5404	chr4	29725791	29725991	+	1.95002	NA	Intergenic	Intergenic	657812	NR_151693	102634169		NR_151693		Gm11917	-	predicted gene 11917	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-888	chr10	73007021	73007221	+	1.95002	NA	intron (NR_040646, intron 2 of 4)	intron (NR_040646, intron 2 of 4)	79584	NR_040646	327768	Mm.417745	NR_040646	ENSMUSG00000111994	A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7629	chr9	43191654	43191854	+	1.95002	NA	intron (NM_011139, intron 2 of 12)	intron (NM_011139, intron 2 of 12)	14001	NM_011139	18988	Mm.436650	NM_011139	ENSMUSG00000032015	Pou2f3	Epoc-1|Oct-11a|Oct11|Otf-11|Otf11|Skin|Skin-1a|Skn-1a|Skn-li	POU domain, class 2, transcription factor 3	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6704	chr6	120385496	120385696	+	1.95002	NA	intron (NM_145997, intron 6 of 27)	intron (NM_145997, intron 6 of 27)	-21227	NR_045558	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding	0.010000	0.308458			68(CATTTAACATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8143	chrX	162539074	162539274	+	1.95002	NA	intron (NM_178256, intron 5 of 17)	L1MC4a|LINE|L1	26342	NM_001359104	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8070	chrX	127407323	127407523	+	1.95002	NA	Intergenic	RLTR13D6|LTR|ERVK	13130	NR_003646	245598	Mm.72281	NM_207250	ENSMUSG00000049815	4921511C20Rik	Gm383	high density lipoprotein (HDL) binding protein pseudogene	pseudo	0.005000	0.393035			30(TTTTTCTTATGTATAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3719	chr18	16432666	16432866	+	1.95002	NA	Intergenic	Intergenic	376480	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1078	chr10	117870608	117870808	+	1.95002	NA	Intergenic	Intergenic	-24734	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7594	chr9	31851861	31852061	+	1.95002	NA	intron (NM_013800, intron 3 of 3)	intron (NM_013800, intron 3 of 3)	61324	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding	0.030000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3975	chr18	84384406	84384606	+	1.95002	NA	intron (NM_001033341, intron 4 of 8)	ORR1D1|LTR|ERVL-MaLR	204998	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding	0.005000	0.522388			-42(GTTTGAATGAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4572	chr2	124264537	124264737	+	1.95002	NA	intron (NM_001290997, intron 2 of 20)	L2b|LINE|L2	-42279	NR_040612	75946	Mm.415059	NR_040612	ENSMUSG00000086954	4930583P06Rik	-	RIKEN cDNA 4930583P06 gene	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7091	chr7	130899982	130900182	+	1.95002	NA	intron (NM_001357696, intron 6 of 12)	L1MD|LINE|L1	-8186	NR_106028	102466219		NR_106028	ENSMUSG00000104914	Mir7061	mmu-mir-7061	microRNA 7061	ncRNA	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8081	chrX	131942168	131942368	+	1.95002	NA	Intergenic	Intergenic	-1745512	NR_153117	102632590	Mm.403836	NR_153117	ENSMUSG00000096978	Gm26851	-	predicted gene, 26851	ncRNA	0.005000	0.328358			12(ATAAACATCATAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6484	chr6	62944395	62944595	+	1.94997	NA	Intergenic	Lx2A1|LINE|L1	-311511	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding	0.000000	0.303483			-74(ATTTGCCTAAGAATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6233	chr5	141567604	141567804	+	1.93805	NA	intron (NM_177879, intron 1 of 44)	intron (NM_177879, intron 1 of 44)	326170	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3302	chr16	70412355	70412555	+	1.93805	NA	intron (NM_028803, intron 3 of 15)	Lx8|LINE|L1	98506	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding	0.025000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2549	chr14	75947421	75947621	+	1.93783	NA	intron (NM_026816, intron 5 of 7)	intron (NM_026816, intron 5 of 7)	-7482	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding	0.000000	0.313433			-98(ATTAAAACCACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-748	chr10	28114672	28114872	+	1.93783	NA	intron (NM_001359355, intron 1 of 33)	intron (NM_001359355, intron 1 of 33)	39952	NM_001359356	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding	0.020000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6938	chr7	83820655	83820855	+	1.93770	NA	Intergenic	Intergenic	-25916	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	Cfap161	1700026D08Rik|AW047638|AW551802	cilia and flagella associated protein 161	protein-coding	0.020000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1629	chr12	43696623	43696823	+	1.93770	NA	Intergenic	RLTR13D6|LTR|ERVK	513345	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2315	chr13	115118806	115119006	+	1.93723	NA	Intergenic	Intergenic	-16942	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding	0.020000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-794	chr10	42562146	42562346	+	1.93723	NA	3' UTR (NM_152229, exon 9 of 9)	3' UTR (NM_152229, exon 9 of 9)	21344	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding	0.005000	0.437811			-80(ATTTCCATAAGTATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5389	chr4	25796267	25796467	+	1.93723	NA	intron (NM_010243, intron 1 of 2)	PB1D7|SINE|Alu	3636	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.005000	0.407960			-90(ATTTGCAATAAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4881	chr3	27498789	27498989	+	1.93723	NA	intron (NM_001356953, intron 9 of 26)	intron (NM_001356953, intron 9 of 26)	86106	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA	0.010000	0.417910			24(TCACAGTTATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-793	chr10	42562049	42562249	+	1.93723	NA	3' UTR (NM_152229, exon 9 of 9)	3' UTR (NM_152229, exon 9 of 9)	21441	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding	0.010000	0.447761			17(ATTTCCATAAGTATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7535	chr9	14890834	14891034	+	1.93723	NA	intron (NM_176807, intron 4 of 4)	intron (NM_176807, intron 4 of 4)	13017	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6582	chr6	91322410	91322610	+	1.93723	NA	Intergenic	MER2|DNA|TcMar-Tigger	88843	NM_001363757	22421	Mm.56964	NM_009527	ENSMUSG00000030093	Wnt7a	AI849442|Wnt-7a|px|tw	wingless-type MMTV integration site family, member 7A	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-72	chr1	23958534	23958734	+	1.93662	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	-36253	NM_001357395	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-822	chr10	53015201	53015401	+	1.93661	NA	intron (NM_178675, intron 2 of 7)	intron (NM_178675, intron 2 of 7)	-219886	NR_152766	102639992	Mm.375738	NR_152766	ENSMUSG00000112835	Gm36173	-	predicted gene, 36173	ncRNA	0.000000	0.328358			-100(ATTTAATCATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7606	chr9	34425021	34425221	+	1.93661	NA	Intergenic	Intergenic	-63610	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kirre like nephrin family adhesion molecule 3	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5655	chr4	103046894	103047094	+	1.93661	NA	intron (NM_146254, intron 16 of 16)	intron (NM_146254, intron 16 of 16)	-19723	NM_001290648	23919	Mm.100163	NM_011831	ENSMUSG00000066090	Insl5	RIF2	insulin-like 5	protein-coding	0.005000	0.288557	76(TATGAAAAATGCATT,+,0.00),76(TATGAAAAATGCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5695	chr4	112433758	112433958	+	1.93661	NA	intron (NM_177864, intron 1 of 6)	intron (NM_177864, intron 1 of 6)	127	NM_177864	329918	Mm.246783	NM_177864	ENSMUSG00000049972	Skint9	A030013N09Rik|Skint-9	selection and upkeep of intraepithelial T cells 9	protein-coding	0.000000	0.313433			-81(CTTTCCATTAGAAAAC,-,0.00),-20(ATTAGAATTAAAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5206	chr3	135300046	135300246	+	1.93661	NA	intron (NM_001172055, intron 7 of 9)	intron (NM_001172055, intron 7 of 9)	-7554	NM_178877	97086	Mm.441764	NM_178877	ENSMUSG00000037994	Slc9b2	C80638|NHA2|NHE10|Nhedc2|nha-oc|nhaoc	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4317	chr2	55580307	55580507	+	1.93661	NA	intron (NM_001355118, intron 4 of 4)	intron (NM_001355118, intron 4 of 4)	144437	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding	0.005000	0.343284			-41(ATTAGAATAAAAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2691	chr14	111033187	111033387	+	1.93661	NA	Intergenic	Intergenic	-278138	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	SLIT and NTRK-like family, member 6	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7815	chr9	92913620	92913820	+	1.93661	NA	Intergenic	Intergenic	92013	NR_040756	78349	Mm.52612	NR_040756	ENSMUSG00000100294	1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	ncRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6496	chr6	65132612	65132812	+	1.93661	NA	intron (NM_019455, intron 3 of 5)	intron (NM_019455, intron 3 of 5)	12018	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-548	chr1	173636649	173636849	+	1.93661	NA	intron (NM_175026, intron 1 of 6)	ORR1C1|LTR|ERVL-MaLR	5890	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2280	chr13	109063070	109063270	+	1.93661	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-261574	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA	0.020000	0.373134			53(TTATTGTTGTATAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-338	chr1	122480898	122481098	+	1.93661	NA	Intergenic	Intergenic	275853	NR_151524	102638832	Mm.112794	NR_151524	ENSMUSG00000099960	Gm28590	-	predicted gene 28590	ncRNA	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4597	chr2	127175106	127175306	+	1.93661	NA	Intergenic	Intergenic	-31749	NM_001163527	73338	Mm.57559	NM_001163527	ENSMUSG00000074825	Itpripl1	1700041B20Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 1	protein-coding	0.005000	0.268657			79(CCTTACTTATTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2848	chr15	30469365	30469565	+	1.93661	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	296931	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3893	chr18	62470041	62470241	+	1.93661	NA	intron (NM_001364957, intron 5 of 5)	intron (NM_001364957, intron 5 of 5)	73711	NM_001361091	107035	Mm.21295	NM_134136	ENSMUSG00000042211	Fbxo38	6030410I24Rik|AU044865|AW214031|Moka|SP329	F-box protein 38	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7178	chr8	26107328	26107528	+	1.93661	NA	intron (NM_207659, intron 2 of 21)	L1MA4|LINE|L1	11796	NM_207659	320191	Mm.334464	NM_207659	ENSMUSG00000037234	Hook3	5830454D03Rik|AI317159|E330005F07Rik	hook microtubule tethering protein 3	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5694	chr4	111803318	111803518	+	1.93661	NA	intron (NM_026470, intron 10 of 12)	intron (NM_026470, intron 10 of 12)	25821	NM_001357231	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7502	chr9	3428991	3429191	+	1.93661	NA	intron (NM_027545, intron 7 of 17)	RSINE1|SINE|B4	25006	NM_027545	244672	Mm.245482	NM_027545	ENSMUSG00000025898	Cwf19l2	3230401L03Rik|9030209E10	CWF19-like 2, cell cycle control (S. pombe)	protein-coding	0.000000	0.383085		-80(TGTGCATATGCAAA,-,0.00)	8(ATTTGCATCCCAAGAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1353	chr11	74907195	74907395	+	1.93614	NA	3' UTR (NM_001362742, exon 8 of 8)	3' UTR (NM_001362742, exon 8 of 8)	1849	NR_028562	100217469		NR_028562		Snord91a	MBII-296	small nucleolar RNA, C/D box 91A	snoRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3781	chr18	34303814	34304014	+	1.93614	NA	intron (NM_001360980, intron 12 of 16)	intron (NM_001360980, intron 12 of 16)	-27231	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4101	chr19	47384140	47384340	+	1.93614	NA	intron (NM_001164717, intron 3 of 13)	MER5A1|DNA|hAT-Charlie	80171	NM_008018	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding	0.025000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1883	chr12	108917106	108917306	+	1.93614	NA	intron (NM_177602, intron 2 of 6)	intron (NM_177602, intron 2 of 6)	22934	NM_177602	212198	Mm.342082	NM_177602	ENSMUSG00000040877	Wdr25	B930090D16Rik	WD repeat domain 25	protein-coding	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1349	chr11	73899286	73899486	+	1.93614	NA	Intergenic	Intergenic	8104	NM_147005	259007	Mm.425696	NM_147005	ENSMUSG00000062186	Olfr395	MOR135-10	olfactory receptor 395	protein-coding	0.000000	0.273632			-44(ATTTACATAATAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1499	chr11	119558150	119558350	+	1.93614	NA	intron (NR_045099, intron 1 of 3)	intron (NR_045099, intron 1 of 3)	9620	NR_045099	100503830	Mm.428077	NR_045099	ENSMUSG00000087675	Gm11762	-	predicted gene 11762	ncRNA	0.025000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4633	chr2	134227594	134227794	+	1.93614	NA	Intergenic	L1MB1|LINE|L1	326658	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	hydroxyacid oxidase 1, liver	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7351	chr8	81207199	81207399	+	1.93614	NA	Intergenic	Lx5c|LINE|L1	-135263	NM_001297596	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding	0.000000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-384	chr16	83022785	83022985	+	1.93590	NA	Intergenic	Intergenic	-1348258	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5622	chr4	96398522	96398722	+	1.93590	NA	Intergenic	Intergenic	-49942	NM_001004141	100066	Mm.26915	NM_001004141	ENSMUSG00000066097	Cyp2j11	AI314783|Cyp2j11-ps	cytochrome P450, family 2, subfamily j, polypeptide 11	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3346	chr16	83022764	83022964	+	1.93590	NA	Intergenic	Intergenic	-1348279	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5140	chr3	117283243	117283443	+	1.93439	NA	Intergenic	Intergenic	77533	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	Plppr4	A330086D10|D3Bwg0562e|Lppr4|PRG-1|mKIAA0455	phospholipid phosphatase related 4	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-147	chr1	51650118	51650318	+	1.93439	NA	Intergenic	Intergenic	-53500	NR_151621	100045066	Mm.404734	NR_151621		Gm17767	-	predicted gene, 17767	ncRNA	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5482	chr4	55379629	55379829	+	1.93439	NA	intron (NM_009011, intron 5 of 9)	intron (NM_009011, intron 5 of 9)	29687	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23 homolog B, nucleotide excision repair protein	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1010	chr10	107952617	107952817	+	1.93439	NA	intron (NR_131147, intron 1 of 5)	LTR109A2|LTR|ERV1	6072	NR_131147	628877	Mm.363120	NR_131147	ENSMUSG00000112910	Gm29685	-	predicted gene, 29685	ncRNA	0.000000	0.328358			12(ATTTACAAGAAATAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4704	chr2	144704404	144704604	+	1.93177	NA	intron (NM_025314, intron 4 of 5)	intron (NM_025314, intron 4 of 5)	104551	NM_025314	66044	Mm.28109	NM_025314	ENSMUSG00000027430	Dtd1	0610006H08Rik|DTD|DUE-B|Hars2	D-tyrosyl-tRNA deacylase 1	protein-coding	0.005000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3875	chr18	56936972	56937172	+	1.93177	NA	non-coding (NR_033455, exon 1 of 1)	non-coding (NR_033455, exon 1 of 1)	812	NR_033455	100038410	Mm.353669	NR_033455		Gm10536	-	predicted gene 10536	ncRNA	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3566	chr17	66976593	66976793	+	1.93177	NA	intron (NM_008984, intron 7 of 30)	intron (NM_008984, intron 7 of 30)	49542	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2982	chr15	68758395	68758595	+	1.93177	NA	Intergenic	Intergenic	-119820	NR_155443	105245971	Mm.380365	NR_155443	ENSMUSG00000069996	Gm41341	-	predicted gene, 41341	ncRNA	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5062	chr3	91030221	91030421	+	1.93177	NA	Intergenic	RLTR13D6|LTR|ERVK	-41341	NR_033593	619677	Mm.396622	NR_033593	ENSMUSG00000086377	4930529C04Rik	-	zinc finger, BED domain containing 4 pseudogene	pseudo	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2313	chr13	113996448	113996648	+	1.93177	NA	intron (NM_172595, intron 4 of 4)	intron (NM_172595, intron 4 of 4)	155044	NR_045836	319803	Mm.386896	NM_177004	ENSMUSG00000114213	A430090L17Rik	-	RIKEN cDNA A430090L17 gene	ncRNA	0.015000	0.417910			-9(TTTTTATCATGGTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8153	chrX	164880299	164880499	+	1.93177	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	99976	NM_029730	76763	Mm.291758	NM_029730	ENSMUSG00000061778	Mospd2	2410013I23Rik	motile sperm domain containing 2	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1205	chr11	26039388	26039588	+	1.93177	NA	intron (NR_027973, intron 1 of 5)	intron (NR_027973, intron 1 of 5)	-162752	NR_105791	102466154		NR_105791	ENSMUSG00000099015	Mir6372	Gm27358|mmu-mir-6372	microRNA 6372	ncRNA	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2764	chr15	6616293	6616493	+	1.93177	NA	intron (NR_155272, intron 4 of 6)	intron (NR_155272, intron 4 of 6)	36546	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Fyb1|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding	0.000000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2534	chr14	70260380	70260580	+	1.93177	NA	intron (NM_001304992, intron 2 of 12)	intron (NM_001304992, intron 2 of 12)	29017	NM_001304991	19057	Mm.439683	NM_008915	ENSMUSG00000022092	Ppp3cc	Calnc|PP2BA gamma	protein phosphatase 3, catalytic subunit, gamma isoform	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8059	chrX	109101141	109101341	+	1.93031	NA	intron (NM_019989, intron 1 of 3)	intron (NM_019989, intron 1 of 3)	5834	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6357	chr6	23923858	23924058	+	1.92933	NA	Intergenic	Intergenic	46102	NM_207022	387347	Mm.377909	NM_207022	ENSMUSG00000043865	Tas2r118	Gm465|T2R16|T2R18|Tas2r16|Tas2r18|mGR18|mt2r40	taste receptor, type 2, member 118	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6580	chr6	89508574	89508774	+	1.92927	NA	intron (NM_025351, intron 4 of 7)	Tigger1|DNA|TcMar-Tigger	86978	NM_025351	66098	Mm.20313	NM_025351	ENSMUSG00000030086	Chchd6	0710001P09Rik|1700021B03Rik|Micos25	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5977	chr5	60989405	60989605	+	1.92792	NA	Intergenic	RLTR13D6|LTR|ERVK	-819338	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6031	chr5	74633291	74633491	+	1.92792	NA	intron (NM_001159577, intron 2 of 10)	intron (NM_001159577, intron 2 of 10)	44481	NM_001159580	16924	Mm.440403	NM_010727	ENSMUSG00000029228	Lnx1	Lnx	ligand of numb-protein X 1	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1468	chr11	111015341	111015541	+	1.92792	NA	intron (NM_001252209, intron 1 of 1)	intron (NM_001252209, intron 1 of 1)	-4144	NM_001252210	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding	0.000000	0.283582			55(ATATTATTTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4179	chr2	13360460	13360660	+	1.92792	NA	intron (NM_001081084, intron 32 of 66)	intron (NM_001081084, intron 32 of 66)	-89145	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-46	chr1	17121767	17121967	+	1.92792	NA	Intergenic	Intergenic	-23506	NM_010267	14545	Mm.18218	NM_010267	ENSMUSG00000025777	Gdap1	-	ganglioside-induced differentiation-associated-protein 1	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7533	chr9	14839085	14839285	+	1.92792	NA	Intergenic	Intergenic	-21025	NM_010287	14608	Mm.4672	NM_010287	ENSMUSG00000031932	Gpr83	AW045253|Gir|Gpr72|RP105|RP39|RP82	G protein-coupled receptor 83	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6534	chr6	74966703	74966903	+	1.92792	NA	Intergenic	Intergenic	-1358130	NR_157242	102634075	Mm.78553	NR_157242	ENSMUSG00000107441	Gm31747	-	predicted gene, 31747	ncRNA	0.005000	0.388060			24(ATATTCATGATAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-181	chr1	62302406	62302606	+	1.92792	NA	intron (NM_001081050, intron 16 of 22)	intron (NM_001081050, intron 16 of 22)	-166397	NR_151537	105243940		NR_151537		Pard3bos2	Gm12747	par-3 family cell polarity regulator beta, opposite strand 2	ncRNA	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6227	chr5	139921732	139921932	+	1.92792	NA	intron (NM_175522, intron 1 of 1)	L1ME1|LINE|L1	13889	NM_175522	243312	Mm.237102	NM_175522	ENSMUSG00000048988	Elfn1	A930017N06Rik|AI197272|Ppp1r28	leucine rich repeat and fibronectin type III, extracellular 1	protein-coding	0.025000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6626	chr6	101854260	101854460	+	1.92792	NA	Intergenic	Intergenic	80111	NR_027989	207157	Mm.57632	NM_177579	ENSMUSG00000052236	Gm9871	0610005I04|EG207157	predicted gene 9871	ncRNA	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1692	chr12	64521252	64521452	+	1.92792	NA	Intergenic	Intergenic	-46454	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0.000000	0.363184			-100(ATTACAATGGCAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6074	chr5	88797116	88797316	+	1.92792	NA	Intergenic	Intergenic	32203	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding	0.010000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4714	chr2	147073413	147073613	+	1.92792	NA	intron (NM_011917, intron 28 of 29)	intron (NM_011917, intron 28 of 29)	11832	NM_023504	228731	Mm.315498	NM_023504	ENSMUSG00000054160	Nkx2-4	1700001P03Rik|Nkx-2.4|tinman	NK2 homeobox 4	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2648	chr14	99332025	99332225	+	1.92792	NA	Intergenic	Intergenic	33434	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4656	chr2	137072968	137073168	+	1.92792	NA	Intergenic	Intergenic	43452	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-684	chr10	7265454	7265654	+	1.92236	NA	Intergenic	Intergenic	-53317	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding	0.025000	0.437811			6(ATTTGCAAGTGAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2849	chr15	30554050	30554250	+	1.92236	NA	intron (NM_008729, intron 3 of 22)	intron (NM_008729, intron 3 of 22)	381616	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6788	chr7	10464003	10464203	+	1.92236	NA	Intergenic	Intergenic	17314	NM_134229	171263	Mm.377216	NM_134229	ENSMUSG00000046716	Vmn1r67	V1re10	vomeronasal 1 receptor 67	protein-coding	0.000000	0.407960			-52(TCTTTCTCATGCACAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2981	chr15	68498388	68498588	+	1.92236	NA	Intergenic	Intergenic	-157199	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA	0.005000	0.318408			-43(ATTTGAATTAAAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1033	chr10	111632592	111632792	+	1.92236	NA	Intergenic	Intergenic	-38419	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7396	chr8	97815690	97815890	+	1.92236	NA	Intergenic	BGLII|LTR|ERVK	-1196097	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	-	predicted gene 15679	ncRNA	0.000000	0.407960			4(ATTTGTAAAATAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6195	chr5	131354331	131354531	+	1.92236	NA	Intergenic	Lx5|LINE|L1	-46909	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Galnt17	AA388321|E330012B09Rik|Galnt19|Gcap8|Wbscr17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6168	chr5	121890074	121890274	+	1.92236	NA	intron (NM_007804, intron 5 of 22)	PB1D10|SINE|Alu	41177	NM_001359950	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Pheta1	A230106M15Rik|AU017694|Fam109a|IPIP27A|Ses1	PH domain containing endocytic trafficking adaptor 1	protein-coding	0.020000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7595	chr9	32095647	32095847	+	1.92236	NA	intron (NM_001370958, intron 1 of 22)	intron (NM_001370958, intron 1 of 22)	-20241	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding	0.010000	0.422886			11(TGTTTGTCATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7358	chr8	82955383	82955583	+	1.92236	NA	intron (NM_177378, intron 1 of 6)	intron (NM_177378, intron 1 of 6)	92127	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1709	chr12	68908501	68908701	+	1.92236	NA	Intergenic	Lx8|LINE|L1	250585	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding	0.005000	0.457711			10(GTTCTGTTTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6951	chr7	88347623	88347823	+	1.92236	NA	Intergenic	Intergenic	69638	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding	0.005000	0.368159	28(TGTAAATTATTCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1108	chr10	123383384	123383584	+	1.92236	NA	intron (NM_001252387, intron 1 of 4)	intron (NM_001252387, intron 1 of 4)	119408	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Tafa2	6330575M02|FAM19A2 TAFA-2|Fam19a2|Sam2|Tafa-2	TAFA chemokine like family member 2	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7864	chr9	105413095	105413295	+	1.92236	NA	intron (NM_001359822, intron 28 of 28)	intron (NM_001359822, intron 28 of 28)	12407	NM_001164828	66595	Mm.84941	NM_025651	ENSMUSG00000032567	Aste1	1100001A21Rik|AV006403	asteroid homolog 1	protein-coding	0.010000	0.393035			-7(ATCTGAAAGAGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3508	chr17	50048019	50048219	+	1.92236	NA	intron (NM_181397, intron 5 of 9)	intron (NM_181397, intron 5 of 9)	142378	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3524	chr17	52631496	52631696	+	1.92236	NA	intron (NM_001031811, intron 1 of 15)	Tigger17c|DNA|TcMar-Tigger	28887	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding	0.010000	0.412935	72(AATGCTTTATATATG,-,0.00)		16(ATTTCTATGAGAAGGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique	chr1	3046260	3046460	+	1.91841	NA	Intergenic	RLTR13C1|LTR|ERVK	625138	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4372	chr2	68181291	68181491	+	1.91841	NA	Intergenic	MLT2B4|LTR|ERVL	76719	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6296	chr6	7968542	7968742	+	1.91841	NA	Intergenic	Intergenic	123418	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3416	chr17	9536298	9536498	+	1.91831	NA	Intergenic	Charlie19a|DNA|hAT-Charlie	133306	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	poly(A) binding protein, cytoplasmic 6	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7790	chr9	85473470	85473670	+	1.91774	NA	Intergenic	Intergenic	-146420	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Tent5a	BAP014|D930050G01Rik|Fam46a	terminal nucleotidyltransferase 5A	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6387	chr6	34187519	34187719	+	1.91774	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-10565	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6879	chr7	65346885	65347085	+	1.91713	NA	intron (NM_001163574, intron 2 of 26)	MER33|DNA|hAT-Charlie	24259	NM_009386	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding	0.010000	0.378109			-55(CTTTACATGACTATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6981	chr7	96207939	96208139	+	1.91713	NA	intron (NM_001310762, intron 1 of 32)	L1MC4|LINE|L1	-2598	NM_011858	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7272	chr8	57922464	57922664	+	1.91628	NA	intron (NM_175032, intron 6 of 11)	intron (NM_175032, intron 6 of 11)	-269509	NM_001167981	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.010000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-269	chr13	111373792	111373992	+	1.91569	NA	Intergenic	Intergenic	116235	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1996	chr13	28629407	28629607	+	1.91477	NA	intron (NR_045054, intron 5 of 7)	intron (NR_045054, intron 5 of 7)	81366	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA	0.020000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-57	chr1	20923446	20923646	+	1.91477	NA	intron (NM_001355122, intron 1 of 2)	intron (NM_001355122, intron 1 of 2)	5706	NM_001355122	74229	Mm.40780	NM_028829	ENSMUSG00000025931	Paqr8	1700019B16Rik|3110001D06Rik	progestin and adipoQ receptor family member VIII	protein-coding	0.020000	0.368159	20(CATGCATTATTTATA,+,0.00),20(CATGCATTATTTATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7444	chr8	109338925	109339125	+	1.91477	NA	TTS (NR_002928)	TTS (NR_002928)	1883	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo	0.000000	0.328358			75(ATATGAATTAGAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4387	chr2	72122957	72123157	+	1.91477	NA	intron (NM_001355478, intron 1 of 26)	L1ME1|LINE|L1	68440	NM_001355478	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8145	chrX	163117749	163117949	+	1.91477	NA	intron (NR_038088, intron 1 of 5)	intron (NR_038088, intron 1 of 5)	-153250	NM_009789	12309	Mm.6891	NM_009789	ENSMUSG00000040808	S100g	AU042539|CABP1|CaBP-D9K|Cabp9k|Calb3	S100 calcium binding protein G	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1985	chr13	23873389	23873589	+	1.91430	NA	intron (NR_121611, intron 2 of 12)	L1ME1|LINE|L1	3216	NM_001170638	20504	Mm.2656	NM_009198	ENSMUSG00000021335	Slc17a1	NAPI-1|Napi1|Npt1	solute carrier family 17 (sodium phosphate), member 1	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-205	chr1	71957344	71957544	+	1.91430	NA	Intergenic	Intergenic	47751	NR_040454	71134	Mm.370574	NR_040454	ENSMUSG00000101848	4933417E11Rik	-	RIKEN cDNA 4933417E11 gene	ncRNA	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3672	chr17	92554830	92555030	+	1.91430	NA	Intergenic	ORR1D2-int|LTR|ERVL-MaLR	-644087	NM_001315503	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3945	chr18	78455208	78455408	+	1.91430	NA	intron (NM_030683, intron 2 of 11)	intron (NM_030683, intron 2 of 11)	141642	NM_030683	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7850	chr9	100963808	100964008	+	1.91430	NA	Intergenic	Intergenic	70976	NM_025835	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding	0.005000	0.378109			-62(GTCTTCTTATTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7437	chr8	108055556	108055756	+	1.91430	NA	Intergenic	Intergenic	-467174	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding	0.005000	0.417910			-27(TGATTCTCATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4929	chr3	46106257	46106457	+	1.91430	NA	Intergenic	Intergenic	341584	NM_001101479	241989	Mm.119234	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	poly(A) binding protein, cytoplasmic 4-like	protein-coding	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4042	chr19	21188069	21188269	+	1.91430	NA	Intergenic	Intergenic	83459	NR_126458	75354	Mm.243873	NR_126458	ENSMUSG00000118047	4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3313	chr16	73052157	73052357	+	1.91430	NA	Intergenic	Intergenic	389108	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2892	chr15	43360277	43360477	+	1.91430	NA	Intergenic	Lx7|LINE|L1	-77641	NM_008388	16341	Mm.289992	NM_008388	ENSMUSG00000022336	Eif3e	48kDa|Eif3s6|Int6|eIF3-p46|eIF3-p48	eukaryotic translation initiation factor 3, subunit E	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8035	chrX	99995156	99995356	+	1.91430	NA	intron (NM_001177940, intron 1 of 6)	L2|LINE|L2	19650	NM_001177937	13607	Mm.328086	NM_010099	ENSMUSG00000059327	Eda	EDA1|Ed1|Eda-A1|Eda-A2|HED|Ta|Tnlg7c|XLHED|tabby	ectodysplasin-A	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5162	chr3	123010937	123011137	+	1.91430	NA	intron (NM_001355462, intron 6 of 6)	L1M5|LINE|L1	23950	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-551	chr1	174560456	174560656	+	1.91430	NA	intron (NM_019445, intron 2 of 17)	intron (NM_019445, intron 2 of 17)	58731	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5429	chr4	36099300	36099500	+	1.91430	NA	intron (NM_001165999, intron 5 of 7)	intron (NM_001165999, intron 5 of 7)	-254196	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6447	chr6	52607819	52608019	+	1.91430	NA	intron (NM_145567, intron 4 of 7)	intron (NM_145567, intron 4 of 7)	32381	NM_145567	58875	Mm.286458	NM_145567	ENSMUSG00000029776	Hibadh	6430402H10Rik|AI265272	3-hydroxyisobutyrate dehydrogenase	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3624	chr17	80937652	80937852	+	1.91430	NA	Intergenic	L2|LINE|L2	-6880	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3730	chr18	20097793	20097993	+	1.91430	NA	intron (NM_013504, intron 7 of 16)	MTEa|LTR|ERVL-MaLR	16880	NM_001291804	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6493	chr6	63963957	63964157	+	1.91290	NA	intron (NM_001370966, intron 4 of 15)	intron (NM_001370966, intron 4 of 15)	708051	NM_001370966									0.000000	0.442786			73(ATTTTGCTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4616	chr2	131503587	131503787	+	1.91290	NA	intron (NM_001177838, intron 1 of 4)	intron (NM_001177838, intron 1 of 4)	11825	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5259	chr3	147030436	147030636	+	1.91290	NA	Intergenic	Intergenic	178169	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.030000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6268	chr5	150814651	150814851	+	1.91290	NA	Intergenic	URR1A|DNA|hAT-Charlie	-137856	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding	0.025000	0.427861			67(TAGTTGTCGTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4673	chr2	140235703	140235903	+	1.91214	NA	intron (NM_001033296, intron 18 of 19)	L1Md_F2|LINE|L1	65157	NM_027093	69487	Mm.287921	NM_027093	ENSMUSG00000027384	Ndufaf5	2310003L22Rik	NADH:ubiquinone oxidoreductase complex assembly factor 5	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2447	chr14	37738400	37738600	+	1.91214	NA	Intergenic	Intergenic	-603178	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding	0.000000	0.268657			62(CTTTGTTCTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6782	chr7	3423334	3423534	+	1.91214	NA	promoter-TSS (NR_126426)	promoter-TSS (NR_126426)	11	NR_126426	70230	Mm.458356	NR_126426	ENSMUSG00000107585	3300002P13Rik	-	RIKEN cDNA 3300002P13 gene	ncRNA	0.040000	0.582090			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7220	chr8	41075588	41075788	+	1.91214	NA	intron (NM_001005863, intron 3 of 13)	MTC|LTR|ERVL-MaLR	-20892	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1837	chr12	98699631	98699831	+	1.91214	NA	intron (NM_001146199, intron 9 of 18)	intron (NM_001146199, intron 9 of 18)	34914	NM_011877	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding	0.000000	0.358209			-27(ATTTAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2415	chr14	29472612	29472812	+	1.91214	NA	intron (NM_009785, intron 3 of 37)	intron (NM_009785, intron 3 of 37)	249152	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8089	chrX	134674031	134674231	+	1.91214	NA	Intergenic	Intergenic	12331	NR_045454	77983	Mm.153204	NR_045454	ENSMUSG00000087024	B230119M05Rik	-	RIKEN cDNA B230119M05 gene	ncRNA	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-445	chr1	149695410	149695610	+	1.91214	NA	Intergenic	Intergenic	226929	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding	0.000000	0.358209			36(TTTGTGCCATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1043	chr10	113433106	113433306	+	1.91214	NA	Intergenic	RLTR13B1|LTR|ERVK	-504180	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132	ataxin 7-like 3B	protein-coding	0.020000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7943	chrX	36073886	36074086	+	1.91214	NA	intron (NM_001009947, intron 52 of 52)	intron (NM_001009947, intron 52 of 52)	-38122	NM_133990	16164	Mm.24208	NM_133990	ENSMUSG00000017057	Il13ra1	AI882074|CD213a1|IL-13R-alpha-1|IL-13r[a]|Il13ra|NR4	interleukin 13 receptor, alpha 1	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3704	chr18	10572200	10572400	+	1.91214	NA	intron (NM_001081222, intron 9 of 10)	B2_Mm2|SINE|B2	38052	NM_001081222	77805	Mm.210996	NM_144542	ENSMUSG00000024293	Esco1	A930014I12Rik	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4043	chr19	21495371	21495571	+	1.91040	NA	Intergenic	Intergenic	-22810	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding	0.025000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4373	chr2	68266711	68266911	+	1.91040	NA	intron (NM_016866, intron 15 of 17)	intron (NM_016866, intron 15 of 17)	162139	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding	0.010000	0.402985			-44(ATTTCCATGAAAAGCT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-730	chr6	23923886	23924086	+	1.90991	NA	Intergenic	Intergenic	46074	NM_207022	387347	Mm.377909	NM_207022	ENSMUSG00000043865	Tas2r118	Gm465|T2R16|T2R18|Tas2r16|Tas2r18|mGR18|mt2r40	taste receptor, type 2, member 118	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4829	chr3	7683065	7683265	+	1.90709	NA	Intergenic	RLTR13D6|LTR|ERVK	-69405	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3513	chr17	51262663	51262863	+	1.90709	NA	Intergenic	Intergenic	-15225	NR_037257	100526552		NR_037257	ENSMUSG00000096134	Mir669p-1	Mir699p-1|mmu-mir-669p-1	microRNA 669p-1	ncRNA	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5996	chr5	65620671	65620871	+	1.90709	NA	intron (NM_001081321, intron 28 of 32)	intron (NM_001081321, intron 28 of 32)	77465	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|B230308N11Rik|E230024D05Rik	PDS5 cohesin associated factor A	protein-coding	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3581	chr17	71352867	71353067	+	1.90709	NA	intron (NM_028887, intron 45 of 47)	intron (NM_028887, intron 45 of 47)	-11163	NR_028023	100043644	Mm.362377	NR_028023	ENSMUSG00000117199	Gm4566	-	ubiquitin specific peptidase 16 pseudogene	pseudo	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5701	chr4	115033812	115034012	+	1.90709	NA	intron (NM_001304555, intron 14 of 16)	intron (NM_001304555, intron 14 of 16)	-22514	NM_011527	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6837	chr7	46801773	46801973	+	1.90709	NA	intron (NM_001360076, intron 3 of 15)	intron (NM_001360076, intron 3 of 15)	5202	NM_001291075	14884	Mm.22700	NM_008186	ENSMUSG00000006599	Gtf2h1	62kDa|AW743425|AW822074|BTF2 p62|C77871|p62	general transcription factor II H, polypeptide 1	protein-coding	0.000000	0.328358			4(ATTTTAATTAGAATAA,-,0.00),10(ATTAGAATAACAGATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4280	chr2	44621547	44621747	+	1.90709	NA	intron (NM_001362986, intron 6 of 10)	L1MA5A|LINE|L1	239975	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding	0.005000	0.363184			-4(ATCTACATATGAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-538	chr1	171787297	171787497	+	1.90305	NA	intron (NM_013730, intron 3 of 6)	intron (NM_013730, intron 3 of 6)	20265	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2301	chr13	111373894	111374094	+	1.90305	NA	Intergenic	Intergenic	116133	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3487	chr17	42346973	42347173	+	1.90274	NA	intron (NM_001355270, intron 1 of 2)	L1ME3B|LINE|L1	30473	NM_001355270	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1542	chr12	12613992	12614192	+	1.90274	NA	Intergenic	Intergenic	55825	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6744	chr6	138209061	138209261	+	1.90274	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	67574	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding	0.010000	0.313433			-64(GATTTCTCATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6070	chr5	86248364	86248564	+	1.90274	NA	intron (NM_001030297, intron 5 of 9)	intron (NM_001030297, intron 5 of 9)	40844	NM_001030297	435845	Mm.359654	NM_001030297	ENSMUSG00000061184	Tmprss11c	Tmprss13	transmembrane protease, serine 11c	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7937	chrX	21935052	21935252	+	1.90274	NA	Intergenic	Intergenic	-190041	NR_163859									0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6849	chr7	50270122	50270322	+	1.90274	NA	intron (NM_001037906, intron 11 of 19)	intron (NM_001037906, intron 11 of 19)	294872	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding	0.015000	0.368159			69(AATTACAAAAGAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4381	chr2	70757264	70757464	+	1.90274	NA	intron (NR_156421, intron 5 of 6)	intron (NR_156421, intron 5 of 6)	67440	NM_001362963	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding	0.010000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6924	chr7	80313728	80313928	+	1.90268	NA	intron (NM_145150, intron 13 of 13)	intron (NM_145150, intron 13 of 13)	10626	NM_173445	269955	Mm.474502	NM_173445	ENSMUSG00000038930	Rccd1	5830436H09|E430018M08Rik	RCC1 domain containing 1	protein-coding	0.025000	0.407960			33(ATTTACAAAACCAAAT,-,0.00),47(ATTAGAAAAGGAAAAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-736	chr6	34187447	34187647	+	1.90268	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-10493	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7634	chr9	45473986	45474186	+	1.90243	NA	intron (NM_001081270, intron 3 of 32)	intron (NM_001081270, intron 3 of 32)	-42854	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4293	chr2	49500252	49500452	+	1.90243	NA	intron (NM_172663, intron 2 of 13)	L1M3|LINE|L1	48866	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1597	chr12	34915485	34915685	+	1.90243	NA	intron (NM_001271386, intron 1 of 27)	intron (NM_001271386, intron 1 of 27)	1510	NM_001271386	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding	0.010000	0.378109			53(GTTTAAATAACAATCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2631	chr14	93229013	93229213	+	1.90243	NA	intron (NM_001081377, intron 4 of 4)	intron (NM_001081377, intron 4 of 4)	661556	NM_001081377	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding	0.005000	0.407960			-43(ATTTAAATAAGAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4799	chr2	173482634	173482834	+	1.90243	NA	Intergenic	MTB-int|LTR|ERVL-MaLR	-39858	NM_028158	72221	Mm.46132	NM_028158	ENSMUSG00000027518	1700021F07Rik	-	RIKEN cDNA 1700021F07 gene	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2189	chr13	90343309	90343509	+	1.90243	NA	Intergenic	Intergenic	253742	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0.005000	0.393035			-77(GTTTGCTTAACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5276	chr3	148883185	148883385	+	1.90243	NA	intron (NM_001081298, intron 2 of 23)	intron (NM_001081298, intron 2 of 23)	71350	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7007	chr7	105244850	105245050	+	1.90243	NA	Intergenic	Intergenic	-40609	NM_147069	259072	Mm.377823	NM_147069	ENSMUSG00000048425	Olfr686	MOR35-1	olfactory receptor 686	protein-coding	0.000000	0.373134	-32(AATGAATCATTCATG,+,0.00),-32(AATGAATCATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3854	chr18	53199615	53199815	+	1.90243	NA	intron (NM_026386, intron 5 of 14)	intron (NM_026386, intron 5 of 14)	23423	NM_001357463	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding	0.000000	0.353234			-78(ATTTGCAAAACAGAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7109	chr7	136232378	136232578	+	1.90243	NA	Intergenic	Intergenic	-35846	NR_102277	77383	Mm.227745	NR_102277	ENSMUSG00000110027	C030029H02Rik	-	RIKEN cDNA C030029H02 gene	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-271	chr1	93130348	93130548	+	1.90243	NA	Intergenic	Intergenic	-4792	NM_001276710	11611	Mm.7457	NM_016702	ENSMUSG00000026272	Agxt	AGT|Agt1|Agxt1|SPT	alanine-glyoxylate aminotransferase	protein-coding	0.020000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6302	chr6	10860535	10860735	+	1.90243	NA	Intergenic	LTRIS2|LTR|ERV1	113743	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	ncRNA	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4767	chr2	161196835	161197035	+	1.90243	NA	Intergenic	Intergenic	-87849	NM_173368	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding	0.000000	0.422886			-29(CCATTGATATGCAAAT,+,0.00),51(ATTTGCATTAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-849	chr10	61795720	61795920	+	1.90243	NA	Intergenic	Intergenic	-11956	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding	0.025000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1179	chr11	19274299	19274499	+	1.90243	NA	Intergenic	Lx10|LINE|L1	209124	NR_046037	74059	Mm.292321	NR_046037	ENSMUSG00000086025	4933406G16Rik	-	RIKEN cDNA 4933406G16 gene	ncRNA	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2864	chr15	37436222	37436422	+	1.90243	NA	intron (NM_029113, intron 2 of 3)	intron (NM_029113, intron 2 of 3)	-3658	NR_045283	100503538	Mm.445166	NR_045283	ENSMUSG00000086992	Gm15941	-	predicted gene 15941	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7706	chr9	67850102	67850302	+	1.90243	NA	intron (NM_177184, intron 1 of 84)	intron (NM_177184, intron 1 of 84)	9851	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3991	chr18	86531704	86531904	+	1.90243	NA	Intergenic	Intergenic	136852	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0.000000	0.323383			68(GTATTCTTATTGTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4683	chr2	141578332	141578532	+	1.90243	NA	intron (NM_001013802, intron 6 of 18)	intron (NM_001013802, intron 6 of 18)	-906956	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0.000000	0.427861			8(ATTAACAAGAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6073	chr5	88734850	88735050	+	1.90156	NA	intron (NM_026735, intron 1 of 5)	B3|SINE|B2	14079	NM_026735	68473	Mm.35764	NM_026735	ENSMUSG00000006262	Mob1b	1110003E08Rik|AU015450|B230364F10|Mobkl1a	MOB kinase activator 1B	protein-coding	0.010000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-247	chr13	66912974	66913174	+	1.89955	NA	intron (NM_025547, intron 7 of 7)	intron (NM_025547, intron 7 of 7)	7659	NM_001177750	100038538	Mm.405005	NM_001177750	ENSMUSG00000074826	Gm10767	-	predicted gene 10767	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2115	chr13	66912938	66913138	+	1.89955	NA	intron (NM_025547, intron 7 of 7)	intron (NM_025547, intron 7 of 7)	7623	NM_001177750	100038538	Mm.405005	NM_001177750	ENSMUSG00000074826	Gm10767	-	predicted gene 10767	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8093	chrX	136611388	136611588	+	1.89698	NA	intron (NM_001359279, intron 3 of 4)	intron (NM_001359279, intron 3 of 4)	20646	NM_001359279	594844	Mm.260515	NM_001029978	ENSMUSG00000044550	Tceal3	1100001D19Rik	transcription elongation factor A (SII)-like 3	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2987	chr15	70944048	70944248	+	1.89698	NA	Intergenic	Intergenic	783690	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding	0.005000	0.268657			-89(ATTATAATAATAAAAA,-,0.00),38(ATTTAAAAGAAAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4505	chr2	107405311	107405511	+	1.89698	NA	Intergenic	L1M2|LINE|L1	114822	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4395	chr2	74073528	74073728	+	1.89698	NA	Intergenic	Intergenic	-162302	NM_001301721	228033	Mm.2966	NM_175015	ENSMUSG00000018770	Atp5g3	6030447M23|Atp5mc3	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4647	chr2	135730989	135731189	+	1.89698	NA	intron (NM_001355153, intron 1 of 38)	intron (NM_001355153, intron 1 of 38)	-33749	NM_001355154	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6253	chr5	147532698	147532898	+	1.89698	NA	intron (NM_001359433, intron 14 of 19)	intron (NM_001359433, intron 14 of 19)	102642	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding	0.000000	0.318408			16(TTTGTGTTTTGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6914	chr7	76551001	76551201	+	1.89698	NA	intron (NM_001199224, intron 17 of 22)	intron (NM_001199224, intron 17 of 22)	321214	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0.000000	0.368159			-26(CTTTGCATTACAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4504	chr2	107405218	107405418	+	1.89698	NA	Intergenic	L1M2|LINE|L1	114729	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1504	chr11	121231142	121231342	+	1.89626	NA	Intergenic	Intergenic	-1933	NM_144832	217370	Mm.27182	NM_144832	ENSMUSG00000039294	Cybc1	-	cytochrome b 245 chaperone 1	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6779	chr6	149037487	149037687	+	1.89626	NA	intron (NM_177192, intron 6 of 20)	intron (NM_177192, intron 6 of 20)	64093	NM_177192	320560	Mm.426874	NM_177192	ENSMUSG00000030313	Dennd5b	9330160C06Rik|AI852444|D030011O10Rik|Gm17524	DENN/MADD domain containing 5B	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5267	chr3	147974809	147975009	+	1.89397	NA	Intergenic	Intergenic	979726	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1216	chr11	28539945	28540145	+	1.89397	NA	intron (NM_181577, intron 2 of 4)	MARNA|DNA|TcMar-Mariner	44279	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6537	chr6	76620804	76621004	+	1.89110	NA	Intergenic	Intergenic	-621573	NR_155299	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6346	chr6	21123067	21123267	+	1.89110	NA	Intergenic	Intergenic	-92179	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121	potassium voltage-gated channel, Shal-related family, member 2	protein-coding	0.000000	0.348259			-20(ATATGCATAACTAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7555	chr9	23728864	23729064	+	1.88933	NA	Intergenic	Intergenic	-369054	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7580	chr9	29721378	29721578	+	1.88933	NA	intron (NM_001357597, intron 1 of 8)	intron (NM_001357597, intron 1 of 8)	241791	NM_001357598	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3271	chr16	63091137	63091337	+	1.88933	NA	Intergenic	Intergenic	236930	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding	0.000000	0.283582			62(CTTTTCATAAAAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5107	chr3	107996099	107996299	+	1.88933	NA	Intergenic	RLTR13D6|LTR|ERVK	-9779	NM_008183	14863	Mm.440086	NM_008183	ENSMUSG00000040562	Gstm2	Gstb-2|Gstb2	glutathione S-transferase, mu 2	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8010	chrX	86950906	86951106	+	1.88933	NA	intron (NM_001160403, intron 6 of 10)	intron (NM_001160403, intron 6 of 10)	-596012	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-266	chr1	91669984	91670184	+	1.88933	NA	Intergenic	Intergenic	129004	NM_023046	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding	0.030000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3479	chr17	36982710	36982910	+	1.88752	NA	TTS (NR_160897)	TTS (NR_160897)	-1573	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3171	chr16	37817250	37817450	+	1.88752	NA	intron (NM_008047, intron 3 of 10)	L1MC4a|LINE|L1	40295	NM_008047	14314	Mm.182434	NM_008047	ENSMUSG00000022816	Fstl1	AI316791|AW107808|Fstl|TSC-36	follistatin-like 1	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5629	chr4	97818725	97818925	+	1.88712	NA	intron (NM_001122953, intron 2 of 9)	intron (NM_001122953, intron 2 of 9)	41199	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1905	chr12	117054051	117054251	+	1.88695	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	97118	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.035000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1712	chr12	69696882	69697082	+	1.88449	NA	intron (NM_145443, intron 9 of 9)	MER20|DNA|hAT-Charlie	-15130	NM_001135559	20663	Mm.3770	NM_001135559	ENSMUSG00000034801	Sos2	SOS-2|mSOS-2	SOS Ras/Rho guanine nucleotide exchange factor 2	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7428	chr8	106077381	106077581	+	1.88449	NA	intron (NM_010901, intron 1 of 9)	intron (NM_010901, intron 1 of 9)	17891	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5653	chr4	102383059	102383259	+	1.88449	NA	intron (NM_019840, intron 1 of 14)	intron (NM_019840, intron 1 of 14)	128220	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-443	chr1	149254325	149254525	+	1.88449	NA	Intergenic	Intergenic	668014	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2598	chr14	85480118	85480318	+	1.88449	NA	Intergenic	Intergenic	-765752	NR_040457	75155	Mm.399239	NR_040457	ENSMUSG00000115271	4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA	0.000000	0.333333			-39(ATTTGAAAGACATATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5940	chr5	49618025	49618225	+	1.88449	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-332466	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8014	chrX	92060092	92060292	+	1.88449	NA	Intergenic	Lx7|LINE|L1	-43859	NM_010759	17145	Mm.377100	NM_010759	ENSMUSG00000062162	Mageb1	MAGE-Xp|Mage-b1|Mage-rs1|Magel1|Smage1|dam1	melanoma antigen, family B, 1	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5659	chr4	103913258	103913458	+	1.88449	NA	intron (NM_001369049, intron 1 of 19)	intron (NM_001369049, intron 1 of 19)	293858	NM_001369048	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1366	chr11	77530556	77530756	+	1.88449	NA	3' UTR (NM_144825, exon 20 of 20)	3' UTR (NM_144825, exon 20 of 20)	15539	NM_026185	67477	Mm.432526	NM_026185	ENSMUSG00000000686	Abhd15	1300007F04Rik	abhydrolase domain containing 15	protein-coding	0.005000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2063	chr13	48042195	48042395	+	1.88449	NA	Intergenic	Intergenic	-23687	NR_038004	70971	Mm.158514	NR_038004	ENSMUSG00000047324	4931429P17Rik	-	RIKEN cDNA 4931429P17 gene	ncRNA	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1693	chr12	64641873	64642073	+	1.88449	NA	Intergenic	Intergenic	-167075	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6307	chr6	12542492	12542692	+	1.88449	NA	intron (NM_001164805, intron 2 of 26)	MIRc|SINE|MIR	206661	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding	0.010000	0.323383			-12(TTTTGCATGACAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7014	chr7	109072966	109073166	+	1.88449	NA	intron (NM_178780, intron 1 of 4)	L1ME4a|LINE|L1	10258	NM_001038624	320360	Mm.71007	NM_178780	ENSMUSG00000048330	Ric3	E130307J04Rik	RIC3 acetylcholine receptor chaperone	protein-coding	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-768	chr10	35102470	35102670	+	1.88449	NA	Intergenic	Intergenic	619170	NM_001358769	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0.000000	0.283582			-39(ATTTGAATGAAAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2363	chr14	12767144	12767344	+	1.88449	NA	intron (NM_001359921, intron 1 of 29)	intron (NM_001359921, intron 1 of 29)	55835	NM_012061	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding	0.005000	0.452736			-83(AATTGCATGATAGAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7447	chr8	110519452	110519652	+	1.88449	NA	intron (NM_172916, intron 42 of 86)	intron (NM_172916, intron 42 of 86)	-17196	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA	0.040000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5077	chr3	98956674	98956874	+	1.88449	NA	Intergenic	L1_Mur3|LINE|L1	-63544	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2106	chr13	63554501	63554701	+	1.88449	NA	intron (NM_008957, intron 2 of 23)	intron (NM_008957, intron 2 of 23)	11134	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes|wig	patched 1	protein-coding	0.035000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3789	chr18	35482822	35483022	+	1.88449	NA	intron (NM_030749, intron 1 of 9)	intron (NM_030749, intron 1 of 9)	-12970	NM_001360814	81500	Mm.291482	NM_030749	ENSMUSG00000024357	Sil1	1810057E01Rik|AI042831|wz	endoplasmic reticulum chaperone SIL1 homolog (S. cerevisiae)	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7500	chr8	128622920	128623120	+	1.88449	NA	Intergenic	Intergenic	-62634	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1595	chr12	34461822	34462022	+	1.88449	NA	intron (NM_024124, intron 2 of 11)	intron (NM_024124, intron 2 of 11)	66967	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4900	chr3	31907175	31907375	+	1.88449	NA	intron (NM_028231, intron 1 of 5)	intron (NM_028231, intron 1 of 5)	4572	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5163	chr3	123906591	123906791	+	1.88449	NA	Intergenic	Intergenic	-215839	NR_121616	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding	0.000000	0.288557			-44(CATTTATTTTTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8131	chrX	157809920	157810120	+	1.88449	NA	Intergenic	RLTR25A|LTR|ERVK	-8415	NM_001081667	245683	Mm.295846	NM_001081667	ENSMUSG00000047485	Klhl34	Gm388	kelch-like 34	protein-coding	0.000000	0.358209			39(GCATTGATATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-117	chr1	41114778	41114978	+	1.88449	NA	Intergenic	Intergenic	66374	NR_040475	74897	Mm.243822	NR_040475	ENSMUSG00000104072	4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	ncRNA	0.000000	0.333333			19(CATTTCCCTTGTATAT,+,0.00),61(CCATTGTGATTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4313	chr2	55181742	55181942	+	1.88305	NA	Intergenic	L1MB3|LINE|L1	-254128	NM_001355118	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7946	chrX	36554193	36554393	+	1.88305	NA	Intergenic	L1MA8|LINE|L1	-43900	NM_016783	53328	Mm.9052	NM_016783	ENSMUSG00000006373	Pgrmc1	AA415812|HPR6.6|PPMR|Vema|mPR	progesterone receptor membrane component 1	protein-coding	0.000000	0.378109		-54(CATCCATTTTCATG,-,0.00)	-51(CCATTTTCATGCAGAT,+,0.00),44(ATAAACATGAGAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5242	chr3	142340972	142341172	+	1.88305	NA	intron (NM_001190856, intron 3 of 14)	intron (NM_001190856, intron 3 of 14)	50778	NM_001190857	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding	0.005000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-761	chr6	89581685	89581885	+	1.88274	NA	intron (NM_001167736, intron 1 of 6)	intron (NM_001167736, intron 1 of 6)	13867	NM_025351	66098	Mm.20313	NM_025351	ENSMUSG00000030086	Chchd6	0710001P09Rik|1700021B03Rik|Micos25	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding	0.015000	0.363184			51(ATAACCATGACAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7558	chr9	24078415	24078615	+	1.88064	NA	Intergenic	L1M4|LINE|L1	-19503	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.000000	0.243781			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2881	chr15	41429318	41429518	+	1.87902	NA	Intergenic	Intergenic	-18064	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2174	chr13	83536769	83536969	+	1.87902	NA	intron (NM_001347581, intron 1 of 9)	intron (NM_001347581, intron 1 of 9)	12126	NM_001347578	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2929	chr15	54099078	54099278	+	1.87902	NA	Intergenic	Intergenic	179306	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)	protein-coding	0.000000	0.348259			-7(TCATACTAATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5766	chr4	138107819	138108019	+	1.87902	NA	intron (NM_001355700, intron 7 of 30)	intron (NM_001355700, intron 7 of 30)	30599	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6042	chr5	77906293	77906493	+	1.87902	NA	Intergenic	Intergenic	440905	NR_131050	69370	Mm.426881	NR_131050	ENSMUSG00000107232	1700017L05Rik	-	RIKEN cDNA 1700017L05 gene	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5363	chr4	18349348	18349548	+	1.87902	NA	Intergenic	Intergenic	495990	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5445	chr4	47559021	47559221	+	1.87902	NA	Intergenic	Intergenic	84460	NM_024171	66212	Mm.20188	NM_024171	ENSMUSG00000053317	Sec61b	1190006C12Rik|AI326121|AW122942	Sec61 beta subunit	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2612	chr14	87804205	87804405	+	1.87902	NA	Intergenic	MLTR18B_MM|LTR|ERVK	387722	NM_001253755	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding	0.005000	0.388060			-89(CATTTCTTTTGCAAAG,+,0.00),11(ATAAGCATAACAGTAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3870	chr18	56258540	56258740	+	1.87744	NA	Intergenic	Intergenic	-141700	NM_001360917	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|Gramd2b|NS3TP2	GRAM domain containing 3	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3500	chr17	48588383	48588583	+	1.87744	NA	Intergenic	L1MB3|LINE|L1	133582	NM_152823	76589	Mm.311629	NM_152823	ENSMUSG00000043592	Unc5cl	2510009H09Rik|BB155270|Zud	unc-5 family C-terminal like	protein-coding	0.015000	0.398010			-35(CTTTGAAAGGCAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6373	chr6	29392691	29392891	+	1.87744	NA	Intergenic	Intergenic	-3784	NM_001347071	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6252	chr5	147501607	147501807	+	1.87744	NA	intron (NM_028291, intron 5 of 18)	intron (NM_028291, intron 5 of 18)	71551	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding	0.000000	0.437811			-26(ATTTGAATCAGAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7862	chr9	104914410	104914610	+	1.87744	NA	intron (NM_028719, intron 5 of 15)	Lx8|LINE|L1	-138758	NM_001364513	94062	Mm.29746	NM_053159	ENSMUSG00000032563	Mrpl3	2010320L16Rik|5930422H18Rik|AA407889|L3mt	mitochondrial ribosomal protein L3	protein-coding	0.015000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-760	chr6	89508283	89508483	+	1.87660	NA	intron (NM_025351, intron 4 of 7)	Tigger1|DNA|TcMar-Tigger	87269	NM_025351	66098	Mm.20313	NM_025351	ENSMUSG00000030086	Chchd6	0710001P09Rik|1700021B03Rik|Micos25	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-609	chr1	185243009	185243209	+	1.87508	NA	TTS (NR_034044)	TTS (NR_034044)	134	NR_035529	100316737		NR_035529	ENSMUSG00000105770	Mir664	mir-664|mmu-mir-664	microRNA 664	ncRNA	0.020000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6092	chr5	92490911	92491111	+	1.87508	NA	intron (NM_007644, intron 1 of 11)	intron (NM_007644, intron 1 of 11)	14646	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP II|LIMP-2|MLGP85	scavenger receptor class B, member 2	protein-coding	0.015000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1015	chr10	108621444	108621644	+	1.87302	NA	intron (NM_001252342, intron 8 of 10)	intron (NM_001252342, intron 8 of 10)	78616	NM_203660	368203	Mm.452758	NM_203660	ENSMUSG00000112039	Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding	0.000000	0.278607		-6(AATACATATTCAAT,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-482	chr2	53586112	53586312	+	1.87302	NA	Intergenic	MTD|LTR|ERVL-MaLR	394128	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding	0.000000	0.417910			-83(ATTTGCATTAAAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2029	chr13	36530523	36530723	+	1.87143	NA	intron (NM_001039189, intron 5 of 5)	RMER1A|Other|Other	203854	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2040	chr13	40645776	40645976	+	1.87036	NA	Intergenic	Intergenic	-81932	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7461	chr8	115311041	115311241	+	1.87036	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	395753	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding	0.000000	0.378109			-43(ATTTAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5600	chr4	91342635	91342835	+	1.87036	NA	intron (NM_001347149, intron 1 of 7)	intron (NM_001347149, intron 1 of 7)	29320	NM_010486	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV like RNA binding protein 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7053	chr7	122134786	122134986	+	1.87036	NA	intron (NM_021608, intron 2 of 5)	intron (NM_021608, intron 2 of 5)	1845	NM_021608	59288	Mm.478285	NM_021608	ENSMUSG00000030868	Dctn5	4930427E12Rik|C78178|b2b315Clo	dynactin 5	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2284	chr13	109690857	109691057	+	1.86945	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-212852	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2	chr1	3046418	3046618	+	1.86720	NA	Intergenic	RLTR13C1|LTR|ERVK	624980	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-514	chr1	164113261	164113461	+	1.86702	NA	Intergenic	Intergenic	-1903	NM_011347	20344	Mm.3337	NM_011347	ENSMUSG00000026580	Selp	CD62P|GMP-140|Grmp|LECAM3|PADGEM	selectin, platelet	protein-coding	0.010000	0.378109			21(CTATTATTATACAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6160	chr5	115177139	115177339	+	1.86702	NA	intron (NM_001310712, intron 1 of 5)	intron (NM_001310712, intron 1 of 5)	8882	NM_013879	29867	Mm.38551	NM_013879	ENSMUSG00000029544	Cabp1	caldendrin	calcium binding protein 1	protein-coding	0.000000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-317	chr1	109095245	109095445	+	1.86702	NA	Intergenic	Lx|LINE|L1	-887555	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding	0.000000	0.502488			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-592	chr3	147030541	147030741	+	1.86702	NA	Intergenic	Intergenic	178274	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.030000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8128	chrX	156589123	156589323	+	1.86702	NA	Intergenic	Intergenic	49740	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo	0.010000	0.353234	39(TATAAATAATTCAGT,+,0.00),39(TATAAATAATTCAGT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3725	chr18	18169744	18169944	+	1.86487	NA	Intergenic	Intergenic	-588854	NR_045374	75162	Mm.60874	NR_045374	ENSMUSG00000117615	4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	ncRNA	0.010000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7494	chr8	127534739	127534939	+	1.86487	NA	intron (NM_001363431, intron 22 of 24)	intron (NM_001363431, intron 22 of 24)	235227	NM_001013581	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding	0.000000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1912	chr12	118423016	118423216	+	1.86487	NA	Intergenic	L1ME4a|LINE|L1	107077	NR_045947	100384890	Mm.484658	NR_045947	ENSMUSG00000113875	D230030E09Rik	Npe	Riken cDNA D230030E09 gene	ncRNA	0.010000	0.333333			-52(TATTTATAATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3117	chr16	22941990	22942190	+	1.86487	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-8982	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5608	chr4	94305876	94306076	+	1.86487	NA	Intergenic	Intergenic	250820	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3869	chr18	55628359	55628559	+	1.86487	NA	Intergenic	Intergenic	-635868	NM_001360787	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding	0.010000	0.348259			-68(ATTAAAAAAAAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-84	chr1	28091131	28091331	+	1.86487	NA	Intergenic	Intergenic	207185	NR_151583	433281	Mm.329306	NR_151583	ENSMUSG00000101514	Gm5524	AI875557|EG433281	predicted gene 5524	ncRNA	0.000000	0.353234			-86(ATTTTCATGGTAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4937	chr3	50898433	50898633	+	1.86487	NA	Intergenic	Intergenic	-325914	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding	0.020000	0.393035			-2(TCTGTGTTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5261	chr3	147261438	147261638	+	1.86487	NA	Intergenic	Intergenic	409171	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.010000	0.368159			-56(TTTTTCTTTTTCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6897	chr7	70789084	70789284	+	1.86487	NA	Intergenic	Intergenic	-422438	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding	0.015000	0.492537			-78(CTTTCCAACACAAATG,-,0.00),6(ATTTGAAAACCAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-743	chr10	25405358	25405558	+	1.86487	NA	intron (NM_001358753, intron 1 of 18)	intron (NM_001358753, intron 1 of 18)	-2910	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding	0.010000	0.348259			-33(TAATTGTTATTAATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5871	chr5	26170861	26171061	+	1.86487	NA	Intergenic	Intergenic	-49536	NM_001134299	434689	Mm.484129	NM_001134299	ENSMUSG00000067698	Gm10220	-	predicted gene 10220	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3165	chr16	34356019	34356219	+	1.86487	NA	intron (NM_177357, intron 5 of 59)	intron (NM_177357, intron 5 of 59)	157908	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding	0.005000	0.378109			-77(TTTTCCATAACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6553	chr6	82012359	82012559	+	1.86487	NA	Intergenic	Intergenic	21618	NR_157232	100504740	Mm.383522	NR_157232	ENSMUSG00000107412	Gm20383	-	predicted gene, 20383	ncRNA	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7652	chr9	51154889	51155089	+	1.86487	NA	Intergenic	MER2|DNA|TcMar-Tigger	38988	NM_019493	56057	Mm.431317	NM_019493	ENSMUSG00000032056	Btg4	C86116|PC3B	B cell translocation gene 4	protein-coding	0.005000	0.333333			-19(CTATACTTATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5456	chr4	49811374	49811574	+	1.86487	NA	intron (NM_001033351, intron 1 of 8)	intron (NM_001033351, intron 1 of 8)	34295	NM_001033351	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3007	chr15	86230408	86230608	+	1.86487	NA	intron (NM_145476, intron 1 of 12)	intron (NM_145476, intron 1 of 12)	16049	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2184	chr13	85886808	85887008	+	1.86487	NA	Intergenic	Intergenic	159887	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit 7C	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4858	chr3	14478667	14478867	+	1.86487	NA	Intergenic	Intergenic	-1930	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding	0.000000	0.338308			36(CTTCAGTCATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3883	chr18	57791886	57792086	+	1.86457	NA	intron (NR_152225, intron 1 of 2)	intron (NR_152225, intron 1 of 2)	347	NR_152225	100503033	Mm.381112	NR_152224	ENSMUSG00000118391	Gm19519	-	predicted gene, 19519	ncRNA	0.010000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-440	chr18	57791790	57791990	+	1.86457	NA	intron (NR_152225, intron 1 of 2)	intron (NR_152225, intron 1 of 2)	443	NR_152225	100503033	Mm.381112	NR_152224	ENSMUSG00000118391	Gm19519	-	predicted gene, 19519	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3409	chr17	5204690	5204890	+	1.86457	NA	intron (NM_001085355, intron 4 of 19)	intron (NM_001085355, intron 4 of 19)	209716	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|BAF250B|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding	0.030000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4073	chr19	34454621	34454821	+	1.86167	NA	Intergenic	Intergenic	20427	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6091	chr5	92229519	92229719	+	1.86167	NA	intron (NM_011148, intron 15 of 16)	MER2|DNA|TcMar-Tigger	-14211	NR_033483	57425	Mm.2548	NM_020562	ENSMUSG00000029409	U90926	-	cDNA sequence U90926	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2550	chr14	75947578	75947778	+	1.86167	NA	intron (NM_026816, intron 5 of 7)	intron (NM_026816, intron 5 of 7)	-7325	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-177	chr1	61310535	61310735	+	1.86148	NA	Intergenic	Intergenic	-67797	NR_040483	77341	Mm.402964	NR_040483	ENSMUSG00000085447	9530026F06Rik	-	RIKEN cDNA 9530026F06 gene	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1746	chr12	75939155	75939355	+	1.86148	NA	intron (NM_001005510, intron 34 of 115)	intron (NM_001005510, intron 34 of 115)	30152	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA	0.020000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5755	chr4	133218816	133219016	+	1.86132	NA	Intergenic	Intergenic	-1893	NM_027152	69655	Mm.285685	NM_027152	ENSMUSG00000028865	Cd164l2	2310047N01Rik	CD164 sialomucin-like 2	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-685	chr10	7787358	7787558	+	1.86132	NA	Intergenic	Lx8|LINE|L1	-5436	NM_026141	67418	Mm.38927	NM_026141	ENSMUSG00000015757	Ppil4	3732410E19Rik|3830425H19Rik|AI788954|AW146233|PPIase	peptidylprolyl isomerase (cyclophilin)-like 4	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7704	chr9	67415563	67415763	+	1.86132	NA	intron (NM_001081242, intron 2 of 57)	intron (NM_001081242, intron 2 of 57)	144040	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding	0.005000	0.358209			2(ATTTGAATCCTAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1040	chr10	112308391	112308591	+	1.86132	NA	intron (NM_001359753, intron 2 of 4)	intron (NM_001359753, intron 2 of 4)	37218	NM_001359753	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding	0.020000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6491	chr6	63874049	63874249	+	1.86132	NA	intron (NM_001370966, intron 2 of 15)	intron (NM_001370966, intron 2 of 15)	618143	NM_001370966									0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3932	chr18	71520082	71520282	+	1.86132	NA	intron (NM_007831, intron 12 of 28)	intron (NM_007831, intron 12 of 28)	830887	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0.000000	0.298507			-75(ATTAGCATTAGAATAA,-,0.00),-69(ATTAGAATAAAAAGAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7039	chr7	117299347	117299547	+	1.86132	NA	Intergenic	Intergenic	-81532	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5266	chr3	147959450	147959650	+	1.86132	NA	Intergenic	Intergenic	995085	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1348	chr11	73079964	73080164	+	1.86132	NA	3' UTR (NM_025818, exon 13 of 13)	3' UTR (NM_025818, exon 13 of 13)	-10519	NM_001361245	16407	Mm.96	NM_008399	ENSMUSG00000005947	Itgae	A530055J10|CD103|aM290|alpha-E1|alpha-M290	integrin alpha E, epithelial-associated	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4978	chr3	63904691	63904891	+	1.86132	NA	Intergenic	Intergenic	-5329	NM_001370984									0.005000	0.427861			-84(ATTTACAAGTTAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6912	chr7	76234877	76235077	+	1.85982	NA	intron (NM_001199224, intron 1 of 22)	intron (NM_001199224, intron 1 of 22)	5090	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0.000000	0.363184			24(TCTTTGTCATCAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3616	chr17	80729474	80729674	+	1.85785	NA	Intergenic	Intergenic	-1549	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.010000	0.378109			21(GTTTGCATCACTAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4985	chr3	65456256	65456456	+	1.85779	NA	Intergenic	Intergenic	-63803	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5895	chr5	32574347	32574547	+	1.85609	NA	Intergenic	B2_Mm2|SINE|B2	-36724	NM_009535	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4873	chr3	23272422	23272622	+	1.85609	NA	Intergenic	LTRIS2|LTR|ERV1	1021152	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6687	chr6	117703483	117703683	+	1.85609	NA	intron (NR_045731, intron 2 of 3)	intron (NR_045731, intron 2 of 3)	48186	NR_045731	72263	Mm.443289	NR_045731	ENSMUSG00000099869	1700030F04Rik	-	RIKEN cDNA 1700030F04 gene	ncRNA	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-995	chr10	105960215	105960415	+	1.85609	NA	Intergenic	MER53|DNA|hAT	118836	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding	0.010000	0.308458			-17(CGATACTTATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3101	chr16	17343227	17343427	+	1.85609	NA	3' UTR (NM_001331047, exon 5 of 5)	3' UTR (NM_001331047, exon 5 of 5)	11956	NM_008223	15160	Mm.6609	NM_008223	ENSMUSG00000022766	Serpind1	AA985900|AI303446|HC-II|HCII|Hcf2	serine (or cysteine) peptidase inhibitor, clade D, member 1	protein-coding	0.010000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8065	chrX	113503948	113504148	+	1.85609	NA	intron (NM_033605, intron 2 of 12)	intron (NM_033605, intron 2 of 12)	205792	NM_033605	93837	Mm.79760	NM_033605	ENSMUSG00000025592	Dach2	9430028N04Rik	dachshund family transcription factor 2	protein-coding	0.015000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5249	chr3	145093599	145093799	+	1.85609	NA	intron (NM_178697, intron 3 of 13)	MLTR25A|LTR|ERVK	5407	NM_178697	229933	Mm.331420	NM_178697	ENSMUSG00000036960	Clca2	4732440A06|AI586120|Clca5	chloride channel accessory 2	protein-coding	0.015000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3673	chr17	93091174	93091374	+	1.85609	NA	Intergenic	L1_Mur1|LINE|L1	-107743	NM_001315503	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-936	chr10	90926658	90926858	+	1.85609	NA	intron (NM_001359242, intron 7 of 10)	(T)n|Simple_repeat|Simple_repeat	96915	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1|AIDA-1b|C030032C09Rik|E530015N03Rik|EB-1|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.000000	0.323383			0(TTTTTTTTTTGTTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-882	chr10	71699779	71699979	+	1.85609	NA	Intergenic	Intergenic	280826	NR_003644	108950	Mm.212793	NM_175390		1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3644	chr17	86081859	86082059	+	1.85609	NA	intron (NM_030133, intron 14 of 20)	intron (NM_030133, intron 14 of 20)	63216	NM_030133	78586	Mm.146236	NM_030133	ENSMUSG00000024135	Srbd1	AI461933|C85414|D530025C17Rik	S1 RNA binding domain 1	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4988	chr3	65612861	65613061	+	1.85609	NA	Intergenic	Intergenic	-46327	NR_106200	102465905		NR_106200	ENSMUSG00000098944	Mir8120	Gm27637|mmu-mir-8120	microRNA 8120	ncRNA	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1674	chr12	57036432	57036632	+	1.85609	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	124111	NM_001167976	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2372	chr14	16313082	16313282	+	1.85609	NA	Intergenic	Intergenic	-52024	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding	0.000000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-23	chr1	89835362	89835562	+	1.85546	NA	intron (NM_001037136, intron 13 of 16)	intron (NM_001037136, intron 13 of 16)	95714	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6987	chr7	97376086	97376286	+	1.85515	NA	intron (NM_199035, intron 2 of 12)	intron (NM_199035, intron 2 of 12)	4569	NM_199035	381903	Mm.279683	NM_199035	ENSMUSG00000035704	Alg8	AI447372|Gm1089	asparagine-linked glycosylation 8 (alpha-1,3-glucosyltransferase)	protein-coding	0.005000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3867	chr18	55344182	55344382	+	1.85515	NA	Intergenic	Intergenic	-351691	NM_001360787	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5666	chr4	104560863	104561063	+	1.85515	NA	intron (NM_001369049, intron 5 of 19)	L1MA8|LINE|L1	193425	NR_104385	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.020000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3861	chr18	54057980	54058180	+	1.85515	NA	Intergenic	Intergenic	195967	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3501	chr17	48588592	48588792	+	1.85515	NA	Intergenic	L1MB3|LINE|L1	133791	NM_152823	76589	Mm.311629	NM_152823	ENSMUSG00000043592	Unc5cl	2510009H09Rik|BB155270|Zud	unc-5 family C-terminal like	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3340	chr16	79878677	79878877	+	1.85515	NA	Intergenic	Intergenic	-120599	NM_030146	78654		NM_030146		1700066C05Rik	-	RIKEN cDNA 1700066C05 gene	protein-coding	0.000000	0.308458	-12(CATAAATCATTCATT,+,0.00),-12(CATAAATCATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6886	chr7	67469063	67469263	+	1.85358	NA	Intergenic	Intergenic	-96305	NM_001291191	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding	0.010000	0.447761			-37(GAATTTGCATGTAAAT,+,0.00),-35(ATTTGCATGTAAATAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-140	chr11	35306963	35307163	+	1.85278	NA	intron (NM_011412, intron 4 of 35)	intron (NM_011412, intron 4 of 35)	185607	NM_011412	20564	Mm.478604	NM_011412	ENSMUSG00000056427	Slit3	Slil2|Slit1|b2b2362.1Clo	slit guidance ligand 3	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-427	chr18	26642610	26642810	+	1.84971	NA	Intergenic	MER2|DNA|TcMar-Tigger	-888553	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3759	chr18	26642614	26642814	+	1.84971	NA	Intergenic	MER2|DNA|TcMar-Tigger	-888557	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.015000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6076	chr5	89240213	89240413	+	1.84965	NA	TTS (NM_001197147)	TTS (NM_001197147)	212347	NM_001359213	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3374	chr16	88617695	88617895	+	1.84965	NA	Intergenic	Intergenic	-5516	NM_001163141	239932	Mm.120273	NM_001163141	ENSMUSG00000050239	Krtap24-1	Gm312	keratin associated protein 24-1	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7952	chrX	42189317	42189517	+	1.84965	NA	intron (NM_021465, intron 1 of 32)	intron (NM_021465, intron 1 of 32)	38716	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4180	chr2	14141894	14142094	+	1.84965	NA	intron (NM_001356337, intron 12 of 12)	intron (NM_001356337, intron 12 of 12)	-32530	NM_001081310	625286	Mm.158781	NM_001081310	ENSMUSG00000061531	Tmem236	2010003H20Rik|Fam23a|Gm613	transmembrane protein 236	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2484	chr14	49255581	49255781	+	1.84965	NA	Intergenic	Intergenic	-10253	NM_025956	67082	Mm.87439	NM_025956	ENSMUSG00000021850	ccdc198	1700011H14Rik	coiled-coil domain containing 198	protein-coding	0.010000	0.398010			-52(TCTTTGGCCTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-581	chr1	178836997	178837197	+	1.84965	NA	intron (NM_001161665, intron 5 of 14)	intron (NM_001161665, intron 5 of 14)	307972	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7344	chr8	79722032	79722232	+	1.84965	NA	intron (NM_026904, intron 3 of 4)	MTE-int|LTR|ERVL-MaLR	10283	NM_001357235	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding	0.015000	0.457711			76(TGTTTCCATTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1623	chr12	42590135	42590335	+	1.84965	NA	Intergenic	Intergenic	443982	NR_148724	102636207		NR_148724		Gm33340	Gm40882	predicted gene, 33340	ncRNA	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2937	chr15	57102696	57102896	+	1.84965	NA	Intergenic	Intergenic	162365	NM_001357930	210463	Mm.26555	NM_172378	ENSMUSG00000022366	Slc22a22	oat-pg	solute carrier family 22 (organic cation transporter), member 22	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3031	chr15	93258570	93258770	+	1.84715	NA	intron (NM_001357006, intron 3 of 6)	ORR1C1|LTR|ERVL-MaLR	16509	NM_001033275	223827	Mm.22819	NM_001033275	ENSMUSG00000036197	Gxylt1	Glt8d3|Gm1228|Gm87	glucoside xylosyltransferase 1	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3582	chr17	71353012	71353212	+	1.84715	NA	intron (NM_028887, intron 45 of 47)	intron (NM_028887, intron 45 of 47)	-11308	NR_028023	100043644	Mm.362377	NR_028023	ENSMUSG00000117199	Gm4566	-	ubiquitin specific peptidase 16 pseudogene	pseudo	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-997	chr10	106115657	106115857	+	1.84715	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	274278	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5421	chr4	34867189	34867389	+	1.84715	NA	intron (NM_013889, intron 1 of 7)	intron (NM_013889, intron 1 of 7)	15659	NM_013889	30046	Mm.38193	NM_013889	ENSMUSG00000039967	Zfp292	5730450D02Rik|5830493J20Rik|9430062L07Rik|AI449016|Krox-10|Zfp-15|Zfp15|Zn-15|Zn-16|mKIAA0530	zinc finger protein 292	protein-coding	0.005000	0.238806			-28(CTTTCCAAAATAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5319	chr3	158840758	158840958	+	1.84493	NA	Intergenic	Intergenic	-235506	NR_040750	624759	Mm.491054	NR_040750	ENSMUSG00000106053	Gm20752	-	predicted gene, 20752	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3621	chr17	80878125	80878325	+	1.84493	NA	Intergenic	Intergenic	-18568	NR_131127	320784	Mm.474182	NR_131127	ENSMUSG00000112121	C230072F16Rik	-	RIKEN cDNA C230072F16 gene	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-128	chr1	43856529	43856729	+	1.84493	NA	Intergenic	BGLII_B|LTR|ERVK	-28790	NR_160749	67883	Mm.387202	NM_026430	ENSMUSG00000057363	Uxs1	1600025I13Rik|AI451869|AI649125|AW550562	UDP-glucuronate decarboxylase 1	protein-coding	0.005000	0.452736			2(GAATTATGATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5948	chr5	51125839	51126039	+	1.84493	NA	Intergenic	Intergenic	427982	NM_008904	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7944	chrX	36103138	36103338	+	1.84493	NA	Intergenic	Intergenic	-8870	NM_133990	16164	Mm.24208	NM_133990	ENSMUSG00000017057	Il13ra1	AI882074|CD213a1|IL-13R-alpha-1|IL-13r[a]|Il13ra|NR4	interleukin 13 receptor, alpha 1	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6934	chr7	83470800	83471000	+	1.84493	NA	Intergenic	Intergenic	-114031	NM_177695	233424	Mm.486619	NM_177695	ENSMUSG00000038540	Tmc3	9030203A06	transmembrane channel-like gene family 3	protein-coding	0.005000	0.373134		5(TGTGCATATTTATT,-,0.00)	25(ATTTACATGAAAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6843	chr7	49819634	49819834	+	1.84493	NA	intron (NM_133740, intron 11 of 15)	intron (NM_133740, intron 11 of 15)	41376	NM_133740	71974	Mm.33202	NM_133740	ENSMUSG00000030505	Prmt3	2010005E20Rik|2410018A17Rik|AL033309|Hrmt1l3	protein arginine N-methyltransferase 3	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4899	chr3	31732070	31732270	+	1.84493	NA	Intergenic	L1MC1|LINE|L1	-170533	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-349	chr1	124811029	124811229	+	1.84493	NA	Intergenic	MLTR25A|LTR|ERVK	624598	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7146	chr8	10575713	10575913	+	1.84493	NA	intron (NM_001319151, intron 32 of 34)	intron (NM_001319151, intron 32 of 34)	306641	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4211	chr2	22914454	22914654	+	1.84493	NA	intron (NM_001355467, intron 5 of 6)	ID_B1|SINE|B4	19032	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2706	chr14	115987825	115988025	+	1.84493	NA	intron (NM_175500, intron 7 of 7)	intron (NM_175500, intron 7 of 7)	-578373	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA	0.000000	0.353234	-77(ACTGAAATATGCATG,+,0.00)		-71(ATATGCATGTAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-925	chr10	88790814	88791014	+	1.84493	NA	intron (NM_175158, intron 25 of 61)	ID_B1|SINE|B4	35900	NM_175158	70683	Mm.29631	NM_175158	ENSMUSG00000004356	Utp20	3830408P06Rik|AA617408|Drim|mDRIM|mDRIN	UTP20 small subunit processome component	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-703	chr10	13156169	13156369	+	1.84493	NA	intron (NM_029172, intron 4 of 5)	intron (NM_029172, intron 4 of 5)	21754	NM_029172	75122	Mm.159433	NM_029172	ENSMUSG00000019815	Zc2hc1b	4930519B02Rik|Fam164b	zinc finger, C2HC-type containing 1B	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2153	chr13	76538212	76538412	+	1.84493	NA	intron (NM_030174, intron 1 of 20)	intron (NM_030174, intron 1 of 20)	153351	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6643	chr6	106263311	106263511	+	1.84493	NA	intron (NM_001109749, intron 5 of 25)	MARNA|DNA|TcMar-Mariner	144469	NM_001364565	269784	Mm.321683	NM_173004	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5688	chr4	111139662	111139862	+	1.84493	NA	intron (NM_001284190, intron 5 of 12)	(TG)n|Simple_repeat|Simple_repeat	-275244	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0.005000	0.417910			35(ATTTTGCTATTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-409	chr1	139026598	139026798	+	1.84493	NA	intron (NM_001166501, intron 3 of 21)	intron (NM_001166501, intron 3 of 21)	49041	NR_108103	78229	Mm.437838	NR_108103	ENSMUSG00000104900	4930596I21Rik	-	RIKEN cDNA 4930596I21 gene	ncRNA	0.000000	0.288557			34(ATATTTTCATGTTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5382	chr4	24218947	24219147	+	1.84493	NA	Intergenic	Intergenic	-277404	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2932	chr15	54385105	54385305	+	1.84493	NA	Intergenic	Intergenic	-25569	NM_173422	239447	Mm.82400	NM_173422	ENSMUSG00000038591	Colec10	CL-L1	collectin sub-family member 10	protein-coding	0.000000	0.308458			-39(TTATTTTCATACTAAT,+,0.00),18(AATTGCAAAAAAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5838	chr5	16324990	16325190	+	1.84493	NA	intron (NM_001110843, intron 19 of 38)	intron (NM_001110843, intron 19 of 38)	-228405	NM_001289459	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1552	chr12	15093381	15093581	+	1.84493	NA	Intergenic	Intergenic	-43092	NR_045960	73972	Mm.107680	NR_045960	ENSMUSG00000113644	4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-481	chr1	156913025	156913225	+	1.84493	NA	intron (NM_001159965, intron 1 of 19)	intron (NM_001159965, intron 1 of 19)	26262	NM_001357392	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding	0.010000	0.393035			32(ATTTAAAAGGCAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1636	chr12	44948718	44948918	+	1.84493	NA	intron (NM_144552, intron 2 of 5)	intron (NM_144552, intron 2 of 5)	125665	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.000000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4584	chr2	125225778	125225978	+	1.84493	NA	intron (NM_183354, intron 24 of 26)	intron (NM_183354, intron 24 of 26)	-21370	NM_001159646	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2074	chr13	52947477	52947677	+	1.84493	NA	Intergenic	RLTR20B4_MM|LTR|ERVK	-17900	NM_016709	11992	Mm.252034	NM_016709	ENSMUSG00000021460	Auh	C77140|W91705	AU RNA binding protein/enoyl-coenzyme A hydratase	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7808	chr9	92341040	92341240	+	1.84493	NA	intron (NM_001033184, intron 1 of 6)	intron (NM_001033184, intron 1 of 6)	31763	NM_001033184	78459	Mm.179195	NM_001033184	ENSMUSG00000074139	1700057G04Rik	-	RIKEN cDNA 1700057G04 gene	protein-coding	0.010000	0.368159			63(TCCTTCTTGTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2842	chr15	29254481	29254681	+	1.84493	NA	Intergenic	L1MA6|LINE|L1	458823	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	ncRNA	0.000000	0.233831		31(TTTGAATATGTATT,+,0.00)	55(TTTTATTTTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6860	chr7	55558882	55559082	+	1.84493	NA	Intergenic	Intergenic	-209202	NM_178706	233274	Mm.44425	NM_178706	ENSMUSG00000051504	Siglech	6430529G09Rik|Siglec-H	sialic acid binding Ig-like lectin H	protein-coding	0.000000	0.343284			25(ATTTGAATGAATATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6855	chr7	54274992	54275192	+	1.84493	NA	Intergenic	Intergenic	-383203	NR_105746	102466619		NR_105746	ENSMUSG00000099176	Mir6238	Gm27982|mmu-mir-6238	microRNA 6238	ncRNA	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6186	chr5	128620262	128620462	+	1.84252	NA	Intergenic	Intergenic	19256	NM_175284	93897	Mm.197628	NM_175284	ENSMUSG00000081683	Fzd10	Fz-10	frizzled class receptor 10	protein-coding	0.025000	0.407960			-31(TATTTGCTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2002	chr13	29610381	29610581	+	1.84252	NA	intron (NR_131896, intron 9 of 16)	intron (NR_131896, intron 9 of 16)	245192	NM_144536	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6892	chr7	68549309	68549509	+	1.84252	NA	Intergenic	Intergenic	-69047	NR_003648	384639	Mm.261760	NM_001013781		Gm5334	EG384639	tetraspanin 7 pseudogene	pseudo	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1432	chr11	101296739	101296939	+	1.84252	NA	intron (NM_001359819, intron 2 of 10)	intron (NM_001359819, intron 2 of 10)	5447	NM_001359819	56208	Mm.178947	NM_019584	ENSMUSG00000035086	Becn1	Atg6	beclin 1, autophagy related	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3757	chr18	26506584	26506784	+	1.84252	NA	Intergenic	Intergenic	-752527	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6011	chr5	68648999	68649199	+	1.84252	NA	Intergenic	Intergenic	617264	NM_001018019	433899	Mm.332422	NM_001018019	ENSMUSG00000068082	Grxcr1	Tg(Eno2-Gabrb3)0370Brll|pi|tde	glutaredoxin, cysteine rich 1	protein-coding	0.000000	0.318408			20(ACTTTATATTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4308	chr2	53586042	53586242	+	1.84239	NA	Intergenic	MTD|LTR|ERVL-MaLR	394058	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding	0.000000	0.358209			-13(ATTTGCATTAAAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2300	chr13	111373618	111373818	+	1.84024	NA	Intergenic	Intergenic	116409	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding	0.030000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7856	chr9	103524736	103524936	+	1.83721	NA	intron (NM_001359465, intron 2 of 4)	intron (NM_001359465, intron 2 of 4)	-32254	NR_040764	319215	Mm.425597	NR_040764	ENSMUSG00000099616	4932413F04Rik	-	RIKEN cDNA 4932413F04 gene	ncRNA	0.010000	0.477612	17(TTTGCATAATGAATT,+,0.00),24(AATGAATTATTCATC,+,0.00),24(AATGAATTATTCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1543	chr12	12614170	12614370	+	1.83721	NA	Intergenic	Charlie25|DNA|hAT-Charlie	55647	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3137	chr16	27467336	27467536	+	1.83721	NA	Intergenic	MER70A|LTR|ERVL	78480	NM_026202	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5345	chr4	12694645	12694845	+	1.83721	NA	Intergenic	Intergenic	-212092	NM_173746	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818	triple QxxK/R motif containing	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6593	chr6	94184410	94184610	+	1.83592	NA	intron (NR_130996, intron 1 of 1)	intron (NR_130996, intron 1 of 1)	52932	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7314	chr8	75375751	75375951	+	1.83592	NA	Intergenic	Intergenic	-72843	NM_027944	71831	Mm.443238	NM_027944	ENSMUSG00000031620	Iqcm	1700007B14Rik	IQ motif containing M	protein-coding	0.000000	0.368159			52(ACTCTGCTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7315	chr8	75375817	75376017	+	1.83592	NA	Intergenic	Intergenic	-72777	NM_027944	71831	Mm.443238	NM_027944	ENSMUSG00000031620	Iqcm	1700007B14Rik	IQ motif containing M	protein-coding	0.000000	0.402985			-14(ACTCTGCTATGTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-836	chr8	75375839	75376039	+	1.83592	NA	Intergenic	Intergenic	-72755	NM_027944	71831	Mm.443238	NM_027944	ENSMUSG00000031620	Iqcm	1700007B14Rik	IQ motif containing M	protein-coding	0.000000	0.402985			-36(ACTCTGCTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-92	chr1	29912579	29912779	+	1.83534	NA	Intergenic	Intergenic	226157	NR_157039	102633704		NR_157037		Gm31465	-	predicted gene, 31465	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4760	chr2	160252473	160252673	+	1.83534	NA	Intergenic	Intergenic	74921	NM_001033411	329554	Mm.291144	NM_001033411	ENSMUSG00000074623	Gm826	-	predicted gene 826	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3565	chr17	66975766	66975966	+	1.83534	NA	intron (NM_008984, intron 7 of 30)	intron (NM_008984, intron 7 of 30)	50369	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1367	chr11	77667244	77667444	+	1.83429	NA	Intergenic	Lx9|LINE|L1	-18795	NM_001024205	68564	Mm.428996	NM_001024205	ENSMUSG00000037857	Nufip2	1110001M19Rik|9530056D24Rik|AI256692|AI461731|PIG1|mKIAA1321	nuclear fragile X mental retardation protein interacting protein 2	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1032	chr10	111632420	111632620	+	1.83429	NA	Intergenic	Intergenic	-38247	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA	0.005000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7691	chr9	64709031	64709231	+	1.83429	NA	TTS (NM_001134399)	TTS (NM_001134399)	28625	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding	0.000000	0.308458		-92(AATTAATATGTATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-915	chr10	86218458	86218658	+	1.83429	NA	intron (NM_013722, intron 6 of 13)	intron (NM_013722, intron 6 of 13)	-81854	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding	0.015000	0.462687			12(CATTTCTTTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1918	chr12	119254556	119254756	+	1.83429	NA	Intergenic	RLTR13B3|LTR|ERVK	-16380	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2333	chr14	7772136	7772336	+	1.83429	NA	Intergenic	Intergenic	-45721	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3585	chr17	72356623	72356823	+	1.83429	NA	intron (NM_007439, intron 3 of 28)	intron (NM_007439, intron 3 of 28)	247584	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3764	chr18	29172730	29172930	+	1.83429	NA	Intergenic	Intergenic	-269370	NR_045395	78199	Mm.243850	NR_045395	ENSMUSG00000117554	4930527G23Rik	-	RIKEN cDNA 4930527G23 gene	ncRNA	0.000000	0.303483			-99(CTATTTTCTTACAAAT,+,0.00),-22(TTCTTGTCATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7374	chr8	92174170	92174370	+	1.83429	NA	Intergenic	Intergenic	181850	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1355	chr11	75022090	75022290	+	1.83429	NA	intron (NM_001002764, intron 10 of 18)	Lx5|LINE|L1	43801	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA	0.005000	0.422886			-59(TCCTTGTTATTTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6451	chr6	52870825	52871025	+	1.83429	NA	intron (NM_173406, intron 2 of 4)	intron (NM_173406, intron 2 of 4)	38695	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding	0.010000	0.388060			-67(CCTTTGTAATTCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7419	chr8	103109551	103109751	+	1.83429	NA	Intergenic	Intergenic	237883	NR_036588	69794	Mm.396139	NR_036588	ENSMUSG00000110340	1600027J07Rik	-	RIKEN cDNA 1600027J07 gene	ncRNA	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3371	chr16	88315115	88315315	+	1.83174	NA	Intergenic	Intergenic	-24950	NM_001346964	14805	Mm.5134	NM_010348	ENSMUSG00000022935	Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	glutamate receptor, ionotropic, kainate 1	protein-coding	0.005000	0.303483			-37(TAATAGTCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3034	chr15	93700992	93701192	+	1.83174	NA	Intergenic	Intergenic	-105190	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding	0.025000	0.422886	-98(AATGAATATTTTATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1775	chr12	82649814	82650014	+	1.82670	NA	intron (NM_001282061, intron 1 of 16)	intron (NM_001282061, intron 1 of 16)	32415	NM_001282061	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4964	chr3	59257808	59258008	+	1.82670	NA	intron (NM_177855, intron 29 of 43)	intron (NM_177855, intron 29 of 43)	5077	NM_001357008	70839	Mm.422675	NM_027571	ENSMUSG00000036353	P2ry12	2900079B22Rik|4921504D23Rik|P2Y12	purinergic receptor P2Y, G-protein coupled 12	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4586	chr2	125447512	125447712	+	1.82670	NA	intron (NM_007993, intron 6 of 65)	intron (NM_007993, intron 6 of 65)	58826	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2554	chr14	76168727	76168927	+	1.82524	NA	Intergenic	Intergenic	57936	NM_013745	27275	Mm.21138	NM_013745	ENSMUSG00000022009	Nufip1	Nufip	nuclear fragile X mental retardation protein interacting protein 1	protein-coding	0.015000	0.398010		11(TATACATATTTATT,+,0.00),11(TATACATATTTATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3044	chr15	95812286	95812486	+	1.82478	NA	intron (NM_175344, intron 1 of 19)	intron (NM_175344, intron 1 of 19)	17686	NR_155277	102634389	Mm.440563	NR_155276	ENSMUSG00000078648	LOC102634389	-	uncharacterized LOC102634389	ncRNA	0.010000	0.447761	30(TATGCATAATTTAAA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1677	chr12	57354784	57354984	+	1.82473	NA	intron (NM_001164370, intron 7 of 9)	ORR1C2|LTR|ERVL-MaLR	124459	NM_001164370	73490	Mm.268180	NM_001164370	ENSMUSG00000047022	Mipol1	1700081O04Rik|6030439O22Rik|AU021838|AW536152|D12Ertd19e	mirror-image polydactyly 1	protein-coding	0.005000	0.452736		30(TATGAATATGCGTG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2389	chr14	21011617	21011817	+	1.82473	NA	intron (NM_009502, intron 13 of 20)	intron (NM_009502, intron 13 of 20)	40725	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding	0.000000	0.353234			14(TTTTTATTATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1526	chr12	5840105	5840305	+	1.82473	NA	Intergenic	Intergenic	464485	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4342	chr2	61143650	61143850	+	1.82473	NA	Intergenic	Lx5c|LINE|L1	-168599	NR_045335	100038493	Mm.388076	NR_045335	ENSMUSG00000075325	Gm13582	-	predicted gene 13582	ncRNA	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1622	chr12	42589972	42590172	+	1.82473	NA	Intergenic	Intergenic	444145	NR_148724	102636207		NR_148724		Gm33340	Gm40882	predicted gene, 33340	ncRNA	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8006	chrX	86133922	86134122	+	1.82473	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-57753	NM_007430	11614	Mm.5180	NM_007430	ENSMUSG00000025056	Nr0b1	AHX|Ahc|Ahch|DAX-1|Dax1	nuclear receptor subfamily 0, group B, member 1	protein-coding	0.000000	0.398010			-27(GTTTGAATAAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-870	chr10	68512000	68512200	+	1.82473	NA	intron (NM_028491, intron 4 of 7)	intron (NM_028491, intron 4 of 7)	29775	NM_028491	73287	Mm.141830	NM_028491	ENSMUSG00000019945	Cabcoco1	1700040L02Rik	ciliary associated calcium binding coiled-coil 1	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1392	chr11	87311164	87311364	+	1.82473	NA	intron (NM_177167, intron 1 of 6)	intron (NM_177167, intron 1 of 6)	47730	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7678	chr9	61112018	61112218	+	1.82473	NA	Intergenic	Intergenic	-6732	NR_105026	66785	Mm.158134	NR_105026	ENSMUSG00000111807	4933433G08Rik	-	RIKEN cDNA 4933433G08 gene	ncRNA	0.030000	0.442786			-7(CCATTGATATGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6214	chr5	136511452	136511652	+	1.82473	NA	intron (NM_001291234, intron 1 of 22)	intron (NM_001291234, intron 1 of 22)	54429	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding	0.025000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7040	chr7	117299781	117299981	+	1.82473	NA	Intergenic	MamRep434|DNA|TcMar-Tigger	-81098	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3335	chr16	78954602	78954802	+	1.82473	NA	intron (NM_178855, intron 26 of 26)	RMER20B|LTR|ERVK	23754	NM_139134	246048	Mm.77895	NM_139134	ENSMUSG00000022860	Chodl	3110074E07Rik|MT75|PRED12	chondrolectin	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8152	chrX	164734066	164734266	+	1.82473	NA	Intergenic	Intergenic	236263	NM_027027	69299	Mm.79031	NM_027027	ENSMUSG00000031384	Asb9	1700011M07Rik	ankyrin repeat and SOCS box-containing 9	protein-coding	0.000000	0.383085			-30(CTTTTTATATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2497	chr14	59595025	59595225	+	1.82473	NA	intron (NR_153387, intron 2 of 10)	MIR|SINE|MIR	2834	NM_027986	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-843	chr10	58477192	58477392	+	1.82308	NA	exon (NM_011240, exon 20 of 29)	exon (NM_011240, exon 20 of 29)	-20645	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding	0.005000	0.393035			-47(CCTTGATTATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2615	chr14	88411160	88411360	+	1.82235	NA	Intergenic	Intergenic	60136	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0.000000	0.303483	30(CATTCATTATTCATT,+,0.00),30(CATTCATTATTCATT,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-688	chr5	88734888	88735088	+	1.81884	NA	intron (NM_026735, intron 1 of 5)	B3|SINE|B2	14117	NM_026735	68473	Mm.35764	NM_026735	ENSMUSG00000006262	Mob1b	1110003E08Rik|AU015450|B230364F10|Mobkl1a	MOB kinase activator 1B	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3143	chr16	28939153	28939353	+	1.81759	NA	Intergenic	Intergenic	-9555	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3214	chr16	49089870	49090070	+	1.81619	NA	intron (NM_001166210, intron 9 of 40)	intron (NM_001166210, intron 9 of 40)	32570	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding	0.005000	0.358209			43(GTATGCATAAGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6937	chr7	83820455	83820655	+	1.81619	NA	Intergenic	Intergenic	-25716	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	Cfap161	1700026D08Rik|AW047638|AW551802	cilia and flagella associated protein 161	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2287	chr13	109713965	109714165	+	1.81619	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-189744	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.010000	0.343284			-1(ATTTTGCCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6587	chr6	92461687	92461887	+	1.81619	NA	intron (NM_001081146, intron 2 of 8)	intron (NM_001081146, intron 2 of 8)	19605	NM_001134460	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-226	chr1	82407435	82407635	+	1.81619	NA	intron (NM_029777, intron 6 of 6)	intron (NM_029777, intron 6 of 6)	68486	NM_001122685	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding	0.000000	0.363184	-23(TATGAATAATGTAGG,+,0.00),-23(TATGAATAATGTAGG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5997	chr5	65620818	65621018	+	1.81619	NA	intron (NM_001081321, intron 28 of 32)	B1_Mm|SINE|Alu	77318	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|B230308N11Rik|E230024D05Rik	PDS5 cohesin associated factor A	protein-coding	0.005000	0.368159			74(TTATTTTTATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7198	chr8	34492634	34492834	+	1.81576	NA	Intergenic	Intergenic	147582	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA	0.020000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7544	chr9	17100296	17100496	+	1.81576	NA	Intergenic	Intergenic	-598342	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-355	chr1	126413834	126414034	+	1.81576	NA	intron (NM_172484, intron 2 of 14)	intron (NM_172484, intron 2 of 14)	78993	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5219	chr3	136989097	136989297	+	1.81576	NA	Intergenic	Intergenic	-300420	NR_163863									0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5686	chr4	109768597	109768797	+	1.81576	NA	intron (NM_007983, intron 7 of 18)	intron (NM_007983, intron 7 of 18)	92070	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2119	chr13	68935511	68935711	+	1.81576	NA	intron (NM_153534, intron 2 of 24)	intron (NM_153534, intron 2 of 24)	63930	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding	0.015000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5860	chr5	23074595	23074795	+	1.81576	NA	intron (NM_029990, intron 1 of 2)	intron (NM_029990, intron 1 of 2)	-327811	NR_027362	330052	Mm.459265	NR_027362	ENSMUSG00000105076	A930003O13Rik	-	RIKEN cDNA A930003O13 gene	ncRNA	0.020000	0.368159			69(CGTTTGTTGTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6408	chr6	38778645	38778845	+	1.81576	NA	intron (NM_001294144, intron 2 of 14)	intron (NM_001294144, intron 2 of 14)	58566	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4244	chr2	30870995	30871195	+	1.81576	NA	intron (NM_009116, intron 1 of 3)	intron (NM_009116, intron 1 of 3)	25728	NM_009116	20204	Mm.1802	NM_009116	ENSMUSG00000039476	Prrx2	Prx2|S8	paired related homeobox 2	protein-coding	0.015000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5238	chr3	141198720	141198920	+	1.81576	NA	Intergenic	Intergenic	13535	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6028	chr5	73756606	73756806	+	1.81576	NA	Intergenic	Intergenic	105326	NM_178387	73472	Mm.87067	NM_178387	ENSMUSG00000029155	Spata18	1700067I02Rik	spermatogenesis associated 18	protein-coding	0.005000	0.343284			-64(ATTAACATAATCATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-278	chr1	94040583	94040783	+	1.81576	NA	intron (NM_008798, intron 3 of 4)	intron (NM_008798, intron 3 of 4)	11870	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6864	chr7	56348641	56348841	+	1.81576	NA	intron (NR_157031, intron 17 of 22)	intron (NR_157031, intron 17 of 22)	108982	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p|p<cas>	oculocutaneous albinism II	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4828	chr3	7600465	7600665	+	1.81576	NA	intron (NM_001313889, intron 3 of 6)	intron (NM_001313889, intron 3 of 6)	12328	NM_001313890	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding	0.000000	0.417910			-40(CCTTTGTCTTGCTAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7711	chr9	69374427	69374627	+	1.81576	NA	intron (NM_013646, intron 8 of 10)	intron (NM_013646, intron 8 of 10)	-10280	NR_136934	102642202	Mm.415363	NR_136934	ENSMUSG00000086648	Gm15511	-	predicted gene 15511	ncRNA	0.010000	0.383085			17(ATGTGCATCATAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2480	chr14	48352780	48352980	+	1.81576	NA	Intergenic	RLTR19|LTR|ERVK	-93243	NM_001310584	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3187	chr16	42203624	42203824	+	1.81576	NA	Intergenic	MER2|DNA|TcMar-Tigger	99745	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA	0.000000	0.278607			-5(TTATTCTTATGTAATT,+,0.00),47(ATTTGCATTACACTAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2845	chr15	30364652	30364852	+	1.81576	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	192218	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4775	chr2	165337106	165337306	+	1.81576	NA	Intergenic	MIR|SINE|MIR	-10727	NM_207706	140579	Mm.35064	NM_080287	ENSMUSG00000017670	Elmo2	1190002F24Rik|CED-12	engulfment and cell motility 2	protein-coding	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7675	chr9	59648511	59648711	+	1.81576	NA	intron (NM_029922, intron 20 of 23)	L2b|LINE|L2	-7757	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1054	chr10	115224520	115224720	+	1.81576	NA	intron (NM_025706, intron 5 of 16)	intron (NM_025706, intron 5 of 16)	26873	NM_025706	66687	Mm.22252	NM_025706	ENSMUSG00000020130	Tbc1d15	4432405K22Rik|AU022358|AU023730|AW557774|Ly6dl|Rab7-GAP	TBC1 domain family, member 15	protein-coding	0.005000	0.308458			-7(CTTTAAATGATAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-567	chr1	176088339	176088539	+	1.81576	NA	intron (NM_001357846, intron 2 of 8)	intron (NM_001357846, intron 2 of 8)	125503	NM_001357845	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding	0.020000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-298	chr1	105246252	105246452	+	1.81576	NA	Intergenic	Intergenic	-109655	NR_151539	100504568	Mm.321153	NR_151538	ENSMUSG00000097482	Gm17634	-	predicted gene, 17634	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7859	chr9	104170914	104171114	+	1.81576	NA	intron (NM_001163026, intron 45 of 55)	intron (NM_001163026, intron 45 of 55)	-44371	NM_145700	252837	Mm.269254	NM_145700	ENSMUSG00000079355	Ackr4	A630091E18Rik|CCBP2|CCR11|CCX-CKR|CCX-CKR1|Ccrl1|Cmkbrl1|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5758	chr4	134528121	134528321	+	1.81576	NA	intron (NM_001256112, intron 6 of 6)	intron (NM_001256112, intron 6 of 6)	6875	NM_001355188	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5012	chr3	74623863	74624063	+	1.81576	NA	Intergenic	RLTR28B|LTR|ERVL	519809	NM_001310529	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	zinc finger, B-box domain containing	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8062	chrX	111604597	111604797	+	1.81576	NA	intron (NM_001290459, intron 4 of 8)	B4|SINE|B4	-66738	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding	0.000000	0.378109			72(ATTTGCAAGGCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6438	chr6	49147339	49147539	+	1.81576	NA	intron (NM_023670, intron 3 of 14)	intron (NM_023670, intron 3 of 14)	67515	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-387	chr1	134845770	134845970	+	1.81576	NA	intron (NM_001081307, intron 13 of 24)	MER3|DNA|hAT-Charlie	-42028	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory subunit 12B	protein-coding	0.000000	0.373134			-76(CTTTGTATAATAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7497	chr8	127838530	127838730	+	1.81576	NA	Intergenic	Intergenic	439595	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5064	chr3	92714128	92714328	+	1.81576	NA	Intergenic	L1M2|LINE|L1	-5154	NM_026811	68694	Mm.290624	NM_026811	ENSMUSG00000068889	Lce1e	1110031B11Rik|AI507275	late cornified envelope 1E	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6581	chr6	89581772	89581972	+	1.81404	NA	intron (NM_001167736, intron 1 of 6)	ORR1F|LTR|ERVL-MaLR	13780	NM_025351	66098	Mm.20313	NM_025351	ENSMUSG00000030086	Chchd6	0710001P09Rik|1700021B03Rik|Micos25	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding	0.000000	0.407960			-36(ATAACCATGACAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-277	chr1	93802557	93802757	+	1.81404	NA	promoter-TSS (NM_001105667)	promoter-TSS (NM_001105667)	-723	NM_001105667	21915	Mm.250332	NM_023136	ENSMUSG00000026281	Dtymk	AU044245|CDC8|D10Ertd203e|TMPK|TYPK|Tmk|mtmk	deoxythymidylate kinase	protein-coding	0.000000	0.393035			85(ATGTGCAACACAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5451	chr4	49227858	49228058	+	1.81364	NA	intron (NM_178756, intron 2 of 7)	intron (NM_178756, intron 2 of 7)	168496	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	Plppr1	E130309F12Rik|Lppr1|PRG-3|mKIAA4247	phospholipid phosphatase related 1	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-803	chr10	45132518	45132718	+	1.81364	NA	intron (NM_011156, intron 10 of 14)	intron (NM_011156, intron 10 of 14)	65402	NM_011156	19072	Mm.37294	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PE|PEP|Pop	prolyl endopeptidase	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3950	chr18	79340568	79340768	+	1.81364	NA	Intergenic	Intergenic	-231277	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2282	chr13	109238109	109238309	+	1.81364	NA	intron (NM_011056, intron 3 of 16)	U2|snRNA|snRNA	-86535	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA	0.005000	0.427861			78(GTGTGCATTACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3984	chr18	85709374	85709574	+	1.81364	NA	Intergenic	Intergenic	-685478	NM_001360910	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3222	chr16	50026246	50026446	+	1.81364	NA	intron (NR_045935, intron 3 of 3)	MER5A1|DNA|hAT-Charlie	45886	NR_045001	628951	Mm.428032	NR_045001		Gm6936	-	predicted gene 6936	ncRNA	0.000000	0.402985			43(CATCTCTTATGCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7963	chrX	51290891	51291091	+	1.81364	NA	Intergenic	Intergenic	-85001	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind like splicing factor 3	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4840	chr3	10655877	10656077	+	1.81364	NA	Intergenic	Intergenic	-215847	NM_029068	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2949	chr15	59397325	59397525	+	1.81364	NA	intron (NM_001164604, intron 2 of 4)	ORR1D2|LTR|ERVL-MaLR	23227	NM_026746	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7614	chr9	38407616	38407816	+	1.81364	NA	Intergenic	RLTR13D6|LTR|ERVK	6005	NM_146869	258869	Mm.335067	NM_146869	ENSMUSG00000049098	Olfr147	M3|MOR164-1	olfactory receptor 147	protein-coding	0.005000	0.447761			-18(CCATGGCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4109	chr19	49605957	49606157	+	1.81364	NA	Intergenic	Intergenic	1072589	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.010000	0.363184			6(ATTAACATGACTCAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-204	chr1	71594347	71594547	+	1.81364	NA	intron (NM_001276411, intron 39 of 43)	intron (NM_001276411, intron 39 of 43)	37291	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5652	chr4	102368253	102368453	+	1.81364	NA	intron (NM_019840, intron 1 of 14)	intron (NM_019840, intron 1 of 14)	113414	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5061	chr3	90556617	90556817	+	1.81364	NA	Intergenic	L1ME3D|LINE|L1	15556	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2683	chr14	105833639	105833839	+	1.81364	NA	Intergenic	Intergenic	63080	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty RTK signaling antagonist 2	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-23	chr1	8914652	8914852	+	1.81364	NA	intron (NM_027671, intron 3 of 20)	Lx8b|LINE|L1	385125	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5792	chr4	150721343	150721543	+	1.81364	NA	Intergenic	MIR|SINE|MIR	-69269	NM_001355737	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6783	chr7	4394490	4394690	+	1.81364	NA	intron (NM_001163014, intron 1 of 7)	intron (NM_001163014, intron 1 of 7)	3154	NM_001163014	243816	Mm.248662	NM_001163014	ENSMUSG00000078810	Gp6	9830166G18Rik|Gm469|Gpvi	glycoprotein 6 (platelet)	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7357	chr8	82219865	82220065	+	1.81364	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	182621	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3497	chr17	45039860	45040060	+	1.81364	NA	intron (NR_158206, intron 9 of 11)	intron (NR_158206, intron 9 of 11)	-159075	NM_029257	75341	Mm.386821	NM_029257		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6721	chr6	134282623	134282823	+	1.81364	NA	Intergenic	RLTR17|LTR|ERVK	-113606	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding	0.010000	0.378109			-4(GTATTTTGATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7296	chr8	65768978	65769178	+	1.81364	NA	intron (NM_175188, intron 1 of 7)	intron (NM_175188, intron 1 of 7)	150553	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2918	chr15	51811093	51811293	+	1.81364	NA	intron (NM_080635, intron 2 of 7)	intron (NM_080635, intron 2 of 7)	54268	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding	0.015000	0.388060			41(CCATTGTCTTTGTAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4394	chr2	73865020	73865220	+	1.81364	NA	intron (NM_001284371, intron 3 of 11)	L1_Mur3|LINE|L1	27519	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-366	chr1	128382796	128382996	+	1.81364	NA	intron (NM_177445, intron 7 of 15)	intron (NM_177445, intron 7 of 15)	-23191	NM_001313695	17219	Mm.4933	NM_008567	ENSMUSG00000026355	Mcm6	ASP-l1|D1Wsu22e|Mcmd6	minichromosome maintenance complex component 6	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6351	chr6	22577107	22577307	+	1.81364	NA	Intergenic	Intergenic	-221126	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6985	chr7	97164272	97164472	+	1.81364	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	82621	NM_001162477	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3994	chr18	87744456	87744656	+	1.81364	NA	Intergenic	Intergenic	1032245	NM_001361145	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0.000000	0.383085			-73(ATTTGCAAAGCAAAAC,-,0.00),58(GCATTTTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6524	chr6	72175305	72175505	+	1.81364	NA	Intergenic	MERVL_2A-int|LTR|ERVL	-52208	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA	0.000000	0.373134			59(CTTTTATTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1120	chr10	125213847	125214047	+	1.81137	NA	Intergenic	Intergenic	94869	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3659	chr17	90355125	90355325	+	1.80955	NA	intron (NM_001346957, intron 15 of 18)	intron (NM_001346957, intron 15 of 18)	100655	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2473	chr14	47709668	47709868	+	1.80881	NA	intron (NM_008477, intron 27 of 41)	intron (NM_008477, intron 27 of 41)	46012	NM_008477	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding	0.005000	0.442786			8(TCTTTGTTATTTACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4613	chr2	130953365	130953565	+	1.80881	NA	intron (NM_009730, intron 6 of 28)	intron (NM_009730, intron 6 of 28)	46970	NM_009730	11990	Mm.119936	NM_009730	ENSMUSG00000027312	Atrn	AW558010|Mgca|mg	attractin	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2139	chr13	72896423	72896623	+	1.80881	NA	Intergenic	Intergenic	-79760	NR_046196	78446	Mm.244082	NR_046196	ENSMUSG00000113082	D730050B12Rik	-	RIKEN cDNA D730050B12 gene	ncRNA	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2934	chr15	55012860	55013060	+	1.80881	NA	Intergenic	Intergenic	-26097	NR_155513	100039911	Mm.252735	NR_155513	ENSMUSG00000115245	Gm2491	4930478E11Rik	predicted gene 2491	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1899	chr12	116877091	116877291	+	1.80881	NA	intron (NM_011215, intron 9 of 22)	RLTR17B_Mm|LTR|ERVK	274078	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1598	chr12	35314420	35314620	+	1.80881	NA	Intergenic	Intergenic	-119623	NR_030449	751520		NR_030449	ENSMUSG00000076253	Mir680-3	Mirn680-3	microRNA 680-3	ncRNA	0.010000	0.338308			43(TCTTTGTCTTGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5991	chr5	64387082	64387282	+	1.80881	NA	Intergenic	ORR1D2-int|LTR|ERVL-MaLR	80760	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-37	chr1	13261888	13262088	+	1.80881	NA	intron (NM_008678, intron 2 of 22)	intron (NM_008678, intron 2 of 22)	110441	NM_001302702	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6110	chr5	100667013	100667213	+	1.80881	NA	intron (NM_027978, intron 2 of 6)	intron (NM_027978, intron 2 of 6)	7143	NM_027978	71883	Mm.260661	NM_027978	ENSMUSG00000029319	Coq2	2310002F18Rik|PHB:PPT	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	protein-coding	0.000000	0.402985		-37(CATTCATATGCAGA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2262	chr13	104027425	104027625	+	1.80881	NA	intron (NM_029447, intron 12 of 12)	intron (NM_029447, intron 12 of 12)	82089	NM_029447	75805	Mm.127692	NM_029447	ENSMUSG00000021710	Nln	4930472G13Rik|C79345	neurolysin (metallopeptidase M3 family)	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4248	chr2	32044742	32044942	+	1.80881	NA	intron (NM_172268, intron 32 of 35)	intron (NM_172268, intron 32 of 35)	-6104	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8101	chrX	142852834	142853034	+	1.80881	NA	3' UTR (NM_019496, exon 6 of 6)	3' UTR (NM_019496, exon 6 of 6)	113792	NM_019496	56068	Mm.143724	NM_019496	ENSMUSG00000042225	Ammecr1	6230420G18Rik	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5059	chr3	89978047	89978247	+	1.80881	NA	Intergenic	RLTR23|LTR|ERV1	-14809	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	ATPase, class I, type 8B, member 2	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1100	chr10	122308696	122308896	+	1.80881	NA	Intergenic	Intergenic	-139703	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1226	chr11	29779538	29779738	+	1.80881	NA	intron (NM_146016, intron 26 of 41)	L1M2|LINE|L1	46030	NM_176829	216622	Mm.443260	NM_176829	ENSMUSG00000078157	4931440F15Rik	Fem1ab	RIKEN cDNA 4931440F15 gene	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7831	chr9	95058642	95058842	+	1.80881	NA	intron (NM_177909, intron 12 of 15)	intron (NM_177909, intron 12 of 15)	306913	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA	0.000000	0.457711			10(TCATAGCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2884	chr15	41859879	41860079	+	1.80881	NA	non-coding (NR_152565, exon 18 of 18)	non-coding (NR_152565, exon 18 of 18)	9741	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4650	chr2	135874737	135874937	+	1.80881	NA	intron (NM_001355153, intron 3 of 38)	intron (NM_001355153, intron 3 of 38)	109999	NM_001355154	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding	0.005000	0.393035			-63(ATTTGCTTGACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-98	chr1	34409560	34409760	+	1.80851	NA	Intergenic	Intergenic	23539	NR_039562	100628580		NR_039562	ENSMUSG00000092852	Mir5103	mir-5103|mmu-mir-5103|mu-mir-5103	microRNA 5103	ncRNA	0.005000	0.383085			-95(TATTTGCTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-447	chr1	150220808	150221008	+	1.80851	NA	Intergenic	RLTR17|LTR|ERVK	-55960	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA	0.010000	0.477612			-64(CCTTTGTGGTGCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7337	chr8	79105441	79105641	+	1.80851	NA	intron (NM_178267, intron 5 of 14)	intron (NM_178267, intron 5 of 14)	77104	NM_178267	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1521	chr12	5283845	5284045	+	1.80851	NA	intron (NM_001164493, intron 2 of 13)	intron (NM_001164493, intron 2 of 13)	91737	NM_001164493	208439	Mm.388281	NM_001164493	ENSMUSG00000020627	Klhl29	A230106N14Rik|Gm68|Kbtbd9|mKIAA1921	kelch-like 29	protein-coding	0.005000	0.402985			30(ATTTACCAGATAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6974	chr7	93055362	93055562	+	1.80776	NA	Intergenic	ORR1F-int|LTR|ERVL-MaLR	-24417	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6327	chr6	17114836	17115036	+	1.80776	NA	intron (NR_153844, intron 1 of 2)	intron (NR_153844, intron 1 of 2)	49787	NM_207176	21753	Mm.436548	NM_011570	ENSMUSG00000029552	Tes	D6Ertd352e|TESS|Tes1|Tes2|testin2	testis derived transcript	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3358	chr16	85585676	85585876	+	1.80776	NA	Intergenic	Intergenic	-35403	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7723	chr9	72553079	72553279	+	1.80776	NA	intron (NM_001033536, intron 1 of 8)	MER2|DNA|TcMar-Tigger	20939	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7270	chr8	57883964	57884164	+	1.80776	NA	intron (NM_175032, intron 7 of 11)	RLTR13B1|LTR|ERVK	-231009	NM_001167981	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3574	chr17	69588242	69588442	+	1.80776	NA	Intergenic	RLTR13B3|LTR|ERVK	149016	NM_001145192	320722	Mm.400254	NM_001145192	ENSMUSG00000091636	Akain1	A330050F15Rik	A kinase (PRKA) anchor inhibitor 1	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8133	chrX	158766839	158767039	+	1.80776	NA	Intergenic	LTR41|LTR|ERVL	-488843	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6846	chr7	50186247	50186447	+	1.80776	NA	intron (NM_001037906, intron 5 of 19)	MLT1H|LTR|ERVL-MaLR	210997	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6333	chr6	17604947	17605147	+	1.80776	NA	Intergenic	L1M2|LINE|L1	-31963	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5220	chr3	137123901	137124101	+	1.80776	NA	Intergenic	RMER6C|LTR|ERVK	-165616	NR_163863									0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2912	chr15	51572186	51572386	+	1.80776	NA	Intergenic	Intergenic	-176676	NR_045092	100502643	Mm.131987	NR_045092	ENSMUSG00000115654	Gm19303	-	predicted gene, 19303	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-260	chr1	89835427	89835627	+	1.80660	NA	intron (NM_001037136, intron 13 of 16)	intron (NM_001037136, intron 13 of 16)	95649	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6196	chr5	131438861	131439061	+	1.80456	NA	3' UTR (NM_001363480, exon 20 of 20)	3' UTR (NM_001363480, exon 20 of 20)	-24243	NR_152164	545809	Mm.357553	NR_152164	ENSMUSG00000105387	Gm29681	Gm42590	predicted gene, 29681	ncRNA	0.030000	0.388060			32(TTTCTCTTTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6563	chr6	83927663	83927863	+	1.80327	NA	intron (NM_008717, intron 1 of 26)	intron (NM_008717, intron 1 of 26)	13410	NM_001166371	18139	Mm.132392	NM_008717	ENSMUSG00000030016	Zfp638	AI323587|Np220|Zfml|Znf638|mNP220	zinc finger protein 638	protein-coding	0.000000	0.368159			36(TGATTTCAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-272	chr1	93380039	93380239	+	1.80327	NA	intron (NM_207031, intron 3 of 23)	intron (NM_207031, intron 3 of 23)	6243	NM_207031	404545	Mm.297411	NM_207031	ENSMUSG00000034107	Ano7	Ngep|Ngep-L|Pcanap5|Tmem16g	anoctamin 7	protein-coding	0.000000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7422	chr8	103464868	103465068	+	1.80327	NA	Intergenic	Intergenic	-117434	NR_036588	69794	Mm.396139	NR_036588	ENSMUSG00000110340	1600027J07Rik	-	RIKEN cDNA 1600027J07 gene	ncRNA	0.005000	0.412935	-34(GATGCATAATGCATA,+,0.00),-34(GATGCATAATGCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3253	chr16	57292258	57292458	+	1.80327	NA	intron (NM_027651, intron 1 of 7)	intron (NM_027651, intron 1 of 7)	493	NM_027651	71027	Mm.158563	NM_027651	ENSMUSG00000022753	Tmem30c	4933401B01Rik|4933409A18Rik|Cdc50c	transmembrane protein 30C	protein-coding	0.010000	0.398010		-62(AATGCAAATGCATA,+,0.00),-62(AATGCAAATGCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7805	chr9	89375463	89375663	+	1.80327	NA	Intergenic	Intergenic	164179	NM_001359993	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1871	chr12	105774831	105775031	+	1.80327	NA	intron (NM_030187, intron 16 of 17)	L1M2|LINE|L1	-9766	NM_011112	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding	0.020000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-861	chr9	24078118	24078318	+	1.80237	NA	Intergenic	Intergenic	-19800	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.000000	0.417910			46(ATCTAAATGGCAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-167	chr1	57106086	57106286	+	1.80237	NA	Intergenic	Lx5c|LINE|L1	108810	NR_037990	407809	Mm.134505	NR_037990	ENSMUSG00000101429	BC055402	-	cDNA sequence BC055402	ncRNA	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-823	chr10	53505529	53505729	+	1.80157	NA	intron (NR_037973, intron 3 of 3)	intron (NR_037973, intron 3 of 3)	13360	NR_037973	100502868	Mm.297722	NR_037973	ENSMUSG00000112739	Gm20597	B230314j19	predicted gene, 20597	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5009	chr3	72014378	72014578	+	1.80157	NA	Intergenic	Intergenic	953385	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0.005000	0.338308			6(CTTTGAAAAAGAAACC,-,0.00),23(ATTTCCAAAACTAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3578	chr17	70361511	70361711	+	1.79765	NA	intron (NM_001347411, intron 3 of 14)	intron (NM_001347411, intron 3 of 14)	-63181	NM_177639	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	DLG associated protein 1	protein-coding	0.005000	0.412935			2(ATTAGCATGGAAGTGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6836	chr7	46801627	46801827	+	1.79765	NA	exon (NM_008186, exon 2 of 15)	exon (NM_008186, exon 2 of 15)	5056	NM_001291075	14884	Mm.22700	NM_008186	ENSMUSG00000006599	Gtf2h1	62kDa|AW743425|AW822074|BTF2 p62|C77871|p62	general transcription factor II H, polypeptide 1	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-795	chr10	42562353	42562553	+	1.79765	NA	3' UTR (NM_152229, exon 9 of 9)	3' UTR (NM_152229, exon 9 of 9)	21137	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding	0.030000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7750	chr9	79051391	79051591	+	1.79765	NA	Intergenic	Intergenic	435945	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding	0.005000	0.328358			25(ATTTTTTCATTTACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7922	chrX	11899667	11899867	+	1.79765	NA	Intergenic	Intergenic	180786	NM_029510	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding	0.015000	0.562189			-67(CTCAGCAAGAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5842	chr5	17641935	17642135	+	1.79765	NA	intron (NM_013657, intron 2 of 17)	intron (NM_013657, intron 2 of 17)	67219	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding	0.000000	0.298507			-24(ATTAGCAACAAAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5753	chr4	131962289	131962489	+	1.79524	NA	intron (NM_001128607, intron 12 of 17)	intron (NM_001128607, intron 12 of 17)	40618	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-439	chr1	147455639	147455839	+	1.79524	NA	Intergenic	Intergenic	958052	NM_001145807	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding	0.015000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-653	chr4	131962318	131962518	+	1.79524	NA	intron (NM_001128607, intron 12 of 17)	intron (NM_001128607, intron 12 of 17)	40647	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6940	chr7	84379777	84379977	+	1.79517	NA	intron (NM_007488, intron 1 of 18)	intron (NM_007488, intron 1 of 18)	30161	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding	0.010000	0.303483			-61(GTTTACACAACAATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6805	chr7	29071067	29071267	+	1.79372	NA	intron (NM_009109, intron 49 of 105)	intron (NM_009109, intron 49 of 105)	12527	NR_035489	100316710		NR_035489	ENSMUSG00000089219	Mir1963	mir-1963|mmu-mir-1963	microRNA 1963	ncRNA	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5260	chr3	147030687	147030887	+	1.79221	NA	Intergenic	Intergenic	178420	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-513	chr1	164112940	164113140	+	1.79221	NA	Intergenic	Intergenic	-2224	NM_011347	20344	Mm.3337	NM_011347	ENSMUSG00000026580	Selp	CD62P|GMP-140|Grmp|LECAM3|PADGEM	selectin, platelet	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3572	chr17	69062113	69062313	+	1.78993	NA	Intergenic	Intergenic	-13464	NM_001355732	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding	0.005000	0.373134			-26(TTTGTGTTATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6592	chr6	94184298	94184498	+	1.78993	NA	intron (NR_130996, intron 1 of 1)	intron (NR_130996, intron 1 of 1)	53044	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3912	chr18	66287249	66287449	+	1.78943	NA	intron (NM_178793, intron 2 of 10)	intron (NM_178793, intron 2 of 10)	4489	NM_178793	320924	Mm.442049	NM_178793	ENSMUSG00000046318	Ccbe1	4933426F18Rik|9430093N24Rik|mKIAA1983	collagen and calcium binding EGF domains 1	protein-coding	0.010000	0.353234			59(CGATTGTCTTTTACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6207	chr5	132911934	132912134	+	1.78811	NA	Intergenic	Intergenic	-368814	NM_001363480	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0.010000	0.467662			37(ATTTGCAAATGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4098	chr19	45153803	45154003	+	1.78811	NA	intron (NM_021901, intron 2 of 2)	CpG-7577	3188	NM_021901	21908	Mm.391203	NM_021901	ENSMUSG00000025215	Tlx1	Hox-11|Hox11|Tlx-1	T cell leukemia, homeobox 1	protein-coding	0.045000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3489	chr17	42505666	42505866	+	1.78811	NA	3' UTR (NM_028474, exon 4 of 4)	3' UTR (NM_028474, exon 4 of 4)	105547	NM_181753	353344	Mm.184937	NM_181753	ENSMUSG00000043972	Opn5	Gpr136|Neuropsin|PGR12|TMEM13	opsin 5	protein-coding	0.000000	0.283582			-94(CTTTAAAAAACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6173	chr5	124235731	124235931	+	1.78811	NA	intron (NR_045369, intron 4 of 5)	intron (NR_045369, intron 4 of 5)	6106	NR_045369	75927	Mm.410803	NR_045369	ENSMUSG00000090220	Pitpnm2os1	4930568K20Rik	phosphatidylinositol transfer protein, membrane-associated 2, opposite strand 1	ncRNA	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-348	chr1	124787450	124787650	+	1.78811	NA	Intergenic	Intergenic	648177	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4868	chr3	21357262	21357462	+	1.78811	NA	Intergenic	Intergenic	-719290	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2000	chr13	29555235	29555435	+	1.78811	NA	intron (NR_131896, intron 9 of 16)	intron (NR_131896, intron 9 of 16)	300338	NM_144536	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2971	chr15	66591812	66592012	+	1.78811	NA	intron (NM_001081409, intron 2 of 20)	T-rich|Low_complexity|Low_complexity	14340	NM_001081409	239510	Mm.267473	NM_178718	ENSMUSG00000072501	Phf20l1	CGI-72|E130113K22Rik	PHD finger protein 20-like 1	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-709	chr10	14930548	14930748	+	1.78811	NA	Intergenic	Intergenic	170701	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-935	chr10	90915297	90915497	+	1.78811	NA	intron (NM_001359241, intron 20 of 25)	intron (NM_001359241, intron 20 of 25)	85554	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1|AIDA-1b|C030032C09Rik|E530015N03Rik|EB-1|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4705	chr2	144708945	144709145	+	1.78811	NA	intron (NM_025314, intron 4 of 5)	MamRep1879|DNA|hAT-Tip100?	109092	NM_025314	66044	Mm.28109	NM_025314	ENSMUSG00000027430	Dtd1	0610006H08Rik|DTD|DUE-B|Hars2	D-tyrosyl-tRNA deacylase 1	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2367	chr14	14490642	14490842	+	1.78811	NA	Intergenic	Intergenic	144247	NM_008369	16188	Mm.425857	NM_008369	ENSMUSG00000068758	Il3ra	CD123|CDw123|SUT-1	interleukin 3 receptor, alpha chain	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-425	chr1	143035263	143035463	+	1.78811	NA	Intergenic	Intergenic	-605334	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6686	chr6	117223616	117223816	+	1.78811	NA	Intergenic	Intergenic	55181	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding	0.005000	0.298507			46(ATATTTTCATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-590	chr1	181196634	181196834	+	1.78811	NA	intron (NM_145514, intron 6 of 13)	ID4|SINE|ID	15244	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1137	chr11	3363110	3363310	+	1.78717	NA	intron (NM_010718, intron 2 of 15)	intron (NM_010718, intron 2 of 15)	-7069	NM_001034030	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1925	chr13	4032554	4032754	+	1.78717	NA	Intergenic	Intergenic	-26937	NM_134072	105387	Mm.26838	NM_134072	ENSMUSG00000033715	Akr1c14	9030611N15Rik|AW557061	aldo-keto reductase family 1, member C14	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3493	chr17	44702579	44702779	+	1.78717	NA	intron (NM_001146038, intron 5 of 8)	intron (NM_001146038, intron 5 of 8)	33497	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7619	chr9	40759394	40759594	+	1.78717	NA	intron (NM_133733, intron 1 of 6)	intron (NM_133733, intron 1 of 6)	-41782	NM_001364480	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding	0.025000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2009	chr13	30493982	30494182	+	1.78717	NA	Intergenic	Intergenic	51234	NM_025710	66694	Mm.181933	NM_025710	ENSMUSG00000038462	Uqcrfs1	4430402G14Rik|AI875505	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1209	chr11	26583677	26583877	+	1.78717	NA	intron (NM_001252447, intron 2 of 11)	intron (NM_001252447, intron 2 of 11)	10143	NM_001252447	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7253	chr8	53065294	53065494	+	1.78717	NA	Intergenic	RLTR13D6|LTR|ERVK	-446308	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4818	chr2	181357362	181357562	+	1.78717	NA	TTS (NM_001166668)	TTS (NM_001166668)	-7469	NM_144894	229007	Mm.87720	NM_144894	ENSMUSG00000027582	Zgpat	1500006I01Rik|BC021513	zinc finger, CCCH-type with G patch domain	protein-coding	0.000000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-123	chr10	125213890	125214090	+	1.78655	NA	Intergenic	Intergenic	94826	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2707	chr14	116496376	116496576	+	1.78498	NA	intron (NM_175500, intron 7 of 7)	intron (NM_175500, intron 7 of 7)	-428821	NM_001079844	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding	0.005000	0.333333	-16(TCTACATAATTCATA,+,0.00),-16(TCTACATAATTCATA,-,0.00)		-89(GTTTTGTTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5973	chr5	57796554	57796754	+	1.78498	NA	intron (NM_001310608, intron 1 of 3)	MTC|LTR|ERVL-MaLR	78573	NM_001310606	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6067	chr5	85799917	85800117	+	1.78498	NA	Intergenic	Intergenic	265566	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding	0.000000	0.308458		79(CATAAAAATTCATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1291	chr11	52511886	52512086	+	1.78498	NA	Intergenic	Intergenic	115558	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7832	chr9	95066030	95066230	+	1.78498	NA	intron (NM_177909, intron 12 of 15)	intron (NM_177909, intron 12 of 15)	314301	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6746	chr6	139506488	139506688	+	1.78498	NA	Intergenic	B3|SINE|B2	-4679	NM_001128090	632971	Mm.475610	NM_001128090	ENSMUSG00000092164	Rergl	EG632971	RERG/RAS-like	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6200	chr5	132006601	132006801	+	1.78498	NA	intron (NM_001363480, intron 4 of 19)	RMER10B|LTR|ERVL	126432	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1273	chr11	45082489	45082689	+	1.78498	NA	Intergenic	Lx10|LINE|L1	34339	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA	0.000000	0.348259		-57(TATACATATGTATG,+,0.00),-57(TATACATATGTATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6546	chr6	81000314	81000514	+	1.78498	NA	Intergenic	Intergenic	895249	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1113	chr10	123852876	123853076	+	1.78498	NA	Intergenic	Intergenic	588900	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Tafa2	6330575M02|FAM19A2 TAFA-2|Fam19a2|Sam2|Tafa-2	TAFA chemokine like family member 2	protein-coding	0.000000	0.303483			-97(TTTTACTATTGCAAAT,+,0.00),-10(ATTTAAATAAAAATAG,-,0.00),29(ATTTACAGAAGAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1972	chr13	20151149	20151349	+	1.78498	NA	intron (NM_080288, intron 1 of 21)	intron (NM_080288, intron 1 of 21)	60742	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.025000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7593	chr9	31567844	31568044	+	1.78498	NA	Intergenic	Intergenic	-103706	NM_144936	235135	Mm.390134	NM_144936	ENSMUSG00000041737	Tmem45b	BC018222	transmembrane protein 45b	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-427	chr1	143375379	143375579	+	1.78498	NA	Intergenic	Lx6|LINE|L1	-265218	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-126	chr1	43284717	43284917	+	1.78498	NA	Intergenic	BGLII|LTR|ERVK	-88056	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding	0.000000	0.407960			-77(CCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4432	chr2	83773297	83773497	+	1.78498	NA	intron (NM_008402, intron 12 of 29)	ORR1E|LTR|ERVL-MaLR	-39215	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding	0.015000	0.487562			79(GTATTGTTATGTAGAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1647	chr12	49121420	49121620	+	1.78498	NA	Intergenic	Intergenic	-261363	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7849	chr9	100471027	100471227	+	1.78498	NA	intron (NM_001033543, intron 3 of 6)	intron (NM_001033543, intron 3 of 6)	15346	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding	0.020000	0.626866			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3874	chr18	56819938	56820138	+	1.78498	NA	intron (NM_177115, intron 1 of 4)	intron (NM_177115, intron 1 of 4)	105510	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7022	chr7	110703207	110703407	+	1.78453	NA	Intergenic	Intergenic	-64899	NM_001276301	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4481	chr2	102325149	102325349	+	1.78453	NA	intron (NM_020267, intron 4 of 4)	intron (NM_020267, intron 4 of 4)	75651	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5605	chr4	93382200	93382400	+	1.78453	NA	Intergenic	Intergenic	-46789	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5086	chr3	100721828	100722028	+	1.78453	NA	Intergenic	RLTR23|LTR|ERV1	-36455	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3251	chr16	56266133	56266333	+	1.78453	NA	intron (NM_174876, intron 16 of 19)	intron (NM_174876, intron 16 of 19)	61920	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4236	chr2	29468899	29469099	+	1.78453	NA	intron (NM_001290489, intron 2 of 6)	intron (NM_001290489, intron 2 of 6)	6295	NR_105753	102465170		NR_105753	ENSMUSG00000098539	Mir133c	Gm27865|mmu-mir-133c	microRNA 133c	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4906	chr3	34568132	34568332	+	1.78453	NA	intron (NR_015580, intron 2 of 4)	intron (NR_015580, intron 2 of 4)	7851	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5709	chr4	118029877	118030077	+	1.78453	NA	intron (NM_001285520, intron 4 of 11)	intron (NM_001285520, intron 4 of 11)	-100214	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4380	chr2	70756985	70757185	+	1.78453	NA	intron (NR_156421, intron 5 of 6)	intron (NR_156421, intron 5 of 6)	67719	NM_001362963	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding	0.000000	0.278607			-61(GTTTGCATCACAAAGT,-,0.00),28(TAATTGTTTTTTTAAT,+,0.00),42(ATAAAAAAGAGAATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-550	chr3	11328624	11328824	+	1.78395	NA	Intergenic	RMER13B|LTR|ERVK	515635	NR_040751	100038545	Mm.388494	NR_040751	ENSMUSG00000104015	Gm10745	-	predicted gene 10745	ncRNA	0.000000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2018	chr13	34337348	34337548	+	1.78116	NA	intron (NM_001033167, intron 1 of 10)	intron (NM_001033167, intron 1 of 10)	7734	NM_001033167	73102	Mm.23932	NM_001033167	ENSMUSG00000038267	Slc22a23	3110004L20Rik	solute carrier family 22, member 23	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3001	chr15	76877083	76877283	+	1.78116	NA	Intergenic	RLTR13D3|LTR|ERVK	-2070	NM_145916	223669	Mm.38948	NM_145916	ENSMUSG00000033669	Zfp7	KRAB20|KRAB7|Krox-2|Zfp-7|Zfp65|Zfp80|Zfp86-rs1|mszf73-2	zinc finger protein 7	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4623	chr2	132738970	132739170	+	1.78116	NA	intron (NM_001358261, intron 2 of 2)	intron (NM_001358261, intron 2 of 2)	-42572	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1|cgB|sgI	chromogranin B	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3495	chr17	44815758	44815958	+	1.78116	NA	intron (NR_158206, intron 2 of 11)	intron (NR_158206, intron 2 of 11)	-1061	NR_073392	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding	0.005000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-793	chr7	76788709	76788909	+	1.77961	NA	intron (NM_001199224, intron 21 of 22)	intron (NM_001199224, intron 21 of 22)	558922	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0.005000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-105	chr10	108621349	108621549	+	1.77908	NA	intron (NM_001252342, intron 8 of 10)	intron (NM_001252342, intron 8 of 10)	78711	NM_203660	368203	Mm.452758	NM_203660	ENSMUSG00000112039	Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding	0.005000	0.328358			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-91	chr10	58477222	58477422	+	1.77908	NA	exon (NM_011240, exon 20 of 29)	exon (NM_011240, exon 20 of 29)	-20615	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding	0.000000	0.378109			-77(CCTTGATTATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4348	chr2	62795202	62795402	+	1.77749	NA	intron (NM_133207, intron 6 of 15)	intron (NM_133207, intron 6 of 15)	130975	NM_145523	227960	Mm.219877	NM_145523	ENSMUSG00000026893	Gca	5133401E04Rik|AI573844	grancalcin	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8095	chrX	138588795	138588995	+	1.77749	NA	intron (NM_030688, intron 6 of 10)	RLTR13D6|LTR|ERVK	-325535	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2120	chr13	69029359	69029559	+	1.77373	NA	Intergenic	Intergenic	-29918	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5150	chr3	119725860	119726060	+	1.77373	NA	intron (NM_001310711, intron 9 of 13)	intron (NM_001310711, intron 9 of 13)	57428	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.005000	0.268657		5(AATGAATATACATA,+,0.00),5(AATGAATATACATA,-,0.00)	10(ATATACATAAAAAGAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2466	chr14	45184752	45184952	+	1.77306	NA	intron (NM_172597, intron 6 of 20)	Charlie1b|DNA|hAT-Charlie	34573	NM_001310534	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-510	chr1	163627814	163628014	+	1.77070	NA	Intergenic	RLTR13D6|LTR|ERVK	97318	NM_001143956	240879	Mm.484621	NM_001143956	ENSMUSG00000040113	Mettl11b	Gm207|NTM1B	methyltransferase like 11B	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1314	chr11	62360280	62360480	+	1.77070	NA	intron (NM_011308, intron 21 of 44)	intron (NM_011308, intron 21 of 44)	78135	NM_011308	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1690	chr12	63449717	63449917	+	1.77070	NA	Intergenic	Intergenic	762030	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6828	chr7	40033355	40033555	+	1.77070	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	515689	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-444	chr1	149376944	149377144	+	1.77070	NA	Intergenic	Intergenic	545395	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding	0.000000	0.243781			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1994	chr13	28010331	28010531	+	1.77070	NA	Intergenic	L1MA4A|LINE|L1	-5781	NM_011165	19110	Mm.18607	NM_011165	ENSMUSG00000005891	Prl4a1	AA409771|Ghd23|PLP-A|Prlpa	prolactin family 4, subfamily a, member 1	protein-coding	0.005000	0.273632			-13(ATCTACATGTTAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3993	chr18	86927041	86927241	+	1.77070	NA	Intergenic	Intergenic	214830	NM_001361145	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-200	chr1	70676253	70676453	+	1.77070	NA	intron (NM_025728, intron 7 of 7)	intron (NM_025728, intron 7 of 7)	-49362	NM_177164	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding	0.010000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3754	chr18	26268560	26268760	+	1.77070	NA	Intergenic	Intergenic	-514503	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.010000	0.378109		-12(GATACATATTGATT,-,0.00)	-32(CATTTGGAATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4346	chr2	62544636	62544836	+	1.77070	NA	intron (NM_007986, intron 9 of 25)	intron (NM_007986, intron 9 of 25)	29285	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding	0.015000	0.383085			35(GTCTGAAAGAGAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2776	chr15	9415308	9415508	+	1.77070	NA	Intergenic	Intergenic	-20620	NM_029341	75568	Mm.82143	NM_029341	ENSMUSG00000039676	Capsl	1700028N11Rik|AW125205	calcyphosine-like	protein-coding	0.005000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3885	chr18	59007954	59008154	+	1.77070	NA	intron (NM_175506, intron 17 of 22)	intron (NM_175506, intron 17 of 22)	-54327	NM_001167925	225583	Mm.209711	NM_173759	ENSMUSG00000050875	Minar2	A730017C20Rik	membrane integral NOTCH2 associated receptor 2	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4706	chr2	145623253	145623453	+	1.77070	NA	intron (NM_053195, intron 15 of 16)	intron (NM_053195, intron 15 of 16)	-68371	NM_001037929	627302	Mm.445953	NM_001037929		Gm14092	-	predicted gene 14092	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-318	chr1	112742582	112742782	+	1.77070	NA	Intergenic	Intergenic	-325764	NR_157044	102635484		NR_157044		Gm32810	Gm18406	predicted gene, 32810	ncRNA	0.000000	0.373134			32(TTTTTGGTTTTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3196	chr16	43557531	43557731	+	1.77070	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-83024	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA	0.025000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1199	chr11	24708799	24708999	+	1.77070	NA	Intergenic	Intergenic	21823	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	-	predicted gene 10466	ncRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3752	chr18	25963282	25963482	+	1.77070	NA	Intergenic	Intergenic	-209225	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4292	chr2	48974033	48974233	+	1.77070	NA	intron (NM_029924, intron 1 of 16)	intron (NM_029924, intron 1 of 16)	-23899	NM_001355296	26428	Mm.291059	NM_011958	ENSMUSG00000026761	Orc4	Orc4P|Orc4l|mMmORC4	origin recognition complex, subunit 4	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-501	chr1	161840480	161840680	+	1.77070	NA	intron (NR_151684, intron 15 of 24)	intron (NR_151684, intron 15 of 24)	36102	NR_151683	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7600	chr9	32989943	32990143	+	1.77007	NA	Intergenic	MER45B|DNA|hAT-Tip100	-61077	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA	0.000000	0.338308			-52(GTATTGTATAGCAAAT,+,0.00),5(ATTTAAATGTGAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8146	chrX	163653227	163653427	+	1.76849	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-103591	NM_008177	14829	Mm.4687	NM_008177	ENSMUSG00000031364	Grpr	GRP-R	gastrin releasing peptide receptor	protein-coding	0.000000	0.363184	28(CCTGAATAATACATG,+,0.00),28(CCTGAATAATACATG,-,0.00)		-48(ATATGCATGAAAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4541	chr2	116189517	116189717	+	1.76849	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-113521	NR_033447	69974	Mm.440293	NR_033447		2810405F15Rik	-	RIKEN cDNA 2810405F15 gene	ncRNA	0.000000	0.393035			-60(GTTTGAATAAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-732	chr10	23343768	23343968	+	1.76849	NA	intron (NM_001347372, intron 1 of 18)	intron (NM_001347372, intron 1 of 18)	6022	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding	0.000000	0.378109			-7(ATTTGAATAAAAGAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3403	chr16	97940424	97940624	+	1.76849	NA	Intergenic	Intergenic	-17891	NM_174847	207781	Mm.1465	NM_174847	ENSMUSG00000045975	C2cd2	5730563M15|5830404H04Rik|AI314146|AI449533|BF168443|ORF25|mKIAA4045	C2 calcium-dependent domain containing 2	protein-coding	0.010000	0.412935			45(CTTTACATGCCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5245	chr3	143443636	143443836	+	1.76849	NA	Intergenic	Intergenic	200681	NR_040551	320072	Mm.136397	NR_040551	ENSMUSG00000105923	A830019L24Rik	-	RIKEN cDNA A830019L24 gene	ncRNA	0.005000	0.238806			-48(AAATTCTGATGTTAAT,+,0.00),-16(CTATTATAATGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6584	chr6	91547984	91548184	+	1.76849	NA	Intergenic	Intergenic	32049	NM_026309	67678	Mm.246693	NM_026309	ENSMUSG00000034192	Lsm3	1010001J12Rik|2610005D18Rik|6030401D18Rik|SMX4|USS2	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2749	chr14	123624204	123624404	+	1.76849	NA	intron (NM_177393, intron 1 of 43)	intron (NM_177393, intron 1 of 43)	2840	NM_177393	338370	Mm.255348	NM_177393	ENSMUSG00000000197	Nalcn	A530023G15Rik|AI849508|Vgcnl1	sodium leak channel, non-selective	protein-coding	0.000000	0.293532			22(CCTTTATTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7557	chr9	24021702	24021902	+	1.76849	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-76216	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6675	chr6	114266341	114266541	+	1.76849	NA	Intergenic	Intergenic	-16194	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7058	chr7	122984482	122984682	+	1.76800	NA	intron (NM_011247, intron 4 of 17)	intron (NM_011247, intron 4 of 17)	14018	NM_011247	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6, ubiquitin ligase	protein-coding	0.005000	0.338308	-17(AATGCTTAATGCATA,+,0.00),-17(AATGCTTAATGCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1335	chr11	70829130	70829330	+	1.76800	NA	Intergenic	Intergenic	-15531	NM_001291142	54189	Mm.7087	NM_019400	ENSMUSG00000020817	Rabep1	Rab5ep|rabaptin-5|rabaptin-5alpha	rabaptin, RAB GTPase binding effector protein 1	protein-coding	0.030000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-21	chr1	7498745	7498945	+	1.76800	NA	Intergenic	Intergenic	409925	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7835	chr9	96213128	96213328	+	1.76800	NA	intron (NM_178667, intron 2 of 13)	Lx8b|LINE|L1	16953	NM_178667	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2678	chr14	105388397	105388597	+	1.76782	NA	Intergenic	Intergenic	-39062	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1761	chr12	79530383	79530583	+	1.76676	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	233132	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding	0.020000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-864	chr10	67560115	67560315	+	1.76676	NA	Intergenic	Intergenic	9793	NR_155445	105245193	Mm.72938	NR_155444		4930563J15Rik	-	RIKEN cDNA 4930563J15 gene	ncRNA	0.030000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4038	chr19	19083131	19083331	+	1.76676	NA	intron (NM_001043354, intron 1 of 9)	L2a|LINE|L2	27965	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1379	chr11	82569984	82570184	+	1.76676	NA	Intergenic	Intergenic	-63269	NR_033582	791422	Mm.341562	NR_033582	ENSMUSG00000069796	Gm11426	-	predicted gene 11426	ncRNA	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2665	chr14	103378718	103378918	+	1.76676	NA	Intergenic	Intergenic	-32018	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2, E3 ubiquitin protein ligase	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2572	chr14	77678075	77678275	+	1.76676	NA	intron (NM_172813, intron 16 of 18)	intron (NM_172813, intron 16 of 18)	120793	NR_157389	380920	Mm.297771	NM_001033440		Gm1587	-	predicted gene 1587	ncRNA	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4255	chr2	35136434	35136634	+	1.76676	NA	intron (NM_001290635, intron 3 of 8)	intron (NM_001290635, intron 3 of 8)	4300	NM_001290635	26920	Mm.231332	NM_012018	ENSMUSG00000057110	Cntrl	6720467O09Rik|AA968343|Cep1|Cep110|IB3/5|Ma2a8|b2b1468.1Clo|b2b1468Clo	centriolin	protein-coding	0.005000	0.338308			55(TCTTTCTTTTGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2722	chr14	119771325	119771525	+	1.76676	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	22198	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA	0.005000	0.447761		10(CATTTATATTCATT,+,0.00)	3(GCTTTGACATTTATAT,+,0.00),13(TTATATTCATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1730	chr12	71824215	71824415	+	1.76676	NA	Intergenic	Intergenic	-6753	NM_026102	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.020000	0.388060		43(CATTCATATGAATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8056	chrX	106583584	106583784	+	1.76676	NA	intron (NM_001033541, intron 1 of 3)	intron (NM_001033541, intron 1 of 3)	498	NM_001033541	331493	Mm.249319	NM_001033541	ENSMUSG00000073010	Gm5127	B130007I08|EG331493	predicted gene 5127	protein-coding	0.005000	0.333333			-34(ACATTGTCTGGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3153	chr16	31584569	31584769	+	1.76676	NA	Intergenic	Intergenic	-33464	NM_001357870	224098	Mm.125439	NM_001357870		Gm536	Gm1777	predicted gene 536	protein-coding	0.010000	0.383085			42(ACTTTTTCATGGAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4462	chr2	96218431	96218631	+	1.76676	NA	Intergenic	Intergenic	-99638	NM_001363048	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4207	chr2	21810198	21810398	+	1.76676	NA	intron (NM_001004761, intron 7 of 10)	intron (NM_001004761, intron 7 of 10)	-417205	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0.000000	0.328358			8(ATTAACAAAACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7655	chr9	52804860	52805060	+	1.76636	NA	Intergenic	L1MC5a|LINE|L1	125097	NR_045333	382139	Mm.335162	NR_045333	ENSMUSG00000111020	Gm1715	-	predicted gene 1715	ncRNA	0.005000	0.358209			-39(ATTTATACAACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4378	chr2	70105112	70105312	+	1.76636	NA	intron (NM_177376, intron 4 of 34)	intron (NM_177376, intron 4 of 34)	66086	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-306	chr1	106316956	106317156	+	1.76636	NA	intron (NM_133821, intron 3 of 16)	intron (NM_133821, intron 3 of 16)	145187	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-608	chr1	185242587	185242787	+	1.76636	NA	promoter-TSS (NR_034044)	promoter-TSS (NR_034044)	-239	NR_034044	100217449	Mm.429560	NR_034044	ENSMUSG00000077571	Snora36b	MBI-87	small nucleolar RNA, H/ACA box 36B	snoRNA	0.005000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4984	chr3	65455985	65456185	+	1.76497	NA	Intergenic	Intergenic	-63532	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding	0.020000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4463	chr2	96323640	96323840	+	1.76411	NA	intron (NM_001363047, intron 1 of 8)	intron (NM_001363047, intron 1 of 8)	5571	NM_001289743	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4782	chr2	167487307	167487507	+	1.76279	NA	intron (NM_001356523, intron 1 of 3)	L2b|LINE|L2	-5238	NM_030743	81018	Mm.22225	NM_030743	ENSMUSG00000006418	Rnf114	1110008J21Rik|AI225886|AW549494|Zfp228|Zfp313|Znf228	ring finger protein 114	protein-coding	0.025000	0.527363			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-544	chr2	167487282	167487482	+	1.76279	NA	intron (NM_001356523, intron 1 of 3)	L2b|LINE|L2	-5263	NM_030743	81018	Mm.22225	NM_030743	ENSMUSG00000006418	Rnf114	1110008J21Rik|AI225886|AW549494|Zfp228|Zfp313|Znf228	ring finger protein 114	protein-coding	0.025000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2168	chr13	81343162	81343362	+	1.76279	NA	intron (NM_054053, intron 83 of 89)	intron (NM_054053, intron 83 of 89)	289882	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Adgrv1	Frings|Gpr98|Mass1|Mgr1|VLGR1	adhesion G protein-coupled receptor V1	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-654	chr1	194239300	194239500	+	1.76154	NA	Intergenic	Intergenic	-16641	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.005000	0.358209			77(TATTTCTCATACAGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-353	chr15	95812312	95812512	+	1.76123	NA	intron (NM_175344, intron 1 of 19)	intron (NM_175344, intron 1 of 19)	17660	NR_155277	102634389	Mm.440563	NR_155276	ENSMUSG00000078648	LOC102634389	-	uncharacterized LOC102634389	ncRNA	0.015000	0.427861	4(TATGCATAATTTAAA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7769	chr9	81323877	81324077	+	1.76048	NA	Intergenic	Intergenic	-307953	NR_040393	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA	0.000000	0.383085			-91(TCTTTGTTATGGAGAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3185	chr16	41948328	41948528	+	1.76048	NA	intron (NM_001361281, intron 4 of 8)	MER53|DNA|hAT	355041	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-478	chr1	155966880	155967080	+	1.76048	NA	intron (NM_001039184, intron 1 of 37)	intron (NM_001039184, intron 1 of 37)	6275	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4745	chr2	157685266	157685466	+	1.76048	NA	Intergenic	ORR1B2-int|LTR|ERVL-MaLR	-52035	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding	0.005000	0.442786			26(ATCTGCATGAGACTGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5069	chr3	95467463	95467663	+	1.76048	NA	intron (NM_001037737, intron 5 of 21)	B4|SINE|B4	-31647	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4778	chr2	165740409	165740609	+	1.76048	NA	intron (NM_010165, intron 9 of 15)	Tigger10|DNA|TcMar-Tigger	85211	NM_010165	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.015000	0.592040			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4604	chr2	129178648	129178848	+	1.76048	NA	non-coding (NR_045264, exon 3 of 3)	non-coding (NR_045264, exon 3 of 3)	1925	NR_045264	100048701	Mm.428544	NR_045264	ENSMUSG00000084826	AI847159	-	expressed sequence AI847159	ncRNA	0.020000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6647	chr6	106600167	106600367	+	1.76048	NA	intron (NM_001109749, intron 14 of 25)	intron (NM_001109749, intron 14 of 25)	148770	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-379	chr1	130777674	130777874	+	1.76048	NA	intron (NR_151623, intron 2 of 3)	Lx8b|LINE|L1	11390	NR_151623	433347	Mm.325009	NR_151623	ENSMUSG00000100106	Gm28856	-	predicted gene 28856	ncRNA	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3182	chr16	39858980	39859180	+	1.76048	NA	Intergenic	L1_Mus1|LINE|L1	-125284	NM_001361282	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Gm29907|Lam|Lamp	limbic system-associated membrane protein	protein-coding	0.005000	0.437811			81(ATTTGCAAAACACAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6910	chr7	74783260	74783460	+	1.76048	NA	Intergenic	Intergenic	-228580	NM_001038643	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5177	chr3	127512223	127512423	+	1.76048	NA	Intergenic	Intergenic	-13208	NM_001327938	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding	0.025000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-178	chr1	61471443	61471643	+	1.76048	NA	Intergenic	Intergenic	93111	NR_040483	77341	Mm.402964	NR_040483	ENSMUSG00000085447	9530026F06Rik	-	RIKEN cDNA 9530026F06 gene	ncRNA	0.005000	0.343284	54(CATTTATTATGTATA,+,0.00)		54(CATTTATTATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4329	chr2	59141305	59141505	+	1.76048	NA	intron (NM_001001178, intron 1 of 14)	intron (NM_001001178, intron 1 of 14)	19278	NM_001001178	227933	Mm.330234	NM_177650	ENSMUSG00000036641	Ccdc148	5830402J09|Gm38473	coiled-coil domain containing 148	protein-coding	0.015000	0.373134			-75(GACTTGTTTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3807	chr18	40117553	40117753	+	1.76048	NA	Intergenic	Intergenic	101746	NM_023311	67180	Mm.270382	NM_023311	ENSMUSG00000024487	Yipf5	2610311I19Rik|AA408236|Yip1a	Yip1 domain family, member 5	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1663	chr12	53629749	53629949	+	1.76048	NA	intron (NM_001370964, intron 4 of 12)	intron (NM_001370964, intron 4 of 12)	381417	NM_001370960	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1657	chr12	52010187	52010387	+	1.76048	NA	Intergenic	Intergenic	-3780	NM_029545	328092	Mm.2821	NM_029545	ENSMUSG00000020956	Dtd2	4930578F06Rik|6530401N04Rik|ATD|B830049N13Rik	D-tyrosyl-tRNA deacylase 2	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2166	chr13	80743818	80744018	+	1.76048	NA	Intergenic	Intergenic	-139466	NR_153410	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7191	chr8	32437690	32437890	+	1.76048	NA	Intergenic	Intergenic	285895	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	ncRNA	0.000000	0.353234			-92(TTTCTGTTTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4805	chr2	177319156	177319356	+	1.76048	NA	Intergenic	Intergenic	-145486	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420	zinc finger protein 970	protein-coding	0.005000	0.398010	67(ATTCAATTATGCATG,+,0.00),67(ATTCAATTATGCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-781	chr10	39263687	39263887	+	1.76048	NA	Intergenic	L2a|LINE|L2	-99993	NM_001127376	327743	Mm.208111	NM_001127376	ENSMUSG00000062074	Ccn6	Gm735|WISP-3|Wisp3	cellular communication network factor 6	protein-coding	0.010000	0.432836			43(ACATTCTTATGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4700	chr2	144136957	144137157	+	1.76048	NA	Intergenic	Intergenic	52233	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-663	chr1	194861333	194861533	+	1.76048	NA	Intergenic	L1MEf|LINE|L1	39432	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4630	chr2	133363044	133363244	+	1.75936	NA	Intergenic	Intergenic	-189015	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6916	chr7	76788720	76788920	+	1.75859	NA	intron (NM_001199224, intron 21 of 22)	intron (NM_001199224, intron 21 of 22)	558933	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1827	chr12	94691371	94691571	+	1.75768	NA	Intergenic	Intergenic	764133	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA	0.000000	0.422886			56(GATTTTCAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4097	chr19	44882737	44882937	+	1.75327	NA	Intergenic	Intergenic	-46899	NR_045315	73322	Mm.250457	NR_045315	ENSMUSG00000092369	1700039E22Rik	-	RIKEN cDNA 1700039E22 gene	ncRNA	0.030000	0.497512			-24(ATTTGCATGGCAGATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6138	chr5	107148284	107148484	+	1.75327	NA	intron (NM_011578, intron 6 of 16)	intron (NM_011578, intron 6 of 16)	141245	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding	0.015000	0.467662			-47(GTTTACATAACAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2705	chr14	115947650	115947850	+	1.75327	NA	intron (NM_175500, intron 7 of 7)	intron (NM_175500, intron 7 of 7)	-538198	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5096	chr3	103332719	103332919	+	1.75327	NA	intron (NM_053170, intron 11 of 19)	intron (NM_053170, intron 11 of 19)	53526	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding	0.010000	0.402985			7(TTTTTTTTTTTTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1974	chr13	20354657	20354857	+	1.75327	NA	intron (NM_080288, intron 14 of 21)	intron (NM_080288, intron 14 of 21)	-118233	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1813	chr12	91523035	91523235	+	1.75299	NA	TTS (NM_001113404)	TTS (NM_001113404)	66514	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding	0.020000	0.373134			20(AATTAGTGATGCTAAT,+,0.00),68(TTTTTCTCTTGAAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-138	chr1	47014322	47014522	+	1.75299	NA	Intergenic	Intergenic	-88646	NM_001356417	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|Zip10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2001	chr13	29610034	29610234	+	1.75299	NA	intron (NR_131896, intron 9 of 16)	intron (NR_131896, intron 9 of 16)	245539	NM_144536	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding	0.020000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2677	chr14	105388048	105388248	+	1.75256	NA	Intergenic	Intergenic	-39411	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3481	chr17	37454761	37454961	+	1.75215	NA	Intergenic	Intergenic	9381	NM_146465	258457	Mm.377511	NM_146465	ENSMUSG00000059687	Olfr108	MOR156-5	olfactory receptor 108	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5376	chr4	22301568	22301768	+	1.75215	NA	Intergenic	Intergenic	-55875	NR_104378	269514	Mm.40708	NM_172988	ENSMUSG00000040410	Fbxl4	AI836810|FBL4|FBL5	F-box and leucine-rich repeat protein 4	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4157	chr2	6703160	6703360	+	1.75215	NA	intron (NM_001160293, intron 2 of 13)	Lx9|LINE|L1	18402	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding	0.020000	0.457711			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-560	chr3	65455951	65456151	+	1.75037	NA	Intergenic	Intergenic	-63498	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding	0.020000	0.542289			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-196	chr12	75939527	75939727	+	1.75030	NA	intron (NM_001005510, intron 34 of 115)	intron (NM_001005510, intron 34 of 115)	30524	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7373	chr8	91890456	91890656	+	1.74857	NA	Intergenic	Intergenic	-88902	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding	0.000000	0.447761			83(ATTTGGTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8060	chrX	109136767	109136967	+	1.74857	NA	intron (NM_019989, intron 1 of 3)	intron (NM_019989, intron 1 of 3)	41460	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4037	chr19	19082927	19083127	+	1.74857	NA	intron (NM_001043354, intron 1 of 9)	intron (NM_001043354, intron 1 of 9)	28169	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5593	chr4	89363244	89363444	+	1.74857	NA	intron (NR_132431, intron 2 of 9)	B1F|SINE|Alu	-52312	NM_007670	12579	Mm.423094	NM_007670	ENSMUSG00000073802	Cdkn2b	AV083695|INK4b|MTS2|p15|p15(INK4b)|p15INK4b	cyclin dependent kinase inhibitor 2B	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5103	chr3	107650114	107650314	+	1.74857	NA	Intergenic	Intergenic	-18504	NM_153563	229707	Mm.278643	NM_153563	ENSMUSG00000014601	Strip1	6330569M22Rik|6530401O14Rik|Fam40a	striatin interacting protein 1	protein-coding	0.020000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1564	chr12	24929239	24929439	+	1.74857	NA	intron (NM_026037, intron 4 of 12)	Tigger7|DNA|TcMar-Tigger	-45593	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4142	chr19	59950154	59950354	+	1.74857	NA	Intergenic	MLTR18D_MM|LTR|ERVK	-6600	NM_001164367	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-188	chr1	65370259	65370459	+	1.74857	NA	intron (NM_139270, intron 9 of 12)	MER99|DNA|hAT?	59102	NM_139270	213527	Mm.294225	NM_139270	ENSMUSG00000025946	Pth2r	Pthr2	parathyroid hormone 2 receptor	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2821	chr15	22936450	22936650	+	1.74857	NA	Intergenic	RLTR13D6|LTR|ERVK	-99913	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l|Tg(GFAP-APOE_i4)1Hol	cadherin 18	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4141	chr19	59949922	59950122	+	1.74857	NA	Intergenic	MLTR18D_MM|LTR|ERVK	-6368	NM_001164367	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1666	chr12	54233303	54233503	+	1.74857	NA	promoter-TSS (NR_108033)	promoter-TSS (NR_108033)	-212	NR_108033	73592	Mm.416874	NR_108033	ENSMUSG00000112821	1700104L18Rik	-	RIKEN cDNA 1700104L18 gene	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3918	chr18	69086285	69086485	+	1.74857	NA	Intergenic	Intergenic	-64112	NR_105780	102465187		NR_105780	ENSMUSG00000098366	Mir145b	Gm27644|mmu-mir-145b	microRNA 145b	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4645	chr2	135470905	135471105	+	1.74840	NA	intron (NM_019677, intron 32 of 32)	intron (NM_019677, intron 32 of 32)	112215	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4883	chr3	27585809	27586009	+	1.74413	NA	promoter-TSS (NR_037275)	promoter-TSS (NR_037275)	-914	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3316	chr16	73294907	73295107	+	1.74351	NA	Intergenic	Intergenic	631858	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.005000	0.333333		58(ACTGAATATGCATT,+,0.00),58(ACTGAATATGCATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5908	chr5	37869265	37869465	+	1.74351	NA	Intergenic	Intergenic	-24407	NR_153822	102637176	Mm.332343	NR_153822		Gm20052	Gm34055	predicted gene, 20052	ncRNA	0.000000	0.358209		2(CATACATTTGCATG,+,0.00),2(CATACATTTGCATG,-,0.00)	7(ATTTGCATGCTAGATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-493	chr1	160289979	160290179	+	1.74351	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	5893	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA	0.010000	0.348259			-10(ATTTTGTTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4295	chr2	50284904	50285104	+	1.74351	NA	intron (NM_001348198, intron 6 of 7)	intron (NM_001348198, intron 6 of 7)	11797	NM_133839	109129	Mm.29214	NM_133839	ENSMUSG00000026766	Mmadhc	2010311D03Rik|AI314967|CblD	methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8154	chrX	165254791	165254991	+	1.74351	NA	intron (NM_001357099, intron 6 of 9)	intron (NM_001357099, intron 6 of 9)	72502	NM_001357100	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	glycine receptor, alpha 2 subunit	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7962	chrX	49452442	49452642	+	1.74351	NA	Intergenic	L1ME3A|LINE|L1	-11403	NM_001356394	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding	0.005000	0.353234	47(ATTGACTTATGCATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5574	chr4	83648369	83648569	+	1.74351	NA	intron (NM_001355549, intron 10 of 24)	intron (NM_001355549, intron 10 of 24)	122893	NM_001369173	320226	Mm.180032	NM_029117	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6053	chr5	81157153	81157353	+	1.74351	NA	intron (NM_001359828, intron 2 of 26)	intron (NM_001359828, intron 2 of 26)	135660	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.005000	0.363184		20(TATGCATATGTATG,+,0.00),20(TATGCATATGTATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5968	chr5	55876936	55877136	+	1.74351	NA	Intergenic	Intergenic	1527044	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13	predicted gene 10440	ncRNA	0.005000	0.243781			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7989	chrX	75368877	75369077	+	1.74351	NA	intron (NM_001161373, intron 1 of 24)	RLTR12B|LTR|ERVK	11064	NM_007977	14069	Mm.1805	NM_007977	ENSMUSG00000031196	F8	Cf-8|Cf8|FVIII	coagulation factor VIII	protein-coding	0.000000	0.427861			72(ATAAGCATTACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2585	chr14	79648705	79648905	+	1.74351	NA	intron (NM_010701, intron 4 of 6)	intron (NM_010701, intron 4 of 6)	13378	NM_001310655	16840	Mm.46561	NM_010701	ENSMUSG00000022025	Cnmd	Bricd3|ChM-I|Chmd|Lect1	chondromodulin	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7135	chr8	4347775	4347975	+	1.74351	NA	intron (NR_033527, intron 2 of 5)	intron (NR_033527, intron 2 of 5)	-1713	NM_009138	20300	Mm.7275	NM_009138	ENSMUSG00000023235	Ccl25	A130072A22Rik|AI852536|CKb15|Scya25|TECK	chemokine (C-C motif) ligand 25	protein-coding	0.015000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4993	chr3	68456675	68456875	+	1.74351	NA	intron (NM_001113420, intron 1 of 6)	intron (NM_001113420, intron 1 of 6)	-11408	NM_001282045	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0.005000	0.338308			76(TCATTGTGTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4275	chr2	44060907	44061107	+	1.74351	NA	intron (NR_040622, intron 2 of 2)	intron (NR_040622, intron 2 of 2)	4317	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3067	chr16	4194583	4194783	+	1.74351	NA	intron (NM_001025432, intron 1 of 30)	Lx|LINE|L1	18721	NM_001025432	12914	Mm.132238	NM_001025432	ENSMUSG00000022521	Crebbp	AW558298|CBP|CBP/p300|KAT3A|p300/CBP	CREB binding protein	protein-coding	0.005000	0.388060			-54(ATATTAAAAACAATGG,-,0.00),-31(AAATTCTTAGGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3770	chr18	31105121	31105321	+	1.74351	NA	intron (NM_009065, intron 4 of 4)	intron (NM_009065, intron 4 of 4)	211907	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5353	chr4	13879397	13879597	+	1.74351	NA	intron (NM_009822, intron 9 of 10)	intron (NM_009822, intron 9 of 10)	94715	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	RUNX1 translocation partner 1	protein-coding	0.000000	0.313433	-51(AATGCATAATTTAAA,-,0.00)	66(CTTGAATATTCAAA,+,0.00)	-62(ATTAGAATAGGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5604	chr4	93184221	93184421	+	1.74351	NA	Intergenic	Intergenic	151190	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5027	chr3	78530190	78530390	+	1.74351	NA	Intergenic	Intergenic	615456	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0.010000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3760	chr18	26724224	26724424	+	1.74351	NA	Intergenic	Intergenic	-970167	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.000000	0.253731			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7247	chr8	51496097	51496297	+	1.74351	NA	Intergenic	Helitron3Na_Mam|RC|Helitron	-860414	NR_151738	330767	Mm.246790	NR_151738	ENSMUSG00000110013	1190028D05Rik	-	RIKEN cDNA 1190028D05 gene	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-766	chr10	34358032	34358232	+	1.74351	NA	intron (NM_001347463, intron 5 of 10)	intron (NM_001347463, intron 5 of 10)	-31849	NM_009925	12813	Mm.443177	NM_009925	ENSMUSG00000039462	Col10a1	Col10|Col10a-1	collagen, type X, alpha 1	protein-coding	0.000000	0.368159			84(CTTTGCATAAAACAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-916	chr10	86877737	86877937	+	1.74351	NA	intron (NM_138673, intron 45 of 68)	intron (NM_138673, intron 45 of 68)	98832	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3847	chr18	50890351	50890551	+	1.74351	NA	Intergenic	Intergenic	-227447	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding	0.000000	0.417910			-99(CTTAACATAGGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3235	chr16	54855408	54855608	+	1.74351	NA	Intergenic	Intergenic	427729	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-174	chr1	60536287	60536487	+	1.74351	NA	intron (NM_001045513, intron 1 of 13)	intron (NM_001045513, intron 1 of 13)	30378	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1073	chr10	117663289	117663489	+	1.74190	NA	intron (NM_027468, intron 3 of 8)	intron (NM_027468, intron 3 of 8)	33889	NM_027468	70574	Mm.339332	NM_027468	ENSMUSG00000020183	Cpm	1110060I01Rik|5730456K23Rik|AA589379|E030045M14Rik	carboxypeptidase M	protein-coding	0.020000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-867	chr9	32989996	32990196	+	1.74190	NA	Intergenic	MER45B|DNA|hAT-Tip100	-61130	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA	0.000000	0.398010			-48(ATTTAAATGTGAATAT,-,0.00),58(CTTTGAATGACAGAGT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-664	chr5	23920488	23920688	+	1.74083	NA	intron (NM_001310471, intron 10 of 10)	intron (NM_001310471, intron 10 of 10)	68355	NR_028536	100217436		NR_028536		Snord93	Gm22397|MBII-336	small nucleolar RNA, C/D box 93	snoRNA	0.010000	0.402985			-2(GTTAACATGACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5865	chr5	23920549	23920749	+	1.74083	NA	intron (NM_001310471, intron 10 of 10)	intron (NM_001310471, intron 10 of 10)	68416	NR_028536	100217436		NR_028536		Snord93	Gm22397|MBII-336	small nucleolar RNA, C/D box 93	snoRNA	0.000000	0.412935			-63(GTTAACATGACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3040	chr15	95028951	95029151	+	1.74067	NA	intron (NM_178789, intron 6 of 7)	intron (NM_178789, intron 6 of 7)	120267	NR_015482	100043315	Mm.159041	NR_015482	ENSMUSG00000100603	LOC100043315	-	uncharacterized LOC100043315	ncRNA	0.020000	0.368159		-11(AAGGAATATGCATA,+,0.00)	-25(TTTTGCATGACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2818	chr15	22403903	22404103	+	1.74035	NA	Intergenic	Lx2B2|LINE|L1	310981	NM_001165971	545091	Mm.475598	NM_001165971		Hnrnpa1l2-ps2	EG545091|Gm5803	heterogeneous nuclear ribonucleoprotein A1-like 2, pseudogene 2	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4452	chr2	92293305	92293505	+	1.74035	NA	intron (NM_001362832, intron 6 of 18)	MIRb|SINE|MIR	71933	NM_001109690	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|BHC80a|Bhc|Bhc80|D030065N23Rik|PFTF1|mBHC80	PHD finger protein 21A	protein-coding	0.000000	0.393035			0(ATTTGCAAACTAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1529	chr12	6939278	6939478	+	1.74035	NA	Intergenic	Intergenic	440952	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA	0.005000	0.333333			-26(CTGTTGTGATGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3872	chr18	56586029	56586229	+	1.74035	NA	intron (NM_019996, intron 4 of 4)	intron (NM_019996, intron 4 of 4)	-2219	NM_026099	67343	Mm.87057	NM_026099	ENSMUSG00000032900	Tex43	1700065I17Rik|Tseg7	testis expressed 43	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-475	chr1	154822235	154822435	+	1.74035	NA	Intergenic	Intergenic	-96415	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1471	chr11	111843948	111844148	+	1.74035	NA	Intergenic	Intergenic	777884	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3533	chr17	54621911	54622111	+	1.74035	NA	Intergenic	RLTR13B3|LTR|ERVK	-251937	NR_045825	69418	Mm.391004	NR_045825	ENSMUSG00000099747	1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	ncRNA	0.005000	0.393035	-40(CATGAATAATGCAAT,+,0.00),-40(CATGAATAATGCAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4602	chr2	128625585	128625785	+	1.74035	NA	intron (NM_008569, intron 39 of 47)	intron (NM_008569, intron 39 of 47)	33344	NM_001310641	241634	Mm.297682	NM_001310641	ENSMUSG00000074812	Spdye4c	Gm355|SpeedyB3|SpyB3	speedy/RINGO cell cycle regulator family, member E4C	protein-coding	0.005000	0.283582			80(ATTTAAAAAAAAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2646	chr14	99083543	99083743	+	1.74035	NA	intron (NM_001360050, intron 15 of 21)	intron (NM_001360050, intron 15 of 21)	-15781	NM_029320	52023	Mm.22835	NM_029320	ENSMUSG00000022064	Pibf1	-	progesterone immunomodulatory binding factor 1	protein-coding	0.005000	0.348259			-76(ATTTAATTATTCAAAT,+,0.00),64(ATTTACATCACCAGAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8015	chrX	92082015	92082215	+	1.74035	NA	Intergenic	Intergenic	-65782	NM_010759	17145	Mm.377100	NM_010759	ENSMUSG00000062162	Mageb1	MAGE-Xp|Mage-b1|Mage-rs1|Magel1|Smage1|dam1	melanoma antigen, family B, 1	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8043	chrX	102330586	102330786	+	1.74035	NA	intron (NM_027382, intron 9 of 10)	L1M4|LINE|L1	78035	NR_040285	434825	Mm.447373	NR_040285	ENSMUSG00000085568	Gm14858	-	predicted gene 14858	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6823	chr7	38008584	38008784	+	1.74035	NA	intron (NM_011274, intron 1 of 10)	L1M4|LINE|L1	10868	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding	0.020000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7295	chr8	64881938	64882138	+	1.74035	NA	Intergenic	Intergenic	-32114	NM_178633	77113	Mm.350347	NM_178633	ENSMUSG00000031605	Klhl2	6030411N21Rik|8530402H02Rik|ABP-KELCH|AU020744|Mav	kelch-like 2, Mayven	protein-coding	0.010000	0.457711			30(ATTTGAATTGAAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4091	chr19	41492789	41492989	+	1.74035	NA	intron (NM_001370767, intron 2 of 7)	intron (NM_001370767, intron 2 of 7)	10207	NM_001370767	212391	Mm.422910	NM_172154	ENSMUSG00000025019	Lcor	3110023F06Rik|A630025C20Rik|Mlr2|mKIAA1795	ligand dependent nuclear receptor corepressor	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6194	chr5	131349156	131349356	+	1.74035	NA	Intergenic	ID|SINE|ID	-41734	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Galnt17	AA388321|E330012B09Rik|Galnt19|Gcap8|Wbscr17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7556	chr9	23919385	23919585	+	1.74035	NA	Intergenic	Cheshire|DNA|hAT-Charlie	-178533	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.000000	0.323383			24(ATTTTGTTATGTTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6078	chr5	89264220	89264420	+	1.74035	NA	Intergenic	Intergenic	193578	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	vitamin D binding protein	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5624	chr4	97108496	97108696	+	1.74035	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-323436	NM_001081284	620779	Mm.439625	NM_001081284	ENSMUSG00000078639	Gm12695	-	predicted gene 12695	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4841	chr3	10656038	10656238	+	1.74035	NA	Intergenic	CYRA11_Mm|Unknown|Y-chromosome	-216008	NM_029068	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2886	chr15	42009109	42009309	+	1.74035	NA	Intergenic	Intergenic	-139489	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding	0.000000	0.288557	64(AATGAATAAAGCATG,+,0.00),64(AATGAATAAAGCATG,-,0.00)		23(ATTAACATGACTGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6401	chr6	37047501	37047701	+	1.74035	NA	intron (NM_001347104, intron 12 of 32)	L1M2|LINE|L1	-237422	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding	0.000000	0.363184			44(ATATTCAAGAAAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5198	chr3	132833237	132833437	+	1.74035	NA	intron (NM_001163455, intron 25 of 25)	intron (NM_001163455, intron 25 of 25)	45259	NR_102298	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-938	chr10	91504998	91505198	+	1.74035	NA	Intergenic	Intergenic	-284479	NR_151510	102633753	Mm.416936	NR_151510		4930534H03Rik	-	RIKEN cDNA 4930534H03 gene	ncRNA	0.030000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3039	chr15	94869689	94869889	+	1.74035	NA	intron (NM_178789, intron 3 of 7)	intron (NM_178789, intron 3 of 7)	240604	NM_178789	320709	Mm.74873	NM_178789	ENSMUSG00000063296	Tmem117	B930062P21Rik	transmembrane protein 117	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5454	chr4	49689283	49689483	+	1.74003	NA	intron (NM_001033351, intron 6 of 8)	intron (NM_001033351, intron 6 of 8)	-7400	NM_001004025	19059	Mm.46125	NM_001004025	ENSMUSG00000028310	Ppp3r2	CaNB2|CnB2	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type II)	protein-coding	0.005000	0.402985			35(GCTTTCTCATGGAAAC,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-317	chr14	105387988	105388188	+	1.73999	NA	Intergenic	Intergenic	-39471	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4274	chr2	43964024	43964224	+	1.73770	NA	intron (NM_001364029, intron 5 of 12)	intron (NM_001364029, intron 5 of 12)	101200	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5175	chr3	127463228	127463428	+	1.73770	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	35787	NM_001327938	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding	0.025000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6771	chr6	146946811	146947011	+	1.73770	NA	intron (NM_001170433, intron 2 of 27)	Tigger17a|DNA|TcMar-Tigger	7510	NM_028509	73344	Mm.391543	NM_028509	ENSMUSG00000040163	1700034J05Rik	-	RIKEN cDNA 1700034J05 gene	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5430	chr4	36106410	36106610	+	1.73770	NA	intron (NM_001165999, intron 5 of 7)	ORR1C1-int|LTR|ERVL-MaLR	-261306	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.000000	0.348259	18(AATGCAAAATTCATT,+,0.00),18(AATGCAAAATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1721	chr12	71189281	71189481	+	1.73770	NA	intron (NM_029818, intron 23 of 27)	intron (NM_029818, intron 23 of 27)	52533	NM_001163378	76967	Mm.87290	NM_029818	ENSMUSG00000034601	2700049A03Rik	Ta3|Talpid3|mKIAA0586	RIKEN cDNA 2700049A03 gene	protein-coding	0.010000	0.442786		-39(TATGCATATGAATG,+,0.00),-39(TATGCATATGAATG,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-392	chr17	28756527	28756727	+	1.73739	NA	Intergenic	Intergenic	-12690	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3116	chr16	22917515	22917715	+	1.73388	NA	promoter-TSS (NM_001083905)	promoter-TSS (NM_001083905)	-767	NM_001083905	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6654	chr6	108335531	108335731	+	1.73282	NA	intron (NM_010585, intron 4 of 61)	intron (NM_010585, intron 4 of 61)	122535	NM_010585	16438	Mm.227912	NM_010585	ENSMUSG00000030102	Itpr1	D6Pas2|Gm10429|IP3R 1|IP3R1|InsP3R|Ip3r|Itpr-1|P400|Pcp-1|Pcp1|insP3R1|opt|wblo	inositol 1,4,5-trisphosphate receptor 1	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-182	chr1	62447670	62447870	+	1.73282	NA	intron (NM_001081050, intron 19 of 22)	intron (NM_001081050, intron 19 of 22)	-255547	NM_010939	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2274	chr13	107585413	107585613	+	1.73282	NA	Intergenic	Intergenic	-101884	NR_045900	72257	Mm.234155	NR_045900	ENSMUSG00000102000	1700006H21Rik	-	RIKEN cDNA 1700006H21 gene	ncRNA	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5952	chr5	51900326	51900526	+	1.73282	NA	Intergenic	Intergenic	235591	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3767	chr18	30163646	30163846	+	1.73282	NA	Intergenic	Intergenic	-109119	NR_151699	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.010000	0.502488			-65(GTTTGCATAACAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2207	chr13	93072882	93073082	+	1.73282	NA	promoter-TSS (NR_036451)	promoter-TSS (NR_036451)	-322	NR_036451	100502942	Mm.441946	NM_177623	ENSMUSG00000114382	Gm4814	C920025J10|EG218444	predicted gene 4814	ncRNA	0.025000	0.582090			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4513	chr2	109119028	109119228	+	1.73282	NA	intron (NM_029790, intron 5 of 5)	intron (NM_029790, intron 5 of 5)	159162	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0.010000	0.308458			7(ATTTGTATGTGAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4887	chr3	28784255	28784455	+	1.73282	NA	intron (NM_177586, intron 3 of 4)	intron (NM_177586, intron 3 of 4)	3078	NM_177586	208691	Mm.193670	NM_177586	ENSMUSG00000050192	Eif5a2	9630038B20|eIF5AII	eukaryotic translation initiation factor 5A2	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1791	chr12	86295845	86296045	+	1.73282	NA	Intergenic	Intergenic	54087	NM_001324488	70373	Mm.252967	NM_027405	ENSMUSG00000021254	Gpatch2l	1700020O03Rik|4732487G21Rik|A630090I05Rik|Kiaa1152	G patch domain containing 2 like	protein-coding	0.010000	0.437811			-30(ATCTACATGAAAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7101	chr7	134472466	134472666	+	1.73282	NA	Intergenic	Intergenic	-95735	NM_001081331	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding	0.005000	0.298507			48(ATTTGCAACATTAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4393	chr2	73213516	73213716	+	1.73282	NA	intron (NM_025942, intron 1 of 10)	ID4|SINE|ID	831	NM_030091	67059	Mm.22661	NM_025942	ENSMUSG00000027108	Ola1	2510025G09Rik|2810405J23Rik|2810409H07Rik|Gtpbp9|PTD004	Obg-like ATPase 1	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6857	chr7	54408056	54408256	+	1.73282	NA	Intergenic	L1_Mur2|LINE|L1	-427089	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0.005000	0.353234			37(TCATTGTTTTGTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-845	chr10	59259704	59259904	+	1.73282	NA	Intergenic	Intergenic	37882	NM_172939	268301	Mm.3036	NM_172939	ENSMUSG00000098188	Sowahc	4921515A04Rik|9430099J10Rik|Ankrd57|C820004L04Rik	sosondowah ankyrin repeat domain family member C	protein-coding	0.005000	0.402985			8(ATTTGCATGAATACAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4420	chr2	79645718	79645918	+	1.73032	NA	intron (NM_080558, intron 8 of 17)	intron (NM_080558, intron 8 of 17)	10393	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Itprid2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|Ssfa2|mKIAA1927	ITPR interacting domain containing 2	protein-coding	0.005000	0.407960	5(TATGCATAATGTAAT,+,0.00),5(TATGCATAATGTAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1628	chr12	43696417	43696617	+	1.73032	NA	Intergenic	RLTR13D6|LTR|ERVK	513551	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding	0.000000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-904	chrX	103472280	103472480	+	1.73022	NA	intron (NR_001463, intron 1 of 6)	intron (NR_001463, intron 1 of 6)	10853	NR_001463	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA	0.005000	0.457711			36(TTTTTTCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8048	chrX	103472355	103472555	+	1.73022	NA	intron (NR_001463, intron 1 of 6)	intron (NR_001463, intron 1 of 6)	10778	NR_001463	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA	0.005000	0.388060			-39(TTTTTTCCTTGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-231	chr13	20139947	20140147	+	1.72971	NA	intron (NM_080288, intron 1 of 21)	MER2|DNA|TcMar-Tigger	49540	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2438	chr14	33759756	33759956	+	1.72971	NA	Intergenic	Intergenic	51427	NR_131114	218902	Mm.107791	NR_131113	ENSMUSG00000115751	4930503F20Rik	4930453C15	RIKEN cDNA 4930503F20 gene	ncRNA	0.025000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-407	chr17	69062157	69062357	+	1.72965	NA	Intergenic	Intergenic	-13420	NM_001355732	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding	0.000000	0.358209			-70(TTTGTGTTATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-964	chr10	96847085	96847285	+	1.72965	NA	Intergenic	Intergenic	-188583	NR_045358	75301	Mm.108650	NR_045358	ENSMUSG00000111924	4930556N09Rik	-	RIKEN cDNA 4930556N09 gene	ncRNA	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6740	chr6	137945731	137945931	+	1.72965	NA	Intergenic	Intergenic	134085	NM_177787	277898	Mm.269823	NM_177787	ENSMUSG00000044378	Slc15a5	9830102E05Rik	solute carrier family 15, member 5	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7589	chr9	30677116	30677316	+	1.72806	NA	Intergenic	L1ME4a|LINE|L1	243734	NM_001329420	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15	protein-coding	0.000000	0.283582			72(TTTTTTTCTTTCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4494	chr2	106720345	106720545	+	1.72806	NA	intron (NM_001356555, intron 2 of 5)	intron (NM_001356555, intron 2 of 5)	24844	NM_029837	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding	0.025000	0.417910	19(CATGATTTTTGCATG,-,0.00)		25(TTTTGCATGACTATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-781	chr6	146221165	146221365	+	1.72760	NA	intron (NM_019923, intron 45 of 56)	intron (NM_019923, intron 45 of 56)	280958	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5269	chr3	147975361	147975561	+	1.72760	NA	Intergenic	Intergenic	979174	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6303	chr6	10861069	10861269	+	1.72481	NA	Intergenic	L1_Mus3|LINE|L1	113209	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3551	chr17	62949502	62949702	+	1.72481	NA	Intergenic	Intergenic	-68285	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0.020000	0.383085	82(CATGCATGATGTATA,+,0.00),82(CATGCATGATGTATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-299	chr1	105864127	105864327	+	1.72481	NA	Intergenic	L1ME1|LINE|L1	83504	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5152	chr3	119951416	119951616	+	1.72481	NA	Intergenic	Intergenic	-168128	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.005000	0.328358			43(GCTATGTTATGTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1910	chr12	117973189	117973389	+	1.72481	NA	intron (NM_010060, intron 60 of 81)	intron (NM_010060, intron 60 of 81)	129428	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7754	chr9	79729931	79730131	+	1.72481	NA	Intergenic	Intergenic	-11309	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6450	chr6	52779787	52779987	+	1.72481	NA	intron (NM_173406, intron 3 of 4)	intron (NM_173406, intron 3 of 4)	65722	NM_001355596	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2568	chr14	77487747	77487947	+	1.72342	NA	intron (NR_033141, intron 3 of 5)	intron (NR_033141, intron 3 of 5)	19021	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA	0.010000	0.378109	-58(CATTAAAAATTCATA,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2748	chr14	123265245	123265445	+	1.72342	NA	Intergenic	Intergenic	96159	NR_045143	380934	Mm.393838	NR_045143	ENSMUSG00000115016	AA536875	Gm1591	expressed sequence AA536875	ncRNA	0.000000	0.402985			-60(TATTTGTGATTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7099	chr7	134151708	134151908	+	1.72342	NA	intron (NM_007400, intron 2 of 22)	intron (NM_007400, intron 2 of 22)	73289	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-921	chr10	87944547	87944747	+	1.72342	NA	Intergenic	Lx8|LINE|L1	-22024	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5403	chr4	29689503	29689703	+	1.72342	NA	Intergenic	Intergenic	621524	NR_151693	102634169		NR_151693		Gm11917	-	predicted gene 11917	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-769	chr10	35838188	35838388	+	1.72342	NA	Intergenic	RLTR47|LTR|ERVK	-668519	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4407	chr2	76852941	76853141	+	1.72342	NA	intron (NM_011652, intron 129 of 312)	intron (NM_011652, intron 129 of 312)	129506	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1879	chr12	107546146	107546346	+	1.72342	NA	Intergenic	Intergenic	189242	NR_045973	74968	Mm.359821	NR_045973	ENSMUSG00000085641	4930465M20Rik	4930431H15Rik	RIKEN cDNA 4930465M20 gene	ncRNA	0.010000	0.363184		-77(AATGACTATTCATA,+,0.00),-77(AATGACTATTCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6012	chr5	69088778	69088978	+	1.72342	NA	Intergenic	Intergenic	252831	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7742	chr9	77616886	77617086	+	1.72342	NA	Intergenic	Intergenic	-19746	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding	0.010000	0.442786			39(TGATTGTGATGTTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5106	chr3	107995896	107996096	+	1.72342	NA	Intergenic	RLTR13D6|LTR|ERVK	-9576	NM_008183	14863	Mm.440086	NM_008183	ENSMUSG00000040562	Gstm2	Gstb-2|Gstb2	glutathione S-transferase, mu 2	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1978	chr13	20746447	20746647	+	1.72342	NA	Intergenic	Intergenic	-47566	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-539	chr1	171787467	171787667	+	1.72337	NA	intron (NM_013730, intron 3 of 6)	intron (NM_013730, intron 3 of 6)	20435	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4111	chr19	49693844	49694044	+	1.72237	NA	Intergenic	Intergenic	984702	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5433	chr4	36742662	36742862	+	1.72237	NA	intron (NM_001165999, intron 1 of 7)	intron (NM_001165999, intron 1 of 7)	-23799	NM_001166000	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3109	chr16	21728061	21728261	+	1.72237	NA	Intergenic	Intergenic	-33496	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding	0.035000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5428	chr4	36087457	36087657	+	1.72237	NA	intron (NM_001165999, intron 5 of 7)	intron (NM_001165999, intron 5 of 7)	-242353	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4239	chr2	29493588	29493788	+	1.72237	NA	intron (NM_001290489, intron 3 of 6)	intron (NM_001290489, intron 3 of 6)	-18394	NR_105753	102465170		NR_105753	ENSMUSG00000098539	Mir133c	Gm27865|mmu-mir-133c	microRNA 133c	ncRNA	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-192	chr1	66228948	66229148	+	1.72237	NA	intron (NM_008632, intron 2 of 13)	intron (NM_008632, intron 2 of 13)	53719	NM_001039934	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1002	chr10	106966712	106966912	+	1.72237	NA	intron (NM_198636, intron 10 of 10)	intron (NM_198636, intron 10 of 10)	156825	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding	0.005000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-136	chr1	45914673	45914873	+	1.72237	NA	intron (NM_016917, intron 5 of 7)	intron (NM_016917, intron 5 of 7)	10821	NM_016917	53945	Mm.28756	NM_016917	ENSMUSG00000025993	Slc40a1	Dusg|Fpn1|IREG1|MTP|MTP1|Ol5|Pcm|Slc11a3|Slc39a1	solute carrier family 40 (iron-regulated transporter), member 1	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5561	chr4	81502265	81502465	+	1.72237	NA	Intergenic	Intergenic	-15352	NR_030570	100124446		NR_030570	ENSMUSG00000077941	Mir466h	Mirn466h	microRNA 466h	ncRNA	0.005000	0.323383			-67(TTTTTGTTATTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2162	chr13	79063004	79063204	+	1.72237	NA	Intergenic	Intergenic	-864231	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3905	chr18	65066350	65066550	+	1.72237	NA	intron (NM_031881, intron 1 of 29)	intron (NM_031881, intron 1 of 29)	42923	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4927	chr3	44692207	44692407	+	1.72237	NA	Intergenic	MTD|LTR|ERVL-MaLR	685953	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	ncRNA	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2862	chr15	36270736	36270936	+	1.72237	NA	intron (NM_001357631, intron 1 of 7)	B1_Mur2|SINE|Alu	12311	NM_001357631	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-799	chr10	43640968	43641168	+	1.72237	NA	Intergenic	Intergenic	47641	NR_033558	414125	Mm.244305	NR_033558	ENSMUSG00000075184	F930017D23Rik	F830002L21Rik	RIKEN cDNA F930017D23 gene	ncRNA	0.035000	0.502488			-84(ATTTGCAAGGGTAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4717	chr2	149698202	149698402	+	1.72237	NA	Intergenic	Intergenic	-132481	NM_001363096	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|Tmem90b	synapse differentiation inducing 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-196	chr1	67136187	67136387	+	1.72237	NA	intron (NM_001080809, intron 1 of 37)	intron (NM_001080809, intron 1 of 37)	13260	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3188	chr16	42397114	42397314	+	1.72237	NA	Intergenic	Intergenic	-56563	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding	0.005000	0.293532		14(TATGTATATGTATG,+,0.00),14(TATGTATATGTATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7990	chrX	75402073	75402273	+	1.72237	NA	Intergenic	RMER10B|LTR|ERVL	14411	NM_001039373	17763	Mm.16366	NM_001039373	ENSMUSG00000031200	Mtcp1	P13MTCP1	mature T cell proliferation 1	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3296	chr16	68123743	68123943	+	1.72237	NA	Intergenic	Lx9|LINE|L1	-502935	NM_001145977	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.000000	0.313433			67(ATTTTCAGGAAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7433	chr8	107696922	107697122	+	1.72237	NA	Intergenic	Intergenic	-108540	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding	0.035000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3772	chr18	31817306	31817506	+	1.72237	NA	intron (NM_028866, intron 1 of 21)	L1ME1|LINE|L1	13349	NM_001170966	74320	Mm.277705	NM_028866	ENSMUSG00000024400	Wdr33	1110001N06Rik|2310011G05Rik|2810021O11Rik|8430413N20Rik|WDC146	WD repeat domain 33	protein-coding	0.000000	0.298507			-5(GTAGTTTCATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2508	chr14	61531793	61531993	+	1.72237	NA	TTS (NM_001310603)	TTS (NM_001310603)	24993	NM_001310603	66674	Mm.282706	NM_025697	ENSMUSG00000021930	Spryd7	6330409N04Rik|Clld6	SPRY domain containing 7	protein-coding	0.005000	0.323383			23(CTATTCAGATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1166	chr11	13978575	13978775	+	1.72237	NA	Intergenic	RLTR13D6|LTR|ERVK	200366	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-164	chr1	56606257	56606457	+	1.72237	NA	Intergenic	ORR1D2-int|LTR|ERVL-MaLR	31094	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5153	chr3	120200188	120200388	+	1.72237	NA	Intergenic	Intergenic	-416900	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2758	chr15	5557764	5557964	+	1.72237	NA	intron (NR_045274, intron 2 of 4)	intron (NR_045274, intron 2 of 4)	61546	NR_045274	71432	Mm.291087	NR_045274	ENSMUSG00000110018	5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	ncRNA	0.005000	0.368159			-47(ATTTTATTATGTAAAG,+,0.00),62(ACTTTTACTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6630	chr6	102245778	102245978	+	1.72237	NA	intron (NM_008779, intron 10 of 21)	intron (NM_008779, intron 10 of 21)	-20222	NR_131018	75893	Mm.2968	NR_131017	ENSMUSG00000107563	4930587E11Rik	4930523E13Rik|Gm44188	RIKEN cDNA 4930587E11 gene	ncRNA	0.000000	0.353234			-11(CTTTGAAAAAGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1138	chr11	3801118	3801318	+	1.72237	NA	intron (NM_152818, intron 2 of 13)	intron (NM_152818, intron 2 of 13)	-26550	NM_001363164	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1819	chr12	93178027	93178227	+	1.72237	NA	Intergenic	Intergenic	266696	NR_126436	75295	Mm.243878	NR_126436	ENSMUSG00000113164	4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7911	chr9	123843358	123843558	+	1.72237	NA	intron (NM_148925, intron 3 of 18)	intron (NM_148925, intron 3 of 18)	8203	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-365	chr1	128344381	128344581	+	1.72237	NA	intron (NM_001313695, intron 8 of 15)	intron (NM_001313695, intron 8 of 15)	15224	NM_008567	17219	Mm.4933	NM_008567	ENSMUSG00000026355	Mcm6	ASP-l1|D1Wsu22e|Mcmd6	minichromosome maintenance complex component 6	protein-coding	0.030000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7479	chr8	123454014	123454214	+	1.72237	NA	intron (NM_054046, intron 4 of 11)	intron (NM_054046, intron 4 of 11)	10855	NM_001281803	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding	0.005000	0.512438			-27(CAATTCTGTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7202	chr8	35679272	35679472	+	1.72237	NA	TTS (NM_001081279)	TTS (NM_001081279)	-86351	NM_001370844	100502846		NM_001370844	ENSMUSG00000109372	Gm19410	-	predicted gene, 19410	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6699	chr6	119579354	119579554	+	1.72237	NA	intron (NR_155458, intron 18 of 18)	PB1D10|SINE|Alu	-35107	NM_009525	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2659	chr14	101892211	101892411	+	1.72237	NA	intron (NM_201529, intron 11 of 30)	intron (NM_201529, intron 11 of 30)	51688	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding	0.020000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-656	chr4	149312939	149313139	+	1.72072	NA	Intergenic	B1_Mur1|SINE|Alu	-5306	NM_001290995	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-310	chr1	106949381	106949581	+	1.71949	NA	intron (NM_027971, intron 3 of 7)	intron (NM_027971, intron 3 of 7)	10524	NM_001199213	71869	Mm.321740	NM_027971	ENSMUSG00000059956	Serpinb12	2300003F07Rik|4833409F13Rik	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3090	chr16	13353950	13354150	+	1.71949	NA	intron (NM_001122667, intron 3 of 16)	intron (NM_001122667, intron 3 of 16)	-4371	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mrtfb	Gt4-1|MRTF-B|Mkl2|mKIAA1243	myocardin related transcription factor B	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6986	chr7	97373158	97373358	+	1.71949	NA	intron (NM_199035, intron 1 of 12)	RSINE1|SINE|B4	1641	NM_199035	381903	Mm.279683	NM_199035	ENSMUSG00000035704	Alg8	AI447372|Gm1089	asparagine-linked glycosylation 8 (alpha-1,3-glucosyltransferase)	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7771	chr9	81481680	81481880	+	1.71900	NA	Intergenic	Intergenic	-150150	NR_040393	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5910	chr5	39069963	39070163	+	1.71900	NA	Intergenic	Intergenic	-193370	NM_013748	27278	Mm.440845	NM_013748	ENSMUSG00000039315	Clnk	MIST	cytokine-dependent hematopoietic cell linker	protein-coding	0.005000	0.373134			-66(GCCTTGTGATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4684	chr2	141804894	141805094	+	1.71900	NA	intron (NM_001013802, intron 7 of 18)	intron (NM_001013802, intron 7 of 18)	1096470	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.010000	0.348259			69(ATCTTCATCAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5136	chr3	116592737	116592937	+	1.71900	NA	intron (NM_030016, intron 2 of 11)	L1MA8|LINE|L1	2050	NR_152258	229780	Mm.259648	NM_030016	ENSMUSG00000033439	Trmt13	4631408H19Rik|A330067P21|A930028L21Rik|Ccdc76	tRNA methyltransferase 13	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-908	chr10	84501385	84501585	+	1.71900	NA	Intergenic	Intergenic	13192	NR_108059	75804		NR_108059	ENSMUSG00000020033	4930463O16Rik	-	RIKEN cDNA 4930463O16 gene	ncRNA	0.010000	0.467662			42(GTTTACATGACAAGGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3685	chr18	6066039	6066239	+	1.71900	NA	intron (NM_001039692, intron 4 of 18)	ORR1F|LTR|ERVL-MaLR	69959	NM_001039692	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6772	chr6	146968195	146968395	+	1.71900	NA	intron (NM_001170433, intron 2 of 27)	intron (NM_001170433, intron 2 of 27)	-13874	NM_001164236	73344	Mm.391543	NM_028509	ENSMUSG00000040163	1700034J05Rik	-	RIKEN cDNA 1700034J05 gene	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4247	chr2	31593352	31593552	+	1.71900	NA	intron (NM_001363081, intron 3 of 17)	B1_Mm|SINE|Alu	-18969	NR_105964	102466214		NR_105964	ENSMUSG00000098904	Mir6998	Gm28024|mmu-mir-6998	microRNA 6998	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7320	chr8	77256597	77256797	+	1.71900	NA	intron (NM_001363418, intron 21 of 21)	intron (NM_001363418, intron 21 of 21)	195392	NM_001363420	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1719	chr12	70268302	70268502	+	1.71900	NA	intron (NM_001110203, intron 6 of 8)	intron (NM_001110203, intron 6 of 8)	-40103	NR_037248	100526482		NR_037248	ENSMUSG00000078026	Mir466o	Mir4660|mmu-mir-466o	microRNA 466o	ncRNA	0.030000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2407	chr14	25857391	25857591	+	1.71900	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	15336	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding	0.015000	0.527363	-98(CATGCTTAAATCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2729	chr14	120571716	120571916	+	1.71716	NA	Intergenic	Intergenic	93355	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding	0.000000	0.398010	-85(CATGTAGAATGCATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5944	chr5	50178415	50178615	+	1.71716	NA	Intergenic	Intergenic	27182	NR_040696	73965	Mm.243823	NR_040696	ENSMUSG00000104870	4930448I18Rik	-	RIKEN cDNA 4930448I18 gene	ncRNA	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1847	chr12	100407051	100407251	+	1.71320	NA	intron (NM_001033213, intron 7 of 19)	intron (NM_001033213, intron 7 of 19)	113671	NM_001033213	104718	Mm.295441	NM_001033213	ENSMUSG00000033530	Ttc7b	AA408451|Ttc7l1	tetratricopeptide repeat domain 7B	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3000	chr15	76876971	76877171	+	1.71320	NA	Intergenic	RLTR13D3|LTR|ERVK	-2182	NM_145916	223669	Mm.38948	NM_145916	ENSMUSG00000033669	Zfp7	KRAB20|KRAB7|Krox-2|Zfp-7|Zfp65|Zfp80|Zfp86-rs1|mszf73-2	zinc finger protein 7	protein-coding	0.000000	0.412935	-18(ATTGCATTATTCATG,+,0.00),-18(ATTGCATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5588	chr4	87928760	87928960	+	1.71320	NA	intron (NM_027326, intron 2 of 10)	intron (NM_027326, intron 2 of 10)	104547	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6063	chr5	83006166	83006366	+	1.71320	NA	Intergenic	Lx9|LINE|L1	-207201	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mir-1187|mmu-mir-1187	microRNA 1187	ncRNA	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1831	chr12	96873074	96873274	+	1.71317	NA	Intergenic	Intergenic	-825952	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo	0.000000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-905	chrX	109101390	109101590	+	1.71315	NA	intron (NM_019989, intron 1 of 3)	MIRb|SINE|MIR	6083	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4644	chr2	135470654	135470854	+	1.71181	NA	intron (NM_019677, intron 32 of 32)	intron (NM_019677, intron 32 of 32)	112466	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA	0.025000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3620	chr17	80834737	80834937	+	1.71005	NA	Intergenic	L1MB2|LINE|L1	-61956	NR_131127	320784	Mm.474182	NR_131127	ENSMUSG00000112121	C230072F16Rik	-	RIKEN cDNA C230072F16 gene	ncRNA	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3822	chr18	44395720	44395920	+	1.70889	NA	intron (NM_027490, intron 1 of 10)	intron (NM_027490, intron 1 of 10)	15320	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding	0.020000	0.388060			55(GATTTATTTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-983	chr10	103146409	103146609	+	1.70889	NA	intron (NM_001163559, intron 18 of 25)	intron (NM_001163559, intron 18 of 25)	89813	NM_001163559	74978	Mm.483817	NM_029134	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding	0.000000	0.383085			84(CCATTGTGGTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7840	chr9	98375469	98375669	+	1.70889	NA	intron (NM_001357446, intron 2 of 3)	intron (NM_001357446, intron 2 of 3)	-47392	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding	0.000000	0.338308			-48(ATTTACATAAGCAGAA,-,0.00),-18(TATTGGGCATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-813	chr10	50483385	50483585	+	1.70889	NA	Intergenic	BGLII_Mus|LTR|ERVK	-109184	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.000000	0.432836			-22(CCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4569	chr2	122944466	122944666	+	1.70889	NA	Intergenic	Intergenic	162567	NM_021507	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqor	0610039J17Rik|4930557M22Rik|Sqrdl	sulfide quinone oxidoreductase	protein-coding	0.010000	0.363184			-3(ATTTAAATGCCAATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7383	chr8	95131640	95131840	+	1.70889	NA	intron (NM_001145831, intron 3 of 21)	intron (NM_001145831, intron 3 of 21)	10800	NM_010631	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding	0.015000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6863	chr7	56153345	56153545	+	1.70889	NA	exon (NM_010418, exon 41 of 93)	exon (NM_010418, exon 41 of 93)	-86314	NR_157030	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p|p<cas>	oculocutaneous albinism II	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-190	chr1	66160903	66161103	+	1.70889	NA	Intergenic	Intergenic	-14326	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding	0.000000	0.328358			72(CATTTGTCATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7047	chr7	120466942	120467142	+	1.70889	NA	intron (NM_001278944, intron 11 of 29)	intron (NM_001278944, intron 11 of 29)	45341	NM_001278944	233810		NM_001278943	ENSMUSG00000051900	Abca16	AY243472	ATP-binding cassette, sub-family A (ABC1), member 16	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-578	chr1	178441176	178441376	+	1.70889	NA	intron (NM_026626, intron 2 of 6)	ID4_|SINE|ID	35258	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6211	chr5	135485278	135485478	+	1.70889	NA	intron (NM_146001, intron 1 of 30)	intron (NM_146001, intron 1 of 30)	59744	NM_146001	215114	Mm.280805	NM_146001	ENSMUSG00000039959	Hip1	2610109B09Rik|A930014B11Rik|E130315I21Rik|mKIAA4113	huntingtin interacting protein 1	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3523	chr17	52465518	52465718	+	1.70889	NA	Intergenic	Intergenic	137042	NR_155517	108168350	Mm.385076	NR_155517		Gm27217	-	predicted gene 27217	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5960	chr5	53959940	53960140	+	1.70889	NA	Intergenic	Intergenic	-38483	NM_054083	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7397	chr8	97827507	97827707	+	1.70889	NA	Intergenic	Intergenic	-1184280	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	-	predicted gene 15679	ncRNA	0.000000	0.338308	14(CATGAAAAATGTATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2203	chr13	92454266	92454466	+	1.70889	NA	intron (NM_001163627, intron 5 of 5)	ORR1C2|LTR|ERVL-MaLR	28397	NM_175455	218440	Mm.213623	NM_175455	ENSMUSG00000045034	Ankrd34b	6430502M16Rik|DP58	ankyrin repeat domain 34B	protein-coding	0.005000	0.417910			-54(GTTTAAATAAGAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2602	chr14	86788576	86788776	+	1.70853	NA	intron (NM_019670, intron 25 of 27)	intron (NM_019670, intron 25 of 27)	352548	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6267	chr5	150814255	150814455	+	1.70717	NA	Intergenic	ORR1E-int|LTR|ERVL-MaLR	-138252	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding	0.015000	0.427861			11(CCTTTCCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5713	chr4	119029731	119029931	+	1.70717	NA	Intergenic	LTR107_Mam|LTR|LTR	39280	NR_131914	433751	Mm.224312	NR_131914	ENSMUSG00000066060	Gm12866	-	predicted gene 12866	ncRNA	0.025000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-644	chr1	192422280	192422480	+	1.70674	NA	intron (NM_001038607, intron 9 of 10)	intron (NM_001038607, intron 9 of 10)	231603	NM_010600	16510	Mm.4489	NM_010600	ENSMUSG00000058248	Kcnh1	EAG1|Kv10.1|M-eag	potassium voltage-gated channel, subfamily H (eag-related), member 1	protein-coding	0.005000	0.393035			85(ATTTAAAAAAAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2307	chr13	112516192	112516392	+	1.70674	NA	Intergenic	Intergenic	52222	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-734	chr10	23813247	23813447	+	1.70674	NA	intron (NM_001358812, intron 6 of 13)	intron (NM_001358812, intron 6 of 13)	16361	NM_001358812	76306	Mm.294271	NM_183116	ENSMUSG00000037455	Slc18b1	1110021L09Rik	solute carrier family 18, subfamily B, member 1	protein-coding	0.005000	0.457711			-93(ATTAGCATCAAAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2388	chr14	19999687	19999887	+	1.70674	NA	Intergenic	MIR|SINE|MIR	-22538	NM_010315	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5551	chr4	77408849	77409049	+	1.70674	NA	intron (NR_160919, intron 4 of 39)	intron (NR_160919, intron 4 of 39)	802793	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.010000	0.353234			15(ATTTGAATGAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6735	chr6	137540376	137540576	+	1.70599	NA	intron (NM_001271588, intron 1 of 20)	intron (NM_001271588, intron 1 of 20)	-20581	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0.025000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2495	chr14	57932433	57932633	+	1.70523	NA	intron (NM_028643, intron 6 of 11)	intron (NM_028643, intron 6 of 11)	-42197	NM_001360097	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|HK11	zinc finger, DHHC domain containing 20	protein-coding	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6544	chr6	80539464	80539664	+	1.70523	NA	intron (NM_001134743, intron 2 of 2)	intron (NM_001134743, intron 2 of 2)	519921	NM_001347261	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5684	chr4	109192005	109192205	+	1.70523	NA	intron (NM_001368727, intron 1 of 23)	intron (NM_001368727, intron 1 of 23)	10167	NM_133885	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding	0.000000	0.358209		11(TGTGCATATGTATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6279	chr6	3549864	3550064	+	1.70523	NA	intron (NM_001167751, intron 13 of 26)	intron (NM_001167751, intron 13 of 26)	51571	NM_001167751	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6664	chr6	110236056	110236256	+	1.70523	NA	Intergenic	Intergenic	-409356	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding	0.000000	0.273632		-83(TATACATATACATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7900	chr9	117115072	117115272	+	1.70523	NA	intron (NM_001172123, intron 1 of 14)	intron (NM_001172123, intron 1 of 14)	137311	NM_178660	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-396	chr1	136442690	136442890	+	1.70523	NA	Intergenic	Intergenic	-25058	NM_001287179	381293	Mm.458468	NM_001081258	ENSMUSG00000041498	Kif14	D1Ertd367e|E130203M01	kinesin family member 14	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5164	chr3	125072764	125072964	+	1.70523	NA	Intergenic	Lx9|LINE|L1	-331227	NM_022565	64580	Mm.444289	NM_022565	ENSMUSG00000027971	Ndst4	4930439H17Rik	N-deacetylase/N-sulfotransferase (heparin glucosaminyl) 4	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-104	chr1	35973606	35973806	+	1.70523	NA	Intergenic	Intergenic	-94694	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.025000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6755	chr6	141341010	141341210	+	1.70523	NA	non-coding (NR_033555, exon 1 of 1)	non-coding (NR_033555, exon 1 of 1)	557	NR_033555	100093700	Mm.483778	NR_033555	ENSMUSG00000107456	Gm10400	-	predicted gene 10400	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5305	chr3	155850475	155850675	+	1.70523	NA	Intergenic	Lx8b|LINE|L1	-125779	NR_040553	329780	Mm.119000	NR_040553	ENSMUSG00000104553	9330178D15Rik	9330178D15	RIKEN cDNA 9330178D15 gene	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2084	chr13	57955747	57955947	+	1.70523	NA	Intergenic	Intergenic	-47515	NM_001166466	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding	0.005000	0.353234			-17(GCTTTGCTATGCTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5196	chr3	132690647	132690847	+	1.70523	NA	intron (NM_001163455, intron 2 of 25)	intron (NM_001163455, intron 2 of 25)	-6357	NM_001368626	13722	Mm.235137	NM_007926	ENSMUSG00000028029	Aimp1	9830137A06Rik|AIMP1/p43|EMAPII|Emap2|Scye1|p43	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6749	chr6	140193131	140193331	+	1.70523	NA	Intergenic	Intergenic	151674	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding	0.000000	0.552239			-18(ATTTAAATGAGACTCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3626	chr17	81172167	81172367	+	1.70523	NA	Intergenic	Intergenic	-107182	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1890	chr12	110869424	110869624	+	1.70523	NA	3' UTR (NM_028365, exon 8 of 8)	3' UTR (NM_028365, exon 8 of 8)	19245	NM_001199785	72805	Mm.443524	NM_028365	ENSMUSG00000021271	Zfp839	2810455K09Rik	zinc finger protein 839	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6605	chr6	98021697	98021897	+	1.70523	NA	TTS (NM_001178049)	TTS (NM_001178049)	30014	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	melanogenesis associated transcription factor	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1136	chr10	128759587	128759787	+	1.70523	NA	intron (NM_001253704, intron 2 of 3)	B3|SINE|B2	11232	NM_001253704	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-77	chr1	25068773	25068973	+	1.70523	NA	intron (NM_175642, intron 30 of 30)	intron (NM_175642, intron 30 of 30)	209081	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding	0.005000	0.298507			-17(ATTAGCATAATCAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5481	chr4	55214517	55214717	+	1.70523	NA	Intergenic	Intergenic	-135425	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23 homolog B, nucleotide excision repair protein	protein-coding	0.010000	0.412935			-53(GCTTTCTAATGTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4253	chr2	34363832	34364032	+	1.70523	NA	intron (NM_001290576, intron 2 of 7)	intron (NM_001290576, intron 2 of 7)	8113	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding	0.005000	0.422886			-11(ATTAGCATATCAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5849	chr5	19355792	19355992	+	1.70523	NA	intron (NM_001170746, intron 1 of 22)	L1M7|LINE|L1	128846	NM_001170746	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1448	chr11	107079193	107079393	+	1.70523	NA	intron (NM_176850, intron 7 of 27)	intron (NM_176850, intron 7 of 27)	51070	NM_001163473	69066	Mm.40679	NM_001163473	ENSMUSG00000078607	1810010H24Rik	-	RIKEN cDNA 1810010H24 gene	protein-coding	0.005000	0.363184			-92(CCATTGTGGTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1964	chr13	16266980	16267180	+	1.70523	NA	Intergenic	Intergenic	-243657	NR_155430	100503142	Mm.359204	NR_155430		B230303A05Rik	B230303A05|EG328191	U1 small nuclear ribonucleoprotein 1C pseudogene	pseudo	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-340	chr1	123511579	123511779	+	1.70523	NA	intron (NM_199021, intron 5 of 25)	intron (NM_199021, intron 5 of 25)	533880	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.005000	0.303483			67(ATTTACATTCCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7955	chrX	43408468	43408668	+	1.70523	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-133784	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-308	chr1	106782403	106782603	+	1.70523	NA	intron (NM_009190, intron 5 of 10)	intron (NM_009190, intron 5 of 10)	14222	NM_009190	20479	Mm.18705	NM_009190	ENSMUSG00000009907	Vps4b	8030489C12Rik|Skd1	vacuolar protein sorting 4B	protein-coding	0.005000	0.313433			-36(ATTTTAATGAGTATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-714	chr10	18584211	18584411	+	1.70523	NA	Intergenic	MER5A|DNA|hAT-Charlie	-38235	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6785	chr7	5087086	5087286	+	1.70523	NA	intron (NM_001252454, intron 2 of 10)	intron (NM_001252454, intron 2 of 10)	6951	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding	0.015000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6046	chr5	79933255	79933455	+	1.70523	NA	Intergenic	RLTR13B1|LTR|ERVK	-1087216	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2604	chr14	86788905	86789105	+	1.70461	NA	intron (NM_019670, intron 25 of 27)	intron (NM_019670, intron 25 of 27)	352219	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4983	chr3	65455744	65455944	+	1.70349	NA	Intergenic	Intergenic	-63291	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding	0.030000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3515	chr17	51554659	51554859	+	1.70349	NA	intron (NR_037264, intron 3 of 4)	intron (NR_037264, intron 3 of 4)	-106490	NR_046166	328837	Mm.236143	NR_046166	ENSMUSG00000117204	C330011F03Rik	C330011F03	RIKEN cDNA C330011F03 gene	ncRNA	0.000000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7168	chr8	18769332	18769532	+	1.70268	NA	intron (NM_173189, intron 12 of 13)	RMER10B|LTR|ERVL	-27870	NM_007426	11601	Mm.439874	NM_007426	ENSMUSG00000031465	Angpt2	Agpt2|Ang-2|Ang2	angiopoietin 2	protein-coding	0.000000	0.383085			2(GCTTTGGTATGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7218	chr8	40880713	40880913	+	1.70268	NA	intron (NM_001044740, intron 1 of 11)	intron (NM_001044740, intron 1 of 11)	18446	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding	0.025000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5810	chr5	3721978	3722178	+	1.70268	NA	intron (NM_001003909, intron 10 of 19)	Lx6|LINE|L1	50709	NM_001289529	70797	Mm.130148	NM_001003909	ENSMUSG00000040351	Ankib1	2310061P20Rik|4631416I11Rik|AW494740|C80642|mKIAA1386	ankyrin repeat and IBR domain containing 1	protein-coding	0.000000	0.363184			41(CTATTTTCATGAAAAA,+,0.00),43(ATTTTCATGAAAAAAA,-,0.00),57(AATTCCAAGAAAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1074	chr10	117663903	117664103	+	1.70268	NA	intron (NM_027468, intron 3 of 8)	RMER17C|LTR|ERVK	34503	NM_027468	70574	Mm.339332	NM_027468	ENSMUSG00000020183	Cpm	1110060I01Rik|5730456K23Rik|AA589379|E030045M14Rik	carboxypeptidase M	protein-coding	0.020000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1945	chr13	10314243	10314443	+	1.70268	NA	intron (NM_033269, intron 1 of 4)	intron (NM_033269, intron 1 of 4)	46460	NM_033269	12671	Mm.342315	NM_033269	ENSMUSG00000046159	Chrm3	Chrm-3|M3|M3R	cholinergic receptor, muscarinic 3, cardiac	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5311	chr3	156970143	156970343	+	1.70268	NA	intron (NM_001039094, intron 2 of 6)	intron (NM_001039094, intron 2 of 6)	408449	NM_177274	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6671	chr6	113105373	113105573	+	1.70268	NA	intron (NM_173005, intron 1 of 20)	intron (NM_173005, intron 1 of 20)	538	NM_173005	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2087	chr13	58240489	58240689	+	1.70130	NA	intron (NM_019832, intron 8 of 11)	L1MB4|LINE|L1	-24936	NM_026842	56085	Mm.182053	NM_026842	ENSMUSG00000005312	Ubqln1	1110046H03Rik|1810030E05Rik|AU019746|C77538|D13Ertd372e|Da41|Dsk2|Plic-1|Plic1|Xdrp1	ubiquilin 1	protein-coding	0.005000	0.338308			-52(ATTTGCTTTAGAAAAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-9	chr1	21910613	21910813	+	1.69920	NA	intron (NM_001160139, intron 1 of 14)	intron (NM_001160139, intron 1 of 14)	51229	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.005000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-819	chr8	30648685	30648885	+	1.69889	NA	Intergenic	Intergenic	80390	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	ncRNA	0.000000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-249	chr13	69093334	69093534	+	1.69798	NA	Intergenic	Intergenic	-93893	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7775	chr9	82061348	82061548	+	1.69798	NA	intron (NM_001357477, intron 4 of 4)	L1MA4|LINE|L1	197778	NM_001357477	75033	Mm.335329	NM_175213	ENSMUSG00000043289	Mei4	4930486G11Rik	meiotic double-stranded break formation protein 4	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4419	chr2	79645466	79645666	+	1.69798	NA	intron (NM_080558, intron 8 of 17)	intron (NM_080558, intron 8 of 17)	10141	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Itprid2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|Ssfa2|mKIAA1927	ITPR interacting domain containing 2	protein-coding	0.020000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-915	chrX	167972799	167972999	+	1.69744	NA	intron (NM_001033330, intron 3 of 19)	L1MC4a|LINE|L1	-117822	NM_001290428	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-675	chr10	5103821	5104021	+	1.69623	NA	intron (NM_001079686, intron 31 of 54)	intron (NM_001079686, intron 31 of 54)	-34858	NM_022027	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|KASH1|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3917	chr18	68990855	68991055	+	1.69623	NA	Intergenic	Intergenic	31318	NR_105780	102465187		NR_105780	ENSMUSG00000098366	Mir145b	Gm27644|mmu-mir-145b	microRNA 145b	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6804	chr7	27499031	27499231	+	1.69623	NA	promoter-TSS (NM_019412)	promoter-TSS (NM_019412)	-193	NM_019412	19153	Mm.10119	NM_019412	ENSMUSG00000053198	Prx	L-Periaxin	periaxin	protein-coding	0.010000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3060	chr15	100792444	100792644	+	1.69623	NA	intron (NM_021530, intron 11 of 24)	intron (NM_021530, intron 11 of 24)	11290	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding	0.010000	0.572139			-33(CCTTTCTGATGCTGAT,+,0.00),66(TATTTGGGATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5813	chr5	4993375	4993575	+	1.69623	NA	intron (NM_011074, intron 10 of 14)	intron (NM_011074, intron 10 of 14)	-235259	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6754	chr6	141285354	141285554	+	1.69623	NA	intron (NM_018779, intron 1 of 15)	intron (NM_018779, intron 1 of 15)	36185	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding	0.000000	0.353234			18(TAATTGTTTTTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4377	chr2	69904600	69904800	+	1.69623	NA	intron (NM_177783, intron 1 of 38)	intron (NM_177783, intron 1 of 38)	7454	NM_177783	68795	Mm.314576	NM_177783	ENSMUSG00000044308	Ubr3	1110059H15Rik|4833421P10Rik|A130030D10Rik|AA409735|AA414972|AA422631|AI646861|AU016126|Zfp650|Znf650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-100	chr1	34878159	34878359	+	1.69623	NA	3' UTR (NM_145516, exon 8 of 8)	3' UTR (NM_145516, exon 8 of 8)	28270	NM_001357425	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding	0.020000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4629	chr2	133361085	133361285	+	1.69623	NA	Intergenic	Intergenic	-190974	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0.025000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3839	chr18	49863356	49863556	+	1.69576	NA	intron (NM_001081371, intron 10 of 42)	MER5A1|DNA|hAT-Charlie	30459	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3219	chr16	49646972	49647172	+	1.69576	NA	Intergenic	Intergenic	-52222	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7737	chr9	75795086	75795286	+	1.69576	NA	intron (NM_007555, intron 1 of 6)	intron (NM_007555, intron 1 of 6)	19821	NM_007555	12160	Mm.428950	NM_007555	ENSMUSG00000032179	Bmp5	AU023399|se	bone morphogenetic protein 5	protein-coding	0.005000	0.313433			-51(ATATAAATGAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2624	chr14	90293412	90293612	+	1.69576	NA	Intergenic	Intergenic	166621	NR_045712	74967	Mm.390704	NR_045712	ENSMUSG00000115001	4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA	0.000000	0.343284			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-511	chr2	107117757	107117957	+	1.69570	NA	Intergenic	Intergenic	-58206	NM_008045	14308	Mm.249525	NM_008045	ENSMUSG00000027120	Fshb	FSH|FSH-B|FSH-beta|Fshbeta	follicle stimulating hormone beta	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2676	chr14	105387645	105387845	+	1.69444	NA	Intergenic	Intergenic	-39814	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6597	chr6	95293018	95293218	+	1.69308	NA	non-coding (NR_033559, exon 4 of 4)	non-coding (NR_033559, exon 4 of 4)	40875	NR_033559	414067	Mm.355990	NR_033559	ENSMUSG00000068180	AY512915	-	cDNA sequence AY512915	ncRNA	0.000000	0.318408			-87(ATTAAAATAACTAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2123	chr13	69498820	69499020	+	1.69308	NA	3' UTR (NM_198600, exon 13 of 13)	3' UTR (NM_198600, exon 13 of 13)	34944	NM_001169131	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Tent4a	LAK-1|POLK|Papd7|Pols|TRF4|TRF4-1	terminal nucleotidyltransferase 4A	protein-coding	0.035000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3244	chr16	55627782	55627982	+	1.69306	NA	Intergenic	RMER12|LTR|ERVK	133151	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA	0.000000	0.363184			-50(TCTTTGTTATTCTAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-778	chr6	137540370	137540570	+	1.69183	NA	intron (NM_001271588, intron 1 of 20)	intron (NM_001271588, intron 1 of 20)	-20575	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-405	chr1	138497046	138497246	+	1.69092	NA	intron (NM_001311148, intron 7 of 7)	intron (NM_001311148, intron 7 of 7)	122611	NM_001311148	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding	0.025000	0.457711	58(CGTGAAATATTCATG,+,0.00),58(CGTGAAATATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7961	chrX	49099043	49099243	+	1.69092	NA	intron (NM_001271448, intron 2 of 14)	intron (NM_001271448, intron 2 of 14)	189099	NM_001271450	209224	Mm.327730	NM_145951	ENSMUSG00000031109	Enox2	APK1|Cova1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-216	chr1	79394664	79394864	+	1.69092	NA	Intergenic	L1MA10|LINE|L1	45262	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-487	chr1	158362565	158362765	+	1.69092	NA	exon (NM_001205204, exon 1 of 23)	exon (NM_001205204, exon 1 of 23)	361	NM_007495	11899	Mm.329586	NM_007495	ENSMUSG00000026587	Astn1	Astn|GC14|mKIAA0289	astrotactin 1	protein-coding	0.070000	0.661692			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2899	chr15	44904008	44904208	+	1.69092	NA	Intergenic	Intergenic	22714	NR_033609	239410	Mm.352401	NR_033609	ENSMUSG00000060530	A930017M01Rik	Gm305	Smg-5 homolog, nonsense mediated mRNA decay factor pseudogene	pseudo	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3625	chr17	80937805	80938005	+	1.69092	NA	Intergenic	Intergenic	-6727	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4489	chr2	104842686	104842886	+	1.69092	NA	intron (NM_178695, intron 3 of 5)	intron (NM_178695, intron 3 of 5)	7064	NM_178695	228413	Mm.259609	NM_178695	ENSMUSG00000027171	Prrg4	9930111I18Rik|TMG4	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5678	chr4	107724151	107724351	+	1.69092	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-40021	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5341	chr4	10756367	10756567	+	1.69092	NA	intron (NR_045185, intron 2 of 4)	intron (NR_045185, intron 2 of 4)	41335	NR_045185	73624	Mm.67392	NR_045185	ENSMUSG00000086080	1700123O12Rik	-	RIKEN cDNA 1700123O12 gene	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2196	chr13	90680073	90680273	+	1.69092	NA	Intergenic	Intergenic	225182	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	ATPase, H+ transporting, lysosomal accessory protein 1-like	protein-coding	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7552	chr9	22538710	22538910	+	1.69092	NA	intron (NM_001360258, intron 5 of 21)	intron (NM_001360258, intron 5 of 21)	63095	NM_001360258	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4794	chr2	171098639	171098839	+	1.69092	NA	Intergenic	Intergenic	366932	NM_029761	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding	0.010000	0.402985			-37(ATCAGCATGAAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3069	chr16	4759930	4760130	+	1.69092	NA	intron (NM_001357050, intron 1 of 5)	intron (NM_001357050, intron 1 of 5)	3084	NM_001357050	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-839	chr10	57613217	57613417	+	1.69092	NA	Intergenic	Intergenic	-18664	NM_008863	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6968	chr7	92128248	92128448	+	1.69092	NA	intron (NM_001243046, intron 4 of 14)	intron (NM_001243046, intron 4 of 14)	-8837	NR_131016	75845	Mm.437835	NR_131016	ENSMUSG00000109382	4930567K12Rik	Gm45128	RIKEN cDNA 4930567K12 gene	ncRNA	0.005000	0.343284			-31(ATTTAAATTGCAAAAC,-,0.00),18(ATTAACAAGTGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5355	chr4	14398510	14398710	+	1.69092	NA	Intergenic	L1MB8|LINE|L1	-107301	NR_131155	100040030	Mm.366499	NR_131155		Gm2560	-	predicted gene 2560	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6665	chr6	110579307	110579507	+	1.69092	NA	Intergenic	Intergenic	-66105	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7503	chr9	3976250	3976450	+	1.69092	NA	Intergenic	Lx|LINE|L1	333144	NR_136940	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding	0.005000	0.293532			21(TTTTTTTTATTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3344	chr16	82862459	82862659	+	1.69092	NA	Intergenic	Intergenic	-1508584	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.000000	0.323383			64(ATCTGAATAACAAGCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7108	chr7	136021827	136022027	+	1.69092	NA	Intergenic	Intergenic	-246397	NR_102277	77383	Mm.227745	NR_102277	ENSMUSG00000110027	C030029H02Rik	-	RIKEN cDNA C030029H02 gene	ncRNA	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5835	chr5	15842830	15843030	+	1.69092	NA	Intergenic	RMER1A|Other|Other	40836	NR_045974	75058	Mm.183467	NR_045974	ENSMUSG00000105185	4930519H02Rik	-	RIKEN cDNA 4930519H02 gene	ncRNA	0.000000	0.427861			-100(AAAAGCATAACAAAAA,-,0.00),75(CCTGTGTCATGGAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-129	chr1	44139833	44140033	+	1.69092	NA	intron (NM_144558, intron 8 of 9)	RLTR22_Mus|LTR|ERVK	-7811	NM_011729	22592	Mm.2213	NM_011729	ENSMUSG00000026048	Ercc5	Xpg	excision repair cross-complementing rodent repair deficiency, complementation group 5	protein-coding	0.000000	0.383085		-52(CTTACATATGCATT,+,0.00)	62(ATTTGAATGCCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6475	chr6	59452204	59452404	+	1.69092	NA	Intergenic	Intergenic	-25998	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8159	chrX	166596146	166596346	+	1.69092	NA	Intergenic	Intergenic	-10530	NM_019397	54156	Mm.37707	NM_019397	ENSMUSG00000000402	Egfl6	Maeg	EGF-like-domain, multiple 6	protein-coding	0.020000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1376	chr11	82094325	82094525	+	1.69092	NA	Intergenic	L1MCb|LINE|L1	-7420	NM_011331	20293	Mm.867	NM_011331	ENSMUSG00000035352	Ccl12	MCP-5|Scya12	chemokine (C-C motif) ligand 12	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3753	chr18	25999293	25999493	+	1.69092	NA	Intergenic	Intergenic	-245236	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.020000	0.422886			-44(TGTTTCCTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2347	chr14	10945813	10946013	+	1.69092	NA	intron (NM_001308285, intron 2 of 9)	MER5A1|DNA|hAT-Charlie	207360	NR_131139	547334	Mm.434606	NR_131139	ENSMUSG00000089833	Fhitos	Gm16542	fragile histidine triad gene, opposite strand	ncRNA	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6266	chr5	150806542	150806742	+	1.68948	NA	intron (NM_175310, intron 34 of 34)	BGLII|LTR|ERVK	132815	NM_175310	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3879	chr18	57543789	57543989	+	1.68948	NA	intron (NM_001311063, intron 2 of 5)	intron (NM_001311063, intron 2 of 5)	7978	NR_027945	75084	Mm.243841	NR_015494	ENSMUSG00000086607	4930511M06Rik	-	RIKEN cDNA 4930511M06 gene	ncRNA	0.015000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1747	chr12	75939553	75939753	+	1.68948	NA	intron (NM_001005510, intron 34 of 115)	intron (NM_001005510, intron 34 of 115)	30550	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7186	chr8	30648662	30648862	+	1.68809	NA	Intergenic	Intergenic	80367	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	ncRNA	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3299	chr16	68679798	68679998	+	1.68585	NA	Intergenic	B4|SINE|B4	-1058990	NM_001145977	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-55	chr1	20457385	20457585	+	1.68585	NA	intron (NM_153179, intron 35 of 66)	MER58B|DNA|hAT-Charlie	101031	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA	0.000000	0.363184			25(TATTTGTCATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6781	chr6	149507358	149507558	+	1.68585	NA	intron (NM_001112796, intron 3 of 7)	ORR1D1|LTR|ERVL-MaLR	-58624	NM_001360951	436100		NM_001360951		Gm21814	6620401J10Rik	predicted gene, 21814	protein-coding	0.005000	0.348259			-61(ATTAGCATGATAATTG,-,0.00),-33(GTTTAAATGAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5520	chr4	66013922	66014122	+	1.68585	NA	intron (NM_207109, intron 5 of 22)	intron (NM_207109, intron 5 of 22)	390461	NM_019514	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2452	chr14	38325198	38325398	+	1.68585	NA	Intergenic	Intergenic	-573004	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-747	chr10	28114355	28114555	+	1.68555	NA	intron (NM_001359355, intron 1 of 33)	B1_Mus2|SINE|Alu	39635	NM_001359356	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-699	chr5	105867905	105868105	+	1.68555	NA	Intergenic	Intergenic	-8563	NM_018759	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding	0.025000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3162	chr16	33698032	33698232	+	1.68546	NA	intron (NM_175256, intron 1 of 14)	intron (NM_175256, intron 1 of 14)	13666	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629	heart development protein with EGF-like domains 1	protein-coding	0.010000	0.587065			5(GTTTTGCCTTGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-762	chr10	31533629	31533829	+	1.68506	NA	intron (NM_001146349, intron 2 of 5)	intron (NM_001146349, intron 2 of 5)	75996	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8084	chrX	132981464	132981664	+	1.68506	NA	Intergenic	RMER13B|LTR|ERVK	-706216	NR_153117	102632590	Mm.403836	NR_153117	ENSMUSG00000096978	Gm26851	-	predicted gene, 26851	ncRNA	0.000000	0.457711			1(ATCTACATGAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-135	chr1	45472857	45473057	+	1.68506	NA	intron (NM_007737, intron 1 of 53)	intron (NM_007737, intron 1 of 53)	30325	NM_007737	12832	Mm.10299	NM_007737	ENSMUSG00000026042	Col5a2	1110014L14Rik	collagen, type V, alpha 2	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6872	chr7	58727571	58727771	+	1.68506	NA	intron (NM_009728, intron 1 of 20)	intron (NM_009728, intron 1 of 20)	69469	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4916	chr3	40456161	40456361	+	1.68506	NA	Intergenic	RLTR17|LTR|ERVK	66651	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA	0.000000	0.452736			2(TCATTTTGATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4286	chr2	46182228	46182428	+	1.68506	NA	Intergenic	MIR|SINE|MIR	485723	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-729	chr10	23164953	23165153	+	1.68506	NA	intron (NM_001347372, intron 4 of 18)	intron (NM_001347372, intron 4 of 18)	184837	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding	0.000000	0.308458	-99(TATTTATTATGCATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3778	chr18	33203234	33203434	+	1.68506	NA	3' UTR (NM_001347624, exon 6 of 6)	3' UTR (NM_001347624, exon 6 of 6)	10528	NM_001347624	170459	Mm.127058	NM_133774	ENSMUSG00000024378	Stard4	4632419C16Rik|9030213J02Rik	StAR-related lipid transfer (START) domain containing 4	protein-coding	0.000000	0.353234			84(ATTTACATAGCCATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2350	chr14	11248424	11248624	+	1.68506	NA	Intergenic	Intergenic	-33953	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA	0.000000	0.293532		29(TTTTCATATGCATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2214	chr13	94385170	94385370	+	1.68506	NA	intron (NM_009680, intron 1 of 26)	intron (NM_009680, intron 1 of 26)	26310	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-273	chr1	93380787	93380987	+	1.68506	NA	intron (NM_207031, intron 4 of 23)	intron (NM_207031, intron 4 of 23)	6991	NM_207031	404545	Mm.297411	NM_207031	ENSMUSG00000034107	Ano7	Ngep|Ngep-L|Pcanap5|Tmem16g	anoctamin 7	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7921	chrX	11899337	11899537	+	1.68506	NA	Intergenic	MIRb|SINE|MIR	181116	NM_029510	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-887	chr10	72969158	72969358	+	1.68506	NA	Intergenic	Intergenic	117447	NR_040646	327768	Mm.417745	NR_040646	ENSMUSG00000111994	A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA	0.010000	0.278607			16(ATTAGCATAAGAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1971	chr13	20140071	20140271	+	1.68427	NA	intron (NM_080288, intron 1 of 21)	MER2|DNA|TcMar-Tigger	49664	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4786	chr2	169032945	169033145	+	1.68427	NA	Intergenic	Intergenic	54776	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6625	chr6	101732496	101732696	+	1.68427	NA	Intergenic	Intergenic	-41653	NR_027989	207157	Mm.57632	NM_177579	ENSMUSG00000052236	Gm9871	0610005I04|EG207157	predicted gene 9871	ncRNA	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5803	chr4	154600054	154600254	+	1.68427	NA	intron (NM_001291026, intron 1 of 16)	intron (NM_001291026, intron 1 of 16)	36213	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2489	chr14	55077607	55077807	+	1.68159	NA	intron (NM_001039198, intron 1 of 9)	intron (NM_001039198, intron 1 of 9)	4616	NR_004444	432855	Mm.490799	NR_004444		Zfhx2os	Zfhx2as	zinc finger homeobox 2, opposite strand	ncRNA	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7513	chr9	9043535	9043735	+	1.67979	NA	intron (NM_027823, intron 7 of 22)	RLTR11B|LTR|ERVK	143802	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding	0.005000	0.437811			-74(TCTTTGTTGTGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2396	chr14	22477326	22477526	+	1.67979	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	65372	NR_046307	74896	Mm.444661	NR_046307	ENSMUSG00000114412	4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA	0.000000	0.308458			42(TCTTTTTTTTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2513	chr14	62353415	62353615	+	1.67979	NA	intron (NM_026001, intron 4 of 10)	intron (NM_026001, intron 4 of 10)	21447	NM_026001	67153	Mm.26040	NM_026001	ENSMUSG00000021932	Rnaseh2b	1110019N06Rik|2610207P08Rik|Dleu8	ribonuclease H2, subunit B	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7975	chrX	60486174	60486374	+	1.67979	NA	Intergenic	Lx7|LINE|L1	-30079	NM_001039240	631784	Mm.424878	NM_001039240	ENSMUSG00000079583	Gm7073	-	predicted gene 7073	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1639	chr12	45562837	45563037	+	1.67979	NA	Intergenic	Intergenic	-488454	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4066	chr19	31878398	31878598	+	1.67979	NA	intron (NM_001081074, intron 1 of 11)	intron (NM_001081074, intron 1 of 11)	9685	NM_001081074	69865	Mm.5307	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|9130016M20Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|alpha-MHC-MerCreMer|alphaMHC-Cre-Mer-Cre|mer	APOBEC1 complementation factor	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2810	chr15	15329980	15330180	+	1.67979	NA	Intergenic	Intergenic	-1398835	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0.010000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3946	chr18	78713556	78713756	+	1.67979	NA	Intergenic	Lx9|LINE|L1	-116706	NM_207651	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4764	chr2	160955293	160955493	+	1.67979	NA	intron (NR_126509, intron 35 of 35)	intron (NR_126509, intron 35 of 35)	-43054	NM_001291145	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding	0.025000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-902	chr10	80609623	80609823	+	1.67979	NA	TTS (NR_105877)	TTS (NR_105877)	463	NR_105877	102465550		NR_105877	ENSMUSG00000099283	Mir6912	Gm27990|mmu-mir-6912	microRNA 6912	ncRNA	0.020000	0.597015			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4424	chr2	80041285	80041485	+	1.67979	NA	intron (NM_001159582, intron 2 of 15)	intron (NM_001159582, intron 2 of 15)	-2483	NM_001355142	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding	0.010000	0.333333			-13(ATTTAAATGACTAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4901	chr3	31986012	31986212	+	1.67979	NA	intron (NM_028231, intron 2 of 5)	intron (NM_028231, intron 2 of 5)	83409	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding	0.000000	0.378109			-36(CCATTGCCTTGCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4485	chr2	104057031	104057231	+	1.67979	NA	non-coding (NR_149726, exon 10 of 10)	non-coding (NR_149726, exon 10 of 10)	-13935	NM_181858	333883	Mm.359026	NM_181858	ENSMUSG00000068686	Cd59b	-	CD59b antigen	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4736	chr2	153773636	153773836	+	1.67979	NA	TTS (NM_007896)	TTS (NM_007896)	-5510	NM_001370916	100504221	Mm.246778	NM_177849	ENSMUSG00000044083	Efcab8	A630008I04|EG329541|Gm38434	EF-hand calcium binding domain 8	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5602	chr4	91438969	91439169	+	1.67979	NA	Intergenic	Intergenic	-39085	NM_207685	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV like RNA binding protein 1	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6220	chr5	138335714	138335914	+	1.67979	NA	Intergenic	B4A|SINE|B4	-27905	NR_157560	100303731	Mm.392433	NR_157560		Gm10874	-	predicted gene 10874	ncRNA	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6489	chr6	63512419	63512619	+	1.67979	NA	intron (NM_001370966, intron 2 of 15)	Lx7|LINE|L1	256513	NM_001370966									0.000000	0.368159	-53(CATGAATTCTTCATG,+,0.00),-53(CATGAATTCTTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5264	chr3	147881217	147881417	+	1.67979	NA	Intergenic	Intergenic	1028950	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1957	chr13	14556822	14557022	+	1.67979	NA	Intergenic	BGLII_A|LTR|ERVK	-33696	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.005000	0.447761			47(ATTAACATCAAAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2058	chr13	45229162	45229362	+	1.67979	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-160480	NM_153789	218203	Mm.212855	NM_153789	ENSMUSG00000038175	Mylip	9430057C20Rik|Mir	myosin regulatory light chain interacting protein	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1638	chr12	45158953	45159153	+	1.67979	NA	Intergenic	Intergenic	-84570	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3648	chr17	86368093	86368293	+	1.67979	NA	intron (NM_011104, intron 2 of 14)	intron (NM_011104, intron 2 of 14)	-81015	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA	0.035000	0.407960			-78(ATTAAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4625	chr2	133091332	133091532	+	1.67870	NA	Intergenic	Intergenic	-145396	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding	0.005000	0.388060		-2(CATTCATATGTATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2642	chr14	98208618	98208818	+	1.67870	NA	Intergenic	Intergenic	-38953	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund family transcription factor 1	protein-coding	0.000000	0.323383			-81(TTTCTGTTATGTAATT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7903	chr9	118978059	118978259	+	1.67870	NA	intron (NM_133710, intron 1 of 7)	intron (NM_133710, intron 1 of 7)	51623	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5762	chr4	136489268	136489468	+	1.67870	NA	intron (NM_024452, intron 1 of 4)	intron (NM_024452, intron 1 of 4)	19607	NM_024452	269593	Mm.485824	NM_024452	ENSMUSG00000001089	Luzp1	2700072H04Rik|AI266952|Luzp|mFLJ00226	leucine zipper protein 1	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3956	chr18	81082865	81083065	+	1.67870	NA	Intergenic	Intergenic	-95944	NM_001369133	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	spalt like transcription factor 3	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5793	chr4	151466188	151466388	+	1.67870	NA	intron (NM_001081557, intron 4 of 23)	intron (NM_001081557, intron 4 of 23)	376718	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	-	predicted gene 13090	protein-coding	0.020000	0.477612			45(ATTAACACAACAGAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6950	chr7	88343021	88343221	+	1.67870	NA	Intergenic	Intergenic	65036	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4921	chr3	41639691	41639891	+	1.67870	NA	intron (NM_001081411, intron 18 of 20)	intron (NM_001081411, intron 18 of 20)	74911	NM_001130186	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding	0.000000	0.373134			-37(ATTTACATAATTAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5929	chr5	47744862	47745062	+	1.67870	NA	Intergenic	Intergenic	-238193	NM_001291227	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|b2b1200.1Clo|mKIAA4141|slit-2	slit guidance ligand 2	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3444	chr17	24826709	24826909	+	1.67870	NA	intron (NM_029197, intron 6 of 13)	intron (NM_029197, intron 6 of 13)	22427	NM_029197	75178	Mm.52592	NM_029197	ENSMUSG00000024155	Meiob	4930528F23Rik|MLZ-675	meiosis specific with OB domains	protein-coding	0.000000	0.402985			-11(GCCTTCTTTTGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-560	chr1	175813216	175813416	+	1.67870	NA	intron (NM_029453, intron 27 of 27)	intron (NM_029453, intron 27 of 27)	-67462	NM_012012	26909	Mm.283046	NM_012012	ENSMUSG00000039748	Exo1	5730442G03Rik|Msa	exonuclease 1	protein-coding	0.005000	0.303483			-2(TTATTTCTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3252	chr16	56831198	56831398	+	1.67870	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	-35440	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding	0.005000	0.378109			-77(CTTAGCATCAAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2456	chr14	39039064	39039264	+	1.67870	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	140862	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.000000	0.407960			27(ATCTCCATAAAAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5314	chr3	157405043	157405243	+	1.67870	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	128947	NR_152231	381498	Mm.402095	NR_152231	ENSMUSG00000105834	4930592C13Rik	Gm1657|Gm43159	RIKEN cDNA 4930592C13 gene	ncRNA	0.000000	0.323383			53(TTTTACATGAGACAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6156	chr5	112944459	112944659	+	1.67870	NA	intron (NM_177078, intron 11 of 20)	intron (NM_177078, intron 11 of 20)	-48197	NM_028901	74376	Mm.441903	NM_028901	ENSMUSG00000072720	Myo18b	4932408L24Rik|4933411E19Rik|Gm448	myosin XVIIIb	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-757	chr10	30550203	30550403	+	1.67870	NA	intron (NM_028604, intron 11 of 12)	intron (NM_028604, intron 11 of 12)	50397	NM_028604	73681	Mm.294503	NM_028604	ENSMUSG00000019792	Trmt11	2410075D05Rik|3110045I18Rik|AW213713	tRNA methyltransferase 11	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2423	chr14	30562115	30562315	+	1.67833	NA	intron (NM_009388, intron 4 of 13)	AT_rich|Low_complexity|Low_complexity	-9934	NR_037237	100526475		NR_037237	ENSMUSG00000093156	Mir3076	mir-3076|mmu-mir-3076	microRNA 3076	ncRNA	0.010000	0.313433			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-388	chr17	9580148	9580348	+	1.67753	NA	Intergenic	Intergenic	89456	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	poly(A) binding protein, cytoplasmic 6	protein-coding	0.015000	0.472637			-62(ATTTACATTTCAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1545	chr12	12927210	12927410	+	1.67683	NA	Intergenic	Intergenic	14526	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding	0.000000	0.492537			23(ATTAACATGATAGAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4551	chr2	118445771	118445971	+	1.67683	NA	intron (NM_001355383, intron 16 of 35)	intron (NM_001355383, intron 16 of 35)	33825	NM_009273	20813	Mm.363404	NM_009273	ENSMUSG00000009549	Srp14	14kDa|AW536328	signal recognition particle 14	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1511	chr12	3538686	3538886	+	1.67683	NA	Intergenic	Intergenic	-33605	NM_001355528	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6345	chr6	21122851	21123051	+	1.67683	NA	Intergenic	Lx2B2|LINE|L1	-92395	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121	potassium voltage-gated channel, Shal-related family, member 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1962	chr13	15699930	15700130	+	1.67683	NA	intron (NM_008130, intron 10 of 14)	intron (NM_008130, intron 10 of 14)	102600	NR_045507	71071	Mm.380845	NR_045507	ENSMUSG00000113960	4933412O06Rik	-	RIKEN cDNA 4933412O06 gene	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4320	chr2	56146401	56146601	+	1.67683	NA	Intergenic	MER58A|DNA|hAT-Charlie	-639310	NR_105751	102465169		NR_105751	ENSMUSG00000098437	Mir195b	Gm27491|mmu-mir-195b	microRNA 195b	ncRNA	0.005000	0.298507			-88(CTTTTATTTTTTATAT,+,0.00),-16(CTCAACATGACAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2841	chr15	28360391	28360591	+	1.67614	NA	intron (NM_133365, intron 47 of 78)	intron (NM_133365, intron 47 of 78)	156725	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b3491Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7776	chr9	82061608	82061808	+	1.67614	NA	intron (NM_001357477, intron 4 of 4)	L1MA4|LINE|L1	198038	NM_001357477	75033	Mm.335329	NM_175213	ENSMUSG00000043289	Mei4	4930486G11Rik	meiotic double-stranded break formation protein 4	protein-coding	0.005000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-340	chr15	28360375	28360575	+	1.67614	NA	intron (NM_133365, intron 47 of 78)	intron (NM_133365, intron 47 of 78)	156709	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b3491Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3949	chr18	79207326	79207526	+	1.67509	NA	Intergenic	Intergenic	-98035	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding	0.005000	0.363184	73(CATGCATTATTAATA,+,0.00),73(CATGCATTATTAATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5295	chr3	153204059	153204259	+	1.67509	NA	3' UTR (NM_011372, exon 5 of 5)	3' UTR (NM_011372, exon 5 of 5)	-52051	NR_108044	75001		NR_108044		4930482G09Rik	-	RIKEN cDNA 4930482G09 gene	ncRNA	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2627	chr14	91796324	91796524	+	1.67509	NA	Intergenic	Intergenic	1669533	NR_045712	74967	Mm.390704	NR_045712	ENSMUSG00000115001	4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3964	chr18	82932380	82932580	+	1.67509	NA	intron (NM_001177464, intron 1 of 5)	intron (NM_001177464, intron 1 of 5)	-11920	NR_033307	75853	Mm.420737	NR_033307	ENSMUSG00000118339	4930592I03Rik	-	RIKEN cDNA 4930592I03 gene	ncRNA	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7430	chr8	106343467	106343667	+	1.67509	NA	Intergenic	Intergenic	-5602	NM_021491	58994	Mm.23298	NM_021491	ENSMUSG00000031906	Smpd3	4631433G07Rik|AI427456|AW537966|fro|nSMase2	sphingomyelin phosphodiesterase 3, neutral	protein-coding	0.005000	0.457711			-65(TATTAGTTTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5299	chr3	154194537	154194737	+	1.67509	NA	intron (NM_001081263, intron 2 of 21)	intron (NM_001081263, intron 2 of 21)	135923	NM_010713	16875	Mm.15530	NM_010713	ENSMUSG00000096225	Lhx8	L3|Lhx7	LIM homeobox protein 8	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6109	chr5	100492121	100492321	+	1.67509	NA	intron (NM_001359914, intron 1 of 13)	intron (NM_001359914, intron 1 of 13)	6352	NM_001115010	231506	Mm.212568	NM_172714	ENSMUSG00000035310	Lin54	AI461788	lin-54 homolog (C. elegans)	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6093	chr5	92755038	92755238	+	1.67509	NA	intron (NM_015756, intron 1 of 10)	BGLII|LTR|ERVK	33424	NR_035487	100316841		NR_035487	ENSMUSG00000089268	Mir1961	mmu-mir-1961	microRNA 1961	ncRNA	0.010000	0.452736			-41(ATTTGTAAAATAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-142	chr1	47495844	47496044	+	1.67509	NA	Intergenic	Intergenic	-28819	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-565	chr1	176037393	176037593	+	1.67509	NA	intron (NM_001195816, intron 5 of 9)	intron (NM_001195816, intron 5 of 9)	117164	NM_001290692	226720	Mm.11282	NM_001290692	ENSMUSG00000104158	Becn2	Beclin-2|Gm104	beclin 2	protein-coding	0.005000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-526	chr2	133363229	133363429	+	1.67503	NA	Intergenic	Intergenic	-188830	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4622	chr2	132617649	132617849	+	1.67424	NA	non-coding (NR_033468, exon 4 of 6)	non-coding (NR_033468, exon 4 of 6)	19553	NR_033468	767814	Mm.371752	NR_033468	ENSMUSG00000074783	AU019990	-	expressed sequence AU019990	ncRNA	0.015000	0.412935			-40(TTATAGTCATGCAATT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-49	chr1	167969889	167970089	+	1.67173	NA	Intergenic	X8_LINE|LINE|CR1	280431	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5029	chr3	79249504	79249704	+	1.66862	NA	intron (NR_045502, intron 2 of 2)	intron (NR_045502, intron 2 of 2)	36685	NR_045502	70924	Mm.444622	NR_045502	ENSMUSG00000104585	4921511C10Rik	-	RIKEN cDNA 4921511C10 gene	ncRNA	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1864	chr12	103564834	103565034	+	1.66862	NA	intron (NM_028980, intron 3 of 24)	RLTR13E|LTR|ERVK	32369	NM_028980	74521	Mm.248619	NM_028980	ENSMUSG00000021209	Ppp4r4	8430415E04Rik|mKIAA1622	protein phosphatase 4, regulatory subunit 4	protein-coding	0.000000	0.388060			27(TCTTTGTAATGCATAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6223	chr5	138919197	138919397	+	1.66862	NA	Intergenic	Intergenic	74984	NR_156469	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	PDGF-1	platelet derived growth factor, alpha	protein-coding	0.000000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-646	chr4	104837419	104837619	+	1.66827	NA	intron (NM_146148, intron 7 of 10)	intron (NM_146148, intron 7 of 10)	38879	NM_146148	230558	Mm.197638	NM_146148	ENSMUSG00000035031	C8a	-	complement component 8, alpha polypeptide	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4790	chr2	169929863	169930063	+	1.66806	NA	intron (NM_001363022, intron 2 of 2)	intron (NM_001363022, intron 2 of 2)	33224	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA	0.015000	0.482587			-89(ATTTACATGAACAGAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3742	chr18	22480836	22481036	+	1.66806	NA	intron (NM_001167777, intron 9 of 12)	L1M4b|LINE|L1	135847	NM_001167777	211961	Mm.392310	NM_001167777	ENSMUSG00000045215	Asxl3	C230079D11Rik|D430002O22Rik|D930044O18Rik|Gm329|Gm945	additional sex combs like 3, transcriptional regulator	protein-coding	0.000000	0.283582			70(CTTTAGTTATGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-334	chr1	121472574	121472774	+	1.66806	NA	intron (NM_001025156, intron 11 of 23)	intron (NM_001025156, intron 11 of 23)	41607	NM_029955	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1701	chr12	66459689	66459889	+	1.66806	NA	Intergenic	Intergenic	-175388	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6895	chr7	70392478	70392678	+	1.66806	NA	intron (NR_045850, intron 5 of 10)	intron (NR_045850, intron 5 of 10)	-25832	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding	0.000000	0.353234	-60(TATGAATAATTCAAC,+,0.00),-60(TATGAATAATTCAAC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8033	chrX	97360888	97361088	+	1.66806	NA	intron (NM_001161433, intron 3 of 6)	intron (NM_001161433, intron 3 of 6)	16221	NM_175540	245527	Mm.189270	NM_175540	ENSMUSG00000034457	Eda2r	9430060M22Rik|TNFRSF27|Xedar	ectodysplasin A2 receptor	protein-coding	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2609	chr14	87002411	87002611	+	1.66806	NA	intron (NM_019670, intron 8 of 27)	intron (NM_019670, intron 8 of 27)	138713	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.010000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1331	chr11	68592544	68592744	+	1.66806	NA	intron (NM_177779, intron 4 of 6)	L1MC5|LINE|L1	5607	NM_177779	276920	Mm.123046	NM_177779	ENSMUSG00000045915	Ccdc42	A530001H01Rik	coiled-coil domain containing 42	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-256	chr1	88764014	88764214	+	1.66806	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	9224	NR_040493	78650	Mm.243767	NR_040493	ENSMUSG00000097398	Platr5	2410088K16Rik	pluripotency associated transcript 5	ncRNA	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4237	chr2	29476889	29477089	+	1.66806	NA	intron (NM_001290489, intron 3 of 6)	intron (NM_001290489, intron 3 of 6)	-1695	NR_105753	102465170		NR_105753	ENSMUSG00000098539	Mir133c	Gm27865|mmu-mir-133c	microRNA 133c	ncRNA	0.005000	0.467662			-21(TTTTAGTGTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6763	chr6	145471954	145472154	+	1.66806	NA	Intergenic	Intergenic	-37129	NM_028742	74071	Mm.441497	NM_028742	ENSMUSG00000054966	Lmntd1	4933403M22Rik|AI482300|Ifltd1|Lmna-rs1|Lmna1	lamin tail domain containing 1	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6802	chr7	25742249	25742449	+	1.66806	NA	intron (NM_001360789, intron 6 of 14)	intron (NM_001360789, intron 6 of 14)	12410	NM_001360789	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8031	chrX	97069668	97069868	+	1.66806	NA	Intergenic	Intergenic	-2828	NM_001033361	245526	Mm.336164	NM_001033361	ENSMUSG00000031212	Pgr15l	-	G protein-coupled receptor 15-like	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-411	chr1	139106874	139107074	+	1.66806	NA	intron (NM_001166501, intron 13 of 21)	MTE-int|LTR|ERVL-MaLR	129317	NR_108103	78229	Mm.437838	NR_108103	ENSMUSG00000104900	4930596I21Rik	-	RIKEN cDNA 4930596I21 gene	ncRNA	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-240	chr1	84652004	84652204	+	1.66806	NA	intron (NM_152915, intron 1 of 12)	Lx|LINE|L1	-43735	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA	0.010000	0.402985			30(ATTTGCCTAAGAATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7072	chr7	127225413	127225613	+	1.66806	NA	Intergenic	Intergenic	-7068	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4593	chr2	126050598	126050798	+	1.66806	NA	intron (NM_008008, intron 2 of 3)	intron (NM_008008, intron 2 of 3)	16040	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding	0.015000	0.427861			-3(CCATTTTAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4033	chr19	18420437	18420637	+	1.66806	NA	Intergenic	Intergenic	211276	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding	0.015000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4499	chr2	107117734	107117934	+	1.66737	NA	Intergenic	MER102b|DNA|hAT-Charlie	-58183	NM_008045	14308	Mm.249525	NM_008045	ENSMUSG00000027120	Fshb	FSH|FSH-B|FSH-beta|Fshbeta	follicle stimulating hormone beta	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-693	chr10	11293949	11294149	+	1.66735	NA	intron (NM_001168297, intron 2 of 2)	MER2|DNA|TcMar-Tigger	12462	NM_001168297	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2145	chr13	74863455	74863655	+	1.66735	NA	Intergenic	Intergenic	-54795	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6396	chr6	35770437	35770637	+	1.66735	NA	Intergenic	Intergenic	-230649	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6217	chr5	137449824	137450024	+	1.66735	NA	intron (NM_011741, intron 24 of 87)	ID_B1|SINE|B4	27140	NM_011741	22635	Mm.7984	NM_011741	ENSMUSG00000079173	Zan	Zan-test	zonadhesin	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3702	chr18	10461165	10461365	+	1.66735	NA	intron (NM_001083628, intron 4 of 32)	intron (NM_001083628, intron 4 of 32)	136086	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding	0.010000	0.422886			-36(AATTTCTTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4084	chr19	36960936	36961136	+	1.66735	NA	intron (NM_001080706, intron 6 of 37)	B1F1|SINE|Alu	34957	NM_001080706	107182	Mm.295062	NM_001080706	ENSMUSG00000040565	Btaf1	AI414500|AI447930|E430027O22Rik|TAF170	B-TFIID TATA-box binding protein associated factor 1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3995	chr18	88068465	88068665	+	1.66735	NA	Intergenic	Intergenic	825642	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0.010000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1466	chr11	110888579	110888779	+	1.66735	NA	Intergenic	Intergenic	-79354	NM_001252207	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2935	chr15	55456326	55456526	+	1.66735	NA	intron (NM_001368422, intron 34 of 47)	intron (NM_001368422, intron 34 of 47)	100886	NM_026759	68537	Mm.236795	NM_026759	ENSMUSG00000022370	Mrpl13	1110002D09Rik	mitochondrial ribosomal protein L13	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7434	chr8	107876552	107876752	+	1.66735	NA	Intergenic	Intergenic	-288170	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5898	chr5	33640802	33641002	+	1.66735	NA	exon (NM_001289724, exon 7 of 7)	exon (NM_001289724, exon 7 of 7)	-11267	NM_001359462	74504	Mm.294695	NM_178390	ENSMUSG00000037339	Fam53a	2410018C17Rik|5430419M09Rik|Dntnp	family with sequence similarity 53, member A	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-723	chr10	20580924	20581124	+	1.66735	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	-32696	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding	0.015000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2960	chr15	62400298	62400498	+	1.66735	NA	Intergenic	L1_Mus3|LINE|L1	-180947	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5885	chr5	29032679	29032879	+	1.66735	NA	Intergenic	Intergenic	-163214	NR_110371	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7554	chr9	22859325	22859525	+	1.66735	NA	intron (NM_001360258, intron 20 of 21)	Lx8b|LINE|L1	-363651	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5814	chr5	5160005	5160205	+	1.66735	NA	intron (NM_011074, intron 5 of 14)	intron (NM_011074, intron 5 of 14)	105963	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5516	chr4	64978808	64979008	+	1.66735	NA	Intergenic	Intergenic	-145266	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2116	chr13	67533412	67533612	+	1.66735	NA	Intergenic	Intergenic	-7281	NM_133228	170763	Mm.491205	NM_133228	ENSMUSG00000097333	Zfp87	2210039O17Rik|4631412O18Rik|KRAB4|Mzf22|Zfp72	zinc finger protein 87	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7674	chr9	59498059	59498259	+	1.66735	NA	Intergenic	Intergenic	-11785	NM_019927	23806	Mm.305925	NM_019927	ENSMUSG00000025234	Arih1	AU021774|Ari|Ari1|Hari|Hhari|Ubch7bp|Uip77	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5371	chr4	20540015	20540215	+	1.66735	NA	intron (NM_172987, intron 1 of 4)	intron (NM_172987, intron 1 of 4)	238553	NM_001290410	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4917	chr3	40532125	40532325	+	1.66625	NA	Intergenic	Intergenic	-8542	NM_175515	380614	Mm.105309	NM_175515	ENSMUSG00000060798	Intu	9230116I04Rik|9430087H23Rik|Pdzd6|Pdzk6|mKIAA1284	inturned planar cell polarity protein	protein-coding	0.025000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1463	chr11	110642856	110643056	+	1.66611	NA	Intergenic	Intergenic	163616	NM_001356346	26399	Mm.14487	NM_011943	ENSMUSG00000020623	Map2k6	MAPKK 6|MAPKK6|MEK6|MKK6|Prkmk6|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7755	chr9	79730099	79730299	+	1.66611	NA	Intergenic	Intergenic	-11477	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2625	chr14	90293630	90293830	+	1.66611	NA	Intergenic	Intergenic	166839	NR_045712	74967	Mm.390704	NR_045712	ENSMUSG00000115001	4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA	0.000000	0.273632			-97(ATTAACATGATAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-741	chr10	25206487	25206687	+	1.66611	NA	intron (NM_018747, intron 7 of 7)	B4A|SINE|B4	-6417	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding	0.010000	0.452736			43(CCAGTGTTATGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-706	chr10	14546130	14546330	+	1.66611	NA	Intergenic	Intergenic	-1194	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding	0.025000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1330	chr11	68144983	68145183	+	1.66611	NA	intron (NM_001361351, intron 6 of 6)	intron (NM_001361351, intron 6 of 6)	-75809	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6245	chr5	144313255	144313455	+	1.66611	NA	intron (NM_025833, intron 3 of 13)	intron (NM_025833, intron 3 of 13)	36294	NR_040432	100504231	Mm.441035	NR_040432	ENSMUSG00000086894	Gm15708	-	predicted gene 15708	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-386	chr1	134611470	134611670	+	1.66611	NA	intron (NM_152895, intron 14 of 26)	MIRc|SINE|MIR	-35042	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194|sytII	synaptotagmin II	protein-coding	0.000000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-209	chr12	96873220	96873420	+	1.66542	NA	Intergenic	Intergenic	-826098	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5133	chr3	115844696	115844896	+	1.66308	NA	Intergenic	Intergenic	43263	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA	0.000000	0.437811			-70(ATATCCATGCCAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7516	chr9	9549712	9549912	+	1.66161	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-310799	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7586	chr9	30597730	30597930	+	1.66161	NA	Intergenic	Intergenic	170501	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding	0.020000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5028	chr3	79249354	79249554	+	1.66161	NA	intron (NR_045502, intron 2 of 2)	intron (NR_045502, intron 2 of 2)	36535	NR_045502	70924	Mm.444622	NR_045502	ENSMUSG00000104585	4921511C10Rik	-	RIKEN cDNA 4921511C10 gene	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2444	chr14	35673463	35673663	+	1.66098	NA	Intergenic	Intergenic	138415	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding	0.005000	0.343284	22(AATGAATTATTCAAC,+,0.00),22(AATGAATTATTCAAC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-12	chr1	6448263	6448463	+	1.66092	NA	Intergenic	Intergenic	-38868	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5986	chr5	63278403	63278603	+	1.65867	NA	Intergenic	Intergenic	-370600	NM_177006	319807	Mm.319487	NM_028470	ENSMUSG00000090061	Nwd2	3110047P20Rik|B830017A01Rik|Hn1-ps2|mKIAA1239	NACHT and WD repeat domain containing 2	protein-coding	0.000000	0.358209			85(CTATTATCTTTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5288	chr3	150643825	150644025	+	1.65867	NA	Intergenic	Intergenic	379937	NR_039540	100628568		NR_039540	ENSMUSG00000092830	Mir3963	mmu-mir-3963|mu-mir-3963	microRNA 3963	ncRNA	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4220	chr2	24539366	24539566	+	1.65867	NA	Intergenic	Intergenic	-63867	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3628	chr17	82024270	82024470	+	1.65867	NA	Intergenic	Intergenic	-285983	NM_011406	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1648	chr12	49732547	49732747	+	1.65867	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	-251785	NR_045472	69054	Mm.417838	NR_045472	ENSMUSG00000100844	1810007C17Rik	-	RIKEN cDNA 1810007C17 gene	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7126	chr7	143198140	143198340	+	1.65867	NA	intron (NM_008434, intron 10 of 15)	intron (NM_008434, intron 10 of 15)	90986	NM_008434	16535	Mm.439769	NM_008434	ENSMUSG00000009545	Kcnq1	AW559127|KVLQT1|Kcna9	potassium voltage-gated channel, subfamily Q, member 1	protein-coding	0.020000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-468	chr1	153220000	153220200	+	1.65867	NA	3' UTR (NM_010683, exon 28 of 28)	3' UTR (NM_010683, exon 28 of 28)	-33653	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4730	chr2	153089938	153090138	+	1.65867	NA	Intergenic	Intergenic	-18430	NM_001172117	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4453	chr2	92658492	92658692	+	1.65867	NA	Intergenic	Intergenic	57475	NM_001356553	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KS6ST|KSGAL6ST|KSST	carbohydrate sulfotransferase 1	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1893	chr12	116300046	116300246	+	1.65867	NA	intron (NM_028731, intron 1 of 21)	ORR1B1|LTR|ERVL-MaLR	18924	NM_028731	52635	Mm.273755	NM_028731	ENSMUSG00000021171	Esyt2	2410017M09Rik|4921504I16Rik|CHR2SYT|D12Ertd551e|Fam62b	extended synaptotagmin-like protein 2	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5447	chr4	48483182	48483382	+	1.65867	NA	Intergenic	Intergenic	-9819	NM_172304	269536	Mm.272025	NM_172304	ENSMUSG00000028345	Tex10	2610206N19Rik|2810462N03Rik|BC006867	testis expressed gene 10	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3435	chr17	17196077	17196277	+	1.65867	NA	intron (NM_001357988, intron 1 of 3)	LTRIS2|LTR|ERV1	16872	NM_001357988	626854	Mm.436630	NM_001039232		Gm38396	-	predicted gene, 38396	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4847	chr3	13038691	13038891	+	1.65867	NA	Intergenic	Intergenic	-432864	NM_001357035	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3639	chr17	85101826	85102026	+	1.65795	NA	intron (NM_028576, intron 2 of 10)	intron (NM_028576, intron 2 of 10)	11300	NM_001364946	73582	Mm.260753	NM_028576	ENSMUSG00000071037	Camkmt	1700106N22Rik|AI480743|AV099781|CLNMT|CaM KMT	calmodulin-lysine N-methyltransferase	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5100	chr3	105027527	105027727	+	1.65795	NA	intron (NM_030249, intron 3 of 5)	intron (NM_030249, intron 3 of 5)	25326	NM_001163333	80281	Mm.200327	NM_030249	ENSMUSG00000062127	Cttnbp2nl	AA552995|AA589392|AU018624|BC003236|mKIAA1433	CTTNBP2 N-terminal like	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4328	chr2	58516417	58516617	+	1.65795	NA	intron (NM_007394, intron 2 of 11)	intron (NM_007394, intron 2 of 11)	44893	NM_001355049	11477	Mm.689	NM_007394	ENSMUSG00000026836	Acvr1	ALK2|ActR-I|ActRIA|Acvr|Acvr1a|Acvrlk2|Alk-2|Alk8|D330013D15Rik|SKR1|Tsk7L	activin A receptor, type 1	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3496	chr17	44815954	44816154	+	1.65795	NA	intron (NR_158206, intron 2 of 11)	intron (NR_158206, intron 2 of 11)	-1257	NR_073392	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2902	chr15	45081482	45081682	+	1.65795	NA	Intergenic	Intergenic	33352	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-64	chr1	21910633	21910833	+	1.65756	NA	intron (NM_001160139, intron 1 of 14)	intron (NM_001160139, intron 1 of 14)	51209	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7370	chr8	91551161	91551361	+	1.65684	NA	intron (NM_011936, intron 8 of 8)	intron (NM_011936, intron 8 of 8)	237736	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4925	chr3	42773369	42773569	+	1.65684	NA	Intergenic	Intergenic	1030851	NM_001099785	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4086	chr19	37273794	37273994	+	1.65684	NA	intron (NM_031156, intron 21 of 23)	intron (NM_031156, intron 21 of 23)	-9799	NR_040298	77059	Mm.251476	NR_040298		4931408D14Rik	-	RIKEN cDNA 4931408D14 gene	ncRNA	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3249	chr16	55907592	55907792	+	1.65684	NA	intron (NM_028815, intron 10 of 10)	URR1A|DNA|hAT-Charlie	-12413	NM_001134457	385658	Mm.310635	NM_001134457	ENSMUSG00000075033	Nxpe3	Fam55c|Gm1752|Gm611	neurexophilin and PC-esterase domain family, member 3	protein-coding	0.005000	0.398010			9(AAATTGTAATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7786	chr9	85282994	85283194	+	1.65684	NA	Intergenic	Intergenic	44030	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Tent5a	BAP014|D930050G01Rik|Fam46a	terminal nucleotidyltransferase 5A	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1645	chr12	48880091	48880291	+	1.65684	NA	Intergenic	Intergenic	-502692	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6002	chr5	66947439	66947639	+	1.65684	NA	intron (NM_001368863, intron 3 of 25)	intron (NM_001368863, intron 3 of 25)	-20889	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6908	chr7	74269015	74269215	+	1.65684	NA	Intergenic	Intergenic	-255433	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3066	chr15	103590608	103590808	+	1.65684	NA	Intergenic	Intergenic	-25627	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding	0.000000	0.373134			-71(ATCAACAAAACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1093	chr10	121187180	121187380	+	1.65684	NA	Intergenic	Intergenic	15369	NR_152796	74647	Mm.370609	NR_152796	ENSMUSG00000112846	4930432O09Rik	-	RIKEN cDNA 4930432O09 gene	ncRNA	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6003	chr5	66948020	66948220	+	1.65684	NA	intron (NM_001368863, intron 3 of 25)	intron (NM_001368863, intron 3 of 25)	-20308	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding	0.000000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6285	chr6	5417540	5417740	+	1.65684	NA	intron (NM_001355662, intron 2 of 4)	intron (NM_001355662, intron 2 of 4)	27230	NM_001355662	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-269	chr1	92592882	92593082	+	1.65684	NA	Intergenic	RLTR13B3|LTR|ERVK	-3539	NM_146490	258483	Mm.271573	NM_146490	ENSMUSG00000062497	Olfr1411	MOR208-3	olfactory receptor 1411	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3419	chr17	10678076	10678276	+	1.65684	NA	intron (NM_027032, intron 2 of 4)	intron (NM_027032, intron 2 of 4)	162015	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding	0.000000	0.243781			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3046	chr15	96244061	96244261	+	1.65684	NA	intron (NR_130160, intron 2 of 2)	URR1A|DNA|hAT-Charlie	10523	NR_130160	75768	Mm.212701	NR_130160	ENSMUSG00000097619	4833422M21Rik	4933406G12Rik	RIKEN cDNA 4833422M21 gene	ncRNA	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3410	chr17	5316058	5316258	+	1.65684	NA	intron (NM_001085355, intron 11 of 19)	intron (NM_001085355, intron 11 of 19)	102609	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2471	chr14	47573653	47573853	+	1.65684	NA	Intergenic	ID4|SINE|ID	-5319	NM_172599	100504663	Mm.287279	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2132	chr13	71330519	71330719	+	1.65684	NA	Intergenic	Intergenic	223530	NR_130325	100316804		NR_130325	ENSMUSG00000080580	Mir466f-4	Mirn466f-4|mmu-mir-466f-4	microRNA 466f-4	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3769	chr18	30898416	30898616	+	1.65684	NA	Intergenic	Intergenic	418612	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2526	chr14	65387973	65388173	+	1.65684	NA	intron (NM_199029, intron 3 of 9)	intron (NM_199029, intron 3 of 9)	29397	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2031	chr13	37375071	37375271	+	1.65684	NA	intron (NM_010745, intron 2 of 4)	intron (NM_010745, intron 2 of 4)	29826	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding	0.010000	0.452736			27(TCATGATCATGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3890	chr18	60389586	60389786	+	1.65684	NA	intron (NM_001146275, intron 2 of 2)	L1MA9|LINE|L1	13657	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4104	chr19	48475982	48476182	+	1.65684	NA	intron (NM_025696, intron 2 of 26)	intron (NM_025696, intron 2 of 26)	270057	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-904	chr10	82838252	82838452	+	1.65684	NA	intron (NM_001042523, intron 1 of 14)	intron (NM_001042523, intron 1 of 14)	4401	NM_001042523	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding	0.015000	0.373134			40(CCTTTTTCATGTTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1456	chr11	108724618	108724818	+	1.65684	NA	intron (NM_029586, intron 1 of 4)	MTE2a|LTR|ERVL-MaLR	42100	NM_029586	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding	0.005000	0.353234			30(ATATCCATGAAAATTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-971	chr10	97653868	97654068	+	1.65684	NA	intron (NM_007884, intron 3 of 7)	Lx3C|LINE|L1	9900	NM_007884	13516	Mm.148886	NM_007884	ENSMUSG00000019936	Epyc	Dspg3|PG-Lb|SLRR3B	epiphycan	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1655	chr12	51787956	51788156	+	1.65684	NA	intron (NM_144788, intron 15 of 42)	intron (NM_144788, intron 15 of 42)	41480	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain E3 ubiquitin protein ligase 1	protein-coding	0.025000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1743	chr12	75602350	75602550	+	1.65684	NA	Intergenic	Intergenic	-6218	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4318	chr2	55706545	55706745	+	1.65684	NA	Intergenic	Intergenic	270675	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7539	chr9	15853930	15854130	+	1.65684	NA	Intergenic	L1_Mur3|LINE|L1	20526	NM_145712	244701	Mm.222631	NM_145712	ENSMUSG00000050901	Mtnr1b	Mel-1B-R|Mel1b|Mt2	melatonin receptor 1B	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6893	chr7	70155184	70155384	+	1.65684	NA	Intergenic	Intergenic	182538	NR_131145	624549	Mm.116344	NR_131144	ENSMUSG00000109097	Gm29683	Gm44536	predicted gene, 29683	ncRNA	0.000000	0.442786			-7(ATTTACAATGCAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6685	chr6	116986590	116986790	+	1.65684	NA	Intergenic	Intergenic	-181845	NM_013655	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1894	chr12	116331639	116331839	+	1.65684	NA	intron (NM_028731, intron 6 of 21)	Lx7|LINE|L1	50517	NM_028731	52635	Mm.273755	NM_028731	ENSMUSG00000021171	Esyt2	2410017M09Rik|4921504I16Rik|CHR2SYT|D12Ertd551e|Fam62b	extended synaptotagmin-like protein 2	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8115	chrX	146428583	146428783	+	1.65684	NA	Intergenic	RLTR17|LTR|ERVK	-533830	NM_008312	15560	Mm.439670	NM_008312	ENSMUSG00000041380	Htr2c	5-HT2C|5-HT2cR|5-HTR2C|5HT1c|Htr1c|SR1	5-hydroxytryptamine (serotonin) receptor 2C	protein-coding	0.000000	0.462687			-37(CCACTGTTATGGATAT,+,0.00),-3(GTATTTTGATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5669	chr4	104837493	104837693	+	1.65402	NA	intron (NM_146148, intron 7 of 10)	intron (NM_146148, intron 7 of 10)	38805	NM_146148	230558	Mm.197638	NM_146148	ENSMUSG00000035031	C8a	-	complement component 8, alpha polypeptide	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7331	chr8	78119932	78120132	+	1.65396	NA	Intergenic	Intergenic	-93310	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3973	chr18	84267711	84267911	+	1.65396	NA	intron (NM_001033341, intron 8 of 8)	intron (NM_001033341, intron 8 of 8)	179653	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3677	chr18	3901695	3901895	+	1.65396	NA	Intergenic	Intergenic	-264037	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding	0.010000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-307	chr14	86788752	86788952	+	1.65253	NA	intron (NM_019670, intron 25 of 27)	intron (NM_019670, intron 25 of 27)	352372	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-645	chr1	192778771	192778971	+	1.65253	NA	Intergenic	Intergenic	-7652	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7588	chr9	30676935	30677135	+	1.65050	NA	Intergenic	Intergenic	243915	NM_001329420	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2454	chr14	38371913	38372113	+	1.65050	NA	intron (NM_001190187, intron 8 of 9)	intron (NM_001190187, intron 8 of 9)	-526289	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.005000	0.268657			6(ATATTATAATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7877	chr9	110345208	110345408	+	1.65050	NA	intron (NM_001001144, intron 1 of 22)	intron (NM_001001144, intron 1 of 22)	11952	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding	0.000000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2419	chr14	30091706	30091906	+	1.65050	NA	intron (NM_001083616, intron 29 of 46)	intron (NM_001083616, intron 29 of 46)	69173	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding	0.005000	0.487562			-18(GATTTGTGATGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1911	chr12	117973449	117973649	+	1.65050	NA	intron (NM_010060, intron 60 of 81)	intron (NM_010060, intron 60 of 81)	129688	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1441	chr11	104246116	104246316	+	1.65028	NA	intron (NM_001038609, intron 1 of 11)	intron (NM_001038609, intron 1 of 11)	14780	NM_010838	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8030	chrX	97063456	97063656	+	1.65028	NA	Intergenic	Intergenic	-9040	NM_001033361	245526	Mm.336164	NM_001033361	ENSMUSG00000031212	Pgr15l	-	G protein-coupled receptor 15-like	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2948	chr15	59130199	59130399	+	1.65028	NA	Intergenic	Intergenic	-48273	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	MTSS I-BAR domain containing 1	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4144	chr19	60765834	60766034	+	1.65028	NA	intron (NM_010123, intron 19 of 21)	intron (NM_010123, intron 19 of 21)	8451	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5601	chr4	91362504	91362704	+	1.65028	NA	intron (NM_001347149, intron 1 of 7)	intron (NM_001347149, intron 1 of 7)	9451	NM_010486	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV like RNA binding protein 1	protein-coding	0.005000	0.383085			-22(TCTCTGCTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5362	chr4	17946150	17946350	+	1.65028	NA	intron (NR_135158, intron 2 of 11)	intron (NR_135158, intron 2 of 11)	92792	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2141	chr13	73457441	73457641	+	1.65028	NA	Intergenic	Intergenic	-9690	NM_145376	210992	Mm.284649	NM_145376	ENSMUSG00000021608	Lpcat1	2900035H07Rik|Aytl2|BB137372|BC005662|C87117|LPCAT|LPCAT-1|lysoPAFAT|mLPCAT1|rd11	lysophosphatidylcholine acyltransferase 1	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-947	chr10	93306101	93306301	+	1.65028	NA	intron (NM_013508, intron 1 of 4)	intron (NM_013508, intron 1 of 4)	4958	NM_001322265	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2070	chr13	51295295	51295495	+	1.65028	NA	Intergenic	L1M2|LINE|L1	-92329	NR_132443	667728		NR_132443		Hist1h2al	EG667728	histone cluster 1, H2al	pseudo	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-331	chr1	120713317	120713517	+	1.65028	NA	Intergenic	B4A|SINE|B4	110930	NM_010133	13798	Mm.2657	NM_010133	ENSMUSG00000058665	En1	En-1|Mo-en.1|engrailed-1	engrailed 1	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8169	chrX	167972692	167972892	+	1.64914	NA	intron (NM_001033330, intron 3 of 19)	L1_Mus2|LINE|L1	-117715	NM_001290428	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding	0.000000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-570	chr3	115844671	115844871	+	1.64849	NA	Intergenic	Intergenic	43288	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA	0.000000	0.447761			-45(ATATCCATGCCAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5752	chr4	131697192	131697392	+	1.64773	NA	Intergenic	L1MEf|LINE|L1	140986	NM_001083119	19273	Mm.4860	NM_011214	ENSMUSG00000028909	Ptpru	Ftp-1|PCP-2|PTP|PTP-lambda|PTPlambda|Pcp2|Ptpf|Ptprl|R-PTP-U|R-PTP-psi|RPTPlambda	protein tyrosine phosphatase, receptor type, U	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5195	chr3	132678211	132678411	+	1.64773	NA	intron (NM_001368626, intron 1 of 6)	intron (NM_001368626, intron 1 of 6)	5568	NM_007926	13722	Mm.235137	NM_007926	ENSMUSG00000028029	Aimp1	9830137A06Rik|AIMP1/p43|EMAPII|Emap2|Scye1|p43	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1	protein-coding	0.015000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1660	chr12	52300869	52301069	+	1.64773	NA	intron (NM_029760, intron 8 of 10)	intron (NM_029760, intron 8 of 10)	179640	NR_136881	102638611	Mm.363799	NR_136881	ENSMUSG00000111982	Gm35135	-	predicted gene, 35135	ncRNA	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4108	chr19	49242765	49242965	+	1.64773	NA	Intergenic	Intergenic	1036840	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0.005000	0.427861			-55(ATTTACATTACTAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4464	chr2	96331731	96331931	+	1.64773	NA	intron (NM_001363047, intron 1 of 8)	intron (NM_001363047, intron 1 of 8)	13662	NM_001289743	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4122	chr19	53632485	53632685	+	1.64773	NA	intron (NM_007790, intron 18 of 28)	(TTTTTG)n|Simple_repeat|Simple_repeat	32189	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding	0.000000	0.338308			-29(ATCTGAATGAAAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5738	chr4	126730137	126730337	+	1.64773	NA	intron (NM_198960, intron 3 of 6)	L1MB8|LINE|L1	6032	NM_198960	332937	Mm.331881	NM_198960	ENSMUSG00000042477	Tfap2e	AI505200|AP-2e|Tcfap2e	transcription factor AP-2, epsilon	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7884	chr9	113000886	113001086	+	1.64773	NA	Intergenic	L1_Mus3|LINE|L1	586166	NR_040760	102688	Mm.394901	NR_040760	ENSMUSG00000109890	AU023762	-	expressed sequence AU023762	ncRNA	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-397	chr1	136638835	136639035	+	1.64773	NA	Intergenic	Intergenic	14034	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3003	chr15	80768356	80768556	+	1.64773	NA	intron (NM_144812, intron 3 of 24)	intron (NM_144812, intron 3 of 24)	-30154	NM_177124	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5988	chr5	63678061	63678261	+	1.64773	NA	intron (NM_177006, intron 1 of 6)	intron (NM_177006, intron 1 of 6)	29058	NM_177006	319807	Mm.319487	NM_028470	ENSMUSG00000090061	Nwd2	3110047P20Rik|B830017A01Rik|Hn1-ps2|mKIAA1239	NACHT and WD repeat domain containing 2	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1835	chr12	98273576	98273776	+	1.64773	NA	intron (NM_008152, intron 1 of 1)	intron (NM_008152, intron 1 of 1)	5041	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding	0.020000	0.447761	24(CATGTTTTATTCATG,+,0.00),24(CATGTTTTATTCATG,-,0.00)		-21(TTTTCCATCACAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5913	chr5	40359427	40359627	+	1.64773	NA	Intergenic	L1MA9|LINE|L1	-714896	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7597	chr9	32097951	32098151	+	1.64773	NA	intron (NM_001370958, intron 1 of 22)	MTE-int|LTR|ERVL-MaLR	-17937	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7302	chr8	67423844	67424044	+	1.64773	NA	Intergenic	RLTR13D6|LTR|ERVK	-67024	NM_008673	17960	Mm.14125	NM_008673	ENSMUSG00000025588	Nat1	Nat-1	N-acetyl transferase 1	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1107	chr10	123373442	123373642	+	1.64773	NA	intron (NM_001252387, intron 1 of 4)	intron (NM_001252387, intron 1 of 4)	109466	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Tafa2	6330575M02|FAM19A2 TAFA-2|Fam19a2|Sam2|Tafa-2	TAFA chemokine like family member 2	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6967	chr7	91724486	91724686	+	1.64773	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	-337808	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs large MAGUK scaffold protein 2	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4045	chr19	21951287	21951487	+	1.64773	NA	Intergenic	Intergenic	173047	NM_001033759	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Cemip2	Tmem2	cell migration inducing hyaluronidase 2	protein-coding	0.010000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6188	chr5	130338058	130338258	+	1.64773	NA	intron (NM_001015876, intron 15 of 15)	intron (NM_001015876, intron 15 of 15)	-31300	NM_181045	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4470	chr2	101516933	101517133	+	1.64773	NA	Intergenic	Intergenic	104013	NM_001362687	68170	Mm.31263	NM_026592	ENSMUSG00000027165	B230118H07Rik	NWC	RIKEN cDNA B230118H07 gene	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3377	chr16	89294238	89294438	+	1.64773	NA	Intergenic	L1M3|LINE|L1	88477	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding	0.005000	0.467662			-6(ATTTGCAAGGCATTTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5953	chr5	51932573	51932773	+	1.64773	NA	Intergenic	MamTip2|DNA|hAT-Tip100	203344	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3281	chr16	64833802	64834002	+	1.64773	NA	intron (NM_001347245, intron 1 of 8)	intron (NM_001347245, intron 1 of 8)	17821	NM_001347245	72020	Mm.25960	NM_028059	ENSMUSG00000047141	Zfp654	1600021C16Rik|1810008K20Rik|433036|Gm5488|Znf654	zinc finger protein 654	protein-coding	0.000000	0.273632			-15(TATTTGTGATTTAAAG,+,0.00),10(ATTTTGTATTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6796	chr7	16966154	16966354	+	1.64773	NA	Intergenic	RLTR11A|LTR|ERVK	6575	NM_001007569	71691	Mm.275673	NM_001007569	ENSMUSG00000041141	Pnmal1	0710005I19Rik|4930488B01Rik|AI844408|Pnma8a|R74771	PNMA-like 1	protein-coding	0.000000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7604	chr9	34144605	34144805	+	1.64773	NA	Intergenic	Intergenic	102334	NR_040744	77119	Mm.367930	NR_040744	ENSMUSG00000098758	7630403G23Rik	TH-cre|Tg(Th-cre)1Tmd	RIKEN cDNA 7630403G23 gene	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5562	chr4	81898107	81898307	+	1.64773	NA	Intergenic	Intergenic	-167173	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1528	chr12	6919888	6920088	+	1.64773	NA	Intergenic	Intergenic	460342	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4715	chr2	148578016	148578216	+	1.64773	NA	Intergenic	Intergenic	-94499	NM_019761	56488	Mm.34663	NM_019761	ENSMUSG00000036992	Nxt1	1110001N02Rik	NTF2-related export protein 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2209	chr13	93302566	93302766	+	1.64743	NA	Intergenic	Intergenic	-1091	NM_147176	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3260	chr16	58501778	58501978	+	1.64743	NA	intron (NM_018784, intron 2 of 10)	intron (NM_018784, intron 2 of 10)	21548	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding	0.010000	0.487562			-21(GCTTTGCCATTCAGAT,+,0.00),-7(ATTTCTTCATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6890	chr7	68548665	68548865	+	1.64743	NA	Intergenic	Intergenic	-69691	NR_003648	384639	Mm.261760	NM_001013781		Gm5334	EG384639	tetraspanin 7 pseudogene	pseudo	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4653	chr2	136840516	136840716	+	1.64731	NA	Intergenic	Intergenic	-50602	NM_028201	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding	0.000000	0.388060			-40(CATTACTTATTTAAAT,+,0.00),-32(ATTTAAATGGCAACAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1970	chr13	19413674	19413874	+	1.64373	NA	Intergenic	Intergenic	-17961	NM_001347485	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding	0.000000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-230	chr13	19413695	19413895	+	1.64373	NA	Intergenic	Intergenic	-17982	NM_001347485	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-690	chr10	8841439	8841639	+	1.64365	NA	intron (NM_175155, intron 2 of 19)	RMER10B|LTR|ERVL	44531	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1351	chr11	74881159	74881359	+	1.64365	NA	intron (NM_197943, intron 2 of 22)	B4|SINE|B4	-13065	NR_105891	102465558		NR_105891	ENSMUSG00000098317	Mir6926	Gm27949|mmu-mir-6926	microRNA 6926	ncRNA	0.015000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-841	chr8	79498749	79498949	+	1.64320	NA	Intergenic	Intergenic	-99421	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Mad1|Madh1|Madr1|Mlp1|MusMLP|dwf-A|mMad1	SMAD family member 1	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6720	chr6	134014885	134015085	+	1.64271	NA	Intergenic	L1_Mur3|LINE|L1	-20715	NM_001303102	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5423	chr4	35549975	35550175	+	1.64271	NA	Intergenic	Intergenic	295129	NM_175516	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.005000	0.358209			3(TTTTTATGATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-635	chr1	189839288	189839488	+	1.64271	NA	intron (NM_008976, intron 8 of 18)	intron (NM_008976, intron 8 of 18)	82903	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-643	chr1	192421863	192422063	+	1.64271	NA	intron (NM_001038607, intron 9 of 10)	intron (NM_001038607, intron 9 of 10)	231186	NM_010600	16510	Mm.4489	NM_010600	ENSMUSG00000058248	Kcnh1	EAG1|Kv10.1|M-eag	potassium voltage-gated channel, subfamily H (eag-related), member 1	protein-coding	0.025000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5105	chr3	107948836	107949036	+	1.64271	NA	Intergenic	L1MB3|LINE|L1	-5187	NM_008184	14867	Mm.458154	NM_008184	ENSMUSG00000068762	Gstm6	-	glutathione S-transferase, mu 6	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-289	chr1	97821318	97821518	+	1.64271	NA	3' UTR (NM_013626, exon 26 of 26)	3' UTR (NM_013626, exon 26 of 26)	51246	NM_001310773	252876	Mm.86090	NM_026250	ENSMUSG00000026333	Gin1	4930429M06Rik|8430411H10Rik|Gin-1|Zh2c2	gypsy retrotransposon integrase 1	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5385	chr4	25676276	25676476	+	1.64271	NA	intron (NM_010243, intron 2 of 2)	intron (NM_010243, intron 2 of 2)	123627	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1710	chr12	69539593	69539793	+	1.64135	NA	Intergenic	Intergenic	43335	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding	0.020000	0.422886			20(CTATTCATAACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5224	chr3	137880328	137880528	+	1.64135	NA	intron (NM_001033155, intron 1 of 7)	intron (NM_001033155, intron 1 of 7)	12753	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding	0.000000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-163	chr11	96720322	96720522	+	1.64135	NA	intron (NM_001177898, intron 9 of 10)	intron (NM_001177898, intron 9 of 10)	57133	NM_001163389	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding	0.030000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4986	chr3	65457405	65457605	+	1.64135	NA	Intergenic	L1MB3|LINE|L1	-64952	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding	0.000000	0.328358			-55(ATTATGTAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3209	chr16	46296447	46296647	+	1.64135	NA	Intergenic	Intergenic	-141470	NM_001304528	11615	Mm.330692	NM_001304528	ENSMUSG00000048087	Gm4737	AL024110|EG11615	predicted gene 4737	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4759	chr2	159873667	159873867	+	1.64135	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-73574	NR_040498	71081	Mm.383491	NR_040498	ENSMUSG00000085198	4933416E03Rik	-	RIKEN cDNA 4933416E03 gene	ncRNA	0.010000	0.477612			16(CTTTGCAAGGCAGAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7400	chr8	98810746	98810946	+	1.64135	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-201041	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	-	predicted gene 15679	ncRNA	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2873	chr15	39615595	39615795	+	1.63970	NA	intron (NM_053271, intron 21 of 26)	intron (NM_053271, intron 21 of 26)	-43816	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding	0.025000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7661	chr9	54612824	54613024	+	1.63970	NA	intron (NM_053178, intron 11 of 13)	intron (NM_053178, intron 11 of 13)	26413	NM_029573	67834	Mm.279195	NM_029573	ENSMUSG00000032279	Idh3a	1110003P10Rik|1500012E04Rik|AA407078|AI316514	isocitrate dehydrogenase 3 (NAD+) alpha	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3263	chr16	58649971	58650171	+	1.63970	NA	Intergenic	Intergenic	-11668	NM_175011	224247	Mm.26145	NM_175011	ENSMUSG00000055789	E330017A01Rik	-	RIKEN cDNA E330017A01 gene	protein-coding	0.020000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4758	chr2	159871295	159871495	+	1.63970	NA	Intergenic	Intergenic	-75946	NR_040498	71081	Mm.383491	NR_040498	ENSMUSG00000085198	4933416E03Rik	-	RIKEN cDNA 4933416E03 gene	ncRNA	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7359	chr8	83731975	83732175	+	1.63970	NA	intron (NM_011925, intron 4 of 19)	intron (NM_011925, intron 4 of 19)	-8091	NR_106188	102465897		NR_106188	ENSMUSG00000098465	Mir1668	Gm27590|mmu-mir-1668	microRNA 1668	ncRNA	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5597	chr4	90960489	90960689	+	1.63970	NA	Intergenic	Intergenic	411466	NM_010486	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV like RNA binding protein 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5879	chr5	27724603	27724803	+	1.63970	NA	intron (NM_010075, intron 25 of 25)	intron (NM_010075, intron 25 of 25)	66847	NM_018878	55982	Mm.277190	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5186	chr3	129151837	129152037	+	1.63970	NA	Intergenic	Intergenic	-47941	NM_011098	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding	0.010000	0.283582		0(TATACTTATGCATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3321	chr16	75961496	75961696	+	1.63970	NA	Intergenic	Intergenic	-39188	NR_155447	102632240	Mm.417237	NR_155447	ENSMUSG00000087214	Gm15555	-	predicted gene 15555	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6880	chr7	65361789	65361989	+	1.63970	NA	intron (NM_001163574, intron 1 of 26)	intron (NM_001163574, intron 1 of 26)	9355	NM_009386	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6596	chr6	95287499	95287699	+	1.63970	NA	Intergenic	Intergenic	46394	NR_033559	414067	Mm.355990	NR_033559	ENSMUSG00000068180	AY512915	-	cDNA sequence AY512915	ncRNA	0.005000	0.358209			57(ATATGAAACACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5867	chr5	25154365	25154565	+	1.63970	NA	Intergenic	Intergenic	-27015	NM_026449	67909	Mm.141471	NM_026449	ENSMUSG00000028938	Galntl5	1700021B12Rik|Galnt15	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5	protein-coding	0.010000	0.442786			36(TCTTTGTGTGGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8083	chrX	132588366	132588566	+	1.63970	NA	Intergenic	Lx|LINE|L1	-1099314	NR_153117	102632590	Mm.403836	NR_153117	ENSMUSG00000096978	Gm26851	-	predicted gene, 26851	ncRNA	0.000000	0.353234			31(AATTGAATAAAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4756	chr2	159508369	159508569	+	1.63970	NA	Intergenic	L1ME1|LINE|L1	-438872	NR_040498	71081	Mm.383491	NR_040498	ENSMUSG00000085198	4933416E03Rik	-	RIKEN cDNA 4933416E03 gene	ncRNA	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7813	chr9	92806729	92806929	+	1.63970	NA	Intergenic	Intergenic	88113	NR_040770	331003	Mm.50805	NR_040770	ENSMUSG00000101734	4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	ncRNA	0.000000	0.358209			-37(CCTGTGTCTTTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7237	chr8	47703515	47703715	+	1.63970	NA	Intergenic	Intergenic	10316	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding	0.000000	0.378109			-29(ATATACATAAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-820	chr10	52460713	52460913	+	1.63970	NA	Intergenic	Intergenic	43266	NM_030250	52014	Mm.199964	NM_030250	ENSMUSG00000023068	Nus1	1600027K07Rik|AU019165|AW538011|BC003223|D10Ertd438e	NUS1 dehydrodolichyl diphosphate synthase subunit	protein-coding	0.005000	0.427861		71(CTTGCAAATGCATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7300	chr8	66994153	66994353	+	1.63970	NA	Intergenic	MTE2a-int|LTR|ERVL-MaLR	134036	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 ribonucleoprotein	protein-coding	0.000000	0.338308		1(AATGAATTTGCATA,+,0.00),1(AATGAATTTGCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7796	chr9	86728657	86728857	+	1.63970	NA	Intergenic	Intergenic	-14876	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	protease, serine 35	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7355	chr8	81992119	81992319	+	1.63970	NA	intron (NM_001297593, intron 14 of 23)	intron (NM_001297593, intron 14 of 23)	410367	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4359	chr2	65490302	65490502	+	1.63970	NA	intron (NM_001355168, intron 17 of 26)	intron (NM_001355168, intron 17 of 26)	77090	NM_001355171	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	sodium channel, voltage-gated, type III, alpha	protein-coding	0.010000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7793	chr9	86394495	86394695	+	1.63970	NA	intron (NM_027394, intron 8 of 9)	intron (NM_027394, intron 8 of 9)	70321	NM_027394	70348	Mm.53469	NM_027394	ENSMUSG00000032415	Ube2cbp	2610018I03Rik|Ube3d	ubiquitin-conjugating enzyme E2C binding protein	protein-coding	0.005000	0.353234			-52(ATTTGAAAAAAAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-761	chr10	31527731	31527931	+	1.63970	NA	intron (NM_001146349, intron 2 of 5)	intron (NM_001146349, intron 2 of 5)	-81873	NM_001359366	21987	Mm.439966	NM_009413	ENSMUSG00000000296	Tpd52l1	D53	tumor protein D52-like 1	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2784	chr15	10297939	10298139	+	1.63970	NA	intron (NM_001253782, intron 1 of 8)	intron (NM_001253782, intron 1 of 8)	4388	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0.005000	0.333333			-5(CCTTTAGCATGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3635	chr17	83764717	83764917	+	1.63970	NA	intron (NM_001171054, intron 7 of 13)	intron (NM_001171054, intron 7 of 13)	58654	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6130	chr5	105840045	105840245	+	1.63970	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-36423	NM_018759	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2173	chr13	83461640	83461840	+	1.63970	NA	Intergenic	Intergenic	-42294	NM_025282	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1021	chr10	110283441	110283641	+	1.63970	NA	Intergenic	Intergenic	-283151	NM_001368815	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2690	chr14	110341137	110341337	+	1.63970	NA	Intergenic	Intergenic	413912	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	SLIT and NTRK-like family, member 6	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7015	chr7	109082481	109082681	+	1.63970	NA	intron (NM_178780, intron 1 of 4)	intron (NM_178780, intron 1 of 4)	743	NM_001038624	320360	Mm.71007	NM_178780	ENSMUSG00000048330	Ric3	E130307J04Rik	RIC3 acetylcholine receptor chaperone	protein-coding	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1159	chr11	11725560	11725760	+	1.63970	NA	intron (NM_001301865, intron 3 of 6)	intron (NM_001301865, intron 3 of 6)	35483	NM_001301865	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1260	chr11	42594591	42594791	+	1.63970	NA	intron (NM_001362646, intron 8 of 9)	intron (NM_001362646, intron 8 of 9)	173490	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding	0.005000	0.368159			15(CATTTCTCATTCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6806	chr7	29071395	29071595	+	1.63857	NA	intron (NM_009109, intron 49 of 105)	intron (NM_009109, intron 49 of 105)	12199	NR_035489	100316710		NR_035489	ENSMUSG00000089219	Mir1963	mir-1963|mmu-mir-1963	microRNA 1963	ncRNA	0.040000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2603	chr14	86788722	86788922	+	1.63819	NA	intron (NM_019670, intron 25 of 27)	intron (NM_019670, intron 25 of 27)	352402	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3245	chr16	55628046	55628246	+	1.63819	NA	Intergenic	RMER12|LTR|ERVK	133415	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA	0.010000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-458	chr19	22284904	22285104	+	1.63797	NA	intron (NM_001035239, intron 1 of 24)	intron (NM_001035239, intron 1 of 24)	145958	NM_001035243	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6752	chr6	140443926	140444126	+	1.63778	NA	intron (NM_144920, intron 3 of 30)	L1MA5|LINE|L1	19927	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding	0.015000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-528	chr2	135084454	135084654	+	1.63778	NA	intron (NM_001145830, intron 3 of 31)	intron (NM_001145830, intron 3 of 31)	131062	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5945	chr5	50178583	50178783	+	1.63731	NA	Intergenic	Intergenic	27350	NR_040696	73965	Mm.243823	NR_040696	ENSMUSG00000104870	4930448I18Rik	-	RIKEN cDNA 4930448I18 gene	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6753	chr6	140791912	140792112	+	1.63731	NA	Intergenic	Intergenic	165127	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2096	chr13	60079965	60080165	+	1.63731	NA	intron (NR_046142, intron 1 of 2)	intron (NR_046142, intron 1 of 2)	50354	NR_046142	328263	Mm.123405	NR_046142	ENSMUSG00000114531	A530065N20Rik	A530065N20	RIKEN cDNA A530046M15 gene	ncRNA	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6776	chr6	147612755	147612955	+	1.63731	NA	intron (NM_001355713, intron 12 of 12)	intron (NM_001355713, intron 12 of 12)	-77386	NR_033636	100039727	Mm.396220	NR_033636	ENSMUSG00000085077	1700049E15Rik	Gm15761	RIKEN cDNA 1700049E15 gene	ncRNA	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5326	chr4	6115891	6116091	+	1.63731	NA	Intergenic	RLTR13D6|LTR|ERVK	-75114	NM_026534	68053	Mm.404043	NM_026534	ENSMUSG00000028243	Ubxn2b	3110003A22Rik|6430407D20Rik|AI451665|p37	UBX domain protein 2B	protein-coding	0.015000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-901	chrX	83740659	83740859	+	1.63581	NA	intron (NM_007868, intron 17 of 78)	intron (NM_007868, intron 17 of 78)	-252835	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0.005000	0.333333			63(AATTGCACAAGAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5351	chr4	13864895	13865095	+	1.63581	NA	intron (NM_009822, intron 6 of 10)	intron (NM_009822, intron 6 of 10)	80213	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	RUNX1 translocation partner 1	protein-coding	0.000000	0.402985			33(TCATTGTGATTCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7187	chr8	30659654	30659854	+	1.63581	NA	Intergenic	ID_B1|SINE|B4	91359	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	ncRNA	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-500	chr1	161748820	161749020	+	1.63581	NA	Intergenic	Intergenic	39575	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding	0.020000	0.452736			2(TCTTTGCAATGCAAAA,+,0.00),3(CTTTGCAATGCAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6147	chr5	109661420	109661620	+	1.63581	NA	Intergenic	Intergenic	-102527	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding	0.015000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3070	chr16	8189386	8189586	+	1.63581	NA	Intergenic	Intergenic	235650	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Tmem114	4930511J11Rik|Cldn26	transmembrane protein 114	protein-coding	0.000000	0.308458			-35(TTTTCCATTAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3347	chr16	83022879	83023079	+	1.63565	NA	Intergenic	Intergenic	-1348164	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.005000	0.303483			22(ATTATCATAAGAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-525	chr1	167969662	167969862	+	1.63266	NA	Intergenic	Intergenic	280204	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1115	chr10	124317653	124317853	+	1.63251	NA	Intergenic	Lx7|LINE|L1	-151321	NR_028310	75030	Mm.159403	NR_028310	ENSMUSG00000112364	4930503E24Rik	-	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1390	chr11	86743505	86743705	+	1.63251	NA	intron (NM_001003908, intron 1 of 31)	intron (NM_001003908, intron 1 of 31)	13962	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3464	chr17	30506293	30506493	+	1.63251	NA	intron (NM_172618, intron 6 of 11)	intron (NM_172618, intron 6 of 11)	69894	NM_027060	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7394	chr8	97477046	97477246	+	1.63251	NA	Intergenic	Intergenic	-1534741	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	-	predicted gene 15679	ncRNA	0.000000	0.393035			-70(TCTTTCTCATTCAAAA,+,0.00),16(CCATTTACATGTAAAT,+,0.00),18(ATTTACATGTAAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3678	chr18	4243418	4243618	+	1.63251	NA	Intergenic	Intergenic	77686	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1777	chr12	82990738	82990938	+	1.63251	NA	intron (NM_015812, intron 3 of 16)	intron (NM_015812, intron 3 of 16)	-51683	NR_046045	74283	Mm.398247	NR_046045	ENSMUSG00000100890	1700085C21Rik	-	RIKEN cDNA 1700085C21 gene	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2334	chr14	7772257	7772457	+	1.63251	NA	Intergenic	Intergenic	-45600	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding	0.005000	0.427861			26(CTTAACATAACAACAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3562	chr17	66073141	66073341	+	1.63251	NA	intron (NM_001025572, intron 1 of 12)	intron (NM_001025572, intron 1 of 12)	3805	NM_001025572	106585	Mm.34706	NM_001025572	ENSMUSG00000034647	Ankrd12	2900001A12Rik|AI447928|ANCO-2|AV347965|GAC-1|mKIAA0874	ankyrin repeat domain 12	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-830	chr10	56144628	56144828	+	1.63251	NA	intron (NM_001033385, intron 20 of 32)	intron (NM_001033385, intron 20 of 32)	37811	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	MSL3 like 2	protein-coding	0.010000	0.278607			81(TTTTTGTATTTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1913	chr12	118530643	118530843	+	1.63251	NA	promoter-TSS (NR_045947)	promoter-TSS (NR_045947)	-550	NR_045947	100384890	Mm.484658	NR_045947	ENSMUSG00000113875	D230030E09Rik	Npe	Riken cDNA D230030E09 gene	ncRNA	0.045000	0.621891			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2829	chr15	25143885	25144085	+	1.63251	NA	Intergenic	Intergenic	269779	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4549	chr2	118266124	118266324	+	1.63251	NA	Intergenic	Intergenic	-9258	NM_027759	71313	Mm.85046	NM_027759	ENSMUSG00000027344	Fsip1	1700012M13Rik|4933432K11Rik	fibrous sheath-interacting protein 1	protein-coding	0.000000	0.388060	-13(CTTGCATTTTGCATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7833	chr9	95557359	95557559	+	1.63251	NA	Intergenic	ID_B1|SINE|B4	-2358	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3075	chr16	9567385	9567585	+	1.63251	NA	TTS (NM_008170)	TTS (NM_008170)	428328	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|GluRepsilon1|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding	0.005000	0.407960			-31(ATTTGCATGACCCTTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2279	chr13	108614530	108614730	+	1.63251	NA	Intergenic	Intergenic	-39547	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5872	chr5	26404972	26405172	+	1.63251	NA	Intergenic	Intergenic	88242	NR_029445	75942	Mm.50087	NR_029445	ENSMUSG00000029044	4930584F24Rik	1700001J09Rik|4930522C06Rik	RIKEN cDNA 4930584F24 gene	ncRNA	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1049	chr10	114841630	114841830	+	1.63251	NA	Intergenic	Intergenic	40004	NR_155864	102633245		NR_155864		Gm15723	-	predicted gene 15723	ncRNA	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3368	chr16	87633907	87634107	+	1.63251	NA	Intergenic	Intergenic	-64947	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8072	chrX	128430065	128430265	+	1.63251	NA	Intergenic	Intergenic	-621359	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	ncRNA	0.000000	0.303483			64(ATTAATATAATAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5828	chr5	12688405	12688605	+	1.63251	NA	Intergenic	Intergenic	305339	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2560	chr14	77146464	77146664	+	1.63142	NA	Intergenic	Intergenic	-10199	NM_001253759	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.000000	0.343284			53(ATTAGAATAAAAGAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5470	chr4	53508102	53508302	+	1.63142	NA	intron (NM_133891, intron 3 of 15)	intron (NM_133891, intron 3 of 15)	67789	NM_133891	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5116	chr3	110011372	110011572	+	1.63142	NA	intron (NM_030699, intron 2 of 7)	intron (NM_030699, intron 2 of 7)	132000	NM_001163348	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding	0.025000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3465	chr17	30506962	30507162	+	1.63030	NA	intron (NM_172618, intron 6 of 11)	intron (NM_172618, intron 6 of 11)	69225	NM_027060	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3792	chr18	36215598	36215798	+	1.62950	NA	Intergenic	L1M5|LINE|L1	-18307	NM_001167891	100042150	Mm.380390	NM_001167891	ENSMUSG00000060275	Nrg2	Don1|NTAK	neuregulin 2	protein-coding	0.000000	0.313433			-89(ATTTGAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1444	chr11	105210369	105210569	+	1.62950	NA	intron (NM_001361996, intron 5 of 19)	intron (NM_001361996, intron 5 of 19)	28942	NM_001294329	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding	0.005000	0.373134	39(TTTGAATTATTCATA,+,0.00),39(TTTGAATTATTCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-850	chr10	63318539	63318739	+	1.62950	NA	TTS (NM_030114)	TTS (NM_030114)	20396	NM_019812	93759	Mm.351459	NM_019812	ENSMUSG00000020063	Sirt1	AA673258|SIR2L1|Sir2|Sir2a|Sir2alpha	sirtuin 1	protein-coding	0.010000	0.452736			-44(CCTTTTTCCTTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4621	chr2	132601907	132602107	+	1.62950	NA	intron (NR_033469, intron 1 of 3)	intron (NR_033469, intron 1 of 3)	3811	NR_033468	767814	Mm.371752	NR_033468	ENSMUSG00000074783	AU019990	-	expressed sequence AU019990	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3438	chr17	20966684	20966884	+	1.62950	NA	TTS (NM_016891)	TTS (NM_016891)	21330	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding	0.000000	0.388060			-50(TTTTGCAAAAGAATTC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-603	chr3	157487935	157488135	+	1.62911	NA	Intergenic	Intergenic	46055	NR_152231	381498	Mm.402095	NR_152231	ENSMUSG00000105834	4930592C13Rik	Gm1657|Gm43159	RIKEN cDNA 4930592C13 gene	ncRNA	0.000000	0.368159			-53(ATTTCAATGAGAAAGA,-,0.00),-24(ATTAACATGAAAACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5315	chr3	157487952	157488152	+	1.62911	NA	Intergenic	Intergenic	46038	NR_152231	381498	Mm.402095	NR_152231	ENSMUSG00000105834	4930592C13Rik	Gm1657|Gm43159	RIKEN cDNA 4930592C13 gene	ncRNA	0.000000	0.353234			-70(ATTTCAATGAGAAAGA,-,0.00),-41(ATTAACATGAAAACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1900	chr12	116877426	116877626	+	1.62601	NA	intron (NM_011215, intron 9 of 22)	intron (NM_011215, intron 9 of 22)	273743	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6008	chr5	67860502	67860702	+	1.62601	NA	Intergenic	Intergenic	-13171	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding	0.010000	0.432836			-6(CCACAGTCATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7842	chr9	98570415	98570615	+	1.62601	NA	intron (NM_015827, intron 3 of 21)	intron (NM_015827, intron 3 of 21)	6784	NM_015827	50797	Mm.400464	NM_015827	ENSMUSG00000032458	Copb2	AI256832	coatomer protein complex, subunit beta 2 (beta prime)	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5917	chr5	42324723	42324923	+	1.62601	NA	Intergenic	Intergenic	256863	NR_131130	433882	Mm.319353	NR_131130	ENSMUSG00000067285	Gm16223	EG433882	predicted gene 16223	ncRNA	0.015000	0.343284			-4(TTATTATTATGCAGAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1221	chr11	29498181	29498381	+	1.62601	NA	intron (NM_001363368, intron 26 of 30)	intron (NM_001363368, intron 26 of 30)	16752	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6058	chr5	82261249	82261449	+	1.62601	NA	Intergenic	Intergenic	-136636	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4821	chr3	3640536	3640736	+	1.62601	NA	intron (NM_013920, intron 2 of 9)	L1MB8|LINE|L1	132606	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7038	chr7	116578222	116578422	+	1.62601	NA	Intergenic	Intergenic	73953	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7759	chr9	80150621	80150821	+	1.62601	NA	Intergenic	Intergenic	-14313	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Myo6<rsv>|Tlc|rsv|sv	myosin VI	protein-coding	0.000000	0.313433			-57(ACATTCTCATGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5041	chr3	83566377	83566577	+	1.62601	NA	intron (NR_036591, intron 1 of 4)	intron (NR_036591, intron 1 of 4)	7641	NR_036591	69460	Mm.389464	NR_036591	ENSMUSG00000101334	1700028M03Rik	-	RIKEN cDNA 1700028M03 gene	ncRNA	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1702	chr12	66459846	66460046	+	1.62601	NA	Intergenic	Intergenic	-175545	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2114	chr13	65309561	65309761	+	1.62601	NA	Intergenic	Intergenic	30807	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5932	chr5	48036221	48036421	+	1.62601	NA	intron (NR_111900, intron 4 of 35)	intron (NR_111900, intron 4 of 35)	53166	NM_001291228	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|b2b1200.1Clo|mKIAA4141|slit-2	slit guidance ligand 2	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-93	chr1	30678043	30678243	+	1.62601	NA	Intergenic	RLTR15|LTR|ERVK	185113	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik	PHD finger protein 3	protein-coding	0.025000	0.388060	-17(AATGATTATTTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1700	chr12	66006199	66006399	+	1.62601	NA	Intergenic	Intergenic	278102	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3850	chr18	52262565	52262765	+	1.62601	NA	Intergenic	Intergenic	-68871	NM_026286	67634	Mm.179144	NM_026286	ENSMUSG00000024510	Ftmt	4930447C24Rik|FerH|Fth3|MtF	ferritin mitochondrial	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4698	chr2	143924652	143924852	+	1.62593	NA	intron (NM_019771, intron 1 of 3)	PB1D10|SINE|Alu	9421	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7341	chr8	79498820	79499020	+	1.62526	NA	Intergenic	Intergenic	-99492	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Mad1|Madh1|Madr1|Mlp1|MusMLP|dwf-A|mMad1	SMAD family member 1	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7034	chr7	114968675	114968875	+	1.62367	NA	intron (NR_040317, intron 2 of 3)	LTR37A|LTR|ERV1	17501	NR_040319	101786	Mm.395157	NR_040317	ENSMUSG00000108379	A730082K24Rik	AU044236	RIKEN cDNA A730082K24 gene	ncRNA	0.005000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-807	chr7	114968678	114968878	+	1.62367	NA	intron (NR_040317, intron 2 of 3)	LTR37A|LTR|ERV1	17504	NR_040319	101786	Mm.395157	NR_040317	ENSMUSG00000108379	A730082K24Rik	AU044236	RIKEN cDNA A730082K24 gene	ncRNA	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5088	chr3	101010824	101011024	+	1.62367	NA	intron (NM_001167906, intron 6 of 8)	ORR1B1|LTR|ERVL-MaLR	18629	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1656	chr12	51858262	51858462	+	1.62078	NA	Intergenic	Intergenic	-28826	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain E3 ubiquitin protein ligase 1	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-176	chr1	61310342	61310542	+	1.62078	NA	Intergenic	Intergenic	-67990	NR_040483	77341	Mm.402964	NR_040483	ENSMUSG00000085447	9530026F06Rik	-	RIKEN cDNA 9530026F06 gene	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1627	chr12	43696228	43696428	+	1.62078	NA	Intergenic	RLTR13D6|LTR|ERVK	513740	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3104	chr16	18644842	18645042	+	1.62050	NA	Intergenic	Intergenic	-15004	NM_213614	18951	Mm.20365	NM_213614	ENSMUSG00000072214	Sept5	Cdcrel-1|Cdcrel1|Pnutl1	septin 5	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1865	chr12	103565213	103565413	+	1.62050	NA	intron (NM_028980, intron 3 of 24)	RLTR13E|LTR|ERVK	32748	NM_028980	74521	Mm.248619	NM_028980	ENSMUSG00000021209	Ppp4r4	8430415E04Rik|mKIAA1622	protein phosphatase 4, regulatory subunit 4	protein-coding	0.015000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-877	chr9	61994970	61995170	+	1.62050	NA	intron (NM_028748, intron 1 of 7)	intron (NM_028748, intron 1 of 7)	31720	NM_028748	74090	Mm.273267	NM_028748	ENSMUSG00000032278	Paqr5	0610010I15Rik|AV002411|BB115488|mPRg	progestin and adipoQ receptor family member V	protein-coding	0.010000	0.447761			-23(ATTAACAAAGGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4050	chr19	22285116	22285316	+	1.62048	NA	intron (NM_001035239, intron 1 of 24)	intron (NM_001035239, intron 1 of 24)	146170	NM_001035243	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding	0.015000	0.393035			-8(ATTTGAATGACTTTAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3436	chr17	17196287	17196487	+	1.62008	NA	intron (NM_001357988, intron 1 of 3)	LTRIS2|LTR|ERV1	17082	NM_001357988	626854	Mm.436630	NM_001039232		Gm38396	-	predicted gene, 38396	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5727	chr4	124825079	124825279	+	1.62008	NA	exon (NM_008636, exon 6 of 11)	exon (NM_008636, exon 6 of 11)	22630	NM_008636	17764	Mm.272397	NM_008636	ENSMUSG00000028890	Mtf1	MTF-1|Thyls	metal response element binding transcription factor 1	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1634	chr12	44840126	44840326	+	1.62008	NA	Intergenic	Intergenic	234257	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5471	chr4	53550619	53550819	+	1.62008	NA	TTS (NM_001159633)	TTS (NM_001159633)	-80705	NM_001369182	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl	fibronectin type III and SPRY domain containing 1-like	protein-coding	0.015000	0.383085			8(CCATAGTAATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2998	chr15	76167760	76167960	+	1.62008	NA	Intergenic	PB1D9|SINE|Alu	27850	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding	0.010000	0.462687			-79(ATTTAAATGCAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4896	chr3	31054526	31054726	+	1.62008	NA	Intergenic	Intergenic	15660	NR_105975	102465610		NR_105975	ENSMUSG00000098890	Mir7008	Gm27752|mmu-mir-7008	microRNA 7008	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5870	chr5	25671199	25671399	+	1.62008	NA	Intergenic	Intergenic	34498	NM_020570	57434	Mm.143767	NM_020570	ENSMUSG00000028933	Xrcc2	4921524O04Rik|8030409M04Rik|RAD51|RecA	X-ray repair complementing defective repair in Chinese hamster cells 2	protein-coding	0.010000	0.447761			-15(TTTTGCATGGTAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-509	chr1	163589475	163589675	+	1.62008	NA	Intergenic	Intergenic	135657	NM_001143956	240879	Mm.484621	NM_001143956	ENSMUSG00000040113	Mettl11b	Gm207|NTM1B	methyltransferase like 11B	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7625	chr9	43029841	43030041	+	1.62008	NA	intron (NM_001359232, intron 4 of 40)	L1ME1|LINE|L1	75777	NM_001359232	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5208	chr3	135565745	135565945	+	1.62008	NA	intron (NM_027288, intron 14 of 16)	intron (NM_027288, intron 14 of 16)	80234	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4777	chr2	165665558	165665758	+	1.62008	NA	intron (NM_010165, intron 2 of 15)	intron (NM_010165, intron 2 of 15)	10360	NM_010165	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6072	chr5	88620248	88620448	+	1.62008	NA	intron (NM_001359209, intron 4 of 17)	intron (NM_001359209, intron 4 of 17)	36835	NM_001359209	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3339	chr16	79713302	79713502	+	1.62008	NA	Intergenic	Intergenic	-285974	NM_030146	78654		NM_030146		1700066C05Rik	-	RIKEN cDNA 1700066C05 gene	protein-coding	0.005000	0.318408			-46(AATAGCATGATAAACA,-,0.00),73(ATTAAAATGACTAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1975	chr13	20404744	20404944	+	1.62008	NA	intron (NM_080288, intron 15 of 21)	intron (NM_080288, intron 15 of 21)	-68146	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4251	chr2	34327531	34327731	+	1.62008	NA	intron (NM_001290576, intron 2 of 7)	intron (NM_001290576, intron 2 of 7)	44414	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3922	chr18	69428860	69429060	+	1.62008	NA	intron (NM_001361127, intron 3 of 19)	intron (NM_001361127, intron 3 of 19)	82800	NM_001361128	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding	0.025000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-885	chr10	72602886	72603086	+	1.62008	NA	Intergenic	Intergenic	-51860	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding	0.000000	0.388060			-39(TTTTCCATAACAAAAC,-,0.00),-19(GTTTACATCACAAAAT,-,0.00),26(TGGTTCTGATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7530	chr9	14509072	14509272	+	1.62008	NA	intron (NM_023153, intron 6 of 6)	intron (NM_023153, intron 6 of 6)	8553	NM_023153	66070	Mm.245938	NM_023153	ENSMUSG00000004096	Cwc15	0610040D20Rik|2900052N06Rik|Ed1|c11orf5|mED1	CWC15 spliceosome-associated protein	protein-coding	0.005000	0.398010	-67(ATTAAATAATGCATC,+,0.00),27(AATGCATAATACATA,+,0.00),27(AATGCATAATACATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7482	chr8	124234259	124234459	+	1.61827	NA	intron (NM_139272, intron 1 of 15)	intron (NM_139272, intron 1 of 15)	2965	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.025000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3959	chr18	81724319	81724519	+	1.61827	NA	Intergenic	Intergenic	267661	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA	0.025000	0.462687			-98(GTTTACATCACAGTGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7876	chr9	110345048	110345248	+	1.61827	NA	intron (NM_001001144, intron 1 of 22)	L2c|LINE|L2	11792	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding	0.010000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-253	chr13	80750587	80750787	+	1.61595	NA	Intergenic	RLTR13C3|LTR|ERVK	-132697	NR_153410	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0.010000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-114	chr10	117663162	117663362	+	1.61466	NA	intron (NM_027468, intron 3 of 8)	intron (NM_027468, intron 3 of 8)	33762	NM_027468	70574	Mm.339332	NM_027468	ENSMUSG00000020183	Cpm	1110060I01Rik|5730456K23Rik|AA589379|E030045M14Rik	carboxypeptidase M	protein-coding	0.035000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3710	chr18	13144561	13144761	+	1.61462	NA	Intergenic	MLT2D|LTR|ERVL	137671	NM_153087	225192	Mm.207073	NM_153087	ENSMUSG00000037346	Hrh4	AXOR35|BG26|GPCR105|GPRv53|H4|H4R|HH4R	histamine receptor H4	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2911	chr15	51565667	51565867	+	1.61462	NA	Intergenic	Intergenic	-170157	NR_045092	100502643	Mm.131987	NR_045092	ENSMUSG00000115654	Gm19303	-	predicted gene, 19303	ncRNA	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7491	chr8	127343145	127343345	+	1.61462	NA	intron (NM_001013580, intron 3 of 13)	intron (NM_001013580, intron 3 of 13)	43633	NM_001013581	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding	0.005000	0.427861			24(ATTTACAAGAAAAGGC,-,0.00),62(AGTTGCATAACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6330	chr6	17477901	17478101	+	1.61462	NA	intron (NM_008591, intron 1 of 21)	intron (NM_008591, intron 1 of 21)	14044	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5497	chr4	59799012	59799212	+	1.61462	NA	Intergenic	L1ME3A|LINE|L1	-6538	NM_172468	209131	Mm.259705	NM_172468	ENSMUSG00000028385	Snx30	4732481H14Rik|C030041J06Rik	sorting nexin family member 30	protein-coding	0.005000	0.298507			15(CCATTGTTATGGATAT,+,0.00),36(ATGTTATTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1607	chr12	37507212	37507412	+	1.61462	NA	intron (NM_178767, intron 12 of 12)	intron (NM_178767, intron 12 of 12)	265673	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding	0.000000	0.303483			-82(TATTTAGTTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3356	chr16	85330402	85330602	+	1.61462	NA	Intergenic	Intergenic	-156795	NM_001198824	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2851	chr15	32338493	32338693	+	1.61462	NA	intron (NM_009154, intron 1 of 22)	intron (NM_009154, intron 1 of 22)	93780	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5782	chr4	144993756	144993956	+	1.61434	NA	intron (NM_001276465, intron 67 of 69)	intron (NM_001276465, intron 67 of 69)	100719	NM_001357274	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6436	chr6	49022569	49022769	+	1.61323	NA	Intergenic	Intergenic	-13849	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6326	chr6	16834574	16834774	+	1.61323	NA	intron (NM_031198, intron 6 of 6)	intron (NM_031198, intron 6 of 6)	57150	NR_157239	102640655		NR_157239	ENSMUSG00000107022	Gm36669	-	predicted gene, 36669	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-141	chr1	47495542	47495742	+	1.61323	NA	Intergenic	Intergenic	-28517	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4638	chr2	135084071	135084271	+	1.61139	NA	intron (NM_001145830, intron 3 of 31)	intron (NM_001145830, intron 3 of 31)	131445	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1714	chr12	69725824	69726024	+	1.61139	NA	intron (NM_001361690, intron 2 of 5)	RMER16B2|LTR|ERVK	979	NM_001361691	68055	Mm.27844	NM_026536	ENSMUSG00000054894	Dmac2l	1110015E18Rik|ATPW|Atp5s	distal membrane arm assembly complex 2 like	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4493	chr2	106706925	106707125	+	1.60956	NA	intron (NM_001356555, intron 2 of 5)	intron (NM_001356555, intron 2 of 5)	11424	NM_029837	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding	0.000000	0.398010			26(ATTAAAAAAAAAAAAC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-881	chr9	81481824	81482024	+	1.60956	NA	Intergenic	Intergenic	-150006	NR_040393	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5011	chr3	73479116	73479316	+	1.60956	NA	intron (NR_040547, intron 1 of 7)	intron (NR_040547, intron 1 of 7)	2435	NR_040547	74693	Mm.292227	NR_040547	ENSMUSG00000102362	4930509J09Rik	-	RIKEN cDNA 4930509J09 gene	ncRNA	0.005000	0.343284			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-419	chr18	4657154	4657354	+	1.60956	NA	intron (NM_001081963, intron 2 of 3)	intron (NM_001081963, intron 2 of 3)	22325	NM_001081963	240185	Mm.33179	NM_001081963	ENSMUSG00000033960	Jcad	1110056P05Rik|9430020K01Rik|Gm328|mKIAA1462	junctional cadherin 5 associated	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7501	chr8	128673577	128673777	+	1.60956	NA	Intergenic	Intergenic	-11977	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3680	chr18	4657115	4657315	+	1.60956	NA	intron (NM_001081963, intron 2 of 3)	intron (NM_001081963, intron 2 of 3)	22286	NM_001081963	240185	Mm.33179	NM_001081963	ENSMUSG00000033960	Jcad	1110056P05Rik|9430020K01Rik|Gm328|mKIAA1462	junctional cadherin 5 associated	protein-coding	0.015000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4049	chr19	22284781	22284981	+	1.60889	NA	intron (NM_001035239, intron 1 of 24)	B4A|SINE|B4	145835	NM_001035243	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3454	chr17	28756656	28756856	+	1.60889	NA	Intergenic	Intergenic	-12561	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4846	chr3	12676479	12676679	+	1.60852	NA	Intergenic	Intergenic	-795076	NM_001357035	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4205	chr2	20735503	20735703	+	1.60852	NA	intron (NM_001081006, intron 6 of 21)	intron (NM_001081006, intron 6 of 21)	216090	NM_001369134	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.010000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2654	chr14	100708082	100708282	+	1.60708	NA	Intergenic	Zaphod3|DNA|hAT-Tip100	491887	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2490	chr14	55077819	55078019	+	1.60708	NA	intron (NM_001039198, intron 1 of 9)	intron (NM_001039198, intron 1 of 9)	4828	NR_004444	432855	Mm.490799	NR_004444		Zfhx2os	Zfhx2as	zinc finger homeobox 2, opposite strand	ncRNA	0.025000	0.557214			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-51	chr1	171787707	171787907	+	1.60687	NA	intron (NM_013730, intron 3 of 6)	intron (NM_013730, intron 3 of 6)	20675	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4163	chr2	8366606	8366806	+	1.60486	NA	Intergenic	L1M4|LINE|L1	-822809	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5799	chr4	152966796	152966996	+	1.60486	NA	Intergenic	Intergenic	269356	NR_033138	330004	Mm.291863	NM_001033414		Gm833	-	predicted gene 833	ncRNA	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6298	chr6	8527473	8527673	+	1.60486	NA	intron (NM_001286729, intron 1 of 7)	Lx8|LINE|L1	7515	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3911	chr18	66046129	66046329	+	1.60486	NA	Intergenic	Intergenic	-43594	NM_027400	70361	Mm.290857	NM_027400	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	lectin, mannose-binding, 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2980	chr15	68396087	68396287	+	1.60486	NA	Intergenic	RLTR13D6|LTR|ERVK	-54898	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-561	chr1	175874749	175874949	+	1.60486	NA	Intergenic	Intergenic	-5929	NM_012012	26909	Mm.283046	NM_012012	ENSMUSG00000039748	Exo1	5730442G03Rik|Msa	exonuclease 1	protein-coding	0.010000	0.482587		-98(AATACATATTAATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2117	chr13	68643653	68643853	+	1.60486	NA	intron (NM_153534, intron 20 of 24)	intron (NM_153534, intron 20 of 24)	46314	NM_027035	69315	Mm.272795	NM_027035	ENSMUSG00000021534	1700001L19Rik	-	RIKEN cDNA 1700001L19 gene	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6478	chr6	60961755	60961955	+	1.60486	NA	intron (NM_001163507, intron 3 of 7)	intron (NM_001163507, intron 3 of 7)	17538	NM_027613	70945	Mm.389770	NM_027613	ENSMUSG00000054641	Mmrn1	4921530G03Rik|Emilin4|Mmrn	multimerin 1	protein-coding	0.000000	0.248756			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7105	chr7	135220375	135220575	+	1.60486	NA	Intergenic	Intergenic	-24473	NR_046050	74314	Mm.415339	NR_046050	ENSMUSG00000100717	1700120G07Rik	-	RIKEN cDNA 1700120G07 gene	ncRNA	0.005000	0.417910		-33(GATGAATATTTAAA,-,0.00)	-1(TCTTTGTTCTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2121	chr13	69093373	69093573	+	1.60409	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-93932	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2039	chr13	40575839	40576039	+	1.60409	NA	Intergenic	Intergenic	-151869	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-127	chr1	43552046	43552246	+	1.60409	NA	intron (NM_010879, intron 3 of 4)	intron (NM_010879, intron 3 of 4)	106395	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding	0.005000	0.427861			47(GAACTCTCATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6190	chr5	130924330	130924530	+	1.60409	NA	intron (NM_145218, intron 6 of 10)	intron (NM_145218, intron 6 of 10)	383092	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Galnt17	AA388321|E330012B09Rik|Galnt19|Gcap8|Wbscr17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7938	chrX	22719107	22719307	+	1.60409	NA	Intergenic	Intergenic	257611	NR_033731	76705	Mm.399727	NM_029707		Ppp1r2-ps7	1700023I07Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 7	pseudo	0.005000	0.447761	74(TATCAAATATGCATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6718	chr6	133060555	133060755	+	1.60045	NA	Intergenic	(CATATA)n|Simple_repeat|Simple_repeat	-4862	NM_021562	387616	Mm.422613	NM_021562	ENSMUSG00000071147	Tas2r140	T2R40|T2r34|TRB3|TRB5|Tas2r13|Tas2r137|Tas2r40|Tas2r8|mTRB3|mt2r64	taste receptor, type 2, member 140	protein-coding	0.000000	0.258706			-44(TCATTTTCATTTACAT,+,0.00),-36(ATTTACATATAAATGT,-,0.00),-18(GCTTTCACATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3086	chr16	12072136	12072336	+	1.60045	NA	intron (NM_028277, intron 2 of 4)	L2b|LINE|L2	88123	NM_001174086	72555	Mm.310139	NM_028277	ENSMUSG00000022494	Shisa9	2700045P11Rik|Ckamp44	shisa family member 9	protein-coding	0.005000	0.407960			-77(TTTAGCAAGACAGTGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-99	chr1	34409901	34410101	+	1.60045	NA	Intergenic	Intergenic	23198	NR_039562	100628580		NR_039562	ENSMUSG00000092852	Mir5103	mir-5103|mmu-mir-5103|mu-mir-5103	microRNA 5103	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2704	chr14	115947470	115947670	+	1.60045	NA	intron (NM_175500, intron 7 of 7)	intron (NM_175500, intron 7 of 7)	-538018	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5750	chr4	129827740	129827940	+	1.60045	NA	intron (NM_001164745, intron 1 of 5)	intron (NM_001164745, intron 1 of 5)	7132	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-518	chr1	164861473	164861673	+	1.60045	NA	Intergenic	Intergenic	-1548	NR_040303	433374	Mm.251149	NR_040303	ENSMUSG00000104117	Gm20743	-	predicted gene, 20743	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5788	chr4	149313017	149313217	+	1.60006	NA	Intergenic	PB1D9|SINE|Alu	-5384	NM_001290995	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding	0.010000	0.422886			72(GTTTTGCTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1310	chr11	61578249	61578449	+	1.59991	NA	intron (NM_001362587, intron 1 of 11)	intron (NM_001362587, intron 1 of 11)	1338	NM_001362585	13855	Mm.139695	NM_010148	ENSMUSG00000001036	Epn2	9530051D10Rik|AA536924|Ibp2	epsin 2	protein-coding	0.020000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3210	chr16	46296597	46296797	+	1.59991	NA	Intergenic	Intergenic	-141620	NM_001304528	11615	Mm.330692	NM_001304528	ENSMUSG00000048087	Gm4737	AL024110|EG11615	predicted gene 4737	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3314	chr16	73201077	73201277	+	1.59991	NA	Intergenic	Intergenic	538028	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.010000	0.393035			18(ATTTGAATGCTAATTG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-326	chr15	4150817	4151017	+	1.59637	NA	intron (NM_024188, intron 16 of 16)	L1MA6|LINE|L1	-123511	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7551	chr9	22329730	22329930	+	1.59632	NA	TTS (NR_033622)	TTS (NR_033622)	860	NR_033622	625603	Mm.37987	NR_033622		Gm6607	EG625603	40S ribosomal protein S20 pseudogene	pseudo	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-838	chr10	57595591	57595791	+	1.59632	NA	Intergenic	Lx4A|LINE|L1	-36290	NM_008863	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1936	chr13	6585173	6585373	+	1.59632	NA	intron (NM_019703, intron 19 of 21)	intron (NM_019703, intron 19 of 21)	37116	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding	0.010000	0.373134			-17(CTTTTAATGATAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-598	chr1	184245354	184245554	+	1.59632	NA	Intergenic	Intergenic	211073	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.025000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5980	chr5	62322252	62322452	+	1.59632	NA	Intergenic	Intergenic	443825	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding	0.005000	0.348259			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-823	chr8	42329106	42329306	+	1.59632	NA	Intergenic	Intergenic	501939	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3417	chr17	9580062	9580262	+	1.59313	NA	Intergenic	Intergenic	89542	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	poly(A) binding protein, cytoplasmic 6	protein-coding	0.015000	0.447761			24(ATTTACATTTCAATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-183	chr12	33303557	33303757	+	1.59313	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	1142	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding	0.020000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5823	chr5	9367902	9368102	+	1.59242	NA	intron (NR_153370, intron 1 of 19)	intron (NR_153370, intron 1 of 19)	-7702	NR_030537	100124492		NR_030537	ENSMUSG00000077896	Mir879	Mirn879|mir-879|mmu-mir-879	microRNA 879	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-871	chr10	68525539	68525739	+	1.59242	NA	exon (NM_028491, exon 3 of 8)	exon (NM_028491, exon 3 of 8)	16236	NM_028491	73287	Mm.141830	NM_028491	ENSMUSG00000019945	Cabcoco1	1700040L02Rik	ciliary associated calcium binding coiled-coil 1	protein-coding	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2653	chr14	100707829	100708029	+	1.59223	NA	Intergenic	Intergenic	492140	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2450	chr14	38321052	38321252	+	1.59050	NA	Intergenic	Intergenic	-577150	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.000000	0.437811			-43(GCATTGATATGGAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-286	chr14	38321051	38321251	+	1.59050	NA	Intergenic	Intergenic	-577151	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.000000	0.432836			-42(GCATTGATATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-14	chr1	6448889	6449089	+	1.58944	NA	Intergenic	Intergenic	-38242	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6189	chr5	130924163	130924363	+	1.58873	NA	intron (NM_145218, intron 6 of 10)	intron (NM_145218, intron 6 of 10)	383259	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Galnt17	AA388321|E330012B09Rik|Galnt19|Gcap8|Wbscr17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5729	chr4	124900099	124900299	+	1.58873	NA	intron (NM_001256432, intron 6 of 16)	intron (NM_001256432, intron 6 of 16)	-5417	NR_040651	73628	Mm.398337	NR_040651	ENSMUSG00000085263	1700125G02Rik	-	RIKEN cDNA 1700125G02 gene	ncRNA	0.015000	0.502488			-30(TTTTGCAAAAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3615	chr17	80729280	80729480	+	1.58867	NA	Intergenic	Intergenic	-1355	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.015000	0.502488			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-313	chr14	100707992	100708192	+	1.58867	NA	Intergenic	Zaphod3|DNA|hAT-Tip100	491977	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4040	chr19	21016711	21016911	+	1.58867	NA	Intergenic	Lx8|LINE|L1	-62609	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5623	chr4	96895773	96895973	+	1.58811	NA	Intergenic	Intergenic	-110713	NM_001081284	620779	Mm.439625	NM_001081284	ENSMUSG00000078639	Gm12695	-	predicted gene 12695	protein-coding	0.010000	0.363184		-73(TATACATATGCACG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7468	chr8	118666144	118666344	+	1.58811	NA	intron (NM_019707, intron 2 of 13)	intron (NM_019707, intron 2 of 13)	382633	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-750	chr10	28461839	28462039	+	1.58811	NA	intron (NM_001359355, intron 7 of 33)	intron (NM_001359355, intron 7 of 33)	-206421	NM_001305663	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding	0.020000	0.402985			9(ATTTAAAACACAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2904	chr15	45912731	45912931	+	1.58811	NA	Intergenic	RLTR13C3|LTR|ERVK	-411754	NR_045509	71120	Mm.158571	NR_045509	ENSMUSG00000099751	1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	ncRNA	0.005000	0.388060	-47(CATGAATAATACAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8155	chrX	165338060	165338260	+	1.58811	NA	Intergenic	MT2A|LTR|ERVL	-10293	NM_001357099	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	glycine receptor, alpha 2 subunit	protein-coding	0.000000	0.363184		55(GAAGAATATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1406	chr11	90356095	90356295	+	1.58811	NA	intron (NM_172563, intron 2 of 3)	intron (NM_172563, intron 2 of 3)	34722	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5703	chr4	115567397	115567597	+	1.58811	NA	intron (NM_001252539, intron 3 of 10)	ORR1B2-int|LTR|ERVL-MaLR	3848	NM_201640	666168	Mm.482086	NM_201640	ENSMUSG00000028712	Cyp4a31	-	cytochrome P450, family 4, subfamily a, polypeptide 31	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4864	chr3	19015569	19015769	+	1.58811	NA	Intergenic	MLT1D-int|LTR|ERVL-MaLR	147426	NM_001357689	74252	Mm.200383	NM_028840	ENSMUSG00000027599	Armc1	2310016N05Rik|2900046P06Rik|3110009G21Rik|AA409258|AW048872|Arcp|C330014L16Rik	armadillo repeat containing 1	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-361	chr1	127692773	127692973	+	1.58811	NA	Intergenic	L1_Mus2|LINE|L1	-14852	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|A-cre|Act-Cre|SV31|Tg(ACTB-cre)2Mrt|actin-cre|cre<actin>	transmembrane protein 163	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-786	chr10	39666511	39666711	+	1.58811	NA	intron (NR_038037, intron 2 of 2)	intron (NR_038037, intron 2 of 2)	-52929	NR_152259	100504626	Mm.440236	NR_152259		Gm16364	Gm16365	predicted gene 16364	ncRNA	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2371	chr14	16289146	16289346	+	1.58811	NA	intron (NM_001362433, intron 8 of 10)	intron (NM_001362433, intron 8 of 10)	-39438	NM_027695	71147	Mm.197960	NM_027695	ENSMUSG00000021786	Oxsm	4933425A18Rik|C80494	3-oxoacyl-ACP synthase, mitochondrial	protein-coding	0.000000	0.358209			-69(TTTTATTTATGGAAAT,+,0.00),41(ATTTGCATAGAAAGTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1853	chr12	101835183	101835383	+	1.58811	NA	Intergenic	Intergenic	-16164	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4000	chr19	3870617	3870817	+	1.58811	NA	intron (NM_013490, intron 2 of 10)	intron (NM_013490, intron 2 of 10)	18944	NM_001271496	12660	Mm.225505	NM_013490	ENSMUSG00000024843	Chka	CK|CK/EK-alpha|Chetk-alpha|Chk|ChoK|EK|EtnK-alpha	choline kinase alpha	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2581	chr14	79313563	79313763	+	1.58811	NA	Intergenic	Intergenic	-12028	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding	0.000000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6522	chr6	71750640	71750840	+	1.58811	NA	intron (NM_178608, intron 1 of 6)	intron (NM_178608, intron 1 of 6)	43059	NM_178608	52250	Mm.146332	NM_178608	ENSMUSG00000052852	Reep1	D6Ertd253e	receptor accessory protein 1	protein-coding	0.005000	0.427861	-9(TATGCATAATTCAGA,+,0.00),-9(TATGCATAATTCAGA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5458	chr4	50180000	50180200	+	1.58811	NA	Intergenic	MT2B1|LTR|ERVL	-334331	NM_001276355	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7354	chr8	81671888	81672088	+	1.58811	NA	intron (NM_001297593, intron 2 of 23)	Lx4B|LINE|L1	329426	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4321	chr2	56259022	56259222	+	1.58811	NA	Intergenic	Intergenic	-526689	NR_105751	102465169		NR_105751	ENSMUSG00000098437	Mir195b	Gm27491|mmu-mir-195b	microRNA 195b	ncRNA	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7275	chr8	58691673	58691873	+	1.58811	NA	intron (NM_175032, intron 1 of 11)	intron (NM_175032, intron 1 of 11)	9023	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	-	predicted gene 15881	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-680	chr10	6182996	6183196	+	1.58811	NA	Intergenic	Intergenic	-260696	NM_001161822	56533	Mm.44606	NM_019958	ENSMUSG00000019775	Rgs17	6430507P11Rik|Rgsz2	regulator of G-protein signaling 17	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7951	chrX	41293209	41293409	+	1.58811	NA	Intergenic	Lx10|LINE|L1	-107545	NM_001358361	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-695	chr10	12005084	12005284	+	1.58811	NA	Intergenic	Intergenic	395960	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5439	chr4	43763530	43763730	+	1.58811	NA	Intergenic	Intergenic	7379	NM_019476	29849	Mm.88845	NM_019476	ENSMUSG00000044801	Olfr159	MOR262-5|Olfr37e|mOR37e	olfactory receptor 159	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4080	chr19	35804783	35804983	+	1.58811	NA	Intergenic	Intergenic	119695	NR_152130	329056	Mm.238105	NR_152130	ENSMUSG00000094707	A830019P07Rik	-	RIKEN cDNA A830019P07 gene	ncRNA	0.005000	0.368159			-13(ATAAACAAGACAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6822	chr7	37625905	37626105	+	1.58811	NA	intron (NM_172385, intron 3 of 5)	intron (NM_172385, intron 3 of 5)	143747	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding	0.025000	0.512438			-12(CTATTTGCATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6612	chr6	99511884	99512084	+	1.58811	NA	intron (NM_001347345, intron 1 of 19)	intron (NM_001347345, intron 1 of 19)	9009	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-220	chr1	80766147	80766347	+	1.58811	NA	Intergenic	Intergenic	-7694	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding	0.005000	0.343284			-73(ATTAGCATCATTATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6050	chr5	80617850	80618050	+	1.58811	NA	Intergenic	Intergenic	-402621	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.005000	0.288557		-11(AATGAATATGCATT,+,0.00),-11(AATGAATATGCATT,-,0.00)	-22(TTTAAAATGAAAATGA,-,0.00),-2(GCATTGATATGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-479	chr1	156809248	156809448	+	1.58811	NA	intron (NM_001159965, intron 19 of 19)	intron (NM_001159965, intron 19 of 19)	-29675	NM_028333	72713	Mm.389206	NM_028333	ENSMUSG00000033544	Angptl1	2810039D03Rik|ANG3|ANGPT3|ANGY|ARP1	angiopoietin-like 1	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2071	chr13	51518006	51518206	+	1.58811	NA	intron (NM_009167, intron 1 of 11)	intron (NM_009167, intron 1 of 11)	51345	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding	0.000000	0.452736	-88(TTTGCATTATGCAGA,+,0.00)		-44(CTATTGTTATGTAACT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5511	chr4	64219891	64220091	+	1.58811	NA	Intergenic	Intergenic	56612	NR_151546	102633436	Mm.411637	NR_151546		Gm11217	-	predicted gene 11217	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6870	chr7	57573507	57573707	+	1.58811	NA	Intergenic	L1MEd|LINE|L1	-7454	NR_105812	102466156		NR_105812	ENSMUSG00000099203	Mir6389	Gm27946|mmu-mir-6389	microRNA 6389	ncRNA	0.000000	0.263682			-14(ATATGAATGACAACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2975	chr15	67524373	67524573	+	1.58811	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	297704	NR_045140	69334	Mm.63770	NR_045140	ENSMUSG00000102069	1700012I11Rik	-	RIKEN cDNA 1700012I11 gene	ncRNA	0.005000	0.492537			76(CCATTCTCATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7505	chr9	5734848	5735048	+	1.58811	NA	Intergenic	Lx2B|LINE|L1	389472	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4323	chr2	56822579	56822779	+	1.58811	NA	Intergenic	Intergenic	36868	NR_105751	102465169		NR_105751	ENSMUSG00000098437	Mir195b	Gm27491|mmu-mir-195b	microRNA 195b	ncRNA	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1102	chr10	122621101	122621301	+	1.58811	NA	Intergenic	Intergenic	-27138	NR_105839	102465223		NR_105839	ENSMUSG00000098522	Mir6412	Gm27364|mmu-mir-6412	microRNA 6412	ncRNA	0.015000	0.373134			76(ATATGCATGACCAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8009	chrX	86444013	86444213	+	1.58811	NA	Intergenic	B3|SINE|B2	-89119	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo	0.000000	0.348259			8(GTCTACTCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-834	chr10	57041255	57041455	+	1.58811	NA	Intergenic	Intergenic	444998	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	ncRNA	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5095	chr3	103153888	103154088	+	1.58811	NA	intron (NM_001356383, intron 6 of 14)	B3|SINE|B2	13662	NM_001356383	329727	Mm.293641	NM_177857	ENSMUSG00000007379	Dennd2c	A930010I20Rik	DENN/MADD domain containing 2C	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6205	chr5	132274027	132274227	+	1.58778	NA	intron (NM_001363480, intron 1 of 19)	intron (NM_001363480, intron 1 of 19)	269093	NM_001363480	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0.000000	0.417910			-59(TTTAACATGAAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3640	chr17	85142931	85143131	+	1.58778	NA	intron (NM_028576, intron 3 of 10)	intron (NM_028576, intron 3 of 10)	52405	NM_001364946	73582	Mm.260753	NM_028576	ENSMUSG00000071037	Camkmt	1700106N22Rik|AI480743|AV099781|CLNMT|CaM KMT	calmodulin-lysine N-methyltransferase	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7415	chr8	101974440	101974640	+	1.58778	NA	Intergenic	Intergenic	810571	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4376	chr2	68967814	68968014	+	1.58778	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	106473	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding	0.005000	0.283582			-77(ATTTTCATCTCAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4353	chr2	64983239	64983439	+	1.58778	NA	intron (NM_016719, intron 2 of 13)	intron (NM_016719, intron 2 of 13)	39427	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2035	chr13	38522462	38522662	+	1.58778	NA	intron (NM_145367, intron 2 of 9)	ORR1F|LTR|ERVL-MaLR	5352	NM_001289599	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2656	chr14	101482224	101482424	+	1.58778	NA	intron (NM_001081278, intron 8 of 18)	Lx4A|LINE|L1	126867	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4632	chr2	134114547	134114747	+	1.58778	NA	Intergenic	RLTR13D5|LTR|ERVK	439705	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	hydroxyacid oxidase 1, liver	protein-coding	0.005000	0.427861	-60(ATTGCATTATTCATG,+,0.00),-60(ATTGCATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4015	chr19	15537337	15537537	+	1.58778	NA	Intergenic	LTR16D|LTR|ERVL	387185	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3283	chr16	64939860	64940060	+	1.58778	NA	intron (NM_008310, intron 2 of 2)	intron (NM_008310, intron 2 of 2)	87959	NM_001357416	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding	0.010000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2479	chr14	48349680	48349880	+	1.58778	NA	Intergenic	Intergenic	-96343	NM_001310584	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding	0.020000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3488	chr17	42393200	42393400	+	1.58778	NA	intron (NM_001355270, intron 2 of 2)	intron (NM_001355270, intron 2 of 2)	76700	NM_001355270	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-442	chr1	149148206	149148406	+	1.58778	NA	Intergenic	Intergenic	774133	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding	0.000000	0.348259			-56(CCATTGTAATGCTTAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5700	chr4	114808970	114809170	+	1.58778	NA	Intergenic	RMER15-int|LTR|ERVL	-12650	NR_033617	433746	Mm.388908	NR_033617	ENSMUSG00000055198	Gm12830	-	predicted gene 12830	ncRNA	0.000000	0.383085			-58(ATCTGCATAGAAATAC,-,0.00),23(GCTTTGGTAAGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2811	chr15	15476504	15476704	+	1.58778	NA	Intergenic	RMER16-int|LTR|ERVK	-1252311	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0.040000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8049	chrX	103529300	103529500	+	1.58778	NA	Intergenic	Intergenic	-16100	NR_033398	668415	Mm.483779	NR_033398		Gm9159	EG668415	predicted gene 9159	pseudo	0.110000	0.691542			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1665	chr12	54160425	54160625	+	1.58778	NA	Intergenic	Intergenic	43349	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding	0.005000	0.512438			37(ATATACATCACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5618	chr4	95867755	95867955	+	1.58778	NA	intron (NM_001113412, intron 14 of 15)	(TA)n|Simple_repeat|Simple_repeat	99180	NR_045777	319247	Mm.473527	NM_175680	ENSMUSG00000044125	9530080O11Rik	-	RIKEN cDNA 9530080O11 gene	ncRNA	0.010000	0.273632	24(TATGCATAAGTCATT,+,0.00),24(TATGCATAAGTCATT,-,0.00)	-2(TATGCATATATATA,-,0.00),18(TATGTATATGCATA,+,0.00),18(TATGTATATGCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7380	chr8	94507279	94507479	+	1.58778	NA	intron (NM_001033207, intron 30 of 48)	B4|SINE|B4	2333	NR_106040	102466800		NR_106040	ENSMUSG00000098511	Mir7072	Gm27665|mmu-mir-7072	microRNA 7072	ncRNA	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3413	chr17	8843857	8844057	+	1.58778	NA	intron (NM_011866, intron 1 of 21)	intron (NM_011866, intron 1 of 21)	-6028	NM_001347321	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding	0.020000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1086	chr10	119793113	119793313	+	1.58778	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	-26176	NM_130891	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding	0.030000	0.442786			-42(ATAATCATGAGAATTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-311	chr1	106968979	106969179	+	1.58778	NA	Intergenic	Intergenic	-11905	NM_172852	241196	Mm.110886	NM_172852	ENSMUSG00000048775	Serpinb13	5430417G24|HUR7|HURPIN|PI13|headpin	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 13	protein-coding	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4938	chr3	51033761	51033961	+	1.58778	NA	Intergenic	Intergenic	-190586	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2171	chr13	82271148	82271348	+	1.58778	NA	Intergenic	Intergenic	427085	NR_039537	100628621		NR_039537	ENSMUSG00000106655	Mir3961	mmu-mir-3961	microRNA 3961	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7596	chr9	32096859	32097059	+	1.58778	NA	intron (NM_001370958, intron 1 of 22)	intron (NM_001370958, intron 1 of 22)	-19029	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1292	chr11	52618636	52618836	+	1.58778	NA	Intergenic	Intergenic	-145970	NM_177059	320027	Mm.44518	NM_177059	ENSMUSG00000036264	Fstl4	B230374F23Rik|SPIG1|mKIAA1061	follistatin-like 4	protein-coding	0.025000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6448	chr6	52769100	52769300	+	1.58778	NA	3' UTR (NM_001168277, exon 5 of 5)	3' UTR (NM_001168277, exon 5 of 5)	55035	NM_001355596	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3827	chr18	45698185	45698385	+	1.58778	NA	intron (NR_040342, intron 3 of 3)	Lx8|LINE|L1	138131	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2863	chr15	37241660	37241860	+	1.58778	NA	intron (NM_026496, intron 1 of 15)	intron (NM_026496, intron 1 of 15)	-8601	NR_155441	105245924	Mm.391911	NR_155441	ENSMUSG00000089804	Gm16136	-	predicted gene 16136	ncRNA	0.025000	0.487562			-82(ATATTATTATGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-274	chr1	93648667	93648867	+	1.58684	NA	Intergenic	Intergenic	-13040	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2311	chr13	113502514	113502714	+	1.58684	NA	intron (NR_045501, intron 1 of 6)	MER90a|LTR|ERV1	230	NR_045501	70917	Mm.491036	NR_045501	ENSMUSG00000114790	4921509O07Rik	-	RIKEN cDNA 4921509O07 gene	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8052	chrX	104565698	104565898	+	1.58684	NA	exon (NM_175358, exon 8 of 12)	exon (NM_175358, exon 8 of 12)	82995	NM_001081189	331487	Mm.40283	NM_001081189	ENSMUSG00000073016	Uprt	D830012I24Rik|Gm774	uracil phosphoribosyltransferase	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5422	chr4	35145799	35145999	+	1.58684	NA	intron (NM_178061, intron 1 of 3)	intron (NM_178061, intron 1 of 3)	-6156	NM_199157	387510	Mm.386929	NM_199157	ENSMUSG00000042993	Ifnk	-	interferon kappa	protein-coding	0.040000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1475	chr11	112476186	112476386	+	1.58684	NA	Intergenic	Intergenic	235070	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6514	chr6	70145164	70145364	+	1.58684	NA	Intergenic	L1Md_F2|LINE|L1	646911	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3510	chr17	50568781	50568981	+	1.58684	NA	intron (NM_013880, intron 1 of 5)	intron (NM_013880, intron 1 of 5)	59334	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7724	chr9	72594596	72594796	+	1.58684	NA	intron (NM_001033536, intron 4 of 8)	L1_Mus2|LINE|L1	62456	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding	0.010000	0.393035			-51(ATTAGTATGAGAGTGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2801	chr15	12945381	12945581	+	1.58684	NA	Intergenic	Intergenic	120666	NM_026799	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding	0.030000	0.417910			49(GGTTTTTCATTCTTAT,+,0.00),55(TCATTCTTATTGAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4056	chr19	27828027	27828227	+	1.58684	NA	intron (NM_001166414, intron 8 of 18)	intron (NM_001166414, intron 8 of 18)	181646	NM_001360358	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3507	chr17	49976850	49977050	+	1.58684	NA	Intergenic	Intergenic	213547	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6169	chr5	122116171	122116371	+	1.58684	NA	intron (NM_183307, intron 9 of 12)	B4A|SINE|B4	15320	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2169	chr13	81430970	81431170	+	1.58684	NA	intron (NM_054053, intron 70 of 89)	intron (NM_054053, intron 70 of 89)	202074	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Adgrv1	Frings|Gpr98|Mass1|Mgr1|VLGR1	adhesion G protein-coupled receptor V1	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2962	chr15	62927687	62927887	+	1.58684	NA	Intergenic	B4A|SINE|B4	551821	NR_045279	432958	Mm.255105	NR_045279	ENSMUSG00000115520	Gm20740	-	predicted gene, 20740	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3603	chr17	78710401	78710601	+	1.58684	NA	intron (NM_011500, intron 1 of 17)	RMER3D-int|LTR|ERVK	26060	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4667	chr2	138966907	138967107	+	1.58684	NA	Intergenic	Intergenic	147078	NR_035477	100316816		NR_035477	ENSMUSG00000088983	Mir1952	mmu-mir-1952	microRNA 1952	ncRNA	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-145	chr1	51230388	51230588	+	1.58684	NA	intron (NR_045151, intron 4 of 4)	intron (NR_045151, intron 4 of 4)	-58638	NM_138741	20324	Mm.398690	NM_138741	ENSMUSG00000045954	Cavin2	Sdpr	caveolae associated 2	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7249	chr8	52664684	52664884	+	1.58684	NA	Intergenic	Intergenic	308173	NR_151738	330767	Mm.246790	NR_151738	ENSMUSG00000110013	1190028D05Rik	-	RIKEN cDNA 1190028D05 gene	ncRNA	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1736	chr12	73002500	73002700	+	1.58684	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-43285	NR_162772	114482235		NR_162772		Mir9718	mmu-mir-9718	microRNA mir-9718	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7211	chr8	38625471	38625671	+	1.58684	NA	intron (NM_145841, intron 1 of 7)	(CA)n|Simple_repeat|Simple_repeat	35937	NM_145841	244431	Mm.210388	NM_145841	ENSMUSG00000039539	Sgcz	C230085N17Rik	sarcoglycan zeta	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2808	chr15	14001003	14001203	+	1.58684	NA	Intergenic	Intergenic	-827428	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.000000	0.398010			28(CATTTCCATTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7280	chr8	61691102	61691302	+	1.58684	NA	intron (NM_001293772, intron 8 of 21)	intron (NM_001293772, intron 8 of 21)	68887	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-191	chr1	66215642	66215842	+	1.58684	NA	intron (NM_008632, intron 2 of 13)	intron (NM_008632, intron 2 of 13)	40413	NM_001039934	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7822	chr9	94222185	94222385	+	1.58684	NA	Intergenic	MTD|LTR|ERVL-MaLR	315796	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	Dipk2a	1190002N15Rik|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3647	chr17	86231272	86231472	+	1.58684	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	55806	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1036	chr10	111810738	111810938	+	1.58684	NA	Intergenic	Intergenic	63538	NR_046029	629206	Mm.391444	NR_046029	ENSMUSG00000112533	Gm20758	-	predicted gene, 20758	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7728	chr9	73911751	73911951	+	1.58684	NA	intron (NM_001081153, intron 2 of 31)	Lx9|LINE|L1	57186	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4352	chr2	64832001	64832201	+	1.58684	NA	Intergenic	Intergenic	190665	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5292	chr3	152376567	152376767	+	1.58654	NA	intron (NM_001076676, intron 15 of 23)	intron (NM_001076676, intron 15 of 23)	-18806	NM_001346655	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2073	chr13	52198918	52199118	+	1.58654	NA	Intergenic	Intergenic	102277	NR_045061	74050	Mm.84860	NR_045061	ENSMUSG00000113211	4921525O09Rik	-	RIKEN cDNA 4921525O09 gene	ncRNA	0.000000	0.522388			74(CCTTTCCCATGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4508	chr2	108441562	108441762	+	1.58654	NA	Intergenic	Intergenic	836628	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1998	chr13	29059691	29059891	+	1.58654	NA	Intergenic	Intergenic	43536	NR_045074	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4137	chr19	59208619	59208819	+	1.58654	NA	Intergenic	Intergenic	-10929	NM_207261	332396	Mm.329947	NM_207261	ENSMUSG00000040901	Kcnk18	Gm781|Tresk|Tresk-2|Trik	potassium channel, subfamily K, member 18	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5015	chr3	75586563	75586763	+	1.58654	NA	intron (NM_001357514, intron 1 of 8)	Lx2|LINE|L1	29170	NM_001357514	20713	Mm.41560	NM_009250	ENSMUSG00000027834	Serpini1	AI837402|Ns|PI-12|PI12|Spi17	serine (or cysteine) peptidase inhibitor, clade I, member 1	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2542	chr14	73878935	73879135	+	1.58654	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	326249	NM_001361638	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS|SCS-betaA	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2122	chr13	69464321	69464521	+	1.58654	NA	Intergenic	L1M2c|LINE|L1	69443	NM_001169131	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Tent4a	LAK-1|POLK|Papd7|Pols|TRF4|TRF4-1	terminal nucleotidyltransferase 4A	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4681	chr2	141174599	141174799	+	1.58654	NA	intron (NM_001013802, intron 5 of 18)	intron (NM_001013802, intron 5 of 18)	-503223	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4892	chr3	29969128	29969328	+	1.58654	NA	intron (NM_007963, intron 8 of 14)	intron (NM_007963, intron 8 of 14)	43976	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0.025000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7773	chr9	81685631	81685831	+	1.58654	NA	Intergenic	Intergenic	-51899	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	5-HT-1B	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6533	chr6	73377848	73378048	+	1.58654	NA	Intergenic	L1M5|LINE|L1	91719	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2571	chr14	77621880	77622080	+	1.58654	NA	intron (NM_172813, intron 13 of 18)	intron (NM_172813, intron 13 of 18)	-115112	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8142	chrX	162441679	162441879	+	1.58654	NA	intron (NM_178256, intron 14 of 17)	intron (NM_178256, intron 14 of 17)	123737	NM_001359104	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5575	chr4	83681893	83682093	+	1.58654	NA	intron (NM_001355549, intron 16 of 24)	intron (NM_001355549, intron 16 of 24)	156417	NM_001369173	320226	Mm.180032	NM_029117	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3348	chr16	83148911	83149111	+	1.58654	NA	Intergenic	RMER19B|LTR|ERVK	-1222132	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.000000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-223	chr1	82245102	82245302	+	1.58654	NA	intron (NM_010570, intron 1 of 1)	intron (NM_010570, intron 1 of 1)	46237	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7858	chr9	103938618	103938818	+	1.58654	NA	Intergenic	Intergenic	-63826	NM_028721	74025	Mm.479273	NM_028721	ENSMUSG00000032558	Nphp3	3632410F03Rik|AI550417|C230078J01|D330020E01Rik|pcy	nephronophthisis 3 (adolescent)	protein-coding	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7725	chr9	72909881	72910081	+	1.58654	NA	intron (NM_175485, intron 18 of 19)	intron (NM_175485, intron 18 of 19)	-15664	NM_028116	72135	Mm.273605	NM_028116	ENSMUSG00000034910	Pygo1	2600014C22Rik	pygopus 1	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3844	chr18	50206209	50206409	+	1.58654	NA	Intergenic	L1M2|LINE|L1	-72060	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	family with sequence similarity 170, member A	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-869	chr10	68494732	68494932	+	1.58654	NA	intron (NM_028491, intron 5 of 7)	intron (NM_028491, intron 5 of 7)	47043	NM_028491	73287	Mm.141830	NM_028491	ENSMUSG00000019945	Cabcoco1	1700040L02Rik	ciliary associated calcium binding coiled-coil 1	protein-coding	0.020000	0.398010		81(GATGAATATTTAAA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6300	chr6	8723685	8723885	+	1.58654	NA	intron (NM_001252266, intron 5 of 11)	Lx7|LINE|L1	34673	NM_001252266	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-43	chr1	15031136	15031336	+	1.58654	NA	Intergenic	Intergenic	-112374	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3207	chr16	46063159	46063359	+	1.58654	NA	intron (NM_032465, intron 8 of 14)	intron (NM_032465, intron 8 of 14)	-52846	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding	0.010000	0.358209			79(CTTTAGTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5210	chr3	135741103	135741303	+	1.58654	NA	Intergenic	Intergenic	-49656	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4797	chr2	172270862	172271062	+	1.58654	NA	Intergenic	LTR33|LTR|ERVL	22470	NM_008561	17201	Mm.57183	NM_008561	ENSMUSG00000038537	Mc3r	MC3-R	melanocortin 3 receptor	protein-coding	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2524	chr14	64426141	64426341	+	1.58654	NA	intron (NM_001253712, intron 1 of 5)	intron (NM_001253712, intron 1 of 5)	-8962	NM_001347639	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1633	chr12	44176151	44176351	+	1.58654	NA	Intergenic	Intergenic	33817	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1178	chr11	18671619	18671819	+	1.58654	NA	Intergenic	Intergenic	347250	NM_010789	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6301	chr6	9329086	9329286	+	1.58654	NA	Intergenic	Intergenic	379167	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7519	chr9	10227543	10227743	+	1.58654	NA	intron (NM_001170787, intron 3 of 24)	intron (NM_001170787, intron 3 of 24)	333212	NR_105745	102466147		NR_105745	ENSMUSG00000098408	Mir6237	Gm27411|mmu-mir-6237	microRNA 6237	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4089	chr19	38482315	38482515	+	1.58528	NA	Intergenic	URR1B|DNA|hAT-Charlie	-41782	NM_019588	74055	Mm.34031	NM_019588	ENSMUSG00000024998	Plce1	4933403A21Rik|PLCepsilon|Plce|mKIAA1516	phospholipase C, epsilon 1	protein-coding	0.020000	0.388060			-23(ATAAGCAAGAAAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5030	chr3	79249660	79249860	+	1.58523	NA	intron (NR_045502, intron 2 of 2)	B1F1|SINE|Alu	36841	NR_045502	70924	Mm.444622	NR_045502	ENSMUSG00000104585	4921511C10Rik	-	RIKEN cDNA 4921511C10 gene	ncRNA	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1359	chr11	75622491	75622691	+	1.58523	NA	intron (NM_008850, intron 10 of 11)	intron (NM_008850, intron 10 of 11)	-8429	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6471	chr6	59327777	59327977	+	1.58476	NA	Intergenic	Intergenic	98429	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0.000000	0.303483			-15(TTTCTTTCATTCAGAT,+,0.00),65(CCTTTTCTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2362	chr14	12445169	12445369	+	1.58476	NA	intron (NM_001359921, intron 24 of 29)	intron (NM_001359921, intron 24 of 29)	-99404	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6997	chr7	100826291	100826491	+	1.58476	NA	intron (NM_178764, intron 5 of 8)	intron (NM_178764, intron 5 of 8)	37022	NM_001358914	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5457	chr4	49811639	49811839	+	1.58476	NA	intron (NM_001033351, intron 1 of 8)	intron (NM_001033351, intron 1 of 8)	34030	NM_001033351	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-616	chr1	186585809	186586009	+	1.58476	NA	Intergenic	Intergenic	-27228	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2511	chr14	62254470	62254670	+	1.58476	NA	Intergenic	Intergenic	38409	NM_173419	239133	Mm.127330	NM_173419	ENSMUSG00000048281	Dleu7	BC038059	deleted in lymphocytic leukemia, 7	protein-coding	0.025000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4939	chr3	51086502	51086702	+	1.58476	NA	Intergenic	Intergenic	-137845	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3943	chr18	78259243	78259443	+	1.58476	NA	intron (NM_030683, intron 3 of 11)	Arthur1|DNA|hAT-Tip100	-52903	NM_001110274	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding	0.005000	0.348259			21(TCTTTCTCATTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6035	chr5	75355462	75355662	+	1.58476	NA	Intergenic	Intergenic	178731	NR_105992	102465620		NR_105992	ENSMUSG00000099060	Mir7025	Gm27860|mmu-mir-7025	microRNA 7025	ncRNA	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6399	chr6	36736833	36737033	+	1.58476	NA	intron (NM_008973, intron 4 of 4)	intron (NM_008973, intron 4 of 4)	73246	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6282	chr6	4620258	4620458	+	1.58476	NA	intron (NM_145398, intron 7 of 17)	intron (NM_145398, intron 7 of 17)	19447	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1|SOAT	CAS1 domain containing 1	protein-coding	0.015000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6099	chr5	97374875	97375075	+	1.58476	NA	Intergenic	Intergenic	17355	NM_001033191	97243	Mm.11746	NM_001033191	ENSMUSG00000046000	Naa11	Ard1b|Ard2|C80008	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4166	chr2	8955158	8955358	+	1.58476	NA	Intergenic	Intergenic	-234257	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2360	chr14	11752745	11752945	+	1.58476	NA	intron (NM_008981, intron 2 of 29)	intron (NM_008981, intron 2 of 29)	199292	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding	0.015000	0.398010	-54(AATGAAATATTCATT,+,0.00),-54(AATGAAATATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3049	chr15	96367945	96368145	+	1.58476	NA	intron (NM_175251, intron 12 of 20)	intron (NM_175251, intron 12 of 20)	80523	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|BAF200|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding	0.005000	0.422886			46(ATTTGCAATGCTAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4614	chr2	131198431	131198631	+	1.58476	NA	TTS (NM_023117)	TTS (NM_023117)	11583	NM_001111075	12531	Mm.38444	NM_023117	ENSMUSG00000027330	Cdc25b	AI604853	cell division cycle 25B	protein-coding	0.000000	0.527363			-28(TGTTTGTTATGCAGAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2176	chr13	83578372	83578572	+	1.58476	NA	intron (NM_001347567, intron 2 of 10)	intron (NM_001347567, intron 2 of 10)	4865	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1670	chr12	54960457	54960657	+	1.58476	NA	intron (NM_013815, intron 3 of 26)	intron (NM_013815, intron 3 of 26)	25779	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7748	chr9	78390209	78390409	+	1.58476	NA	Intergenic	Intergenic	-5468	NM_001191044	100048658	Mm.158166	NM_001191044	ENSMUSG00000070291	Ddx43	-	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	protein-coding	0.005000	0.497512			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-53	chr1	175722782	175722982	+	1.58374	NA	intron (NM_029453, intron 4 of 27)	B4A|SINE|B4	24289	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-63	chr1	21910495	21910695	+	1.58374	NA	intron (NM_001160139, intron 1 of 14)	intron (NM_001160139, intron 1 of 14)	51347	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6038	chr5	76396149	76396349	+	1.58267	NA	Intergenic	Intergenic	-32472	NM_019515	56183	Mm.154879	NM_019515	ENSMUSG00000029236	Nmu	-	neuromedin U	protein-coding	0.005000	0.303483			-17(ATTTGCATAAATAACA,-,0.00),-3(CATTACTTATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8085	chrX	133387920	133388120	+	1.58267	NA	Intergenic	Intergenic	-299760	NR_153117	102632590	Mm.403836	NR_153117	ENSMUSG00000096978	Gm26851	-	predicted gene, 26851	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3361	chr16	86166802	86167002	+	1.58267	NA	Intergenic	Lx6|LINE|L1	-265777	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8021	chrX	93329977	93330177	+	1.58267	NA	intron (NM_008892, intron 36 of 36)	intron (NM_008892, intron 36 of 36)	43570	NM_007492	11878	Mm.275547	NM_007492	ENSMUSG00000035277	Arx	Arx1	aristaless related homeobox	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8150	chrX	164649071	164649271	+	1.58267	NA	Intergenic	Lx9|LINE|L1	151268	NM_027027	69299	Mm.79031	NM_027027	ENSMUSG00000031384	Asb9	1700011M07Rik	ankyrin repeat and SOCS box-containing 9	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4189	chr2	16643023	16643223	+	1.58267	NA	intron (NM_026162, intron 5 of 13)	ORR1C2|LTR|ERVL-MaLR	286819	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1646	chr12	49120158	49120358	+	1.58267	NA	Intergenic	Intergenic	-262625	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1244	chr11	37678790	37678990	+	1.58267	NA	Intergenic	Intergenic	19901	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA	0.000000	0.348259			-10(ATTTGCATAGCCATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1380	chr11	83313190	83313390	+	1.58267	NA	intron (NM_001035854, intron 2 of 21)	intron (NM_001035854, intron 2 of 21)	10593	NM_001035854	71770	Mm.39053	NM_027915	ENSMUSG00000035152	Ap2b1	1300012O03Rik|AI788979|AP105B	adaptor-related protein complex 2, beta 1 subunit	protein-coding	0.010000	0.467662			61(TTTTTCTTATGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2714	chr14	117599774	117599974	+	1.58267	NA	intron (NM_001079844, intron 3 of 9)	intron (NM_001079844, intron 3 of 9)	353973	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5717	chr4	121199306	121199506	+	1.58267	NA	intron (NM_001346660, intron 1 of 7)	RMER5|LTR|ERV1	15678	NM_001346660	109263	Mm.215745	NM_001081013	ENSMUSG00000049878	Rlf	9230110M18Rik|AI195322|MommeD8	rearranged L-myc fusion sequence	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7450	chr8	112336569	112336769	+	1.58267	NA	Intergenic	Intergenic	232906	NR_132433	102640845	Mm.405615	NR_132433	ENSMUSG00000098075	Gm26994	-	predicted gene, 26994	ncRNA	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1989	chr13	24909389	24909589	+	1.58267	NA	3' UTR (NM_172532, exon 10 of 10)	3' UTR (NM_172532, exon 10 of 10)	3889	NR_045182	73326	Mm.458692	NR_045182	ENSMUSG00000086796	4932702P03Rik	1700047I16Rik	RIKEN cDNA 4932702P03 gene	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7705	chr9	67455871	67456071	+	1.58267	NA	intron (NM_001081242, intron 2 of 57)	intron (NM_001081242, intron 2 of 57)	103732	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-383	chr1	131731878	131732078	+	1.58267	NA	Intergenic	Intergenic	-12044	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7427	chr8	105892469	105892669	+	1.58267	NA	promoter-TSS (NM_001301174)	promoter-TSS (NM_001301174)	-998	NM_001301174	234700	Mm.133990	NM_175024	ENSMUSG00000044287	Nrn1l	Cpg15-2|G630049C14Rik	neuritin 1-like	protein-coding	0.000000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1206	chr11	26227820	26228020	+	1.58267	NA	Intergenic	Intergenic	-17344	NR_027973	70626	Mm.379180	NM_027486		5730522E02Rik	-	RIKEN cDNA 5730522E02 gene	ncRNA	0.005000	0.393035			1(ATATTGTTATATTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3720	chr18	16546814	16547014	+	1.58267	NA	Intergenic	Intergenic	262332	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-612	chr1	185726963	185727163	+	1.58267	NA	intron (NR_030555, intron 4 of 6)	B4A|SINE|B4	189727	NR_030555	100124483		NR_030555	ENSMUSG00000076976	Mir297c	Mirn297c	microRNA 297c	ncRNA	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4217	chr2	24296122	24296322	+	1.58267	NA	Intergenic	Intergenic	5026	NM_153077	215274	Mm.218750	NM_153077	ENSMUSG00000046845	Il1f10	-	interleukin 1 family, member 10	protein-coding	0.005000	0.452736			-58(CTATAATTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1566	chr12	25462170	25462370	+	1.58267	NA	Intergenic	L1MD|LINE|L1	333096	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA	0.000000	0.318408			-7(GTCAGCATGATAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7227	chr8	42243313	42243513	+	1.58267	NA	Intergenic	Lx7|LINE|L1	416146	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5347	chr4	12792312	12792512	+	1.58267	NA	Intergenic	Intergenic	-114425	NM_173746	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818	triple QxxK/R motif containing	protein-coding	0.025000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2	chr1	6448918	6449118	+	1.58135	NA	Intergenic	Intergenic	-38213	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6369	chr6	28520850	28521050	+	1.58039	NA	intron (NM_019776, intron 3 of 23)	intron (NM_019776, intron 3 of 23)	40602	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.020000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3169	chr16	35780670	35780870	+	1.58039	NA	intron (NR_152314, intron 1 of 8)	intron (NR_152314, intron 1 of 8)	10384	NR_152314	66667	Mm.45272	NM_175111	ENSMUSG00000022849	Hspbap1	3830421G21Rik	Hspb associated protein 1	protein-coding	0.005000	0.437811			-64(TTATTGTCATAGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-770	chr10	36468808	36469008	+	1.58039	NA	Intergenic	Intergenic	-37899	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5244	chr3	143336757	143336957	+	1.58039	NA	Intergenic	Intergenic	93802	NR_040551	320072	Mm.136397	NR_040551	ENSMUSG00000105923	A830019L24Rik	-	RIKEN cDNA A830019L24 gene	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5387	chr4	25743691	25743891	+	1.58039	NA	intron (NM_010243, intron 1 of 2)	Lx9|LINE|L1	56212	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6926	chr7	80691258	80691458	+	1.58039	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	-2481	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding	0.005000	0.427861	58(AATTCATAATTCATG,+,0.00),58(AATTCATAATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6902	chr7	72627405	72627605	+	1.58039	NA	Intergenic	Intergenic	-320910	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2769	chr15	7159219	7159419	+	1.58039	NA	intron (NM_001358593, intron 3 of 19)	intron (NM_001358593, intron 3 of 19)	18777	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	LIF receptor alpha	protein-coding	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4429	chr2	82169745	82169945	+	1.58039	NA	intron (NM_175513, intron 1 of 3)	intron (NM_175513, intron 1 of 3)	116187	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4242	chr2	29747735	29747935	+	1.58039	NA	intron (NM_001370924, intron 1 of 3)	B4|SINE|B4	3822	NM_001370923	433415	Mm.359309	NM_001370923	ENSMUSG00000079497	Gm13420	Dspd2	predicted gene 13420	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3006	chr15	85126078	85126278	+	1.58039	NA	intron (NM_080470, intron 4 of 24)	MLTR25A|LTR|ERVK	5779	NM_080470	140557	Mm.182737	NM_080470	ENSMUSG00000022432	Smc1b	SMC-1B|SMC1beta|Smc1l2	structural maintenance of chromosomes 1B	protein-coding	0.005000	0.363184			-38(ATATGCTTAACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3709	chr18	12283616	12283816	+	1.58039	NA	intron (NM_001360803, intron 1 of 7)	intron (NM_001360803, intron 1 of 7)	22004	NM_001190371	225187	Mm.53865	NM_001190371	ENSMUSG00000057766	Ankrd29	G630054C21|G630054C21Rik|Gm95	ankyrin repeat domain 29	protein-coding	0.005000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1210	chr11	26753687	26753887	+	1.58039	NA	Intergenic	Intergenic	-31321	NR_002890	654472	Mm.347777	NR_002890		Gm12070	-	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1672	chr12	56077589	56077789	+	1.58039	NA	Intergenic	Intergenic	-175554	NR_045048	100503961	Mm.136732	NR_045048	ENSMUSG00000112164	Gm19990	-	predicted gene, 19990	ncRNA	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4048	chr19	22193374	22193574	+	1.58039	NA	intron (NM_001035239, intron 1 of 24)	intron (NM_001035239, intron 1 of 24)	54428	NM_001035243	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2242	chr13	98842793	98842993	+	1.58039	NA	3' UTR (NM_178716, exon 24 of 24)	3' UTR (NM_178716, exon 24 of 24)	-27444	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding	0.000000	0.358209			-79(ACTTTTTTTTGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-765	chr10	33792223	33792423	+	1.58039	NA	Intergenic	LTRIS3|LTR|ERV1	-10208	NM_001101452	215895	Mm.473684	NM_001101452	ENSMUSG00000090298	Sult3a2	EG215895|Gm4794	sulfotransferase family 3A, member 2	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6764	chr6	146221250	146221450	+	1.57925	NA	intron (NM_019923, intron 45 of 56)	intron (NM_019923, intron 45 of 56)	280873	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding	0.010000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-666	chr5	30763375	30763575	+	1.57895	NA	intron (NM_001356948, intron 2 of 12)	intron (NM_001356948, intron 2 of 12)	-51166	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding	0.030000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-545	chr1	172953562	172953762	+	1.57873	NA	Intergenic	L1MC|LINE|L1	-3106	NM_008763	18313	Mm.377103	NM_008763	ENSMUSG00000037924	Olfr16	MOR23|MOR26713	olfactory receptor 16	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3777	chr18	32997660	32997860	+	1.57873	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	58719	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding	0.005000	0.363184			41(ATTTGCATACAAATAT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-536	chr2	143924599	143924799	+	1.57873	NA	intron (NM_019771, intron 1 of 3)	L1_Rod|LINE|L1	9368	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8168	chrX	167972418	167972618	+	1.57873	NA	intron (NM_001033330, intron 3 of 19)	intron (NM_001033330, intron 3 of 19)	-117441	NM_001290428	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5240	chr3	142309547	142309747	+	1.57803	NA	intron (NM_001190853, intron 4 of 9)	intron (NM_001190853, intron 4 of 9)	82203	NM_001190857	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7339	chr8	79366029	79366229	+	1.57803	NA	intron (NM_008539, intron 2 of 6)	intron (NM_008539, intron 2 of 6)	33299	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Mad1|Madh1|Madr1|Mlp1|MusMLP|dwf-A|mMad1	SMAD family member 1	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-486	chr1	157804192	157804392	+	1.57803	NA	Intergenic	Intergenic	278122	NM_001159986	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding	0.005000	0.323383			-64(AAAGTGTTATGCAAAT,+,0.00),-43(TTTTTGTTATTAATAT,+,0.00),-21(TGATAGTTATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2224	chr13	95832671	95832871	+	1.57803	NA	intron (NM_027711, intron 2 of 35)	intron (NM_027711, intron 2 of 35)	59151	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8104	chrX	142984762	142984962	+	1.57803	NA	Intergenic	Intergenic	-18136	NM_019496	56068	Mm.143724	NM_019496	ENSMUSG00000042225	Ammecr1	6230420G18Rik	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	protein-coding	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-158	chr1	54791503	54791703	+	1.57803	NA	intron (NM_001081433, intron 3 of 27)	intron (NM_001081433, intron 3 of 27)	134784	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5130	chr3	114324630	114324830	+	1.57803	NA	Intergenic	Intergenic	294190	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding	0.005000	0.353234			-85(TTTTTCTTTTTCAGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-634	chr4	85707663	85707863	+	1.57639	NA	Intergenic	Intergenic	-346152	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding	0.010000	0.412935			33(ATCAGAATGACAGAAT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-24	chr1	92004172	92004372	+	1.57599	NA	intron (NM_207225, intron 5 of 26)	intron (NM_207225, intron 5 of 26)	176069	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5735	chr4	126165871	126166071	+	1.57599	NA	intron (NM_001356455, intron 11 of 11)	intron (NM_001356455, intron 11 of 11)	-2630	NM_001162533	66938	Mm.29813	NM_025856	ENSMUSG00000073758	Sh3d21	1700029G01Rik|AU019788	SH3 domain containing 21	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2167	chr13	80750818	80751018	+	1.57570	NA	Intergenic	RLTR13C3|LTR|ERVK	-132466	NR_153410	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6131	chr5	105867710	105867910	+	1.57570	NA	Intergenic	Intergenic	-8758	NM_018759	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7844	chr9	99058009	99058209	+	1.57562	NA	intron (NM_029094, intron 16 of 23)	intron (NM_029094, intron 16 of 23)	-22419	NM_001080776	382097	Mm.293727	NM_001080776	ENSMUSG00000044860	Gm1123	AV052824|CLSP	predicted gene 1123	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6454	chr6	53207377	53207577	+	1.57562	NA	Intergenic	MER45C|DNA|hAT-Tip100	-13687	NR_073371	231989	Mm.372520	NR_073371	ENSMUSG00000107935	Gm4872	D430007I03	predicted gene 4872	ncRNA	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3002	chr15	77111160	77111360	+	1.57562	NA	intron (NM_175387, intron 5 of 12)	intron (NM_175387, intron 5 of 12)	26862	NR_108037	74303	Mm.444304	NR_108037	ENSMUSG00000097267	1700109K24Rik	4933425G21Rik	RIKEN cDNA 1700109K24 gene	ncRNA	0.005000	0.328358			-77(TTTTAAAAGGCAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6513	chr6	70143887	70144087	+	1.57562	NA	Intergenic	Intergenic	648188	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.000000	0.268657			-14(AATTTGTCATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-564	chr1	176037244	176037444	+	1.57562	NA	intron (NM_001195816, intron 5 of 9)	intron (NM_001195816, intron 5 of 9)	117015	NM_001290692	226720	Mm.11282	NM_001290692	ENSMUSG00000104158	Becn2	Beclin-2|Gm104	beclin 2	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-363	chr1	127826842	127827042	+	1.57562	NA	intron (NM_011737, intron 6 of 9)	intron (NM_011737, intron 6 of 9)	13348	NM_011737	22625	Mm.246566	NM_011737	ENSMUSG00000051590	Map3k19	Ysk4	mitogen-activated protein kinase kinase kinase 19	protein-coding	0.010000	0.417910			-28(TCATTGTTTTGCTGAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7999	chrX	83740724	83740924	+	1.57320	NA	intron (NM_007868, intron 17 of 78)	intron (NM_007868, intron 17 of 78)	-252900	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0.005000	0.323383			-2(AATTGCACAAGAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-591	chr1	181333339	181333539	+	1.57320	NA	Intergenic	Intergenic	-19189	NM_001160211	72978	Mm.338083	NM_028408	ENSMUSG00000026514	Cnih3	2900075G08Rik|CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4731	chr2	153092544	153092744	+	1.57320	NA	Intergenic	Intergenic	-15824	NM_001172117	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5552	chr4	77409113	77409313	+	1.57320	NA	intron (NR_160919, intron 4 of 39)	intron (NR_160919, intron 4 of 39)	802529	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-189	chr1	66066764	66066964	+	1.57320	NA	Intergenic	Intergenic	-108465	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding	0.010000	0.358209	-17(TATACATTATTCATG,+,0.00),-17(TATACATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-336	chr1	122327634	122327834	+	1.57320	NA	Intergenic	L1MA4A|LINE|L1	122589	NR_151524	102638832	Mm.112794	NR_151524	ENSMUSG00000099960	Gm28590	-	predicted gene 28590	ncRNA	0.005000	0.298507			34(ATTTGCAAGACAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3212	chr16	47472800	47473000	+	1.57320	NA	Intergenic	Intergenic	685599	NR_152166	619300	Mm.384092	NR_152166		6430553K19Rik	-	RIKEN cDNA 6430553K19 gene	ncRNA	0.015000	0.333333			5(TCTTTCACATGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7799	chr9	87933284	87933484	+	1.57280	NA	Intergenic	Intergenic	-202124	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-778	chr10	39006140	39006340	+	1.57041	NA	intron (NM_010681, intron 2 of 37)	intron (NM_010681, intron 2 of 37)	40725	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4409	chr2	77035804	77036004	+	1.57001	NA	intron (NM_001025576, intron 17 of 23)	intron (NM_001025576, intron 17 of 23)	-53357	NM_011652	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding	0.005000	0.328358			-48(ATATGGTCATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5912	chr5	39541300	39541500	+	1.56842	NA	intron (NR_045416, intron 1 of 5)	intron (NR_045416, intron 1 of 5)	62174	NR_045416	75095	Mm.332354	NR_045416	ENSMUSG00000106741	4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	ncRNA	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4552	chr2	118446035	118446235	+	1.56842	NA	intron (NM_001355383, intron 16 of 35)	intron (NM_001355383, intron 16 of 35)	33561	NM_009273	20813	Mm.363404	NM_009273	ENSMUSG00000009549	Srp14	14kDa|AW536328	signal recognition particle 14	protein-coding	0.020000	0.417910			-72(ATTTGCATAACGGAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7763	chr9	80368691	80368891	+	1.56842	NA	intron (NM_022016, intron 12 of 16)	intron (NM_022016, intron 12 of 16)	96647	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0.005000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-473	chr2	28222837	28223037	+	1.56842	NA	intron (NM_001038613, intron 5 of 5)	intron (NM_001038613, intron 5 of 5)	17248	NM_001038612	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding	0.030000	0.577114			68(CCTTTCTTGTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-56	chr1	20923049	20923249	+	1.56842	NA	intron (NM_001355122, intron 1 of 2)	intron (NM_001355122, intron 1 of 2)	5309	NM_001355122	74229	Mm.40780	NM_028829	ENSMUSG00000025931	Paqr8	1700019B16Rik|3110001D06Rik	progestin and adipoQ receptor family member VIII	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4291	chr2	47977061	47977261	+	1.56842	NA	Intergenic	MamTip2|DNA|hAT-Tip100	-836948	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1808	chr12	90887364	90887564	+	1.56842	NA	Intergenic	Intergenic	-148426	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding	0.000000	0.393035			-17(ATTTGCATATGAGTAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1338	chr11	70931526	70931726	+	1.56842	NA	intron (NM_019400, intron 13 of 17)	L1M4|LINE|L1	38347	NM_001083331	19069	Mm.288962	NM_172394	ENSMUSG00000040667	Nup88	Nup84|Prei2	nucleoporin 88	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5979	chr5	62322143	62322343	+	1.56842	NA	Intergenic	Intergenic	443934	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding	0.000000	0.303483		-14(CATACATATGGATA,+,0.00),-14(CATACATATGGATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6404	chr6	38347890	38348090	+	1.56842	NA	intron (NM_028864, intron 1 of 8)	MER2|DNA|TcMar-Tigger	6613	NM_001347122	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|PARP13|ZAP	zinc finger CCCH type, antiviral 1	protein-coding	0.015000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-744	chr6	57515784	57515984	+	1.56609	NA	non-coding (NR_156745, exon 4 of 7)	non-coding (NR_156745, exon 4 of 7)	19603	NR_156745	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2C-kappa|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-819	chr10	52130727	52130927	+	1.56609	NA	intron (NM_011282, intron 18 of 43)	intron (NM_011282, intron 18 of 43)	64417	NM_011282	19886	Mm.236163	NM_011282	ENSMUSG00000019893	Ros1	Ros-1|c-ros	Ros1 proto-oncogene	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6464	chr6	57515807	57516007	+	1.56609	NA	non-coding (NR_156745, exon 4 of 7)	non-coding (NR_156745, exon 4 of 7)	19580	NR_156745	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2C-kappa|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5546	chr4	76812238	76812438	+	1.56609	NA	intron (NR_160919, intron 8 of 39)	Eulor6B|DNA?|DNA?	-468095	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5579	chr4	85707551	85707751	+	1.56523	NA	Intergenic	Intergenic	-346264	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6617	chr6	101354394	101354594	+	1.56476	NA	exon (NM_018884, exon 3 of 10)	exon (NM_018884, exon 3 of 10)	23403	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4639	chr2	135084291	135084491	+	1.56476	NA	intron (NM_001145830, intron 3 of 31)	intron (NM_001145830, intron 3 of 31)	131225	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7057	chr7	122847880	122848080	+	1.56380	NA	Intergenic	B3|SINE|B2	122479	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5811	chr5	3722196	3722396	+	1.56380	NA	intron (NM_001003909, intron 10 of 19)	intron (NM_001003909, intron 10 of 19)	50491	NM_001289529	70797	Mm.130148	NM_001003909	ENSMUSG00000040351	Ankib1	2310061P20Rik|4631416I11Rik|AW494740|C80642|mKIAA1386	ankyrin repeat and IBR domain containing 1	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7464	chr8	116144071	116144271	+	1.56380	NA	Intergenic	Intergenic	-360844	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding	0.010000	0.517413	-74(CATGAAATATTCATT,+,0.00),-74(CATGAAATATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2535	chr14	70435324	70435524	+	1.56380	NA	intron (NM_001364321, intron 1 of 22)	intron (NM_001364321, intron 1 of 22)	1474	NM_001364321	57746	Mm.85253	NM_021308	ENSMUSG00000033644	Piwil2	Piwil1l|mili	piwi-like RNA-mediated gene silencing 2	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1798	chr12	87435028	87435228	+	1.56380	NA	intron (NM_001102565, intron 3 of 5)	MER77B|LTR|ERVL	2629	NR_037228	100526546		NR_037228	ENSMUSG00000105428	Mir3068	mir-3068|mmu-mir-3068	microRNA 3068	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6261	chr5	149649697	149649897	+	1.56380	NA	Intergenic	Intergenic	-13461	NM_001347534	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding	0.015000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-837	chr8	77340183	77340383	+	1.56238	NA	intron (NM_001363418, intron 18 of 21)	intron (NM_001363418, intron 18 of 21)	111806	NM_001363420	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5889	chr5	30763293	30763493	+	1.56228	NA	intron (NM_001356948, intron 2 of 12)	intron (NM_001356948, intron 2 of 12)	-51248	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding	0.040000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4680	chr2	141042667	141042867	+	1.56156	NA	intron (NM_001013802, intron 5 of 18)	RMER12B|LTR|ERVK	-371291	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2979	chr15	68350132	68350332	+	1.56156	NA	Intergenic	L1ME1|LINE|L1	-8943	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4	chr1	3569136	3569336	+	1.56156	NA	intron (NM_001011874, intron 1 of 2)	Lx7|LINE|L1	102262	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding	0.005000	0.363184			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-346	chr15	68350039	68350239	+	1.56156	NA	Intergenic	L1ME1|LINE|L1	-8850	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA	0.000000	0.328358			-46(ATATCCACAACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2078	chr13	56102771	56102971	+	1.56156	NA	intron (NM_012015, intron 4 of 8)	intron (NM_012015, intron 4 of 8)	32679	NM_001159514	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding	0.000000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique	chr1	3569155	3569355	+	1.56156	NA	intron (NM_001011874, intron 1 of 2)	Lx7|LINE|L1	102243	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding	0.005000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-533	chr2	141042655	141042855	+	1.56156	NA	intron (NM_001013802, intron 5 of 18)	RMER12B|LTR|ERVK	-371279	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1401	chr11	88862450	88862650	+	1.56156	NA	intron (NR_126433, intron 3 of 4)	intron (NR_126433, intron 3 of 4)	2036	NM_001042541	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding	0.010000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-529	chr2	136840591	136840791	+	1.56041	NA	Intergenic	Intergenic	-50527	NM_028201	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4654	chr2	136840725	136840925	+	1.56041	NA	Intergenic	Intergenic	-50393	NM_028201	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-309	chr1	106949091	106949291	+	1.55937	NA	exon (NM_001199213, exon 3 of 8)	exon (NM_001199213, exon 3 of 8)	10234	NM_001199213	71869	Mm.321740	NM_027971	ENSMUSG00000059956	Serpinb12	2300003F07Rik|4833409F13Rik	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7346	chr8	79828897	79829097	+	1.55937	NA	Intergenic	L4_C_Mam|LINE|RTE-X	117148	NM_001357235	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding	0.005000	0.383085			16(ATTTAAATGAACAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2103	chr13	63094339	63094539	+	1.55937	NA	intron (NM_001289926, intron 5 of 15)	intron (NM_001289926, intron 5 of 15)	129546	NM_001289926	72061	Mm.188105	NM_028079	ENSMUSG00000021458	Aopep	2010111I01Rik|2300006M17Rik|AP-O|AW742919|ApO|mir-23b|mir-24-1|mir-27b	aminopeptidase O	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-546	chr1	172953806	172954006	+	1.55723	NA	Intergenic	L1MC|LINE|L1	-2862	NM_008763	18313	Mm.377103	NM_008763	ENSMUSG00000037924	Olfr16	MOR23|MOR26713	olfactory receptor 16	protein-coding	0.000000	0.323383			56(TTATTGACTTGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5154	chr3	120263824	120264024	+	1.55723	NA	Intergenic	Intergenic	-480536	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.328358			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-433	chr18	32997638	32997838	+	1.55723	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	58697	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding	0.000000	0.373134			63(ATTTGCATACAAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-556	chr1	175722810	175723010	+	1.55591	NA	intron (NM_029453, intron 4 of 27)	intron (NM_029453, intron 4 of 27)	24317	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-13	chr1	6448446	6448646	+	1.55591	NA	Intergenic	Intergenic	-38685	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding	0.005000	0.318408			-22(ATTTACAACTCAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2755	chr15	4150879	4151079	+	1.55591	NA	intron (NM_024188, intron 16 of 16)	L1MA6|LINE|L1	-123573	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7324	chr8	77340232	77340432	+	1.55439	NA	intron (NM_001363418, intron 18 of 21)	intron (NM_001363418, intron 18 of 21)	111757	NM_001363420	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1938	chr13	6652545	6652745	+	1.55376	NA	Intergenic	Intergenic	-3874	NM_001291071	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3985	chr18	85949985	85950185	+	1.55310	NA	Intergenic	MamRep1527|LTR|LTR	-444867	NM_001360910	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0.000000	0.348259		-62(CTTGAATATGCAAT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4041	chr19	21016928	21017128	+	1.55111	NA	Intergenic	Intergenic	-62826	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5252	chr3	146044938	146045138	+	1.55111	NA	intron (NM_172864, intron 20 of 22)	intron (NM_172864, intron 20 of 22)	57168	NM_001166064	214804	Mm.268854	NM_001166064	ENSMUSG00000036863	Syde2	C430017H16Rik	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	protein-coding	0.025000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5277	chr3	148899102	148899302	+	1.55111	NA	intron (NM_001081298, intron 1 of 23)	intron (NM_001081298, intron 1 of 23)	55433	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6751	chr6	140443476	140443676	+	1.54916	NA	intron (NM_144920, intron 3 of 30)	intron (NM_144920, intron 3 of 30)	19477	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4500	chr2	107118116	107118316	+	1.54916	NA	Intergenic	Intergenic	-58565	NM_008045	14308	Mm.249525	NM_008045	ENSMUSG00000027120	Fshb	FSH|FSH-B|FSH-beta|Fshbeta	follicle stimulating hormone beta	protein-coding	0.010000	0.298507			-46(TTCTTTTCATTAAAAT,+,0.00),-38(ATTAAAATGGAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7523	chr9	13535759	13535959	+	1.54727	NA	Intergenic	Intergenic	-84130	NM_001013813	270118	Mm.116898	NM_173776	ENSMUSG00000031925	Maml2	5930431H10|BC032967	mastermind like transcriptional coactivator 2	protein-coding	0.005000	0.378109			-87(CCATTACCTTTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1023	chr10	110933466	110933666	+	1.54727	NA	intron (NM_007792, intron 2 of 5)	intron (NM_007792, intron 2 of 5)	13390	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-524	chr1	167969575	167969775	+	1.54541	NA	Intergenic	Intergenic	280117	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding	0.010000	0.522388			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-291	chr14	60403326	60403526	+	1.54541	NA	Intergenic	Intergenic	25734	NM_028113	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-526	chr1	167969848	167970048	+	1.54361	NA	Intergenic	X8_LINE|LINE|CR1	280390	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding	0.010000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-363	chr16	25503655	25503855	+	1.54361	NA	Intergenic	Intergenic	-180010	NM_001127260	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding	0.010000	0.442786			58(TTGTTTTCATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3125	chr16	25503661	25503861	+	1.54361	NA	Intergenic	Intergenic	-180004	NM_001127260	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding	0.010000	0.442786			52(TTGTTTTCATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2341	chr14	9105899	9106099	+	1.54084	NA	Intergenic	Lx5|LINE|L1	439609	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5016	chr3	75607649	75607849	+	1.54084	NA	intron (NM_001357514, intron 1 of 8)	intron (NM_001357514, intron 1 of 8)	47982	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2208	chr13	93073018	93073218	+	1.54084	NA	promoter-TSS (NR_036451)	promoter-TSS (NR_036451)	-186	NR_036451	100502942	Mm.441946	NM_177623	ENSMUSG00000114382	Gm4814	C920025J10|EG218444	predicted gene 4814	ncRNA	0.015000	0.532338		24(CATTCATAGGCATC,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8027	chrX	94012518	94012718	+	1.54084	NA	Intergenic	Intergenic	43962	NR_028320	385493	Mm.328014	NM_001033480	ENSMUSG00000081044	AU015836	-	expressed sequence AU015836	ncRNA	0.025000	0.487562			-59(TATGTATCATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6055	chr5	81725295	81725495	+	1.54084	NA	intron (NM_001359829, intron 16 of 23)	intron (NM_001359829, intron 16 of 23)	399318	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA	0.005000	0.333333		2(CATTCATATGCATG,+,0.00),2(CATTCATATGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3837	chr18	48935075	48935275	+	1.54084	NA	Intergenic	L1_Rod|LINE|L1	-588114	NR_033785	67321	Mm.245802	NR_033785	ENSMUSG00000100297	1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	ncRNA	0.000000	0.298507			-49(ACATTCATATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-362	chr1	127826637	127826837	+	1.54084	NA	intron (NM_011737, intron 6 of 9)	B1_Mus2|SINE|Alu	13553	NM_011737	22625	Mm.246566	NM_011737	ENSMUSG00000051590	Map3k19	Ysk4	mitogen-activated protein kinase kinase kinase 19	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2880	chr15	41352220	41352420	+	1.54084	NA	Intergenic	RLTR9A3|LTR|ERVK	-95162	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2159	chr13	78083924	78084124	+	1.54084	NA	intron (NM_001163419, intron 9 of 9)	intron (NM_001163419, intron 9 of 9)	59122	NM_029315	75507	Mm.443255	NM_029315	ENSMUSG00000093668	Pou5f2	1700013G10Rik|SPRM-1|Sprm1	POU domain class 5, transcription factor 2	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5924	chr5	45207030	45207230	+	1.54084	NA	intron (NR_131933, intron 4 of 5)	intron (NR_131933, intron 4 of 5)	217270	NR_131933	52401	Mm.33854	NR_131933	ENSMUSG00000029092	D5Ertd615e	4930435H24Rik	DNA segment, Chr 5, ERATO Doi 615, expressed	ncRNA	0.000000	0.442786			-49(GTCTGCATCACAATAA,-,0.00),-37(ATAAACAAAAGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5409	chr4	31873240	31873440	+	1.54084	NA	Intergenic	MamRep605|LTR?|LTR?	-90767	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5310	chr3	156852831	156853031	+	1.54084	NA	intron (NM_001039094, intron 1 of 6)	Lx3C|LINE|L1	291137	NM_177274	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4509	chr2	108655539	108655739	+	1.54084	NA	Intergenic	Intergenic	622651	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0.005000	0.323383		-84(TATTCTTATGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8003	chrX	84971610	84971810	+	1.54084	NA	intron (NM_007868, intron 61 of 78)	intron (NM_007868, intron 61 of 78)	-76585	NM_001314037	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1556	chr12	16012031	16012231	+	1.54082	NA	Intergenic	Intergenic	-195346	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3794	chr18	37096323	37096523	+	1.54082	NA	intron (NM_001003671, intron 1 of 3)	Lx9|LINE|L1	6287	NM_001003671	353236	Mm.308500	NM_001003671	ENSMUSG00000103255	Pcdhac1	CNRc1	protocadherin alpha subfamily C, 1	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3158	chr16	33464894	33465094	+	1.54082	NA	intron (NM_001358570, intron 5 of 8)	intron (NM_001358570, intron 5 of 8)	-52334	NM_001370999									0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7059	chr7	123319455	123319655	+	1.54082	NA	intron (NM_001122642, intron 6 of 19)	intron (NM_001122642, intron 6 of 19)	50360	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5873	chr5	26491115	26491315	+	1.54082	NA	intron (NR_029445, intron 1 of 4)	intron (NR_029445, intron 1 of 4)	2099	NR_029445	75942	Mm.50087	NR_029445	ENSMUSG00000029044	4930584F24Rik	1700001J09Rik|4930522C06Rik	RIKEN cDNA 4930584F24 gene	ncRNA	0.000000	0.452736			-26(CTTTACTCATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-118	chr1	41658542	41658742	+	1.54082	NA	Intergenic	Intergenic	-477390	NR_040475	74897	Mm.243822	NR_040475	ENSMUSG00000104072	4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	ncRNA	0.010000	0.318408	-39(TTTGCTTTATGCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5591	chr4	89130446	89130646	+	1.54082	NA	Intergenic	Intergenic	-2320	NR_151607	102637941	Mm.366358	NR_151607		Gm12602	-	predicted gene 12602	ncRNA	0.005000	0.402985			78(ATTAACATGTAAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3686	chr18	6066224	6066424	+	1.54082	NA	intron (NM_001039692, intron 4 of 18)	ORR1F|LTR|ERVL-MaLR	69774	NM_001039692	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1171	chr11	16241044	16241244	+	1.54050	NA	Intergenic	RLTR13B1|LTR|ERVK	-16598	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0.020000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7458	chr8	115201871	115202071	+	1.54050	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	504923	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3826	chr18	44654711	44654911	+	1.54050	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-6854	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4580	chr2	124912143	124912343	+	1.54050	NA	Intergenic	Intergenic	-155884	NM_175034	317750	Mm.330538	NM_175034	ENSMUSG00000035183	Slc24a5	F630045L20Rik|JSX|NCKX5|NCX5|Oca6	solute carrier family 24, member 5	protein-coding	0.005000	0.323383			35(ATTACCATAGCAATGT,-,0.00),60(CTATTATCGTGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3337	chr16	79335194	79335394	+	1.54050	NA	Intergenic	Intergenic	-244197	NM_178855	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	transmembrane protease, serine 15	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3809	chr18	40289811	40290011	+	1.54050	NA	intron (NM_026135, intron 2 of 2)	intron (NM_026135, intron 2 of 2)	32912	NM_001371039									0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2698	chr14	114927744	114927944	+	1.54050	NA	Intergenic	Intergenic	18104	NR_126548	74982		NR_126548	ENSMUSG00000115372	1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA	0.005000	0.323383		25(TATGAATATTCATG,+,0.00),25(TATGAATATTCATG,-,0.00)	18(TTATTGTTATGAATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-156	chr1	53359139	53359339	+	1.54050	NA	Intergenic	Intergenic	-6487	NM_001353501	110599589	Mm.285783	NM_001353501		Asdurf	ASNSD1-SEP|Asnsd1	Asnsd1 upstream reading frame	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4159	chr2	7460459	7460659	+	1.54046	NA	Intergenic	Intergenic	-64361	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1445	chr11	105258050	105258250	+	1.54046	NA	intron (NM_001112705, intron 15 of 21)	intron (NM_001112705, intron 15 of 21)	-34496	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5724	chr4	124360262	124360462	+	1.54046	NA	Intergenic	Intergenic	125597	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	ncRNA	0.015000	0.393035			-28(GTTTTGTGATGCTAAT,+,0.00),81(ATTTGAATAAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4582	chr2	125160269	125160469	+	1.54046	NA	intron (NM_183354, intron 2 of 26)	intron (NM_183354, intron 2 of 26)	7769	NM_183354	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7037	chr7	116545051	116545251	+	1.54046	NA	Intergenic	Intergenic	40782	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3328	chr16	77092160	77092360	+	1.54046	NA	intron (NM_013918, intron 17 of 23)	intron (NM_013918, intron 17 of 23)	78191	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1288	chr11	50666448	50666648	+	1.54046	NA	intron (NM_175643, intron 2 of 21)	intron (NM_175643, intron 2 of 21)	64463	NM_175643	216725	Mm.110597	NM_175643	ENSMUSG00000036545	Adamts2	ADAM-TS 2|ADAM-TS2|ADAMTS-2|PC I-NP|PCINP|pNPI	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6991	chr7	99180357	99180557	+	1.54046	NA	intron (NM_026384, intron 1 of 7)	intron (NM_026384, intron 1 of 7)	2256	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-804	chr10	45136886	45137086	+	1.54046	NA	intron (NM_011156, intron 10 of 14)	intron (NM_011156, intron 10 of 14)	69770	NM_011156	19072	Mm.37294	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PE|PEP|Pop	prolyl endopeptidase	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-341	chr1	123770979	123771179	+	1.54046	NA	intron (NM_199021, intron 3 of 25)	intron (NM_199021, intron 3 of 25)	274480	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7608	chr9	35149210	35149410	+	1.54046	NA	intron (NM_027030, intron 2 of 5)	intron (NM_027030, intron 2 of 5)	26677	NM_027030	69305	Mm.229110	NM_027030	ENSMUSG00000032040	Dcps	1700001E16Rik|AA408441	decapping enzyme, scavenger	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-153	chr1	52465646	52465846	+	1.54046	NA	intron (NM_008667, intron 5 of 7)	intron (NM_008667, intron 5 of 7)	34702	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3397	chr16	96612419	96612619	+	1.54046	NA	intron (NM_031174, intron 30 of 32)	intron (NM_031174, intron 30 of 32)	144913	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding	0.010000	0.402985			-61(AGCTTGTTATTTAAAT,+,0.00),-53(ATTTAAATGCTAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-659	chr1	194320805	194321005	+	1.54011	NA	Intergenic	Intergenic	-98146	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2798	chr15	12878300	12878500	+	1.53997	NA	intron (NM_026799, intron 15 of 34)	intron (NM_026799, intron 15 of 34)	53585	NM_026799	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding	0.010000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-962	chr10	96834445	96834645	+	1.53997	NA	Intergenic	Intergenic	-201223	NR_045358	75301	Mm.108650	NR_045358	ENSMUSG00000111924	4930556N09Rik	-	RIKEN cDNA 4930556N09 gene	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-160	chr1	55380413	55380613	+	1.53997	NA	Intergenic	Intergenic	-16760	NM_001367887	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	boule homolog, RNA binding protein	protein-coding	0.005000	0.378109			-60(CCATTTTCTTTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1094	chr10	121635326	121635526	+	1.53997	NA	Intergenic	Lx7|LINE|L1	-6275	NM_177335	216393	Mm.119759	NM_177335	ENSMUSG00000047642	D930020B18Rik	1500017I17Rik	RIKEN cDNA D930020B18 gene	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-140	chr1	47495242	47495442	+	1.53997	NA	Intergenic	Intergenic	-28217	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4950	chr3	54107016	54107216	+	1.53997	NA	Intergenic	MER2|DNA|TcMar-Tigger	-48941	NM_001253683	22066	Mm.10100	NM_016984	ENSMUSG00000027748	Trpc4	CCE1|STRPC4|Trp4|Trrp4	transient receptor potential cation channel, subfamily C, member 4	protein-coding	0.010000	0.373134			-85(CAAGTCTCATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5032	chr3	81318616	81318816	+	1.53956	NA	Intergenic	Intergenic	282300	NM_001357746	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C|SCDGF|VEGF-E	platelet-derived growth factor, C polypeptide	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7174	chr8	23925272	23925472	+	1.53956	NA	intron (NM_177086, intron 4 of 6)	intron (NM_177086, intron 4 of 6)	255711	NM_001277239	320158	Mm.121274	NM_177086	ENSMUSG00000037492	Zmat4	9630048M01Rik	zinc finger, matrin type 4	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1600	chr12	35450886	35451086	+	1.53956	NA	Intergenic	Intergenic	84003	NM_013464	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding	0.005000	0.348259			10(ATATCCATAAAAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1784	chr12	83841669	83841869	+	1.53956	NA	intron (NR_073563, intron 4 of 10)	intron (NR_073563, intron 4 of 10)	589	NM_001136075	18222	Mm.4390	NM_010949	ENSMUSG00000021224	Numb	Nb	NUMB endocytic adaptor protein	protein-coding	0.010000	0.323383			-57(TTTTTCTTATTTAATT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6121	chr5	103072794	103072994	+	1.53956	NA	intron (NM_001081567, intron 2 of 13)	intron (NM_001081567, intron 2 of 13)	-14502	NM_001318131	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.020000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-86	chr10	33792129	33792329	+	1.53956	NA	Intergenic	LTRIS3|LTR|ERV1	-10114	NM_001101452	215895	Mm.473684	NM_001101452	ENSMUSG00000090298	Sult3a2	EG215895|Gm4794	sulfotransferase family 3A, member 2	protein-coding	0.000000	0.378109			-26(GTTTTGTTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-774	chr10	37357248	37357448	+	1.53956	NA	Intergenic	Intergenic	-218422	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6017	chr5	70603185	70603385	+	1.53956	NA	Intergenic	Intergenic	239332	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1118	chr10	125093722	125093922	+	1.53956	NA	Intergenic	L1_Mur2|LINE|L1	214994	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.000000	0.328358			-33(CCACTGTTATTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4979	chr3	64321976	64322176	+	1.53956	NA	Intergenic	RLTR13D6|LTR|ERVK	-34659	NM_001104614	637004	Mm.469887	NM_001104614	ENSMUSG00000091572	Vmn2r3	EG637004	vomeronasal 2, receptor 3	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5807	chr5	3477894	3478094	+	1.53956	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-65839	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6503	chr6	66263463	66263663	+	1.53956	NA	Intergenic	Intergenic	-8942	NR_136927	102633773	Mm.272086	NR_136927	ENSMUSG00000107653	Gm31520	-	sterol-C5-desaturase pseudogene	pseudo	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7050	chr7	121489846	121490046	+	1.53956	NA	intron (NM_001081327, intron 1 of 1)	intron (NM_001081327, intron 1 of 1)	97650	NM_001081327	195646	Mm.247449	NM_177575	ENSMUSG00000046321	Hs3st2	6430516N12Rik|A830061E14Rik|AW491345	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4208	chr2	21942463	21942663	+	1.53956	NA	Intergenic	Intergenic	-284940	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1154	chr11	9867123	9867323	+	1.53956	NA	Intergenic	Intergenic	675281	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7607	chr9	35043753	35043953	+	1.53926	NA	Intergenic	MIRc|SINE|MIR	-72875	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1534	chr12	9132677	9132877	+	1.53926	NA	Intergenic	Intergenic	102780	NM_029321	75516	Mm.37581	NM_029321	ENSMUSG00000066637	Ttc32	1700013G20Rik	tetratricopeptide repeat domain 32	protein-coding	0.000000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-451	chr18	81439733	81439933	+	1.53926	NA	Intergenic	Intergenic	-452812	NM_001369133	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	spalt like transcription factor 3	protein-coding	0.010000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7578	chr9	28983287	28983487	+	1.53926	NA	Intergenic	Intergenic	429298	NM_001357602	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-300	chr1	105864281	105864481	+	1.53926	NA	Intergenic	L1ME1|LINE|L1	83658	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding	0.020000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-602	chr1	184915487	184915687	+	1.53796	NA	intron (NM_145515, intron 10 of 17)	AT_rich|Low_complexity|Low_complexity	-32551	NM_178692	226777	Mm.169542	NM_178692	ENSMUSG00000039349	C130074G19Rik	-	RIKEN cDNA C130074G19 gene	protein-coding	0.005000	0.348259			-53(ATATACATGAGAACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6366	chr6	27545873	27546073	+	1.53794	NA	intron (NM_008174, intron 7 of 10)	intron (NM_008174, intron 7 of 10)	390777	NR_030420	735266		NR_030420	ENSMUSG00000076067	Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	ncRNA	0.010000	0.427861			7(ATTTGAATAACATTTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7926	chrX	13560000	13560200	+	1.53794	NA	intron (NM_009806, intron 14 of 24)	intron (NM_009806, intron 14 of 24)	-72669	NM_011823	23890	Mm.487326	NM_011823	ENSMUSG00000040229	Gpr34	Lypsr1	G protein-coupled receptor 34	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-488	chr1	158490647	158490847	+	1.53794	NA	intron (NM_007495, intron 2 of 22)	intron (NM_007495, intron 2 of 22)	-14878	NR_030441	735253		NR_030441	ENSMUSG00000070103	Mir488	Mirn488|mir-488|mmu-mir-488	microRNA 488	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-805	chr10	45338102	45338302	+	1.53794	NA	intron (NM_024285, intron 1 of 7)	intron (NM_024285, intron 1 of 7)	2467	NM_024285	23828	Mm.332793	NM_024285	ENSMUSG00000071317	Bves	Pop1|Popdc1|mBVES	blood vessel epicardial substance	protein-coding	0.000000	0.308458		65(AGTGTATATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7872	chr9	108163803	108164003	+	1.53794	NA	intron (NM_007567, intron 1 of 11)	L1M4b|LINE|L1	26480	NM_007567	12217	Mm.20425	NM_007567	ENSMUSG00000032589	Bsn	-	bassoon	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4299	chr2	51090231	51090431	+	1.53794	NA	Intergenic	Intergenic	58780	NM_028810	74194	Mm.46497	NM_028810	ENSMUSG00000017144	Rnd3	2610017M01Rik|AI661404|Arhe|Rhoe	Rho family GTPase 3	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6049	chr5	80202360	80202560	+	1.53794	NA	Intergenic	(CATA)n|Simple_repeat|Simple_repeat	-818111	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6350	chr6	22032465	22032665	+	1.53794	NA	intron (NM_001081351, intron 2 of 21)	intron (NM_001081351, intron 2 of 21)	46655	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2620	chr14	89542942	89543142	+	1.53794	NA	Intergenic	L1_Mur3|LINE|L1	-353182	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	poly(A)-binding protein, cytoplasmic pseudogene	pseudo	0.000000	0.283582			71(CTTTTATTATGTATAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3123	chr16	24932916	24933116	+	1.53794	NA	intron (NM_178665, intron 10 of 12)	intron (NM_178665, intron 10 of 12)	-126623	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4534	chr2	115497571	115497771	+	1.53794	NA	intron (NR_030712, intron 2 of 2)	intron (NR_030712, intron 2 of 2)	14530	NR_030712	100043232	Mm.240112	NR_030712	ENSMUSG00000085582	3110099E03Rik	-	RIKEN cDNA 3110099E03 gene	ncRNA	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6727	chr6	135820368	135820568	+	1.53794	NA	intron (NM_001363750, intron 6 of 14)	intron (NM_001363750, intron 6 of 14)	161555	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8037	chrX	101423627	101423827	+	1.53794	NA	Intergenic	RSINE1|SINE|B4	-3042	NM_001177987	56364	Mm.23458	NM_019831	ENSMUSG00000031310	Zmym3	9030216B10Rik|AW122925|DXS6673El|Zfp261	zinc finger, MYM-type 3	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5760	chr4	136003297	136003497	+	1.53794	NA	TTS (NM_013736)	TTS (NM_013736)	-16153	NM_025411	66193	Mm.29131	NM_025411	ENSMUSG00000028669	Pithd1	1110049F12Rik|AA408179|Trp26	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3370	chr16	88226548	88226748	+	1.53794	NA	intron (NM_146072, intron 1 of 16)	intron (NM_146072, intron 1 of 16)	63610	NM_010348	14805	Mm.5134	NM_010348	ENSMUSG00000022935	Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	glutamate receptor, ionotropic, kainate 1	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5225	chr3	138106625	138106825	+	1.53794	NA	intron (NM_001163457, intron 14 of 19)	intron (NM_001163457, intron 14 of 19)	24928	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2952	chr15	59753828	59754028	+	1.53794	NA	Intergenic	Intergenic	41031	NR_045076	100503021	Mm.402924	NR_045076	ENSMUSG00000115426	Gm19510	-	predicted gene, 19510	ncRNA	0.020000	0.383085			-24(ATTTCCATCACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3903	chr18	64208335	64208535	+	1.53748	NA	intron (NR_045366, intron 2 of 5)	intron (NR_045366, intron 2 of 5)	-45924	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5	chr1	3569314	3569514	+	1.53748	NA	intron (NM_001011874, intron 1 of 2)	Lx7|LINE|L1	102084	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2583	chr14	79461649	79461849	+	1.53748	NA	3' UTR (NM_018765, exon 10 of 10)	3' UTR (NM_018765, exon 10 of 10)	9914	NM_001034882	432879	Mm.308666	NM_001034882	ENSMUSG00000075502	Kbtbd6	EG432879|Gm5465|Zbtbd6	kelch repeat and BTB (POZ) domain containing 6	protein-coding	0.000000	0.278607			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-303	chr14	79461606	79461806	+	1.53748	NA	3' UTR (NM_018765, exon 10 of 10)	3' UTR (NM_018765, exon 10 of 10)	9871	NM_001034882	432879	Mm.308666	NM_001034882	ENSMUSG00000075502	Kbtbd6	EG432879|Gm5465|Zbtbd6	kelch repeat and BTB (POZ) domain containing 6	protein-coding	0.000000	0.248756			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-865	chr9	30597529	30597729	+	1.53748	NA	Intergenic	Intergenic	170300	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4768	chr2	161216344	161216544	+	1.53748	NA	Intergenic	Intergenic	-107358	NM_173368	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3318	chr16	73884177	73884377	+	1.53748	NA	Intergenic	RLTR25B|LTR|ERVK	457790	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA	0.000000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-226	chr13	6652436	6652636	+	1.53637	NA	Intergenic	ERVB3_1-LTR_MM|LTR|ERVK	-3765	NM_001291071	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-790	chr10	40443672	40443872	+	1.53539	NA	intron (NM_001291817, intron 4 of 11)	intron (NM_001291817, intron 4 of 11)	94464	NM_198164	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding	0.015000	0.368159			66(ACATTGTTTTTCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7005	chr7	102711531	102711731	+	1.53539	NA	3' UTR (NM_147093, exon 2 of 2)	3' UTR (NM_147093, exon 2 of 2)	2780	NM_147073	18332	Mm.222837	NM_147073	ENSMUSG00000066273	Olfr33	MOR11-2|MTPCR33|ORL181	olfactory receptor 33	protein-coding	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2230	chr13	96680449	96680649	+	1.53539	NA	Intergenic	Intergenic	-9613	NM_001360166	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding	0.010000	0.363184		-54(TATGCATATTTAAT,-,0.00),72(CATGACTATTCATT,+,0.00),72(CATGACTATTCATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6508	chr6	67487366	67487566	+	1.53539	NA	intron (NM_144548, intron 2 of 10)	intron (NM_144548, intron 2 of 10)	4389	NM_144548	209590	Mm.221227	NM_144548	ENSMUSG00000049093	Il23r	IL-23R	interleukin 23 receptor	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3431	chr17	15541995	15542195	+	1.53533	NA	TTS (NM_144809)	TTS (NM_144809)	-14794	NM_008799	18567	Mm.323	NM_008799	ENSMUSG00000014771	Pdcd2	AI528543|Pcd2|RP-8	programmed cell death 2	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2839	chr15	28206957	28207157	+	1.53533	NA	intron (NM_133365, intron 1 of 78)	intron (NM_133365, intron 1 of 78)	3291	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b3491Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding	0.020000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-621	chr1	187796062	187796262	+	1.53533	NA	intron (NM_001357534, intron 2 of 7)	intron (NM_001357534, intron 2 of 7)	143921	NM_001357535	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding	0.015000	0.398010			27(TCATTGGTATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7664	chr9	56222602	56222802	+	1.53533	NA	intron (NM_172924, intron 6 of 6)	intron (NM_172924, intron 6 of 6)	-61632	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding	0.000000	0.472637	45(TGTGCATTATTCATT,+,0.00),45(TGTGCATTATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2909	chr15	50260227	50260427	+	1.53533	NA	Intergenic	MER3|DNA|hAT-Charlie	628722	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	transcriptional repressor GATA binding 1	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7770	chr9	81470340	81470540	+	1.53533	NA	Intergenic	Intergenic	-161490	NR_040393	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA	0.005000	0.333333			-28(CTATGCATGAGAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8067	chrX	114423335	114423535	+	1.53533	NA	Intergenic	L1_Mur3|LINE|L1	-50898	NM_172781	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding	0.000000	0.313433			-23(TCATTTTCATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7033	chr7	114963320	114963520	+	1.53533	NA	intron (NR_040317, intron 2 of 3)	intron (NR_040317, intron 2 of 3)	12146	NR_040319	101786	Mm.395157	NR_040317	ENSMUSG00000108379	A730082K24Rik	AU044236	RIKEN cDNA A730082K24 gene	ncRNA	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1333	chr11	70125806	70126006	+	1.53533	NA	Intergenic	L1M2|LINE|L1	-4451	NM_145137	216864	Mm.222465	NM_145137	ENSMUSG00000040950	Mgl2	CD301b	macrophage galactose N-acetyl-galactosamine specific lectin 2	protein-coding	0.005000	0.338308			-43(GTTTACTCATTTAAAG,+,0.00),25(ATATGCAAATCAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6903	chr7	72675078	72675278	+	1.53533	NA	Intergenic	Intergenic	-368583	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding	0.015000	0.388060	-37(AATGCATTATGCAGA,+,0.00),-37(AATGCATTATGCAGA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3362	chr16	86320506	86320706	+	1.53533	NA	Intergenic	URR1B|DNA|hAT-Charlie	-419481	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding	0.015000	0.407960			72(GGATTGTAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6911	chr7	74917086	74917286	+	1.53533	NA	Intergenic	Intergenic	-113025	NR_131122	75205	Mm.399304	NR_131122	ENSMUSG00000108803	4930533N22Rik	Gm44904	RIKEN cDNA 4930533N22 gene	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2517	chr14	62774110	62774310	+	1.53533	NA	intron (NR_045503, intron 2 of 6)	intron (NR_045503, intron 2 of 6)	-13098	NM_008715	18130	Mm.319684	NM_008715	ENSMUSG00000035161	Ints6	2900075H24Rik|AI480962|DICE1|Ddx26|HDB|Notch2l	integrator complex subunit 6	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4865	chr3	19208150	19208350	+	1.53533	NA	intron (NM_001253391, intron 3 of 7)	intron (NM_001253391, intron 3 of 7)	19955	NM_001356295	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7683	chr9	62060816	62061016	+	1.53533	NA	exon (NM_033320, exon 5 of 5)	exon (NM_033320, exon 5 of 5)	-34126	NM_028748	74090	Mm.273267	NM_028748	ENSMUSG00000032278	Paqr5	0610010I15Rik|AV002411|BB115488|mPRg	progestin and adipoQ receptor family member V	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6847	chr7	50226125	50226325	+	1.53533	NA	intron (NM_001037906, intron 7 of 19)	intron (NM_001037906, intron 7 of 19)	250875	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4831	chr3	8367674	8367874	+	1.53533	NA	Intergenic	Intergenic	95324	NR_033512	620966	Mm.301719	NR_033512		Gm6194	1700003N22Rik|EG620966	transmembrane protein 189 pseudogene	pseudo	0.005000	0.348259		-2(TGTGATTATGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1966	chr13	17274692	17274892	+	1.53533	NA	intron (NM_138654, intron 11 of 13)	intron (NM_138654, intron 11 of 13)	419973	NM_138654	192136	Mm.364180	NM_138654	ENSMUSG00000055137	Sugct	5033411D12Rik|D17907	succinyl-CoA glutarate-CoA transferase	protein-coding	0.005000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-107	chr1	37194715	37194915	+	1.53533	NA	Intergenic	Intergenic	-23463	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7680	chr9	61607696	61607896	+	1.53533	NA	Intergenic	B4A|SINE|B4	235430	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding	0.015000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2081	chr13	56869014	56869214	+	1.53533	NA	intron (NM_012035, intron 2 of 11)	intron (NM_012035, intron 2 of 11)	26675	NM_001302373	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP7|Trrp8	transient receptor potential cation channel, subfamily C, member 7	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-123	chr1	43202304	43202504	+	1.53533	NA	Intergenic	Intergenic	-5643	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding	0.000000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1717	chr12	70086032	70086232	+	1.53533	NA	intron (NM_008697, intron 4 of 29)	intron (NM_008697, intron 4 of 29)	16722	NM_001081453	18080	Mm.244047	NM_008697	ENSMUSG00000021068	Nin	3110068G20Rik|AI385615|AU024711|mKIAA1565	ninein	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3441	chr17	22447039	22447239	+	1.53533	NA	intron (NM_198003, intron 4 of 6)	intron (NM_198003, intron 4 of 6)	22937	NM_198003	74149	Mm.30767	NM_198003	ENSMUSG00000071266	Zfp946	1300003B13Rik	zinc finger protein 946	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1773	chr12	82348923	82349123	+	1.53533	NA	intron (NM_001167983, intron 5 of 23)	intron (NM_001167983, intron 5 of 23)	37674	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-36	chr1	13146032	13146232	+	1.53533	NA	intron (NM_008678, intron 22 of 22)	intron (NM_008678, intron 22 of 22)	-18969	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3828	chr18	45897011	45897211	+	1.53533	NA	intron (NR_040342, intron 2 of 3)	intron (NR_040342, intron 2 of 3)	148149	NR_040342	107003	Mm.395148	NR_040342		A330093E20Rik	AU043608	RIKEN cDNA A330093E20 gene	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-868	chr10	68268746	68268946	+	1.53533	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	9880	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding	0.015000	0.487562			69(CTGTGCATGAGAATCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5833	chr5	14001546	14001746	+	1.53533	NA	Intergenic	Intergenic	-23630	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7800	chr9	87933477	87933677	+	1.53427	NA	Intergenic	Intergenic	-202317	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding	0.010000	0.388060			-61(ATAAGAATGACAGTTG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-884	chr9	87933521	87933721	+	1.53427	NA	Intergenic	Intergenic	-202361	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4081	chr19	36199552	36199752	+	1.53312	NA	Intergenic	Intergenic	-79808	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding	0.010000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3329	chr16	77250497	77250697	+	1.53312	NA	Intergenic	Intergenic	-78731	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA	0.005000	0.293532	6(GATTCATAATTCATC,+,0.00),6(GATTCATAATTCATC,-,0.00)		76(CTTCTGTTATTTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4326	chr2	57333631	57333831	+	1.53194	NA	intron (NM_001145820, intron 6 of 16)	intron (NM_001145820, intron 6 of 16)	95349	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5132	chr3	115519649	115519849	+	1.53129	NA	Intergenic	Intergenic	195306	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding	0.010000	0.388060			-20(TCATTTTCAGGCTAAT,+,0.00),52(ATTTACATGAAAGTGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3486	chr17	41524615	41524815	+	1.53129	NA	Intergenic	Intergenic	590030	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mmut	D230010K02Rik|Mcm|Mut	methylmalonyl-Coenzyme A mutase	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6915	chr7	76629480	76629680	+	1.53129	NA	intron (NM_001199224, intron 18 of 22)	intron (NM_001199224, intron 18 of 22)	399693	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-133	chr1	44701418	44701618	+	1.53129	NA	intron (NM_028450, intron 2 of 10)	BGLII_A|LTR|ERVK	43431	NR_040602	75066	Mm.416932	NR_040602	ENSMUSG00000101701	4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	ncRNA	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-297	chr1	104824353	104824553	+	1.53129	NA	intron (NM_011800, intron 1 of 11)	intron (NM_011800, intron 1 of 11)	55933	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8123	chrX	153423095	153423295	+	1.53129	NA	Intergenic	Intergenic	63582	NM_001357183	245671	Mm.260751	NM_173780	ENSMUSG00000041649	Klf8	BKLF3|ZNF74	Kruppel-like factor 8	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4519	chr2	110783754	110783954	+	1.53129	NA	intron (NM_001355244, intron 2 of 23)	intron (NM_001355244, intron 2 of 23)	56205	NM_001355244	228432	Mm.483325	NM_001081556	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2528	chr14	67522846	67523046	+	1.53129	NA	Intergenic	Intergenic	46073	NR_153767	328436	Mm.246762	NR_153767	ENSMUSG00000114744	Gm38409	E030037F02	predicted gene, 38409	ncRNA	0.005000	0.393035			-53(ATTTGAAAAACAAATT,-,0.00),3(CTTAACATAACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7565	chr9	25064285	25064485	+	1.53129	NA	Intergenic	Intergenic	87396	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4176	chr2	11747845	11748045	+	1.53129	NA	intron (NM_001348237, intron 18 of 20)	intron (NM_001348237, intron 18 of 20)	29640	NM_001348237	50755	Mm.24088	NM_015792	ENSMUSG00000058594	Fbh1	AU015756|Fbx18|Fbxo18	F-box DNA helicase 1	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2622	chr14	89709447	89709647	+	1.53129	NA	Intergenic	RLTR19|LTR|ERVK	-186677	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	poly(A)-binding protein, cytoplasmic pseudogene	pseudo	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5213	chr3	136084193	136084393	+	1.53129	NA	intron (NM_001033350, intron 10 of 16)	intron (NM_001033350, intron 10 of 16)	241773	NM_001310749	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3250	chr16	56154429	56154629	+	1.53129	NA	intron (NM_001360073, intron 10 of 24)	ID4_|SINE|ID	-49784	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1554	chr12	15394477	15394677	+	1.53129	NA	Intergenic	Intergenic	-344188	NR_045960	73972	Mm.107680	NR_045960	ENSMUSG00000113644	4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6990	chr7	98103383	98103583	+	1.53129	NA	intron (NM_008663, intron 3 of 48)	intron (NM_008663, intron 3 of 48)	5765	NM_001256082	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding	0.045000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3871	chr18	56452079	56452279	+	1.53129	NA	intron (NM_026240, intron 1 of 13)	intron (NM_026240, intron 1 of 13)	20047	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|Gramd2b|NS3TP2	GRAM domain containing 3	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1278	chr11	47389171	47389371	+	1.53129	NA	Intergenic	Intergenic	-9946	NM_011891	24052	Mm.34175	NM_011891	ENSMUSG00000020354	Sgcd	35DAG|A530047J11Rik|AI504364|AW547581|SG-delta|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8068	chrX	116127963	116128163	+	1.53129	NA	Intergenic	Intergenic	-320881	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8147	chrX	163835295	163835495	+	1.53129	NA	Intergenic	Intergenic	-73622	NM_026887	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2907	chr15	49509218	49509418	+	1.53129	NA	Intergenic	Lx9|LINE|L1	-717329	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6291	chr6	7136740	7136940	+	1.53129	NA	Intergenic	Intergenic	180822	NM_001077713	71238	Mm.389086	NM_001077713	ENSMUSG00000042505	Sdhaf3	0610005M07Rik|4933430A16Rik|Acn9	succinate dehydrogenase complex assembly factor 3	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2493	chr14	57690687	57690887	+	1.53129	NA	3' UTR (NM_015771, exon 8 of 8)	3' UTR (NM_015771, exon 8 of 8)	-25549	NM_020506	57258	Mm.202747	NM_020506	ENSMUSG00000021952	Xpo4	B430309A01Rik|mKIAA1721	exportin 4	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7987	chrX	71559280	71559480	+	1.53129	NA	intron (NM_001293623, intron 4 of 4)	intron (NM_001293623, intron 4 of 4)	3463	NM_001293625	15354	Mm.336087	NM_008253	ENSMUSG00000015217	Hmgb3	Hmg2a|Hmg4	high mobility group box 3	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3733	chr18	20459942	20460142	+	1.53129	NA	intron (NM_181564, intron 10 of 15)	intron (NM_181564, intron 10 of 15)	23867	NM_181564	16769	Mm.358619	NM_181564	ENSMUSG00000001804	Dsg4	CDHF13|lah	desmoglein 4	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3802	chr18	39295172	39295372	+	1.53129	NA	intron (NM_175164, intron 18 of 22)	intron (NM_175164, intron 18 of 22)	194007	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7088	chr7	130482215	130482415	+	1.53129	NA	intron (NM_001029895, intron 7 of 11)	intron (NM_001029895, intron 7 of 11)	37265	NM_001136054	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6812	chr7	34492828	34493028	+	1.53129	NA	Intergenic	RLTR11A2|LTR|ERVK	-103223	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral|mRAP55A	LSM14A mRNA processing body assembly factor	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-722	chr10	20434704	20434904	+	1.53129	NA	intron (NM_001347366, intron 6 of 11)	intron (NM_001347366, intron 6 of 11)	86985	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4722	chr2	150117025	150117225	+	1.53129	NA	3' UTR (NM_023266, exon 3 of 3)	3' UTR (NM_023266, exon 3 of 3)	19553	NM_181266	104348	Mm.485851	NM_023266	ENSMUSG00000068134	Zfp120	AI315103|E030042N05Rik|F80|MZF31|Zfp844	zinc finger protein 120	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6255	chr5	148501671	148501871	+	1.53129	NA	Intergenic	Intergenic	49902	NM_001359201	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG|MUB|mmMUB	ubiquitin-like 3	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6652	chr6	107605400	107605600	+	1.53129	NA	Intergenic	Intergenic	75774	NM_008516	16979	Mm.428543	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	leucine rich repeat protein 1, neuronal	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6262	chr5	149762319	149762519	+	1.53129	NA	3' UTR (NM_001081204, exon 15 of 15)	3' UTR (NM_001081204, exon 15 of 15)	49332	NR_077242	100861794	Mm.402054	NR_077242	ENSMUSG00000106740	Gm21221	-	predicted gene, 21221	ncRNA	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4331	chr2	59341109	59341309	+	1.53129	NA	intron (NM_001362991, intron 15 of 20)	intron (NM_001362991, intron 15 of 20)	45473	NR_040510	76676	Mm.110038	NR_040510	ENSMUSG00000087455	5330411J11Rik	-	RIKEN cDNA 5330411J11 gene	ncRNA	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3072	chr16	8696218	8696418	+	1.53129	NA	intron (NM_001003918, intron 20 of 30)	intron (NM_001003918, intron 20 of 30)	15548	NM_001324517	436336	Mm.357666	NM_001324517		Gm5767	EG436336|Gm43786	predicted gene 5767	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2077	chr13	54118407	54118607	+	1.53129	NA	Intergenic	Intergenic	46662	NM_027324	14057	Mm.134191	NM_027324	ENSMUSG00000021474	Sfxn1	2810002O05Rik|A930015P12Rik|f	sideroflexin 1	protein-coding	0.010000	0.437811	28(ATTTAATTATGCATG,+,0.00)		66(ATTTGCATAATAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1673	chr12	57024246	57024446	+	1.53129	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	136297	NM_001167976	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding	0.000000	0.318408	-15(TCTGCATGATGCATG,+,0.00),-15(TCTGCATGATGCATG,-,0.00)		53(GTTTTCTCATTGAATT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5020	chr3	75712066	75712266	+	1.53075	NA	Intergenic	L1M5|LINE|L1	-56435	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA	0.015000	0.328358		-34(GATGCATATGCAGT,+,0.00),-34(GATGCATATGCAGT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7525	chr9	13645235	13645435	+	1.53075	NA	intron (NM_001013813, intron 1 of 3)	intron (NM_001013813, intron 1 of 3)	-17125	NM_173776	270118	Mm.116898	NM_173776	ENSMUSG00000031925	Maml2	5930431H10|BC032967	mastermind like transcriptional coactivator 2	protein-coding	0.015000	0.447761		-80(CATGCATATGCCTC,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4325	chr2	57333298	57333498	+	1.53075	NA	intron (NM_001145820, intron 6 of 16)	intron (NM_001145820, intron 6 of 16)	95016	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-952	chr10	95531521	95531721	+	1.53075	NA	intron (NM_080560, intron 1 of 3)	intron (NM_080560, intron 1 of 3)	16459	NM_080560	93765	Mm.371667	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding	0.010000	0.363184			82(ATATGAATGATTAAGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-564	chr3	75712092	75712292	+	1.53075	NA	Intergenic	L1M5|LINE|L1	-56461	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA	0.010000	0.348259		-60(GATGCATATGCAGT,+,0.00),-60(GATGCATATGCAGT,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-59	chr1	184915173	184915373	+	1.53053	NA	intron (NM_145515, intron 10 of 17)	intron (NM_145515, intron 10 of 17)	-32237	NM_178692	226777	Mm.169542	NM_178692	ENSMUSG00000039349	C130074G19Rik	-	RIKEN cDNA C130074G19 gene	protein-coding	0.005000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-35	chr1	13084976	13085176	+	1.52955	NA	Intergenic	Intergenic	42087	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding	0.010000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-446	chr18	69977494	69977694	+	1.52834	NA	Intergenic	Intergenic	52035	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4882	chr3	27585519	27585719	+	1.52713	NA	promoter-TSS (NR_037275)	promoter-TSS (NR_037275)	-624	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5890	chr5	30763471	30763671	+	1.52713	NA	intron (NM_001356948, intron 2 of 12)	intron (NM_001356948, intron 2 of 12)	-51070	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding	0.025000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4285	chr2	45820369	45820569	+	1.52517	NA	Intergenic	Intergenic	123864	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA	0.000000	0.343284			-7(TTCTTCTTATGCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7636	chr9	46142175	46142375	+	1.52517	NA	intron (NM_027498, intron 3 of 24)	intron (NM_027498, intron 3 of 24)	-86355	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1197	chr11	24551080	24551280	+	1.52517	NA	intron (NR_045857, intron 1 of 3)	intron (NR_045857, intron 1 of 3)	69271	NR_045857	71316	Mm.79162	NR_045857	ENSMUSG00000086892	4933430M04Rik	-	RIKEN cDNA 4933430M04 gene	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3014	chr15	89932669	89932869	+	1.52517	NA	Intergenic	Intergenic	-90909	NM_018803	54526	Mm.261601	NM_018803	ENSMUSG00000063260	Syt10	-	synaptotagmin X	protein-coding	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1167	chr11	14167214	14167414	+	1.52517	NA	intron (NR_131011, intron 1 of 3)	MLTR18B_MM|LTR|ERVK	11727	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4107	chr19	49222278	49222478	+	1.52517	NA	Intergenic	B4|SINE|B4	1016353	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5365	chr4	18756893	18757093	+	1.52517	NA	Intergenic	Intergenic	365557	NM_001371269									0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4254	chr2	34485288	34485488	+	1.52517	NA	intron (NM_001362921, intron 4 of 10)	MIRc|SINE|MIR	78537	NM_001362920	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4330	chr2	59255598	59255798	+	1.52517	NA	intron (NM_001362994, intron 3 of 22)	RLTR12B|LTR|ERVK	93829	NM_001362996	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4221	chr2	24811590	24811790	+	1.52517	NA	intron (NM_001012518, intron 18 of 26)	intron (NM_001012518, intron 18 of 26)	-48538	NM_007579	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7455	chr8	114746395	114746595	+	1.52517	NA	intron (NM_019573, intron 8 of 8)	MER135|DNA|DNA	306843	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5734	chr4	126068095	126068295	+	1.52517	NA	intron (NM_001356446, intron 2 of 10)	intron (NM_001356446, intron 2 of 10)	9630	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6666	chr6	111258272	111258472	+	1.52517	NA	intron (NM_177328, intron 7 of 9)	intron (NM_177328, intron 7 of 9)	612774	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1083	chr10	119444733	119444933	+	1.52517	NA	Intergenic	Kanga1a|DNA|TcMar-Tc2	-9201	NM_001358809	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding	0.015000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2566	chr14	77417329	77417529	+	1.52517	NA	intron (NM_172813, intron 4 of 18)	intron (NM_172813, intron 4 of 18)	89439	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7390	chr8	96385718	96385918	+	1.52517	NA	Intergenic	Intergenic	-497417	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding	0.015000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-895	chr10	76173409	76173609	+	1.52517	NA	intron (NM_133184, intron 9 of 14)	L1_Mur3|LINE|L1	26058	NM_133184	64452	Mm.154797	NM_133184	ENSMUSG00000020229	Slc5a4a	SGLT3-a	solute carrier family 5, member 4a	protein-coding	0.000000	0.318408			-2(TATTTGGTTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1641	chr12	45872332	45872532	+	1.52517	NA	Intergenic	Intergenic	-797949	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4561	chr2	120825377	120825577	+	1.52517	NA	intron (NM_080788, intron 1 of 15)	ID_B1|SINE|B4	24941	NM_001024856	140810	Mm.275698	NM_080788	ENSMUSG00000090100	Ttbk2	2610507N02Rik|AI326283|B930008N24Rik|TTK|Ttbk|Ttbk1|mKIAA0847	tau tubulin kinase 2	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7371	chr8	91561100	91561300	+	1.52517	NA	intron (NM_011936, intron 8 of 8)	MT2B1|LTR|ERVL	240454	NM_008393	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1430	chr11	98981173	98981373	+	1.52517	NA	3' UTR (NM_178596, exon 1 of 1)	3' UTR (NM_178596, exon 1 of 1)	1747	NM_178596	353155	Mm.453253	NM_178596	ENSMUSG00000047197	Gjd3	Gja11|Gjc1|cx30.2	gap junction protein, delta 3	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7930	chrX	17088235	17088435	+	1.52517	NA	Intergenic	L1MD|LINE|L1	-176561	NM_010883	17986	Mm.5014	NM_010883	ENSMUSG00000040138	Ndp	ND|Ndph	Norrie disease (pseudoglioma) (human)	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4014	chr19	14970845	14971045	+	1.52517	NA	Intergenic	Intergenic	-372762	NM_001302950	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6452	chr6	52952458	52952658	+	1.52517	NA	intron (NM_173406, intron 1 of 4)	intron (NM_173406, intron 1 of 4)	-42938	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3836	chr18	48071540	48071740	+	1.52517	NA	intron (NR_045404, intron 3 of 3)	intron (NR_045404, intron 3 of 3)	26305	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno-1|Eno1|Gm5506|NNE	enolase 1B, retrotransposed	protein-coding	0.015000	0.343284			3(ATTTAAATGAGAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2596	chr14	84543993	84544193	+	1.52517	NA	Intergenic	Intergenic	-67669	NR_015539	319903	Mm.440481	NR_015539	ENSMUSG00000115529	9630013A20Rik	lncOL1	RIKEN cDNA 9630013A20 gene	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5756	chr4	133566583	133566783	+	1.52517	NA	Intergenic	L1ME3C|LINE|L1	-8062	NM_172876	242691	Mm.40110	NM_172876	ENSMUSG00000028850	Gpatch3	D930035B09Rik|Gpatc3	G patch domain containing 3	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5234	chr3	140700431	140700631	+	1.52517	NA	Intergenic	Intergenic	511824	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.005000	0.383085	39(TGTGCATTATGCAAT,-,0.00)		-27(ATTTGCATCAGTATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3664	chr17	90558644	90558844	+	1.52517	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	-102864	NM_001346960	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.010000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1283	chr11	48619354	48619554	+	1.52517	NA	Intergenic	Intergenic	-180906	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding	0.000000	0.412935			-51(TCTTTGTGTTTTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4735	chr2	153722654	153722854	+	1.52517	NA	Intergenic	ORR1C2-int|LTR|ERVL-MaLR	-18533	NM_007896	13589	Mm.143877	NM_007896	ENSMUSG00000027479	Mapre1	5530600P05Rik|AI462499|AI504412|AW260097|BIM1p|D2Ertd459e|Eb1	microtubule-associated protein, RP/EB family, member 1	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6313	chr6	13665139	13665339	+	1.52517	NA	intron (NM_175312, intron 1 of 4)	intron (NM_175312, intron 1 of 4)	12727	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	Bmt2	AI666701|B630005N14Rik	base methyltransferase of 25S rRNA 2	protein-coding	0.005000	0.298507			-7(ATTTGAATAACAATCC,-,0.00),34(TCTTTGTGCTGAAAAT,+,0.00),73(ATTTACATGGTAGATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6117	chr5	102613017	102613217	+	1.52517	NA	intron (NM_029270, intron 2 of 9)	intron (NM_029270, intron 2 of 9)	131726	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding	0.015000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6133	chr5	106186947	106187147	+	1.52517	NA	Intergenic	Intergenic	-134293	NR_136913	102635633	Mm.383511	NR_136913	ENSMUSG00000105508	Gm32921	-	predicted gene, 32921	ncRNA	0.020000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-235	chr1	83959623	83959823	+	1.52517	NA	Intergenic	Intergenic	259238	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA	0.000000	0.393035		-73(CATGCATATACATA,+,0.00),-73(CATGCATATACATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7243	chr8	48400665	48400865	+	1.52517	NA	intron (NM_011857, intron 3 of 28)	intron (NM_011857, intron 3 of 28)	273925	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0.030000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4585	chr2	125349572	125349772	+	1.52517	NA	intron (NM_007993, intron 35 of 65)	intron (NM_007993, intron 35 of 65)	102157	NM_023595	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding	0.010000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-846	chr8	100144953	100145153	+	1.52472	NA	Intergenic	Intergenic	728379	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5612	chr4	94388960	94389160	+	1.52340	NA	Intergenic	Lx8b|LINE|L1	167736	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8086	chrX	133549443	133549643	+	1.51586	NA	Intergenic	Intergenic	-138237	NR_153117	102632590	Mm.403836	NR_153117	ENSMUSG00000096978	Gm26851	-	predicted gene, 26851	ncRNA	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4402	chr2	76216265	76216465	+	1.51586	NA	intron (NM_001081033, intron 2 of 19)	intron (NM_001081033, intron 2 of 19)	122428	NM_001081033	241489	Mm.246613	NM_001081033	ENSMUSG00000075270	Pde11a	6330414F14Rik|A630086N24Rik|Gm350|PDE11A1	phosphodiesterase 11A	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2294	chr13	110099459	110099659	+	1.51586	NA	intron (NM_001360099, intron 3 of 4)	MIR3|SINE|MIR	180647	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5366	chr4	19355626	19355826	+	1.51586	NA	intron (NM_013927, intron 3 of 17)	(CTATT)n|Simple_repeat|Simple_repeat	74876	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6101	chr5	97628593	97628793	+	1.51586	NA	Intergenic	Intergenic	-171670	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5964	chr5	54895210	54895410	+	1.51586	NA	Intergenic	Intergenic	545318	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13	predicted gene 10440	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8117	chrX	150541183	150541383	+	1.51586	NA	Intergenic	Intergenic	-6134	NM_009653	11656	Mm.302724	NM_009653	ENSMUSG00000025270	Alas2	ALAS|ALAS-E|ALASE|Alas-2	aminolevulinic acid synthase 2, erythroid	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2872	chr15	39556526	39556726	+	1.51586	NA	intron (NM_053271, intron 19 of 26)	intron (NM_053271, intron 19 of 26)	-102885	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1536	chr12	10652805	10653005	+	1.51586	NA	Intergenic	Lx9|LINE|L1	206517	NR_110487	328061	Mm.56067	NR_110487	ENSMUSG00000112792	Gm38407	4931412M21	predicted gene, 38407	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2854	chr15	32495497	32495697	+	1.51586	NA	intron (NM_009154, intron 5 of 22)	intron (NM_009154, intron 5 of 22)	250784	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7620	chr9	42339463	42339663	+	1.51586	NA	intron (NM_009347, intron 17 of 23)	intron (NM_009347, intron 17 of 23)	60366	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2917	chr15	51736801	51737001	+	1.51586	NA	Intergenic	Intergenic	128560	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding	0.005000	0.487562			54(TTTTTAACTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2605	chr14	86801625	86801825	+	1.51586	NA	intron (NM_019670, intron 25 of 27)	B3|SINE|B2	339499	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7841	chr9	98533760	98533960	+	1.51586	NA	Intergenic	L1ME1|LINE|L1	29751	NR_029444	75881	Mm.483402	NM_175227	ENSMUSG00000051074	4930579K19Rik	-	RIKEN cDNA 4930579K19 gene	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-417	chr1	140659714	140659914	+	1.51586	NA	Intergenic	B2_Mm2|SINE|B2	-3412	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6105	chr5	99083984	99084184	+	1.51586	NA	Intergenic	Intergenic	-47005	NM_008926	19092	Mm.263002	NM_008926	ENSMUSG00000029334	Prkg2	AW212535|CGKII|Prkgr2|cGK-II	protein kinase, cGMP-dependent, type II	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-437	chr1	147116581	147116781	+	1.51586	NA	Intergenic	Intergenic	618994	NM_001145807	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3288	chr16	66592154	66592354	+	1.51586	NA	Intergenic	Intergenic	-64864	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA	0.020000	0.373134			14(ATTTACATAGTAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7372	chr8	91778552	91778752	+	1.51586	NA	Intergenic	Intergenic	23002	NM_008393	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6931	chr7	82606062	82606262	+	1.51586	NA	intron (NM_001190374, intron 27 of 29)	intron (NM_001190374, intron 27 of 29)	42366	NM_177894	330577	Mm.222812	NM_177894	ENSMUSG00000038570	Saxo2	1700129I04Rik|D030069K18|Fam154b	stabilizer of axonemal microtubules 2	protein-coding	0.005000	0.388060		-85(AATGAATAGGCATT,+,0.00),-85(AATGAATAGGCATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4651	chr2	136305528	136305728	+	1.51586	NA	intron (NM_001360384, intron 1 of 10)	intron (NM_001360384, intron 1 of 10)	82339	NM_001360382	241656	Mm.131572	NM_172858	ENSMUSG00000039913	Pak7	2900083L08Rik|PAK-5|PAK-7|Pak5	p21 (RAC1) activated kinase 7	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4972	chr3	62594911	62595111	+	1.51586	NA	exon (NM_001356525, exon 3 of 5)	exon (NM_001356525, exon 3 of 5)	10129	NM_177346	229357	Mm.95181	NM_177346	ENSMUSG00000043441	Gpr149	9630018L10Rik|Ieda|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.030000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1090	chr10	120660600	120660800	+	1.51586	NA	Intergenic	Intergenic	-105032	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA	0.015000	0.462687			40(ATTTACATGCCAGTCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1735	chr12	72950687	72950887	+	1.51586	NA	Intergenic	L1MB7|LINE|L1	10905	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding	0.000000	0.358209			-93(ATTTAAAAGGAAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7012	chr7	107535459	107535659	+	1.51586	NA	intron (NM_021889, intron 6 of 6)	intron (NM_021889, intron 6 of 6)	-31874	NM_172907	244198	Mm.77425	NM_172907	ENSMUSG00000051041	Olfml1	6720478C22|AV321997|BC047207|MVAL564|ONT2|mONT2	olfactomedin-like 1	protein-coding	0.000000	0.502488			81(ATCATCATCACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4755	chr2	159376461	159376661	+	1.51586	NA	Intergenic	Intergenic	-570780	NR_040498	71081	Mm.383491	NR_040498	ENSMUSG00000085198	4933416E03Rik	-	RIKEN cDNA 4933416E03 gene	ncRNA	0.000000	0.358209			15(ATAAGCATTAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3280	chr16	64659642	64659842	+	1.51586	NA	Intergenic	L1MA6|LINE|L1	-57411	NM_173861	224291	Mm.246580	NM_173861	ENSMUSG00000068167	Csnka2ip	Ckt2	casein kinase 2, alpha prime interacting protein	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4556	chr2	120211850	120212050	+	1.51586	NA	intron (NM_001363090, intron 1 of 20)	RCHARR1|DNA|hAT-Charlie	33385	NM_177845	329502	Mm.330505	NM_177845	ENSMUSG00000050211	Pla2g4e	2310026J01Rik|C230096D22|Pla2epsilon	phospholipase A2, group IVE	protein-coding	0.010000	0.318408			63(ATTTGCATGCCTATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6689	chr6	118541124	118541324	+	1.51586	NA	intron (NM_001081112, intron 12 of 33)	intron (NM_001081112, intron 12 of 33)	21047	NM_001081112	232339	Mm.276116	NM_001081112	ENSMUSG00000007827	Ankrd26	5730521P14Rik|BC008111|mKIAA1074	ankyrin repeat domain 26	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-664	chr10	3359229	3359429	+	1.51320	NA	Intergenic	Intergenic	-6821	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory inhibitor subunit 14C	protein-coding	0.005000	0.358209			-41(TTATAGTTATTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3866	chr18	55145941	55146141	+	1.51318	NA	Intergenic	Intergenic	-153450	NM_001360787	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1050	chr10	114949956	114950156	+	1.51318	NA	Intergenic	Intergenic	148330	NR_155864	102633245		NR_155864		Gm15723	-	predicted gene 15723	ncRNA	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5563	chr4	82311064	82311264	+	1.51318	NA	intron (NM_001286131, intron 8 of 9)	intron (NM_001286131, intron 8 of 9)	194615	NM_001286131	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding	0.010000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-111	chr10	115966639	115966839	+	1.51318	NA	Intergenic	Intergenic	-51624	NM_011217	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding	0.015000	0.407960			-73(CATTTATCATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5010	chr3	72014596	72014796	+	1.51318	NA	Intergenic	Intergenic	953167	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0.000000	0.303483			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-413	chr17	82556603	82556803	+	1.51318	NA	Intergenic	Intergenic	521522	NR_045094	100503434	Mm.187281	NR_045094	ENSMUSG00000117399	Gm19689	-	predicted gene, 19689	ncRNA	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2451	chr14	38322634	38322834	+	1.51318	NA	Intergenic	LTRIS2|LTR|ERV1	-575568	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.040000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-883	chr10	72178656	72178856	+	1.51298	NA	Intergenic	RLTR15|LTR|ERVK	-198051	NR_003644	108950	Mm.212793	NM_175390		1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo	0.000000	0.402985	-34(CATGAATAAAACATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5437	chr4	41219751	41219951	+	1.51298	NA	intron (NM_026872, intron 9 of 28)	intron (NM_026872, intron 9 of 28)	55284	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4445	chr2	90566785	90566985	+	1.51298	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	13762	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding	0.015000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-270	chr13	116463494	116463694	+	1.51298	NA	Intergenic	Intergenic	-153906	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	ISL1 transcription factor, LIM/homeodomain	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4678	chr2	140330934	140331134	+	1.51298	NA	intron (NM_001033296, intron 2 of 19)	RCHARR1|DNA|hAT-Charlie	58676	NM_001033296	228684	Mm.486585	NM_001033296	ENSMUSG00000074764	Sel1l2	Gm118	sel-1 suppressor of lin-12-like 2 (C. elegans)	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1844	chr12	99926445	99926645	+	1.51285	NA	intron (NM_028354, intron 13 of 15)	intron (NM_028354, intron 13 of 15)	-37954	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8042	chrX	102035161	102035361	+	1.51285	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	36046	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rtl5	6430402L03Rik|Mar5|Mart5|Rgag4|mKIAA2001	retrotransposon Gag like 5	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3627	chr17	81586753	81586953	+	1.51285	NA	intron (NM_001286684, intron 2 of 11)	intron (NM_001286684, intron 2 of 11)	151534	NM_001112798	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding	0.020000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2791	chr15	11456127	11456327	+	1.51285	NA	Intergenic	MIRb|SINE|MIR	-56569	NM_033074	110960	Mm.286061	NM_033074	ENSMUSG00000022241	Tars	D15Wsu59e|ThrRS	threonyl-tRNA synthetase	protein-coding	0.010000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-412	chr17	81586770	81586970	+	1.51285	NA	intron (NM_001286684, intron 2 of 11)	intron (NM_001286684, intron 2 of 11)	151517	NM_001112798	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7291	chr8	64307922	64308122	+	1.51285	NA	Intergenic	Intergenic	-102014	NM_009390	21892	Mm.418367	NM_009390	ENSMUSG00000053626	Tll1	Tll|Tll-1|b2b2476Clo	tolloid-like	protein-coding	0.000000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-885	chr9	92707074	92707274	+	1.51285	NA	Intergenic	Intergenic	-11542	NR_040770	331003	Mm.50805	NR_040770	ENSMUSG00000101734	4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	ncRNA	0.025000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5613	chr4	94389271	94389471	+	1.51209	NA	Intergenic	Intergenic	167425	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.000000	0.293532			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-635	chr4	94389203	94389403	+	1.51209	NA	Intergenic	Intergenic	167493	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3	chr1	3046611	3046811	+	1.51209	NA	Intergenic	RLTR13C1|LTR|ERVK	624787	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4875	chr3	24826924	24827124	+	1.51191	NA	Intergenic	Intergenic	-43018	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding	0.005000	0.373134			-56(AATTACAAAAGAAAAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4	chr1	13084828	13085028	+	1.51106	NA	Intergenic	Intergenic	42235	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding	0.005000	0.427861			43(TTTGTGTTATGCATAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-779	chr6	137541079	137541279	+	1.51106	NA	intron (NM_001271588, intron 1 of 20)	intron (NM_001271588, intron 1 of 20)	-21284	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1022	chr10	110933274	110933474	+	1.51106	NA	intron (NM_007792, intron 2 of 5)	intron (NM_007792, intron 2 of 5)	13198	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3617	chr17	80735964	80736164	+	1.51106	NA	Intergenic	L2c|LINE|L2	-8039	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6736	chr6	137541086	137541286	+	1.51106	NA	intron (NM_001271588, intron 1 of 20)	intron (NM_001271588, intron 1 of 20)	-21291	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-980	chr10	101140291	101140491	+	1.51092	NA	Intergenic	Intergenic	-398756	NR_152765	102639396	Mm.404529	NR_152765		Gm35722	-	predicted gene, 35722	ncRNA	0.010000	0.298507		80(CATCCATATGCATA,+,0.00),80(CATCCATATGCATA,-,0.00)	85(ATATGCATATCAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1606	chr12	37494280	37494480	+	1.51092	NA	intron (NM_178767, intron 12 of 12)	intron (NM_178767, intron 12 of 12)	252741	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-972	chr10	98155542	98155742	+	1.51092	NA	Intergenic	Intergenic	-188552	NR_033537	100038699	Mm.467933	NR_033537	ENSMUSG00000074776	Gm10754	-	predicted gene 10754	ncRNA	0.000000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-445	chr18	65661124	65661324	+	1.51092	NA	intron (NM_001361052, intron 6 of 8)	RSINE1|SINE|B4	-37044	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding	0.010000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2277	chr13	108288432	108288632	+	1.51092	NA	Intergenic	L1_Mus3|LINE|L1	-27805	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding	0.000000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-206	chr1	72739783	72739983	+	1.51092	NA	Intergenic	Intergenic	28623	NM_009084	19981	Mm.21529	NM_009084	ENSMUSG00000046330	Rpl37a	-	ribosomal protein L37a	protein-coding	0.030000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2211	chr13	93480490	93480690	+	1.51092	NA	intron (NM_021310, intron 1 of 10)	intron (NM_021310, intron 1 of 10)	19218	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding	0.000000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-431	chr18	32990608	32990808	+	1.51046	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	51667	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-566	chr1	176039822	176040022	+	1.51046	NA	intron (NM_001195816, intron 5 of 9)	intron (NM_001195816, intron 5 of 9)	119593	NM_001290692	226720	Mm.11282	NM_001290692	ENSMUSG00000104158	Becn2	Beclin-2|Gm104	beclin 2	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5947	chr5	50960205	50960405	+	1.50982	NA	Intergenic	Intergenic	593616	NM_008904	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding	0.005000	0.303483			-39(GGATTGTGATGATAAT,+,0.00),42(ATATTCTCTTTCATAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-674	chr5	50960213	50960413	+	1.50982	NA	Intergenic	Intergenic	593608	NM_008904	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding	0.005000	0.293532			-47(GGATTGTGATGATAAT,+,0.00),34(ATATTCTCTTTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-32	chr1	12710753	12710953	+	1.50954	NA	intron (NM_001198566, intron 1 of 20)	intron (NM_001198566, intron 1 of 20)	-7692	NM_172294	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding	0.000000	0.388060			30(GTCTGAATGACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4591	chr2	126037545	126037745	+	1.50954	NA	intron (NM_008008, intron 2 of 3)	intron (NM_008008, intron 2 of 3)	2987	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-949	chr10	93908660	93908860	+	1.50954	NA	Intergenic	Intergenic	-17558	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding	0.025000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3681	chr18	4657409	4657609	+	1.50954	NA	intron (NM_001081963, intron 2 of 3)	RSINE1|SINE|B4	22580	NM_001081963	240185	Mm.33179	NM_001081963	ENSMUSG00000033960	Jcad	1110056P05Rik|9430020K01Rik|Gm328|mKIAA1462	junctional cadherin 5 associated	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-492	chr1	159865793	159865993	+	1.50954	NA	intron (NM_022312, intron 7 of 22)	intron (NM_022312, intron 7 of 22)	-178487	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3961	chr18	81929464	81929664	+	1.50954	NA	Intergenic	Intergenic	62516	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA	0.000000	0.437811			-22(CTTTGCAAGCAAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6006	chr5	67628783	67628983	+	1.50915	NA	intron (NM_001038999, intron 35 of 36)	intron (NM_001038999, intron 35 of 36)	21000	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding	0.005000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-657	chr4	149313272	149313472	+	1.50915	NA	Intergenic	B3|SINE|B2	-5639	NM_001290995	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding	0.015000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-633	chr4	85707402	85707602	+	1.50845	NA	Intergenic	Intergenic	-346413	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-186	chr1	64853719	64853919	+	1.50767	NA	intron (NM_001039493, intron 6 of 7)	intron (NM_001039493, intron 6 of 7)	103005	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5054	chr3	86093526	86093726	+	1.50767	NA	intron (NM_001082414, intron 1 of 14)	intron (NM_001082414, intron 1 of 14)	9192	NM_001082414	27059	Mm.2454	NM_012059	ENSMUSG00000028082	Sh3d19	AW011754|Kryn	SH3 domain protein D19	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1125	chr10	125387810	125388010	+	1.50767	NA	Intergenic	Intergenic	-58947	NM_001358496	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7772	chr9	81481879	81482079	+	1.50767	NA	Intergenic	Intergenic	-149951	NR_040393	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7852	chr9	101242868	101243068	+	1.50767	NA	intron (NM_001161362, intron 1 of 13)	intron (NM_001161362, intron 1 of 13)	8864	NM_001161362	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07|C530025M11Rik	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-846	chr10	59723528	59723728	+	1.50767	NA	intron (NM_001359267, intron 1 of 11)	intron (NM_001359267, intron 1 of 11)	21065	NM_001359267	216001	Mm.27199	NM_144822	ENSMUSG00000020111	Micu1	C730016L05Rik|Calc|Cbara1	mitochondrial calcium uptake 1	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2966	chr15	66207756	66207956	+	1.50767	NA	intron (NM_152923, intron 1 of 14)	L1M5|LINE|L1	78773	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1332	chr11	69970785	69970985	+	1.50767	NA	intron (NM_001253700, intron 3 of 6)	intron (NM_001253700, intron 3 of 6)	5464	NM_016887	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding	0.010000	0.462687		64(TTTGCATATTAATG,-,0.00)	63(CTTTGCATATTAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3888	chr18	59241993	59242193	+	1.50767	NA	intron (NM_001081328, intron 2 of 2)	ORR1B1|LTR|ERVL-MaLR	66753	NM_001081328	78923	Mm.84007	NM_001081328	ENSMUSG00000058152	Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-453	chr1	151293747	151293947	+	1.50767	NA	Intergenic	Intergenic	-50639	NM_001359263	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding	0.015000	0.507463			-82(CATTTATTATTGTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5377	chr4	22301773	22301973	+	1.50767	NA	Intergenic	Intergenic	-55670	NR_104378	269514	Mm.40708	NM_172988	ENSMUSG00000040410	Fbxl4	AI836810|FBL4|FBL5	F-box and leucine-rich repeat protein 4	protein-coding	0.000000	0.338308	7(TTTGAATCATTCATG,-,0.00)		-83(ATTTGAATGTCAACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3273	chr16	63869532	63869732	+	1.50767	NA	Intergenic	Intergenic	-5457	NM_010140	13837	Mm.1977	NM_010140	ENSMUSG00000052504	Epha3	AW492086|Cek4|EK4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3138	chr16	27467594	27467794	+	1.50767	NA	Intergenic	MER70A|LTR|ERVL	78738	NM_026202	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5336	chr4	9212667	9212867	+	1.50517	NA	Intergenic	RMER13B|LTR|ERVK	-56526	NM_001355183	74438	Mm.473368	NM_028940	ENSMUSG00000041216	Clvs1	4933402J24Rik|Clvl1|Rlbp1l1	clavesin 1	protein-coding	0.000000	0.482587			3(CTTTTCTTATTCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1142	chr11	5218907	5219107	+	1.50517	NA	intron (NM_032396, intron 3 of 8)	MLT1D|LTR|ERVL-MaLR	42603	NM_032396	84035	Mm.209989	NM_032396	ENSMUSG00000020393	Kremen1	AV002070|Kremen|Krm1	kringle containing transmembrane protein 1	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5590	chr4	89130333	89130533	+	1.50517	NA	Intergenic	Intergenic	-2207	NR_151607	102637941	Mm.366358	NR_151607		Gm12602	-	predicted gene 12602	ncRNA	0.030000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-886	chr10	72968951	72969151	+	1.50517	NA	Intergenic	Intergenic	117654	NR_040646	327768	Mm.417745	NR_040646	ENSMUSG00000111994	A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4813	chr2	180497155	180497355	+	1.50517	NA	Intergenic	B3A|SINE|B2	-2721	NM_018766	18216	Mm.301712	NM_018766	ENSMUSG00000027568	Ntsr1	NT-1R|NTR-1|NTR1	neurotensin receptor 1	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7044	chr7	119595412	119595612	+	1.50517	NA	intron (NM_001177977, intron 13 of 13)	intron (NM_001177977, intron 13 of 13)	-22300	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3967	chr18	83736558	83736758	+	1.50517	NA	Intergenic	Intergenic	349807	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|teashirt1	teashirt zinc finger family member 1	protein-coding	0.010000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-252	chr13	78083786	78083986	+	1.50517	NA	intron (NM_001163419, intron 9 of 9)	intron (NM_001163419, intron 9 of 9)	58984	NM_029315	75507	Mm.443255	NM_029315	ENSMUSG00000093668	Pou5f2	1700013G10Rik|SPRM-1|Sprm1	POU domain class 5, transcription factor 2	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7423	chr8	104098937	104099137	+	1.50517	NA	intron (NR_131138, intron 1 of 2)	MER5A|DNA|hAT-Charlie	-2588	NM_009868	12562	Mm.21767	NM_009868	ENSMUSG00000031871	Cdh5	7B4|AA408225|Cd144|VE-Cad|VECD|VEcad|Vec	cadherin 5	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5410	chr4	31873489	31873689	+	1.50517	NA	Intergenic	Intergenic	-90518	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.020000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-578	chr3	119828482	119828682	+	1.50468	NA	Intergenic	Intergenic	-45194	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8092	chrX	136611158	136611358	+	1.50187	NA	intron (NM_001359279, intron 3 of 4)	LTR41B|LTR|ERVL	20416	NM_001359279	594844	Mm.260515	NM_001029978	ENSMUSG00000044550	Tceal3	1100001D19Rik	transcription elongation factor A (SII)-like 3	protein-coding	0.000000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-282	chr1	96501670	96501870	+	1.50187	NA	Intergenic	Intergenic	160803	NR_040478	75159	Mm.243854	NR_040478	ENSMUSG00000100589	4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	ncRNA	0.000000	0.373134			21(ATTTCCATTAAAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6362	chr6	25537030	25537230	+	1.50187	NA	Intergenic	L1MA7|LINE|L1	152850	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding	0.000000	0.363184			-66(TCATTGTCTGGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3071	chr16	8384499	8384699	+	1.50187	NA	Intergenic	Intergenic	40537	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Tmem114	4930511J11Rik|Cldn26	transmembrane protein 114	protein-coding	0.000000	0.313433			-100(GTTTGAATCACAAATT,-,0.00),-88(AATTGCATGCTAATGG,-,0.00),2(ATTTGCATTGCAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5500	chr4	59964052	59964252	+	1.50187	NA	Intergenic	RLTR9A3A|LTR|ERVK	-3485	NM_008648	17843	Mm.457982	NM_008648	ENSMUSG00000041333	Mup4	Mup-4|Mup1	major urinary protein 4	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3745	chr18	23913117	23913317	+	1.50187	NA	Intergenic	MIRb|SINE|MIR	-41471	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6251	chr5	146969856	146970056	+	1.50187	NA	Intergenic	Intergenic	-6101	NM_001359467	76366	Mm.486234	NM_029581	ENSMUSG00000016510	Mtif3	2810012L14Rik|AI414549	mitochondrial translational initiation factor 3	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1438	chr11	103841039	103841239	+	1.50187	NA	intron (NM_008740, intron 17 of 20)	intron (NM_008740, intron 17 of 20)	66964	NM_009521	22415	Mm.159091	NM_009521	ENSMUSG00000000125	Wnt3	Int-4|Wnt-3	wingless-type MMTV integration site family, member 3	protein-coding	0.045000	0.606965			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7292	chr8	64366917	64367117	+	1.50187	NA	Intergenic	Intergenic	147424	NR_030491	735270		NR_030491	ENSMUSG00000076042	Mir710	Mirn710|mmu-mir-710	microRNA 710	ncRNA	0.035000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1492	chr11	117192934	117193134	+	1.50187	NA	Intergenic	PB1D10|SINE|Alu	-6627	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2593	chr14	80999128	80999328	+	1.50187	NA	Intergenic	Intergenic	998926	NM_001351947	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.005000	0.383085		2(CATTCATATGCAAT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1184	chr11	20751196	20751396	+	1.50187	NA	Intergenic	Intergenic	-9740	NM_181411	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding	0.005000	0.422886			60(ATTAGCATGATCAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3254	chr16	57427174	57427374	+	1.50187	NA	intron (NM_001040397, intron 1 of 4)	intron (NM_001040397, intron 1 of 4)	73997	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1287	chr11	50059773	50059973	+	1.50187	NA	intron (NM_021540, intron 2 of 8)	intron (NM_021540, intron 2 of 8)	-9829	NR_029769	723845		NR_029769	ENSMUSG00000065417	Mir340	Mirn340|mir-340|mmu-mir-340	microRNA 340	ncRNA	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6673	chr6	113154980	113155180	+	1.50187	NA	Intergenic	MT2B1|LTR|ERVL	40304	NM_177763	269788	Mm.37943	NM_177763	ENSMUSG00000042873	Lhfpl4	1190004M23Rik|AI604880|B230384L07|mKIAA4027	lipoma HMGIC fusion partner-like protein 4	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1703	chr12	67620246	67620446	+	1.50187	NA	Intergenic	RLTR13D6|LTR|ERVK	-397797	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1|Tg(Prnp-PFN1*G118V)838Kiaei	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6470	chr6	58931044	58931244	+	1.50145	NA	Intergenic	Intergenic	-24018	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7234	chr8	46637518	46637718	+	1.50145	NA	intron (NM_009810, intron 6 of 6)	intron (NM_009810, intron 6 of 6)	20327	NM_009810	12367	Mm.34405	NM_009810	ENSMUSG00000031628	Casp3	A830040C14Rik|AC-3|CASP-3|CC3|CPP-32|CPP32|Caspase-3|Lice|SCA-1|Yama|mldy	caspase 3	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2963	chr15	66139951	66140151	+	1.50145	NA	intron (NM_152923, intron 1 of 14)	intron (NM_152923, intron 1 of 14)	146578	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6400	chr6	37004618	37004818	+	1.50145	NA	intron (NM_001347104, intron 19 of 32)	MLT1D|LTR|ERVL-MaLR	-194539	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding	0.015000	0.373134			25(CATTTCCAATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8166	chrX	167321049	167321249	+	1.50145	NA	intron (NM_001290758, intron 2 of 3)	intron (NM_001290758, intron 2 of 3)	9422	NM_001290756	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4682	chr2	141489731	141489931	+	1.50145	NA	intron (NM_001013802, intron 5 of 18)	intron (NM_001013802, intron 5 of 18)	-818355	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0.000000	0.328358		-58(TATAAATATTGATT,+,0.00),-58(TATAAATATTGATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2814	chr15	20028671	20028871	+	1.50145	NA	Intergenic	Intergenic	637979	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-940	chr10	91684399	91684599	+	1.50145	NA	Intergenic	Intergenic	-204330	NR_152729	102633867	Mm.351514	NR_152729	ENSMUSG00000111657	Gm31592	-	predicted gene, 31592	ncRNA	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5926	chr5	45810927	45811127	+	1.50145	NA	intron (NM_001359871, intron 1 of 5)	L1M2|LINE|L1	45525	NM_001359872	209707	Mm.71498	NM_172153	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding	0.000000	0.283582			32(ATTTGAAAAACATTTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-165	chr1	56680353	56680553	+	1.50145	NA	Intergenic	RSINE1|SINE|B4	-43002	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-543	chr1	172468470	172468670	+	1.50145	NA	Intergenic	Intergenic	-6790	NM_029612	98365	Mm.150050	NM_029612	ENSMUSG00000026548	Slamf9	2310026I04Rik|AI462096|CD2F-10|CD84-H1|Cd2f10|SF2001	SLAM family member 9	protein-coding	0.025000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6535	chr6	75037394	75037594	+	1.50145	NA	Intergenic	RLTR13E|LTR|ERVK	-1428821	NR_157242	102634075	Mm.78553	NR_157242	ENSMUSG00000107441	Gm31747	-	predicted gene, 31747	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3345	chr16	82937056	82937256	+	1.50145	NA	Intergenic	Intergenic	-1433987	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.000000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6019	chr5	71750683	71750883	+	1.50145	NA	intron (NM_001370968, intron 4 of 9)	intron (NM_001370968, intron 4 of 9)	50851	NM_008069	14400	Mm.38567	NM_008069	ENSMUSG00000029212	Gabrb1	AW061132|B230208N19Rik|Gabrb-1	gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7656	chr9	52821858	52822058	+	1.50145	NA	Intergenic	Intergenic	142095	NR_045333	382139	Mm.335162	NR_045333	ENSMUSG00000111020	Gm1715	-	predicted gene 1715	ncRNA	0.000000	0.323383			-90(CCTTTGTTATTCTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7233	chr8	45056823	45057023	+	1.50145	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	8495	NR_033588	434310	Mm.334512	NR_033588	ENSMUSG00000066158	AY512931	-	cDNA sequence AY512931	ncRNA	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2312	chr13	113723872	113724072	+	1.50145	NA	Intergenic	(CATA)n|Simple_repeat|Simple_repeat	-60296	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding	0.045000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2629	chr14	92854016	92854216	+	1.50145	NA	Intergenic	Intergenic	1036553	NM_001081377	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding	0.010000	0.333333			-96(TCATTGCAATGAAAAT,+,0.00),23(CAATTGACATGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7326	chr8	77387555	77387755	+	1.50145	NA	intron (NM_001363418, intron 11 of 21)	intron (NM_001363418, intron 11 of 21)	64434	NM_001363420	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3811	chr18	40645172	40645372	+	1.50145	NA	Intergenic	Intergenic	388273	NM_001371039									0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4310	chr2	53914880	53915080	+	1.50145	NA	Intergenic	Intergenic	170572	NM_023396	67874	Mm.27086	NM_023396	ENSMUSG00000075334	Rprm	2410012A13Rik|Reprimo	reprimo, TP53 dependent G2 arrest mediator candidate	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1643	chr12	46126183	46126383	+	1.50145	NA	Intergenic	Intergenic	692484	NM_001364637	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0.000000	0.348259	-43(TTTGAATAATTCATC,+,0.00),-43(TTTGAATAATTCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4272	chr2	43555775	43555975	+	1.50145	NA	intron (NM_001289594, intron 1 of 10)	intron (NM_001289594, intron 1 of 10)	550	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7919	chrX	10643270	10643470	+	1.50145	NA	Intergenic	Intergenic	-73995	NM_026524	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2630	chr14	92958322	92958522	+	1.50145	NA	Intergenic	Intergenic	932247	NM_001081377	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-893	chr10	74416373	74416573	+	1.50145	NA	intron (NM_001142747, intron 19 of 26)	intron (NM_001142747, intron 19 of 26)	-550704	NM_010311	14687	Mm.32595	NM_010311	ENSMUSG00000040009	Gnaz	AI847979|Gz	guanine nucleotide binding protein, alpha z subunit	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6355	chr6	23474213	23474413	+	1.50145	NA	intron (NM_153163, intron 8 of 29)	intron (NM_153163, intron 8 of 29)	175992	NM_198251	386611	Mm.436547	NM_198251	ENSMUSG00000051956	Rnf133	Greul2	ring finger protein 133	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6483	chr6	62920250	62920450	+	1.50145	NA	Intergenic	Intergenic	-335656	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4007	chr19	12050241	12050441	+	1.50145	NA	Intergenic	Intergenic	9409	NM_146681	258676	Mm.377634	NM_146681	ENSMUSG00000067528	Olfr1424	MOR239-2	olfactory receptor 1424	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1284	chr11	48992366	48992566	+	1.50145	NA	promoter-TSS (NM_011579)	promoter-TSS (NM_011579)	-220	NM_011579	21822	Mm.15793	NM_011579	ENSMUSG00000078922	Tgtp1	Gtp2|Ifggb6|Irgb6|Mg21|Tgtp|Tgtp2	T cell specific GTPase 1	protein-coding	0.005000	0.402985			-96(AAATTCTTGTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3085	chr16	11675349	11675549	+	1.50145	NA	intron (NM_028964, intron 18 of 20)	Charlie8|DNA|hAT-Charlie	-104253	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA	0.005000	0.383085			80(ATTTGAATGTTAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1041	chr10	112522780	112522980	+	1.50145	NA	Intergenic	Intergenic	-204046	NR_040579	69355	Mm.84337	NR_040579	ENSMUSG00000100314	1700010J16Rik	-	RIKEN cDNA 1700010J16 gene	ncRNA	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2961	chr15	62796768	62796968	+	1.50145	NA	Intergenic	Intergenic	-577417	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5217	chr3	136862367	136862567	+	1.50145	NA	intron (NM_001293622, intron 2 of 12)	intron (NM_001293622, intron 2 of 12)	192401	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding	0.025000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2617	chr14	88543548	88543748	+	1.50145	NA	Intergenic	Intergenic	-72252	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6760	chr6	144503913	144504113	+	1.50145	NA	Intergenic	Intergenic	-168855	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	Sox5os3	4933425H06Rik	SRY (sex determining region Y)-box 5, opposite strand 3	ncRNA	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1790	chr12	86021626	86021826	+	1.50145	NA	intron (NM_001364630, intron 32 of 32)	intron (NM_001364630, intron 32 of 32)	57315	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2382	chr14	18950322	18950522	+	1.50145	NA	Intergenic	L1_Mus3|LINE|L1	-56155	NM_001360327	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2342	chr14	9288281	9288481	+	1.49751	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	-595714	NR_030680	100042415	Mm.235938	NR_030680	ENSMUSG00000089686	Mnd1-ps	Gm3833	Mnd1 retrotransposed pseudogene	pseudo	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1579	chr12	30208377	30208577	+	1.49751	NA	intron (NM_172951, intron 14 of 16)	intron (NM_172951, intron 14 of 16)	-75853	NM_009417	22018	Mm.4991	NM_009417	ENSMUSG00000020673	Tpo	-	thyroid peroxidase	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-783	chr10	39359822	39360022	+	1.49751	NA	Intergenic	Intergenic	-9877	NM_001122893	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1262	chr11	43059700	43059900	+	1.49751	NA	Intergenic	Intergenic	-90077	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7398	chr8	97827645	97827845	+	1.49751	NA	Intergenic	Intergenic	-1184142	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	-	predicted gene 15679	ncRNA	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-227	chr1	82905981	82906181	+	1.49751	NA	Intergenic	Intergenic	66621	NM_010472	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding	0.010000	0.412935		-12(GATCCATATGCATC,+,0.00),-12(GATCCATATGCATC,-,0.00)	-7(ATATGCATCACATAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6710	chr6	126043200	126043400	+	1.49751	NA	Intergenic	Intergenic	121660	NM_001164035	18205	Mm.267570	NM_008742	ENSMUSG00000049107	Ntf3	AI316846|AI835689|HDNF|NGF-2|Nt3|Ntf-3	neurotrophin 3	protein-coding	0.010000	0.412935			13(ATTTGCAAAAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5378	chr4	22623081	22623281	+	1.49751	NA	Intergenic	Intergenic	132633	NR_131335	105500046		NR_131335	ENSMUSG00000107859	Gm30731	Pnky|lnc-pou3f2	predicted gene, 30731	ncRNA	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4480	chr2	102324778	102324978	+	1.49751	NA	intron (NM_020267, intron 4 of 4)	intron (NM_020267, intron 4 of 4)	76022	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-38	chr1	13334408	13334608	+	1.49751	NA	intron (NM_008678, intron 1 of 22)	U6|snRNA|snRNA	37921	NM_001302702	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0.010000	0.368159			-37(ATTTAAACAATAAAGA,-,0.00),-16(ATTTGTAAAAGTATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3349	chr16	83670258	83670458	+	1.49751	NA	Intergenic	Intergenic	-700785	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2149	chr13	75884694	75884894	+	1.49751	NA	intron (NM_028493, intron 8 of 11)	intron (NM_028493, intron 8 of 11)	44908	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2565	chr14	77377577	77377777	+	1.49751	NA	intron (NM_172813, intron 3 of 18)	intron (NM_172813, intron 3 of 18)	129191	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5463	chr4	52319632	52319832	+	1.49751	NA	Intergenic	Intergenic	119232	NR_045175	72648	Mm.391869	NR_045175	ENSMUSG00000085763	Smc2os	2700081L22Rik	structural maintenance of chromosomes 2, opposite strand	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-335	chr1	121597095	121597295	+	1.49751	NA	Intergenic	Intergenic	-29215	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2533	chr14	69867954	69868154	+	1.49751	NA	intron (NM_028560, intron 3 of 6)	Eulor9B|DNA|DNA	27647	NM_028526	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1817	chr12	92676361	92676561	+	1.49751	NA	Intergenic	Intergenic	768362	NR_126436	75295	Mm.243878	NR_126436	ENSMUSG00000113164	4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2449	chr14	38320759	38320959	+	1.49507	NA	Intergenic	Lx2B|LINE|L1	-577443	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.000000	0.447761			51(TAATTATAATGTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-54	chr1	176039884	176040084	+	1.49359	NA	intron (NM_001195816, intron 5 of 9)	intron (NM_001195816, intron 5 of 9)	119655	NM_001290692	226720	Mm.11282	NM_001290692	ENSMUSG00000104158	Becn2	Beclin-2|Gm104	beclin 2	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-792	chr7	76234665	76234865	+	1.49356	NA	intron (NM_001199224, intron 1 of 22)	intron (NM_001199224, intron 1 of 22)	4878	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0.010000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-502	chr2	91971591	91971791	+	1.49356	NA	Intergenic	Intergenic	-8128	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding	0.025000	0.552239			-68(ATTTAAATTACAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4450	chr2	91971620	91971820	+	1.49356	NA	Intergenic	Intergenic	-8157	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding	0.030000	0.592040			-97(ATTTAAATTACAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4996	chr3	68587930	68588130	+	1.49356	NA	intron (NM_013928, intron 1 of 6)	intron (NM_013928, intron 1 of 6)	15662	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0.020000	0.507463			4(ATTACCAAGGCAAAGC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-169	chr11	109749759	109749959	+	1.49343	NA	Intergenic	MER2|DNA|TcMar-Tigger	-27621	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding	0.005000	0.333333			-57(ATTTGAATAAGAAACA,-,0.00),24(ATTTACATGGCATTTA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-218	chr12	117345388	117345588	+	1.49318	NA	Intergenic	Intergenic	-8476	NR_044987	432713	Mm.459210	NR_044987	ENSMUSG00000101930	Gm5441	-	predicted gene 5441	ncRNA	0.025000	0.552239	-53(CATCCATAATTCATT,+,0.00),-53(CATCCATAATTCATT,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-78	chr10	8038591	8038791	+	1.49228	NA	Intergenic	Intergenic	-82568	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding	0.020000	0.447761	34(AATGAATAATTCGTA,+,0.00),34(AATGAATAATTCGTA,-,0.00),74(GATGCATAATTCAAA,+,0.00),74(GATGCATAATTCAAA,-,0.00)		49(CATTTGTAATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7810	chr9	92707120	92707320	+	1.49228	NA	Intergenic	Intergenic	-11496	NR_040770	331003	Mm.50805	NR_040770	ENSMUSG00000101734	4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	ncRNA	0.025000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7517	chr9	9645578	9645778	+	1.49228	NA	Intergenic	B3A|SINE|B2	-248753	NR_105745	102466147		NR_105745	ENSMUSG00000098408	Mir6237	Gm27411|mmu-mir-6237	microRNA 6237	ncRNA	0.005000	0.427861		-80(TATGCATATACATA,+,0.00),-80(TATGCATATACATA,-,0.00),-74(TATACATATGTATG,+,0.00),-74(TATACATATGTATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3971	chr18	84239274	84239474	+	1.49176	NA	intron (NM_001033341, intron 8 of 8)	intron (NM_001033341, intron 8 of 8)	151216	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1947	chr13	11640858	11641058	+	1.49176	NA	intron (NM_023868, intron 77 of 104)	(TATATG)n|Simple_repeat|Simple_repeat	118906	NR_027813	664793	Mm.410565	NR_027813	ENSMUSG00000113593	Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo	0.005000	0.318408		-21(TATGTATATGTATG,+,0.00),-21(TATGTATATGTATG,-,0.00),-11(TATGCATATATATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6469	chr6	58847185	58847385	+	1.49176	NA	intron (NM_001361966, intron 3 of 25)	intron (NM_001361966, intron 3 of 25)	13585	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2590	chr14	80170819	80171019	+	1.49176	NA	Intergenic	Intergenic	170617	NM_001351947	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.030000	0.437811			-64(TCTTTGGTATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-530	chr1	168411119	168411319	+	1.49176	NA	intron (NM_001291508, intron 2 of 7)	intron (NM_001291508, intron 2 of 7)	20950	NM_183355	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2403	chr14	25505231	25505431	+	1.49176	NA	intron (NM_183208, intron 2 of 23)	intron (NM_183208, intron 2 of 23)	-29108	NR_037236	100526533		NR_037236	ENSMUSG00000093081	Mir3075	mir-3075|mmu-mir-3075	microRNA 3075	ncRNA	0.015000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3660	chr17	90378182	90378382	+	1.49176	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	77598	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1973	chr13	20353913	20354113	+	1.49176	NA	intron (NM_080288, intron 14 of 21)	intron (NM_080288, intron 14 of 21)	-118977	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.030000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7393	chr8	97389810	97390010	+	1.49176	NA	Intergenic	Intergenic	-1501509	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding	0.025000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3160	chr16	33616044	33616244	+	1.49176	NA	intron (NM_001083902, intron 7 of 11)	intron (NM_001083902, intron 7 of 11)	-68322	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629	heart development protein with EGF-like domains 1	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7416	chr8	102000564	102000764	+	1.49176	NA	Intergenic	Intergenic	784447	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding	0.000000	0.402985			-63(ATCTGAAACACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6402	chr6	37963446	37963646	+	1.49176	NA	intron (NM_001272064, intron 17 of 18)	intron (NM_001272064, intron 17 of 18)	63059	NM_001272076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding	0.000000	0.383085			41(CTTTAAAAGAAAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2708	chr14	116916808	116917008	+	1.49176	NA	Intergenic	Intergenic	-8389	NM_001079844	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding	0.025000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3408	chr17	5089605	5089805	+	1.49176	NA	intron (NM_001085355, intron 2 of 19)	intron (NM_001085355, intron 2 of 19)	94631	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|BAF250B|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding	0.040000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4283	chr2	45019875	45020075	+	1.49176	NA	intron (NM_001355289, intron 4 of 10)	intron (NM_001355289, intron 4 of 10)	3202	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5000	chr3	68907182	68907382	+	1.49176	NA	intron (NM_026641, intron 18 of 19)	intron (NM_026641, intron 18 of 19)	37696	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5215	chr3	136692553	136692753	+	1.49176	NA	intron (NM_001293622, intron 1 of 12)	intron (NM_001293622, intron 1 of 12)	22587	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5356	chr4	14474172	14474372	+	1.49176	NA	Intergenic	L2a|LINE|L2	147506	NM_145947	208890	Mm.483839	NM_145947	ENSMUSG00000040569	Slc26a7	-	solute carrier family 26, member 7	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-304	chr1	106239001	106239201	+	1.49176	NA	intron (NM_133821, intron 1 of 16)	intron (NM_133821, intron 1 of 16)	67232	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.010000	0.427861			84(ATTTGAATGAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2113	chr13	65093001	65093201	+	1.49176	NA	intron (NM_133680, intron 2 of 11)	L1VL4|LINE|L1	19881	NM_001083901	66631	Mm.239196	NM_133680	ENSMUSG00000038212	Mfsd14b	5730414C17Rik|AU045608|AW539692|Hiatl1	major facilitator superfamily domain containing 14B	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2883	chr15	41846547	41846747	+	1.49176	NA	intron (NR_152565, intron 12 of 17)	intron (NR_152565, intron 12 of 17)	15689	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5151	chr3	119828565	119828765	+	1.49158	NA	Intergenic	Intergenic	-45277	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7489	chr8	126884209	126884409	+	1.49067	NA	Intergenic	Intergenic	35289	NR_151740	414091	Mm.240068	NM_001033546		A630001O12Rik	Gm45803	RIKEN cDNA A630001O12 gene	ncRNA	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6900	chr7	72084303	72084503	+	1.49067	NA	intron (NM_001024703, intron 21 of 22)	intron (NM_001024703, intron 21 of 22)	-122385	NR_126483	102640608	Mm.399138	NR_126483	ENSMUSG00000108480	Gm36633	-	predicted gene, 36633	ncRNA	0.000000	0.427861			81(CATCTGCTTTGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-284	chr14	32504405	32504605	+	1.48951	NA	Intergenic	Intergenic	-9016	NM_001081221	319955	Mm.318310	NM_001081221	ENSMUSG00000054051	Ercc6	4732403I04|C130058G22Rik|CSB	excision repair cross-complementing rodent repair deficiency, complementation group 6	protein-coding	0.000000	0.318408			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-37	chr1	135031461	135031661	+	1.48951	NA	intron (NM_001033409, intron 4 of 17)	MER53|DNA|hAT	68996	NM_001278115	67196	Mm.284587	NM_026024	ENSMUSG00000026429	Ube2t	2700084L22Rik|C80607	ubiquitin-conjugating enzyme E2T	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2432	chr14	32504416	32504616	+	1.48951	NA	Intergenic	Intergenic	-9005	NM_001081221	319955	Mm.318310	NM_001081221	ENSMUSG00000054051	Ercc6	4732403I04|C130058G22Rik|CSB	excision repair cross-complementing rodent repair deficiency, complementation group 6	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3542	chr17	59382613	59382813	+	1.48951	NA	Intergenic	Intergenic	-369391	NM_001368393	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1512	chr12	3550828	3551028	+	1.48805	NA	Intergenic	MTC|LTR|ERVL-MaLR	-21463	NM_001355528	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding	0.010000	0.487562			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-214	chr12	116959437	116959637	+	1.48805	NA	intron (NM_011215, intron 11 of 22)	intron (NM_011215, intron 11 of 22)	191732	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7824	chr9	94582247	94582447	+	1.48805	NA	Intergenic	Intergenic	-44266	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	Dipk2a	1190002N15Rik|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.005000	0.427861			-66(GTTTACATGGGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-246	chr1	86420013	86420213	+	1.48805	NA	Intergenic	Intergenic	-6216	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	Tex44	1700019O17Rik	testis expressed 44	protein-coding	0.015000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5770	chr4	140102943	140103143	+	1.48805	NA	intron (NM_198610, intron 3 of 9)	intron (NM_198610, intron 3 of 9)	-39830	NR_153821	102636673	Mm.449180	NR_153821		Gm13029	Gm33676	predicted gene 13029	ncRNA	0.010000	0.492537			5(ATTTGCATGACCCTTA,-,0.00),20(ATTTACATGGCTGTGA,-,0.00),35(ATTTGCAAGGTAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5325	chr4	6115614	6115814	+	1.48624	NA	Intergenic	L1_Mur2|LINE|L1	-75391	NM_026534	68053	Mm.404043	NM_026534	ENSMUSG00000028243	Ubxn2b	3110003A22Rik|6430407D20Rik|AI451665|p37	UBX domain protein 2B	protein-coding	0.000000	0.407960			-44(AATTTCTCAGGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7336	chr8	78944486	78944686	+	1.48624	NA	Intergenic	Intergenic	-83851	NM_001294279	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3679	chr18	4408559	4408759	+	1.48624	NA	Intergenic	RMER1C|Other|Other	33067	NM_026157	67440	Mm.49826	NM_026157	ENSMUSG00000024234	Mtpap	0610027A18Rik|AW551379|Papd1|Tent6	mitochondrial poly(A) polymerase	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2800	chr15	12922576	12922776	+	1.48624	NA	intron (NM_026799, intron 29 of 34)	intron (NM_026799, intron 29 of 34)	97861	NM_026799	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding	0.015000	0.373134			-80(TCATTGTCAGACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7509	chr9	7845348	7845548	+	1.48410	NA	Intergenic	RMER17C|LTR|ERVK	-8391	NM_007465	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-16	chr1	6940365	6940565	+	1.48410	NA	Intergenic	MLTR14|LTR|ERV1	-148455	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4028	chr19	17211783	17211983	+	1.48410	NA	intron (NM_181348, intron 17 of 19)	intron (NM_181348, intron 17 of 19)	127622	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4723	chr2	150117459	150117659	+	1.48410	NA	exon (NM_181266, exon 4 of 4)	exon (NM_181266, exon 4 of 4)	19119	NM_181266	104348	Mm.485851	NM_023266	ENSMUSG00000068134	Zfp120	AI315103|E030042N05Rik|F80|MZF31|Zfp844	zinc finger protein 120	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7703	chr9	67400639	67400839	+	1.48410	NA	intron (NM_001081242, intron 2 of 57)	intron (NM_001081242, intron 2 of 57)	158964	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding	0.010000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3080	chr16	11510620	11510820	+	1.48410	NA	intron (NM_028964, intron 13 of 20)	intron (NM_028964, intron 13 of 20)	105072	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7142	chr8	9144392	9144592	+	1.48410	NA	promoter-TSS (NR_073360)	promoter-TSS (NR_073360)	-177	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA	0.010000	0.393035			-14(CCATTCTCATTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7945	chrX	36524467	36524667	+	1.48410	NA	Intergenic	Intergenic	-31932	NM_001370943	101055983		NM_001370943	ENSMUSG00000091556	Gm14569	Kiaa1210	predicted gene 14569	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1935	chr13	6482187	6482387	+	1.48410	NA	Intergenic	MER2|DNA|TcMar-Tigger	-65870	NM_001360106	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding	0.005000	0.383085			82(AGTTTGCTTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4991	chr3	68097011	68097211	+	1.48410	NA	intron (NM_001113420, intron 1 of 6)	intron (NM_001113420, intron 1 of 6)	32309	NM_001113421	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2689	chr14	110340902	110341102	+	1.48410	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	414147	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	SLIT and NTRK-like family, member 6	protein-coding	0.000000	0.268657			61(ATTTATATGAAAATCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7666	chr9	56398209	56398409	+	1.48410	NA	intron (NM_172924, intron 1 of 6)	MIR|SINE|MIR	19741	NM_172924	244895	Mm.490331	NM_172924	ENSMUSG00000074305	Peak1	1110049L02Rik|9530046P14|AA690169|BE132841|C230081A13Rik|SGK269|mKIAA2002	pseudopodium-enriched atypical kinase 1	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2660	chr14	102313516	102313716	+	1.48410	NA	Intergenic	Intergenic	472993	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7767	chr9	81103828	81104028	+	1.48410	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-528002	NR_040393	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4190	chr2	17032268	17032468	+	1.48410	NA	Intergenic	Intergenic	-18642	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6958	chr7	90094357	90094557	+	1.48410	NA	Intergenic	Intergenic	35017	NR_046006	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA	0.000000	0.333333	-93(AATGCTTTATTAATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3467	chr17	30732554	30732754	+	1.48410	NA	intron (NM_013811, intron 42 of 92)	intron (NM_013811, intron 42 of 92)	105718	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-540	chr1	172114455	172114655	+	1.48410	NA	intron (NM_009938, intron 21 of 32)	MLT1F2|LTR|ERVL-MaLR	-12200	NM_001356513	19298	Mm.247764	NM_023041	ENSMUSG00000003464	Pex19	Pxf	peroxisomal biogenesis factor 19	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6032	chr5	74734885	74735085	+	1.48410	NA	Intergenic	L1ME1|LINE|L1	-32082	NM_001159577	16924	Mm.440403	NM_010727	ENSMUSG00000029228	Lnx1	Lnx	ligand of numb-protein X 1	protein-coding	0.020000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6590	chr6	93968819	93969019	+	1.48410	NA	intron (NM_001029850, intron 1 of 23)	intron (NM_001029850, intron 1 of 23)	-55229	NM_001083321	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.005000	0.363184			-57(TGCTTTTGATGTAAAT,+,0.00),58(GTATGCAAGACAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7452	chr8	114153446	114153646	+	1.48410	NA	Intergenic	Intergenic	19972	NM_024437	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding	0.010000	0.432836			33(ATTTTCATAACTATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6286	chr6	5876687	5876887	+	1.48410	NA	intron (NM_001191023, intron 5 of 15)	intron (NM_001191023, intron 5 of 15)	100606	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	ncRNA	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2052	chr13	43350962	43351162	+	1.48410	NA	Intergenic	Intergenic	-19654	NM_178848	68346	Mm.35325	NM_178848	ENSMUSG00000054021	Sirt5	0610012J09Rik|1500032M05Rik|AV001953	sirtuin 5	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2968	chr15	66311050	66311250	+	1.48410	NA	Intergenic	Intergenic	-24521	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4397	chr2	74243904	74244104	+	1.48410	NA	Intergenic	Intergenic	63713	NR_040501	73962	Mm.50289	NR_040501	ENSMUSG00000085405	4930441J16Rik	Astx1a|Astx1b|Astx1c	RIKEN cDNA 4930441J16 gene	ncRNA	0.030000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3468	chr17	31317625	31317825	+	1.48410	NA	intron (NM_001242427, intron 5 of 19)	B3A|SINE|B2	21501	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding	0.030000	0.597015			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-833	chr10	56967691	56967891	+	1.48410	NA	Intergenic	Intergenic	518562	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3307	chr16	71007620	71007820	+	1.48410	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	-123356	NR_040561	70972	Mm.399391	NR_040561	ENSMUSG00000116750	4931420L22Rik	-	RIKEN cDNA 4931420L22 gene	ncRNA	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4162	chr2	8223677	8223877	+	1.48410	NA	Intergenic	Intergenic	-827579	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6456	chr6	53976854	53977054	+	1.48410	NA	intron (NM_027749, intron 1 of 12)	intron (NM_027749, intron 1 of 12)	1719	NM_001289713	71287	Mm.158654	NM_027749	ENSMUSG00000052955	Cpvl	4933436L16Rik|HVLP	carboxypeptidase, vitellogenic-like	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6030	chr5	74177005	74177205	+	1.48410	NA	Intergenic	Intergenic	-18221	NM_026878	68939	Mm.293316	NM_026878	ENSMUSG00000049907	Rasl11b	1190017B18Rik	RAS-like, family 11, member B	protein-coding	0.015000	0.482587			12(CTTTTGTTGTGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1220	chr11	29472262	29472462	+	1.48410	NA	intron (NM_001363369, intron 17 of 28)	intron (NM_001363369, intron 17 of 28)	42671	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2417	chr14	29693224	29693424	+	1.48410	NA	intron (NM_009785, intron 2 of 37)	intron (NM_009785, intron 2 of 37)	28540	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3390	chr16	94560885	94561085	+	1.48410	NA	Intergenic	RMER1B|Other|Other	-9221	NM_007890	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2243	chr13	98849192	98849392	+	1.48410	NA	intron (NM_001048267, intron 20 of 23)	intron (NM_001048267, intron 20 of 23)	-33843	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding	0.005000	0.303483			6(ATATTCAACACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7907	chr9	121068744	121068944	+	1.48410	NA	intron (NM_177589, intron 34 of 36)	intron (NM_177589, intron 34 of 36)	113758	NR_106058	102465661		NR_106058	ENSMUSG00000106193	Mir7090	mmu-mir-7090	microRNA 7090	ncRNA	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1180	chr11	19671955	19672155	+	1.48410	NA	Intergenic	Intergenic	-252387	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related EVH1 domain containing 2	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1382	chr11	84357549	84357749	+	1.48410	NA	intron (NM_133360, intron 43 of 53)	L1MC3|LINE|L1	155852	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3063	chr15	102007140	102007340	+	1.48401	NA	Intergenic	Intergenic	-2898	NM_031170	16691	Mm.358618	NM_031170	ENSMUSG00000049382	Krt8	AA960620|AL022697|AU019895|Card2|EndoA|K8|Krt-2.8|Krt2-8	keratin 8	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7228	chr8	42329051	42329251	+	1.48401	NA	Intergenic	Intergenic	501884	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4757	chr2	159680576	159680776	+	1.48127	NA	Intergenic	Intergenic	-266665	NR_040498	71081	Mm.383491	NR_040498	ENSMUSG00000085198	4933416E03Rik	-	RIKEN cDNA 4933416E03 gene	ncRNA	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2181	chr13	85596751	85596951	+	1.48127	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-307365	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding	0.000000	0.407960			-42(CTTTGAATGAAAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2601	chr14	86088513	86088713	+	1.48127	NA	Intergenic	Intergenic	-157357	NR_040457	75155	Mm.399239	NR_040457	ENSMUSG00000115271	4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA	0.005000	0.368159			-32(TCTTTCTCATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4631	chr2	133983133	133983333	+	1.48127	NA	Intergenic	Intergenic	418525	NR_037273	100526500		NR_037273	ENSMUSG00000093338	Mir3090	mmu-mir-3090	microRNA 3090	ncRNA	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1757	chr12	79463390	79463590	+	1.48127	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	166139	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7802	chr9	89334756	89334956	+	1.48127	NA	Intergenic	L1MA8|LINE|L1	123472	NM_001359993	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3505	chr17	49761809	49762009	+	1.47789	NA	intron (NM_177052, intron 13 of 22)	intron (NM_177052, intron 13 of 22)	146737	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding	0.020000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4798	chr2	172428081	172428281	+	1.47789	NA	intron (NM_001276422, intron 5 of 5)	B4|SINE|B4	-12397	NM_025542	66404	Mm.25157	NM_025542	ENSMUSG00000027502	Rtf2	1700067C04Rik|2410001C21Rik|5730427M17Rik|AA589417|Rtfdc1	replication termination factor 2	protein-coding	0.015000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-603	chr1	184917561	184917761	+	1.47789	NA	intron (NM_145515, intron 9 of 17)	ORR1B2|LTR|ERVL-MaLR	-34625	NM_178692	226777	Mm.169542	NM_178692	ENSMUSG00000039349	C130074G19Rik	-	RIKEN cDNA C130074G19 gene	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5809	chr5	3644460	3644660	+	1.47789	NA	intron (NM_026033, intron 3 of 4)	intron (NM_026033, intron 3 of 4)	3376	NM_026033	67210	Mm.178424	NM_026033	ENSMUSG00000007415	Gatad1	2310031E19Rik|2810047M21Rik|8430439A17Rik|9130430G15Rik|B330017N08Rik|Odag	GATA zinc finger domain containing 1	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4312	chr2	55181549	55181749	+	1.47789	NA	Intergenic	L1MB3|LINE|L1	-254321	NM_001355118	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-385	chr1	134611226	134611426	+	1.47789	NA	intron (NM_152895, intron 14 of 26)	ID_B1|SINE|B4	-35286	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194|sytII	synaptotagmin II	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6787	chr7	6487113	6487313	+	1.47789	NA	promoter-TSS (NM_146914)	promoter-TSS (NM_146914)	-400	NM_146914	18349	Mm.358623	NM_146914	ENSMUSG00000096228	Olfr5	MOR103-8|ORL120	olfactory receptor 5	protein-coding	0.000000	0.348259		-57(GTTAAATATGCATA,+,0.00),-51(TATGCATATGAATT,+,0.00),-51(TATGCATATGAATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6800	chr7	25055732	25055932	+	1.47789	NA	intron (NM_001360067, intron 11 of 19)	intron (NM_001360067, intron 11 of 19)	16537	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3422	chr17	13755934	13756134	+	1.47789	NA	intron (NM_022311, intron 1 of 2)	intron (NM_022311, intron 1 of 2)	-4507	NR_151731	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3805	chr18	39928345	39928545	+	1.47789	NA	Intergenic	MIR|SINE|MIR	154948	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1682	chr12	59074203	59074403	+	1.47789	NA	TTS (NM_008891)	TTS (NM_008891)	7384	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5194	chr3	131796960	131797160	+	1.47789	NA	Intergenic	Intergenic	231028	NM_001289477	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.010000	0.353234			-20(CAGTGCTCATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1001	chr10	106928627	106928827	+	1.47789	NA	intron (NM_001359693, intron 29 of 29)	intron (NM_001359693, intron 29 of 29)	194910	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding	0.010000	0.407960	-36(CATGAATAATTTAAC,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-568	chr3	109544126	109544326	+	1.47750	NA	intron (NM_020505, intron 15 of 26)	MTEb|LTR|ERVL-MaLR	-29781	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2503	chr14	60403380	60403580	+	1.47652	NA	Intergenic	Intergenic	25788	NM_028113	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3775	chr18	32990628	32990828	+	1.47652	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	51687	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding	0.005000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-278	chr14	17674212	17674412	+	1.47584	NA	intron (NM_001113417, intron 1 of 9)	intron (NM_001113417, intron 1 of 9)	13352	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-464	chr1	152954710	152954910	+	1.47505	NA	promoter-TSS (NM_175460)	promoter-TSS (NM_175460)	-291	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.015000	0.482587			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-18	chr1	52293157	52293357	+	1.47501	NA	Intergenic	Intergenic	-60025	NM_001113383	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3727	chr18	19730168	19730368	+	1.47402	NA	Intergenic	Intergenic	271829	NM_001291809	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6113	chr5	101538264	101538464	+	1.47402	NA	Intergenic	Intergenic	126347	NM_144955	18096	Mm.193072	NM_144955	ENSMUSG00000035187	Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2008	chr13	30177578	30177778	+	1.47379	NA	intron (NM_153546, intron 1 of 12)	intron (NM_153546, intron 1 of 12)	41188	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.020000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6930	chr7	82445605	82445805	+	1.47379	NA	intron (NM_001190374, intron 5 of 29)	intron (NM_001190374, intron 5 of 29)	110011	NM_001190374	269959	Mm.65306	NM_001190374	ENSMUSG00000070469	Adamtsl3	9230119C12Rik|C130057K09|mKIAA1233	ADAMTS-like 3	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-970	chr10	97493185	97493385	+	1.47379	NA	intron (NM_001190451, intron 2 of 7)	intron (NM_001190451, intron 2 of 7)	10954	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3011	chr15	88033742	88033942	+	1.47379	NA	Intergenic	Intergenic	-237899	NR_105817	102465209		NR_105817	ENSMUSG00000098938	Mir6393	Gm27424|mmu-mir-6393	microRNA 6393	ncRNA	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7950	chrX	40803558	40803758	+	1.47379	NA	Intergenic	Intergenic	-597196	NM_001358361	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5716	chr4	120640257	120640457	+	1.47379	NA	Intergenic	L3b|LINE|CR1	-26206	NM_019563	56222	Mm.272646	NM_019563	ENSMUSG00000070803	Cited4	MRG-2|Mrg2	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6510	chr6	69732995	69733195	+	1.47379	NA	Intergenic	Intergenic	-405921	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6867	chr7	56568690	56568890	+	1.47379	NA	Intergenic	Intergenic	329031	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p|p<cas>	oculocutaneous albinism II	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2137	chr13	72029412	72029612	+	1.47379	NA	Intergenic	Intergenic	-65789	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois homeobox 1	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7303	chr8	68046885	68047085	+	1.47379	NA	Intergenic	Intergenic	-72411	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding	0.000000	0.402985			4(ATTAGCAAGTCAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7622	chr9	42400843	42401043	+	1.47379	NA	Intergenic	Intergenic	-1014	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding	0.005000	0.363184			19(CTTTTGTAAATCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3602	chr17	78284653	78284853	+	1.47379	NA	intron (NM_015800, intron 4 of 16)	intron (NM_015800, intron 4 of 16)	84505	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3323	chr16	76266734	76266934	+	1.47379	NA	Intergenic	Intergenic	106215	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7508	chr9	7691956	7692156	+	1.47379	NA	promoter-TSS (NM_010810)	promoter-TSS (NM_010810)	-34	NM_010810	17393	Mm.4825	NM_010810	ENSMUSG00000018623	Mmp7	MAT|MMP-7	matrix metallopeptidase 7	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-435	chr1	143888698	143888898	+	1.47379	NA	Intergenic	Intergenic	111520	NM_001159866	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2594	chr14	83944279	83944479	+	1.47379	NA	Intergenic	B2_Mm2|SINE|B2	130911	NR_153783	102635012	Mm.399509	NR_153783	ENSMUSG00000115043	Gm32455	-	predicted gene, 32455	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1979	chr13	20884232	20884432	+	1.47379	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	90219	NM_001281854	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding	0.010000	0.398010			-48(ATCACCATAATAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2736	chr14	121161796	121161996	+	1.47379	NA	intron (NM_134082, intron 2 of 26)	intron (NM_134082, intron 2 of 26)	-86810	NR_155502	320268	Mm.435974	NR_155502		B930095G15Rik	-	RIKEN cDNA B930095G15 gene	ncRNA	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7389	chr8	96385225	96385425	+	1.47379	NA	Intergenic	Intergenic	-496924	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2765	chr15	6746713	6746913	+	1.47379	NA	intron (NM_030168, intron 5 of 37)	BGLII|LTR|ERVK	38432	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding	0.000000	0.383085			-79(CCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3426	chr17	14881030	14881230	+	1.47379	NA	intron (NM_175173, intron 22 of 24)	intron (NM_175173, intron 22 of 24)	61994	NM_175173	71682	Mm.122698	NM_175173	ENSMUSG00000046991	Wdr27	0610012K18Rik	WD repeat domain 27	protein-coding	0.005000	0.328358			-31(TGATTCTTTTGTTAAT,+,0.00),31(ATATACATAATAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6966	chr7	91241882	91242082	+	1.47379	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	151196	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs large MAGUK scaffold protein 2	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1571	chr12	25884310	25884510	+	1.47379	NA	Intergenic	Intergenic	326095	NR_131149	629481	Mm.390460	NR_131149	ENSMUSG00000113550	Gm29687	-	predicted gene, 29687	ncRNA	0.005000	0.313433			52(ATTTTCATAACAGTTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-853	chr10	63915724	63915924	+	1.47379	NA	intron (NM_177612, intron 7 of 17)	intron (NM_177612, intron 7 of 17)	94769	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2082	chr13	56869365	56869565	+	1.47379	NA	intron (NM_012035, intron 2 of 11)	MIR|SINE|MIR	26324	NM_001302373	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP7|Trrp8	transient receptor potential cation channel, subfamily C, member 7	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8091	chrX	135085888	135086088	+	1.47379	NA	Intergenic	Intergenic	-25652	NR_040282	320606	Mm.439072	NR_040281	ENSMUSG00000089759	3632454L22Rik	-	RIKEN cDNA 3632454L22 gene	ncRNA	0.025000	0.497512			-54(CCCTTGGGATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1053	chr10	115204497	115204697	+	1.47379	NA	intron (NM_025706, intron 14 of 16)	intron (NM_025706, intron 14 of 16)	-19575	NM_173391	216343	Mm.31597	NM_173391	ENSMUSG00000006764	Tph2	AU043594|Ntph	tryptophan hydroxylase 2	protein-coding	0.020000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3989	chr18	86463182	86463382	+	1.47379	NA	intron (NM_144946, intron 6 of 10)	intron (NM_144946, intron 6 of 10)	68330	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-932	chr10	89621433	89621633	+	1.47379	NA	promoter-TSS (NM_182959)	promoter-TSS (NM_182959)	-284	NM_182959	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8	protein-coding	0.010000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4830	chr3	7748667	7748867	+	1.47379	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-135007	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2020	chr13	35109922	35110122	+	1.47379	NA	Intergenic	MurERV4-int|LTR|ERVK	57782	NR_153831	75197	Mm.234091	NR_153831	ENSMUSG00000113906	4930529N20Rik	-	RIKEN cDNA 4930529N20 gene	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5394	chr4	25895684	25895884	+	1.47379	NA	Intergenic	RMER12B|LTR|ERVK	-95781	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4789	chr2	169756545	169756745	+	1.47379	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	124136	NM_001363023	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2314	chr13	114995350	114995550	+	1.47379	NA	intron (NM_001033228, intron 12 of 28)	intron (NM_001033228, intron 12 of 28)	-63350	NM_008396	16398	Mm.5007	NM_008396	ENSMUSG00000015533	Itga2	CD49B|DX5|GPIa	integrin alpha 2	protein-coding	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2306	chr13	112451886	112452086	+	1.47379	NA	Intergenic	MER5A|DNA|hAT-Charlie	-12084	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-18	chr1	7465695	7465895	+	1.47379	NA	Intergenic	Intergenic	376875	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7751	chr9	79108275	79108475	+	1.47379	NA	Intergenic	Intergenic	410927	NR_045336	100038575	Mm.367838	NR_045336	ENSMUSG00000111765	Gm10635	-	predicted gene 10635	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-280	chr1	95248243	95248443	+	1.47379	NA	Intergenic	Lx8b|LINE|L1	-65285	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding	0.000000	0.363184			41(GTTAACATGACAGTAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4415	chr2	77671336	77671536	+	1.47379	NA	intron (NM_178723, intron 3 of 9)	intron (NM_178723, intron 3 of 9)	31836	NM_001113399	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding	0.000000	0.288557		21(TATGCACATGCATA,+,0.00),21(TATGCACATGCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4838	chr3	10154243	10154443	+	1.47379	NA	Intergenic	Intergenic	29542	NM_001030305	18857	Mm.371777	NM_001030305	ENSMUSG00000052468	Pmp2	P2	peripheral myelin protein 2	protein-coding	0.000000	0.353234	-12(TTTGCATAAATCATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1117	chr10	124667863	124668063	+	1.47379	NA	Intergenic	Intergenic	198889	NR_028310	75030	Mm.159403	NR_028310	ENSMUSG00000112364	4930503E24Rik	-	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7306	chr8	69314958	69315158	+	1.47379	NA	Intergenic	Lx5b|LINE|L1	43978	NM_172491	211135	Mm.294970	NM_172491	ENSMUSG00000079038	D130040H23Rik	-	RIKEN cDNA D130040H23 gene	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3734	chr18	20509659	20509859	+	1.47373	NA	promoter-TSS (NM_030596)	promoter-TSS (NM_030596)	-515	NM_030596	13512	Mm.106811	NM_030596	ENSMUSG00000056632	Dsg3	bal	desmoglein 3	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6909	chr7	74635851	74636051	+	1.47373	NA	Intergenic	Intergenic	-81171	NM_001038643	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2111	chr13	64866189	64866389	+	1.47373	NA	intron (NM_001081129, intron 2 of 23)	B1_Mur1|SINE|Alu	37599	NM_001081129	238680	Mm.390590	NM_001081129	ENSMUSG00000033063	Cntnap3	-	contactin associated protein-like 3	protein-coding	0.000000	0.393035			-29(ATCTACATAGCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5373	chr4	20679904	20680104	+	1.47373	NA	intron (NM_172987, intron 1 of 4)	intron (NM_172987, intron 1 of 4)	98664	NM_001290410	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0.000000	0.298507			-3(AATTGCAAAACTAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3919	chr18	69086522	69086722	+	1.47373	NA	Intergenic	Intergenic	-64349	NR_105780	102465187		NR_105780	ENSMUSG00000098366	Mir145b	Gm27644|mmu-mir-145b	microRNA 145b	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1354	chr11	74954916	74955116	+	1.47373	NA	intron (NM_001002764, intron 8 of 18)	intron (NM_001002764, intron 8 of 18)	-29068	NM_001362744	27364	Mm.131443	NM_013761	ENSMUSG00000001323	Srr	M100034|Rgsc34|Srs	serine racemase	protein-coding	0.000000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7733	chr9	75631127	75631327	+	1.47373	NA	intron (NM_027309, intron 1 of 2)	intron (NM_027309, intron 1 of 2)	5495	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1877	chr12	107285713	107285913	+	1.47373	NA	Intergenic	Intergenic	449675	NR_045973	74968	Mm.359821	NR_045973	ENSMUSG00000085641	4930465M20Rik	4930431H15Rik	RIKEN cDNA 4930465M20 gene	ncRNA	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6311	chr6	13443234	13443434	+	1.47373	NA	Intergenic	Intergenic	29997	NR_038149	69413	Mm.177847	NR_038149	ENSMUSG00000101894	1700016P04Rik	-	RIKEN cDNA 1700016P04 gene	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-677	chr10	5368160	5368360	+	1.47373	NA	exon (NM_001347732, exon 14 of 146)	exon (NM_001347732, exon 14 of 146)	120054	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|KASH1|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-225	chr1	82393132	82393332	+	1.47373	NA	intron (NM_029777, intron 6 of 6)	intron (NM_029777, intron 6 of 6)	54183	NM_001122685	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding	0.000000	0.348259			-29(ATTTGCATTGGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7213	chr8	39404941	39405141	+	1.47373	NA	Intergenic	Intergenic	107061	NR_044988	621335	Mm.208080	NR_044988	ENSMUSG00000109827	Gm6213	EG621335	predicted gene 6213	ncRNA	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8157	chrX	166040889	166041089	+	1.47373	NA	Intergenic	Lx8|LINE|L1	-129465	NM_146238	237221	Mm.209490	NM_146238	ENSMUSG00000040621	Gemin8	B130034M20Rik|B930082C09Rik|BC023488|gemin-8	gem nuclear organelle associated protein 8	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4061	chr19	28560846	28561046	+	1.47283	NA	intron (NM_175459, intron 2 of 10)	intron (NM_175459, intron 2 of 10)	-117278	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4021	chr19	16411149	16411349	+	1.47142	NA	Intergenic	L1M4|LINE|L1	-24418	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding	0.000000	0.318408			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-22	chr1	89173034	89173234	+	1.46974	NA	Intergenic	Intergenic	102719	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding	0.020000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-259	chr1	89172991	89173191	+	1.46974	NA	Intergenic	Intergenic	102676	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8061	chrX	110826483	110826683	+	1.46858	NA	Intergenic	Intergenic	12204	NM_008901	18994	Mm.56946	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	POU domain, class 3, transcription factor 4	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5021	chr3	75753741	75753941	+	1.46858	NA	Intergenic	Intergenic	-98110	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA	0.010000	0.417910	-27(AATAAATGATTCATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6460	chr6	54757548	54757748	+	1.46858	NA	Intergenic	Intergenic	-59268	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1716	chr12	69777832	69778032	+	1.46858	NA	intron (NM_183294, intron 2 of 9)	intron (NM_183294, intron 2 of 9)	-12412	NR_033573	74724	Mm.399254	NR_033573		4930512B01Rik	4930472D12Rik	RIKEN cDNA 4930512B01 gene	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1608	chr12	37507367	37507567	+	1.46858	NA	intron (NM_178767, intron 12 of 12)	intron (NM_178767, intron 12 of 12)	265828	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5329	chr4	6593037	6593237	+	1.46858	NA	Intergenic	RLTR9D|LTR|ERVK	-138866	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4770	chr2	163219464	163219664	+	1.46858	NA	intron (NM_001363063, intron 1 of 8)	intron (NM_001363063, intron 1 of 8)	-5890	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding	0.015000	0.437811			-22(CTGTTGTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4240	chr2	29747277	29747477	+	1.46858	NA	exon (NM_001370923, exon 2 of 4)	exon (NM_001370923, exon 2 of 4)	4280	NM_001370923	433415	Mm.359309	NM_001370923	ENSMUSG00000079497	Gm13420	Dspd2	predicted gene 13420	protein-coding	0.115000	0.746269			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5247	chr3	144089803	144090003	+	1.46858	NA	Intergenic	Intergenic	112429	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding	0.030000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3058	chr15	100521625	100521825	+	1.46858	NA	intron (NM_001355497, intron 6 of 15)	L1M5|LINE|L1	-26486	NM_153407	207785	Mm.294969	NM_153407	ENSMUSG00000044636	Csrnp2	CSRNP-2|Csnrp2|taip-12	cysteine-serine-rich nuclear protein 2	protein-coding	0.000000	0.268657			-7(TAATTGTTAGGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4203	chr2	20642840	20643040	+	1.46858	NA	intron (NM_001081006, intron 3 of 21)	intron (NM_001081006, intron 3 of 21)	123427	NM_001369134	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.030000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1067	chr10	116683397	116683597	+	1.46858	NA	Intergenic	Intergenic	8906	NR_152731	102633950	Mm.356554	NR_152731	ENSMUSG00000097104	Gm26579	-	predicted gene, 26579	ncRNA	0.015000	0.412935			-35(TTTTGCAAAACTAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5006	chr3	70580898	70581098	+	1.46858	NA	Intergenic	Intergenic	226293	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	ncRNA	0.000000	0.427861			14(TGTAGGTCATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1986	chr13	23985247	23985447	+	1.46858	NA	intron (NM_145399, intron 2 of 10)	intron (NM_145399, intron 2 of 10)	5867	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-440	chr1	147601928	147602128	+	1.46776	NA	Intergenic	Intergenic	1104341	NM_001145807	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1063	chr10	115966591	115966791	+	1.46776	NA	Intergenic	Intergenic	-51672	NM_011217	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding	0.010000	0.393035			-25(CATTTATCATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5375	chr4	21922814	21923014	+	1.46776	NA	Intergenic	BGLII_Mur|LTR|ERVK	-8412	NM_175234	76132	Mm.159689	NM_175234	ENSMUSG00000028246	Faxc	6230409E13Rik|AW742931	failed axon connections homolog	protein-coding	0.005000	0.442786			6(GTATTCTGATGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3536	chr17	55626039	55626239	+	1.46776	NA	Intergenic	Lx6|LINE|L1	-1467	NM_001104582	383258	Mm.461682	NM_001104582	ENSMUSG00000091504	Vmn2r118	EG383258|EG668547|Vmn2r119	vomeronasal 2, receptor 118	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5636	chr4	98949363	98949563	+	1.46593	NA	intron (NM_001290636, intron 42 of 48)	intron (NM_001290636, intron 42 of 48)	25653	NM_001301414	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2319	chr13	116463619	116463819	+	1.46543	NA	Intergenic	Intergenic	-154031	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	ISL1 transcription factor, LIM/homeodomain	protein-coding	0.010000	0.323383			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-724	chr6	12318299	12318499	+	1.46543	NA	intron (NM_001164805, intron 25 of 26)	intron (NM_001164805, intron 25 of 26)	-208819	NR_003631	625347	Mm.389084	NM_001039041	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo	0.010000	0.383085			-39(ATTAGCAATGGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1929	chr13	5160315	5160515	+	1.46543	NA	Intergenic	Intergenic	-551251	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding	0.015000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-68	chr1	192778936	192779136	+	1.46523	NA	Intergenic	Intergenic	-7817	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7287	chr8	63460017	63460217	+	1.46267	NA	Intergenic	Intergenic	492053	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgo2b	EG244495|Gm4975|Sgol2b	shugoshin 2B	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1014	chr10	108581094	108581294	+	1.46267	NA	intron (NM_001252342, intron 9 of 10)	intron (NM_001252342, intron 9 of 10)	118966	NM_203660	368203	Mm.452758	NM_203660	ENSMUSG00000112039	Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding	0.035000	0.417910	48(TGTAAATAATTCATT,+,0.00),48(TGTAAATAATTCATT,-,0.00),55(AATTCATTATTCATT,+,0.00),55(AATTCATTATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4999	chr3	68904953	68905153	+	1.46267	NA	intron (NM_026641, intron 18 of 19)	ORR1C1|LTR|ERVL-MaLR	35467	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2774	chr15	7684270	7684470	+	1.46267	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-125678	NM_001301332	14573	Mm.4679	NM_010275	ENSMUSG00000022144	Gdnf	AI385739|ATF	glial cell line derived neurotrophic factor	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7848	chr9	100097226	100097426	+	1.46267	NA	Intergenic	Intergenic	75026	NR_040763	108970	Mm.390215	NR_040763	ENSMUSG00000101584	4930519F24Rik	-	RIKEN cDNA 4930519F24 gene	ncRNA	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5581	chr4	85770032	85770232	+	1.46267	NA	Intergenic	Intergenic	-283783	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3110	chr16	22287537	22287737	+	1.46267	NA	Intergenic	RLTR9A3|LTR|ERVK	-7351	NR_153764	100043507		NR_153764		Gng5-ps	Gm15776	G protein subunit gamma 5, pseudogene	pseudo	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4133	chr19	58244076	58244276	+	1.46219	NA	intron (NM_010279, intron 9 of 10)	intron (NM_010279, intron 9 of 10)	-52028	NR_040449	791347	Mm.452208	NR_040449		Gm10007	-	predicted gene 10007	ncRNA	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6517	chr6	70899508	70899708	+	1.46219	NA	intron (NM_010121, intron 14 of 16)	intron (NM_010121, intron 14 of 16)	19314	NM_028825	74221	Mm.273326	NM_028825	ENSMUSG00000051896	Tex37	1700011F03Rik|Tsc21	testis expressed 37	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6378	chr6	31482712	31482912	+	1.46219	NA	intron (NM_013791, intron 12 of 17)	intron (NM_013791, intron 12 of 17)	81125	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1|Podxl1	podocalyxin-like	protein-coding	0.005000	0.368159			-89(CATTTAATATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7075	chr7	128331614	128331814	+	1.46219	NA	Intergenic	Intergenic	-33583	NM_145590	233913	Mm.220880	NM_145590	ENSMUSG00000030780	BC017158	-	cDNA sequence BC017158	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3154	chr16	31846734	31846934	+	1.46219	NA	exon (NM_007862, exon 19 of 26)	exon (NM_007862, exon 19 of 26)	-31976	NM_013900	30060	Mm.30988	NM_013900	ENSMUSG00000022780	Meltf	CD228|MTf|Mfi2	melanotransferrin	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1704	chr12	67620381	67620581	+	1.46219	NA	Intergenic	RLTR13D6|LTR|ERVK	-397932	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1|Tg(Prnp-PFN1*G118V)838Kiaei	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7106	chr7	135794295	135794495	+	1.46219	NA	Intergenic	Intergenic	-78016	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5120	chr3	110387000	110387200	+	1.46219	NA	Intergenic	Intergenic	-136101	NM_178891	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0.000000	0.313433			-47(CTTTTATTATTCAGAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6561	chr6	83483521	83483721	+	1.46219	NA	intron (NR_149734, intron 4 of 6)	intron (NR_149734, intron 4 of 6)	23348	NM_001162521	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7127	chr7	143289324	143289524	+	1.46219	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	7123	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA	0.000000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1068	chr10	117005270	117005470	+	1.46219	NA	intron (NM_001007583, intron 7 of 9)	intron (NM_001007583, intron 7 of 9)	19056	NM_001007583	382427	Mm.339322	NM_001007583	ENSMUSG00000020169	Best3	Vmd2l3|mBest4	bestrophin 3	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1232	chr11	32420136	32420336	+	1.46219	NA	intron (NM_177364, intron 12 of 12)	intron (NM_177364, intron 12 of 12)	-35134	NM_173784	327900	Mm.260956	NM_173784	ENSMUSG00000044949	Ubtd2	4930571L24|9630054F20Rik|AI645720	ubiquitin domain containing 2	protein-coding	0.010000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7386	chr8	95404420	95404620	+	1.46219	NA	Intergenic	MTB-int|LTR|ERVL-MaLR	30349	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-508	chr1	163537832	163538032	+	1.46219	NA	Intergenic	Intergenic	-134263	NM_001313738	98376	Mm.32901	NM_178883	ENSMUSG00000040124	Gorab	NTKL-BP1|SCYL1-BP1|Scyl1bp1	golgin, RAB6-interacting	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2436	chr14	33722450	33722650	+	1.46219	NA	Intergenic	LTRIS2|LTR|ERV1	88733	NR_131114	218902	Mm.107791	NR_131113	ENSMUSG00000115751	4930503F20Rik	4930453C15	RIKEN cDNA 4930503F20 gene	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4288	chr2	47357065	47357265	+	1.46219	NA	Intergenic	L1ME2|LINE|L1	-1456944	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0.005000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1705	chr12	67620570	67620770	+	1.46219	NA	Intergenic	RLTR13D6|LTR|ERVK	-398121	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1|Tg(Prnp-PFN1*G118V)838Kiaei	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5113	chr3	109544088	109544288	+	1.46140	NA	intron (NM_020505, intron 15 of 26)	MTEb|LTR|ERVL-MaLR	-29819	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6005	chr5	67628586	67628786	+	1.46140	NA	intron (NM_001038999, intron 35 of 36)	intron (NM_001038999, intron 35 of 36)	20803	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-267	chr1	92004114	92004314	+	1.46140	NA	intron (NM_207225, intron 5 of 26)	intron (NM_207225, intron 5 of 26)	176127	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding	0.005000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-810	chr7	122847337	122847537	+	1.46039	NA	Intergenic	Intergenic	123022	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA	0.005000	0.447761			-4(TAATTATCATGCTTAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7667	chr9	57333308	57333508	+	1.45964	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-57662	NR_040729	73772	Mm.444684	NR_040729		4930430J02Rik	-	RIKEN cDNA 4930430J02 gene	ncRNA	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7707	chr9	67864114	67864314	+	1.45964	NA	intron (NM_177184, intron 5 of 84)	intron (NM_177184, intron 5 of 84)	23863	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6163	chr5	119521703	119521903	+	1.45964	NA	Intergenic	Intergenic	58555	NR_045702	100993	Mm.381453	NR_045702	ENSMUSG00000087516	AW549542	-	expressed sequence AW549542	ncRNA	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6136	chr5	106835540	106835740	+	1.45964	NA	Intergenic	Intergenic	90250	NM_001252516	330149	Mm.121664	NM_177873	ENSMUSG00000043410	Hfm1	A330009G12Rik|Gm1046|Mer3|Sec63d1	HFM1, ATP-dependent DNA helicase homolog	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1124	chr10	125228838	125229038	+	1.45964	NA	intron (NM_001358496, intron 5 of 5)	intron (NM_001358496, intron 5 of 5)	79878	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.000000	0.338308			-51(ATCTGAATGAGATTAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3198	chr16	43756801	43757001	+	1.45964	NA	Intergenic	Lx9|LINE|L1	-5320	NM_007877	13490	Mm.439735	NM_007877	ENSMUSG00000022705	Drd3	D3R	dopamine receptor D3	protein-coding	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5346	chr4	12784800	12785000	+	1.45964	NA	Intergenic	Intergenic	-121937	NM_173746	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818	triple QxxK/R motif containing	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2732	chr14	120698063	120698263	+	1.45964	NA	Intergenic	Intergenic	-213031	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5|imp5	importin 5	protein-coding	0.020000	0.507463			-4(GTATTCTCATGGTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4271	chr2	43398437	43398637	+	1.45964	NA	Intergenic	RLTR22_Mus|LTR|ERVK	-156788	NM_001289593	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase	protein-coding	0.000000	0.343284			-100(AATTTATGATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5171	chr3	126813632	126813832	+	1.45964	NA	intron (NM_001025438, intron 14 of 18)	intron (NM_001025438, intron 14 of 18)	129654	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6674	chr6	113296207	113296407	+	1.45964	NA	intron (NM_170673, intron 16 of 19)	ORR1C2|LTR|ERVL-MaLR	-10830	NM_001282127	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding	0.005000	0.502488			53(AATTTAGCATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2954	chr15	60261704	60261904	+	1.45964	NA	Intergenic	Intergenic	-245186	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding	0.005000	0.298507	29(CATATATTATACATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7161	chr8	13948226	13948426	+	1.45964	NA	Intergenic	B2_Mm2|SINE|B2	26451	NM_173744	72148	Mm.5727	NM_173744	ENSMUSG00000050052	Tdrp	2610019F03Rik	testis development related protein	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5025	chr3	76454372	76454572	+	1.45964	NA	intron (NM_178673, intron 6 of 15)	L1ME1|LINE|L1	378889	NM_001253719	213262	Mm.379337	NM_178673	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7615	chr9	38456304	38456504	+	1.45964	NA	Intergenic	Intergenic	7612	NM_146802	258798	Mm.377696	NM_146802	ENSMUSG00000049334	Olfr902	MOR169-1	olfactory receptor 902	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5348	chr4	13218812	13219012	+	1.45964	NA	Intergenic	MamTip1|DNA|hAT-Tip100	312075	NM_001171801	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818	triple QxxK/R motif containing	protein-coding	0.000000	0.398010			71(AATCTGTGATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1425	chr11	96742584	96742784	+	1.45964	NA	intron (NM_001177898, intron 10 of 10)	intron (NM_001177898, intron 10 of 10)	34871	NM_001163389	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4987	chr3	65497861	65498061	+	1.45964	NA	Intergenic	Intergenic	-30486	NM_178892	99929	Mm.246398	NM_178892	ENSMUSG00000034640	Tiparp	ARTD14|AW558171|PARP7	TCDD-inducible poly(ADP-ribose) polymerase	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1824	chr12	94529214	94529414	+	1.45964	NA	Intergenic	RLTR21|LTR|ERVK	601976	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4935	chr3	50278361	50278561	+	1.45964	NA	Intergenic	MLTR11B|LTR|ERVK	165152	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3841	chr18	49947042	49947242	+	1.45964	NA	intron (NM_001081371, intron 37 of 42)	intron (NM_001081371, intron 37 of 42)	-32285	NM_001177759	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1405	chr11	89611549	89611749	+	1.45964	NA	intron (NM_001327810, intron 2 of 19)	intron (NM_001327810, intron 2 of 19)	85287	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding	0.015000	0.432836			71(GCTCTATCATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7248	chr8	52380925	52381125	+	1.45964	NA	intron (NR_151738, intron 2 of 3)	RLTR13C3|LTR|ERVK	24414	NR_151738	330767	Mm.246790	NR_151738	ENSMUSG00000110013	1190028D05Rik	-	RIKEN cDNA 1190028D05 gene	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-261	chr1	89838363	89838563	+	1.45964	NA	intron (NM_001037136, intron 14 of 16)	intron (NM_001037136, intron 14 of 16)	92713	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding	0.025000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-512	chr1	164075026	164075226	+	1.45964	NA	intron (NM_011346, intron 7 of 8)	intron (NM_011346, intron 7 of 8)	13050	NM_001164059	20343	Mm.1461	NM_011346	ENSMUSG00000026581	Sell	AI528707|CD62L|L-selectin|LECAM-1|Lnhr|Ly-22|Ly-m22|Lyam-1|Lyam1	selectin, lymphocyte	protein-coding	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4062	chr19	29130304	29130504	+	1.45964	NA	intron (NM_021525, intron 6 of 8)	intron (NM_021525, intron 6 of 8)	-4875	NR_029778	724062		NR_029778	ENSMUSG00000065556	Mir101b	Mirn101b|mir-101b	microRNA 101b	ncRNA	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7436	chr8	107980675	107980875	+	1.45964	NA	Intergenic	Intergenic	-392293	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3376	chr16	88911929	88912129	+	1.45964	NA	Intergenic	Intergenic	-15580	NM_010676	16704	Mm.3503	NM_010676	ENSMUSG00000051802	Krtap19-5	Krtap8-2	keratin associated protein 19-5	protein-coding	0.015000	0.338308			-94(ATTAACATGTGAATTA,-,0.00),38(CATCTCTCATGCATAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5705	chr4	116857185	116857385	+	1.45964	NA	Intergenic	Intergenic	-20117	NM_001029912	74464	Mm.218946	NM_001029912	ENSMUSG00000033948	Zswim5	4933426E21Rik|AI503093|mKIAA1511	zinc finger SWIM-type containing 5	protein-coding	0.030000	0.412935	44(TATAATTTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1339	chr11	71627100	71627300	+	1.45964	NA	Intergenic	Intergenic	110664	NR_152165	619299	Mm.387056	NR_152165		9230020A06Rik	-	RIKEN cDNA 9230020A06 gene	ncRNA	0.005000	0.407960			-69(TCTTTACCTTGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1319	chr11	64518560	64518760	+	1.45964	NA	intron (NM_178870, intron 1 of 1)	intron (NM_178870, intron 1 of 1)	-81986	NR_028445	654805	Mm.436132	NR_028445		F930015N05Rik	-	RIKEN cDNA F930015N05 gene	ncRNA	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-231	chr1	83699388	83699588	+	1.45964	NA	Intergenic	Intergenic	-291288	NM_001356547	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2860	chr15	35491124	35491324	+	1.45964	NA	intron (NM_177151, intron 17 of 61)	B4A|SINE|B4	120106	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13	vacuolar protein sorting 13B	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2781	chr15	10237437	10237637	+	1.45964	NA	intron (NM_001253781, intron 1 of 9)	intron (NM_001253781, intron 1 of 9)	13631	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7041	chr7	118169887	118170087	+	1.45964	NA	intron (NM_001031814, intron 31 of 62)	RLTR13B1|LTR|ERVK	-40362	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding	0.015000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4973	chr3	63274002	63274202	+	1.45964	NA	Intergenic	Intergenic	-21109	NM_001357335	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding	0.005000	0.412935			-25(ACATTCTCTTGCTCAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-364	chr1	128150352	128150552	+	1.45964	NA	intron (NM_001357482, intron 1 of 26)	intron (NM_001357482, intron 1 of 26)	8465	NM_001357482	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2938	chr15	58011747	58011947	+	1.45964	NA	Intergenic	Intergenic	22447	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4765	chr2	161024723	161024923	+	1.45964	NA	intron (NR_126509, intron 10 of 35)	intron (NR_126509, intron 10 of 35)	84263	NR_126509	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2618	chr14	89182557	89182757	+	1.45964	NA	Intergenic	Intergenic	-711261	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2574	chr14	78215109	78215309	+	1.45964	NA	Intergenic	Intergenic	-23731	NR_035499	100316715		NR_035499	ENSMUSG00000087932	Mir1971	mmu-mir-1971	microRNA 1971	ncRNA	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6209	chr5	134371060	134371260	+	1.45964	NA	intron (NM_001081462, intron 22 of 29)	intron (NM_001081462, intron 22 of 29)	44706	NR_039544	100628570		NR_039544	ENSMUSG00000093311	Mir3965	mmu-mir-3965|mu-mir-3965	microRNA 3965	ncRNA	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-111	chr1	38530931	38531131	+	1.45941	NA	intron (NM_001290814, intron 4 of 21)	intron (NM_001290814, intron 4 of 21)	96213	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding	0.000000	0.348259			-5(ATTTTAAAAACAATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7493	chr8	127511963	127512163	+	1.45941	NA	intron (NM_001363431, intron 22 of 24)	(CA)n|Simple_repeat|Simple_repeat	212451	NM_001013581	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding	0.000000	0.368159			-48(GTTTAAAAAAAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1969	chr13	19413362	19413562	+	1.45923	NA	Intergenic	Intergenic	-17649	NM_001347485	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3926	chr18	69977570	69977770	+	1.45923	NA	Intergenic	Intergenic	52111	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding	0.005000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-418	chr17	91582461	91582661	+	1.45790	NA	Intergenic	Intergenic	-489759	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2916	chr15	51696675	51696875	+	1.45790	NA	Intergenic	Intergenic	168686	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding	0.035000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2377	chr14	17674302	17674502	+	1.45790	NA	intron (NM_001113417, intron 1 of 9)	intron (NM_001113417, intron 1 of 9)	13442	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0.000000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8	chr1	21702929	21703129	+	1.45556	NA	intron (NM_001160139, intron 1 of 14)	intron (NM_001160139, intron 1 of 14)	258913	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5728	chr4	124899824	124900024	+	1.45556	NA	exon (NM_001256432, exon 6 of 17)	exon (NM_001256432, exon 6 of 17)	-5142	NR_040651	73628	Mm.398337	NR_040651	ENSMUSG00000085263	1700125G02Rik	-	RIKEN cDNA 1700125G02 gene	ncRNA	0.045000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3412	chr17	8387476	8387676	+	1.45556	NA	intron (NR_045795, intron 1 of 2)	intron (NR_045795, intron 1 of 2)	1892	NR_045795	100504601	Mm.365131	NR_045795	ENSMUSG00000097796	Gm16702	AU016609	predicted gene, 16702	ncRNA	0.005000	0.373134			82(ATTTACACAACAAACG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6015	chr5	69600688	69600888	+	1.45556	NA	Intergenic	Intergenic	-8484	NM_001359239	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7325	chr8	77340400	77340600	+	1.45477	NA	intron (NM_001363418, intron 18 of 21)	intron (NM_001363418, intron 18 of 21)	111589	NM_001363420	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3564	chr17	66854377	66854577	+	1.45470	NA	intron (NM_008984, intron 14 of 30)	intron (NM_008984, intron 14 of 30)	140021	NR_151453	102639882	Mm.443262	NR_151453		1700016K05Rik	-	RIKEN cDNA 1700016K05 gene	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4526	chr2	114178234	114178434	+	1.45417	NA	Intergenic	RLTR23|LTR|ERV1	-2995	NM_009702	11834	Mm.2545	NM_009702	ENSMUSG00000040383	Aqr	AW495846|mKIAA0560	aquarius	protein-coding	0.000000	0.487562			-87(ATTTCCAAGACAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5101	chr3	105570931	105571131	+	1.45417	NA	intron (NM_019931, intron 2 of 7)	MER103C|DNA|hAT-Charlie	116540	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding	0.005000	0.417910			51(TCTTTAATATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6969	chr7	92151516	92151716	+	1.45417	NA	intron (NM_001243046, intron 4 of 14)	intron (NM_001243046, intron 4 of 14)	-32105	NR_131016	75845	Mm.437835	NR_131016	ENSMUSG00000109382	4930567K12Rik	Gm45128	RIKEN cDNA 4930567K12 gene	ncRNA	0.005000	0.293532			-47(ATTTGCATGAAAATGT,-,0.00),0(ACATTGTGTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6978	chr7	95225183	95225383	+	1.45417	NA	Intergenic	Intergenic	-945961	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.005000	0.393035	26(CTTGCATATTGCATT,+,0.00)		-16(TGATGTTTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6403	chr6	37963622	37963822	+	1.45417	NA	intron (NM_001272064, intron 17 of 18)	L1MA4|LINE|L1	63235	NM_001272076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4250	chr2	33314116	33314316	+	1.45417	NA	intron (NM_001290570, intron 3 of 16)	intron (NM_001290570, intron 3 of 16)	57278	NM_001290572	241308	Mm.274249	NM_175211	ENSMUSG00000038831	Ralgps1	5830418G11Rik|AI853783|AI854138|RALGEF2|RALGPS1A|RalGEF 2|mKIAA0351	Ral GEF with PH domain and SH3 binding motif 1	protein-coding	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-120	chr1	42636903	42637103	+	1.45417	NA	Intergenic	Intergenic	57822	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA	0.005000	0.373134			25(TTTTTGCAATGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-798	chr10	43228207	43228407	+	1.45417	NA	intron (NM_001168289, intron 1 of 7)	L2c|LINE|L2	6821	NM_001168289	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5039	chr3	83232915	83233115	+	1.45417	NA	intron (NM_001357165, intron 1 of 19)	intron (NM_001357165, intron 1 of 19)	-103769	NM_001358023	100038599	Mm.381315	NM_001358023	ENSMUSG00000074517	Gm10710	-	predicted gene 10710	protein-coding	0.000000	0.288557			-56(CTATTGTTTTGTTTAT,+,0.00),-29(CCTTTACCTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2915	chr15	51671231	51671431	+	1.45417	NA	Intergenic	Intergenic	194130	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7090	chr7	130732766	130732966	+	1.45417	NA	intron (NM_021314, intron 4 of 17)	intron (NM_021314, intron 4 of 17)	40248	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5884	chr5	28525374	28525574	+	1.45417	NA	intron (NR_015562, intron 1 of 6)	intron (NR_015562, intron 1 of 6)	-58373	NM_009170	20423	Mm.57202	NM_009170	ENSMUSG00000002633	Shh	9530036O11Rik|Dsh|Hhg1|Hx|Hxl3|M100081|ShhNC	sonic hedgehog	protein-coding	0.000000	0.338308			-40(TATTTGTTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-856	chr10	66098242	66098442	+	1.45417	NA	Intergenic	Intergenic	25722	NR_038039	69433	Mm.23366	NR_038039	ENSMUSG00000100000	1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	ncRNA	0.000000	0.313433			-54(CAATTCTCATGATTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7956	chrX	43885185	43885385	+	1.45417	NA	Intergenic	Intergenic	294296	NM_001195271	637093	Mm.368463	NM_001195271	ENSMUSG00000078320	Tex13c1	Gm362|Tex13c	TEX13 family member C1	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7515	chr9	9499253	9499453	+	1.45417	NA	Intergenic	Intergenic	-260340	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding	0.010000	0.398010			-85(ATGAAAATGACAAACG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6610	chr6	98666660	98666860	+	1.45417	NA	Intergenic	Intergenic	-324006	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding	0.025000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3655	chr17	88498800	88499000	+	1.45417	NA	Intergenic	Intergenic	-31224	NM_028658	73825	Mm.271817	NM_028658	ENSMUSG00000034709	Ppp1r21	1110018J12Rik|AI426045|AW550781|Ccdc128|Klraq1	protein phosphatase 1, regulatory subunit 21	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6126	chr5	103859629	103859829	+	1.45417	NA	Intergenic	Intergenic	51530	NM_178741	246293	Mm.179871	NM_178741	ENSMUSG00000029312	Klhl8	2310001P09Rik|D5Ertd431e	kelch-like 8	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1245	chr11	37808935	37809135	+	1.45417	NA	Intergenic	Intergenic	150046	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA	0.005000	0.338308			52(ATTTATATAATAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7204	chr8	35956513	35956713	+	1.45417	NA	Intergenic	MER2|DNA|TcMar-Tigger	-73656	NR_046181	330737	Mm.381743	NR_046181	ENSMUSG00000109761	5430403N17Rik	5430403N17	RIKEN cDNA 5430403N17 gene	ncRNA	0.005000	0.373134			-63(GTATTATAATGCTAAT,+,0.00),41(TTGTTTTTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5263	chr3	147824376	147824576	+	1.45417	NA	Intergenic	Intergenic	972109	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3558	chr17	65848862	65849062	+	1.45417	NA	3' UTR (NM_001198949, exon 10 of 10)	3' UTR (NM_001198949, exon 10 of 10)	35961	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding	0.025000	0.582090			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-213	chr1	77467504	77467704	+	1.45256	NA	intron (NM_007936, intron 3 of 17)	intron (NM_007936, intron 3 of 17)	29164	NR_105770	102465180		NR_105770	ENSMUSG00000099141	Mir6352	Gm27481|mmu-mir-6352	microRNA 6352	ncRNA	0.005000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-838	chr8	78235364	78235564	+	1.45256	NA	intron (NM_183096, intron 5 of 13)	intron (NM_183096, intron 5 of 13)	22122	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding	0.015000	0.303483			-29(CTCTGCAAAAGAAAGT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-831	chr8	64307998	64308198	+	1.45256	NA	Intergenic	Intergenic	-102090	NM_009390	21892	Mm.418367	NM_009390	ENSMUSG00000053626	Tll1	Tll|Tll-1|b2b2476Clo	tolloid-like	protein-coding	0.000000	0.348259			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-268	chr13	109926572	109926772	+	1.45152	NA	intron (NM_011056, intron 8 of 16)	intron (NM_011056, intron 8 of 16)	22863	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.030000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5733	chr4	126059580	126059780	+	1.45097	NA	intron (NM_172701, intron 1 of 9)	intron (NM_172701, intron 1 of 9)	1115	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2788	chr15	10722601	10722801	+	1.45097	NA	TTS (NR_045065)	TTS (NR_045065)	7801	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000096971	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1848	chr12	100690345	100690545	+	1.45097	NA	intron (NM_153587, intron 1 of 17)	intron (NM_153587, intron 1 of 17)	34675	NM_001330702	73086	Mm.220417	NM_153587	ENSMUSG00000021180	Rps6ka5	3110005L17Rik|6330404E13Rik|AI854034|MSK1|MSPK1|RLPK|RLSK|S6K-alpha-5	ribosomal protein S6 kinase, polypeptide 5	protein-coding	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1133	chr10	127049490	127049690	+	1.45097	NA	intron (NM_010009, intron 2 of 8)	intron (NM_010009, intron 2 of 8)	1344	NM_010009	13115	Mm.6216	NM_010009	ENSMUSG00000006724	Cyp27b1	Cp2b|Cyp1|Cyp27b|Cyp40|P450c1|Pddr|Vdd1|Vddr|VddrI|Vdr	cytochrome P450, family 27, subfamily b, polypeptide 1	protein-coding	0.025000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3519	chr17	51823772	51823972	+	1.45097	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	2716	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding	0.015000	0.373134			-67(GGAATGTCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2143	chr13	73963710	73963910	+	1.45097	NA	promoter-TSS (NM_027704)	promoter-TSS (NM_027704)	-41	NM_027704	71164	Mm.66995	NM_027704	ENSMUSG00000069189	Zdhhc11	4933421L13Rik|DHHC-11|Zdhhc20	zinc finger, DHHC domain containing 11	protein-coding	0.020000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2756	chr15	5069015	5069215	+	1.45097	NA	Intergenic	Intergenic	-5342	NM_001243837	109828	Mm.208034	NM_001243837	ENSMUSG00000079105	C7	A530026G17|Gm1238	complement component 7	protein-coding	0.025000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-233	chr1	83855739	83855939	+	1.45097	NA	Intergenic	RMER4B|LTR|ERVK	363122	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6550	chr6	81552497	81552697	+	1.45097	NA	Intergenic	RMER15|LTR|ERVL	343066	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7086	chr7	129958480	129958680	+	1.45097	NA	Intergenic	Intergenic	-3585	NR_046077	100043150	Mm.334264	NR_046077	ENSMUSG00000108504	Gm4265	-	predicted gene 4265	ncRNA	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7333	chr8	78235459	78235659	+	1.45023	NA	intron (NM_183096, intron 5 of 13)	intron (NM_183096, intron 5 of 13)	22217	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding	0.025000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4885	chr3	28530838	28531038	+	1.45023	NA	intron (NM_001163009, intron 4 of 30)	intron (NM_001163009, intron 4 of 30)	110995	NR_130342	100628591		NR_130342	ENSMUSG00000092990	Mir466q	Mir446q|mmu-mir-466q|mu-mir-446q	microRNA 466q	ncRNA	0.000000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-354	chr15	96029043	96029243	+	1.44756	NA	Intergenic	L1_Mur3|LINE|L1	50410	NR_126493	402773	Mm.210567	NM_001033483	ENSMUSG00000078925	D030018L15Rik	-	nuclear receptor coactivator 2 pseudogene	pseudo	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2671	chr14	105062359	105062559	+	1.44756	NA	Intergenic	Intergenic	114855	NM_134077	74213	Mm.124957	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2782	chr15	10276903	10277103	+	1.44574	NA	intron (NM_001253781, intron 1 of 9)	intron (NM_001253781, intron 1 of 9)	-16648	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0.000000	0.338308			-26(ATATGAATTACAATGA,-,0.00),-4(ATTAGCATTAGAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-779	chr10	39018716	39018916	+	1.44551	NA	intron (NM_010681, intron 4 of 37)	intron (NM_010681, intron 4 of 37)	53301	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4562	chr2	120960170	120960370	+	1.44551	NA	intron (NM_009461, intron 3 of 46)	intron (NM_009461, intron 3 of 46)	10445	NM_009461	22222	Mm.389330	NM_009461	ENSMUSG00000027272	Ubr1	AI504731	ubiquitin protein ligase E3 component n-recognin 1	protein-coding	0.005000	0.407960			20(TCTTTCTCTTATAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-219	chr1	80262064	80262264	+	1.44551	NA	Intergenic	Intergenic	-48220	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding	0.010000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-505	chr2	101585053	101585253	+	1.44551	NA	intron (NM_001362687, intron 4 of 6)	ORR1D2|LTR|ERVL-MaLR	35893	NM_001362687	68170	Mm.31263	NM_026592	ENSMUSG00000027165	B230118H07Rik	NWC	RIKEN cDNA B230118H07 gene	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3457	chr17	29165544	29165744	+	1.44551	NA	intron (NM_001360239, intron 15 of 21)	intron (NM_001360239, intron 15 of 21)	51463	NM_001364848	442827	Mm.20023	NM_001002786	ENSMUSG00000064147	Rab44	9830134C10Rik	RAB44, member RAS oncogene family	protein-coding	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3363	chr16	86918578	86918778	+	1.44551	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-112165	NR_153789	102635020	Mm.132956	NR_153789		Gm32461	-	predicted gene, 32461	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1981	chr13	22218011	22218211	+	1.44551	NA	TTS (NM_134225)	TTS (NM_134225)	1709	NM_134225	171259	Mm.432535	NM_134225	ENSMUSG00000046932	Vmn1r193	V1ri9	vomeronasal 1 receptor 193	protein-coding	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2547	chr14	75412381	75412581	+	1.44551	NA	Intergenic	LTR16C|LTR|ERVL	-24335	NR_030568	100124475		NR_030568	ENSMUSG00000077981	Mir466f-3	Mirn466f-3	microRNA 466f-3	ncRNA	0.000000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-44	chr1	152954650	152954850	+	1.44489	NA	promoter-TSS (NM_175460)	promoter-TSS (NM_175460)	-351	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-463	chr1	152954593	152954793	+	1.44450	NA	promoter-TSS (NM_175460)	promoter-TSS (NM_175460)	-408	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2431	chr14	32504226	32504426	+	1.44448	NA	Intergenic	L1M4|LINE|L1	-9195	NM_001081221	319955	Mm.318310	NM_001081221	ENSMUSG00000054051	Ercc6	4732403I04|C130058G22Rik|CSB	excision repair cross-complementing rodent repair deficiency, complementation group 6	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1759	chr12	79482601	79482801	+	1.44448	NA	intron (NM_009014, intron 7 of 10)	MARNA|DNA|TcMar-Mariner	185350	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3535	chr17	55625843	55626043	+	1.44448	NA	Intergenic	Lx6|LINE|L1	-1271	NM_001104582	383258	Mm.461682	NM_001104582	ENSMUSG00000091504	Vmn2r118	EG383258|EG668547|Vmn2r119	vomeronasal 2, receptor 118	protein-coding	0.000000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-84	chr10	27125759	27125959	+	1.44448	NA	intron (NM_008481, intron 34 of 63)	intron (NM_008481, intron 34 of 63)	-264007	NR_131034	75855	Mm.402080	NR_131034	ENSMUSG00000101636	4930579H20Rik	-	RIKEN cDNA 4930579H20 gene	ncRNA	0.000000	0.358209		-35(TATGAATATACAAG,-,0.00)	-17(CTTTAAATAACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5777	chr4	143120175	143120375	+	1.44448	NA	intron (NM_001081355, intron 8 of 9)	intron (NM_001081355, intron 8 of 9)	15887	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA	0.025000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5005	chr3	70173398	70173598	+	1.44400	NA	Intergenic	Intergenic	165885	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3610	chr17	80153047	80153247	+	1.44400	NA	intron (NM_176963, intron 4 of 6)	intron (NM_176963, intron 4 of 6)	25676	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding	0.035000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6199	chr5	131714753	131714953	+	1.44400	NA	intron (NM_001363480, intron 5 of 19)	intron (NM_001363480, intron 5 of 19)	-165416	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA	0.000000	0.412935			-75(GCATTGTCTTTTAACT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-320	chr1	113533107	113533307	+	1.44400	NA	Intergenic	RLTR17|LTR|ERVK	-1116289	NR_157044	102635484		NR_157044		Gm32810	Gm18406	predicted gene, 32810	ncRNA	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7020	chr7	110230070	110230270	+	1.44400	NA	intron (NM_009302, intron 1 of 11)	intron (NM_009302, intron 1 of 11)	8467	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5374	chr4	21492782	21492982	+	1.44400	NA	Intergenic	RMER15-int|LTR|ERVL	193081	NM_001080771	230025	Mm.208541	NM_001080771	ENSMUSG00000040478	Prdm13	-	PR domain containing 13	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7381	chr8	94832847	94833047	+	1.44400	NA	intron (NM_134141, intron 1 of 8)	intron (NM_134141, intron 1 of 8)	5393	NM_134141	109006	Mm.27582	NM_134141	ENSMUSG00000031781	Ciapin1	2810413N20Rik|AA617265|AU021794|anamorsin	cytokine induced apoptosis inhibitor 1	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1276	chr11	47002575	47002775	+	1.44400	NA	intron (NM_011891, intron 6 of 7)	intron (NM_011891, intron 6 of 7)	191876	NM_178759	276891	Mm.69002	NM_178759	ENSMUSG00000055546	Timd4	B430010N18Rik|TIM-4|Tim4	T cell immunoglobulin and mucin domain containing 4	protein-coding	0.005000	0.422886			59(TCTTTGTTATGCTGAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1685	chr12	61855162	61855362	+	1.44400	NA	intron (NM_001310586, intron 5 of 5)	intron (NM_001310586, intron 5 of 5)	332095	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|Salm5|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.000000	0.318408			-98(ATTTGAAACACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4878	chr3	26093212	26093412	+	1.44400	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	60674	NM_001357096	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding	0.010000	0.447761			23(ATTAGGAAGACAAAAG,-,0.00),76(TTATAACCATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2882	chr15	41797023	41797223	+	1.44400	NA	intron (NM_001130163, intron 1 of 13)	B2_Mm2|SINE|B2	7608	NM_001130163	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1416	chr11	94099521	94099721	+	1.44400	NA	intron (NM_001363157, intron 22 of 29)	PB1D9|SINE|Alu	55491	NM_001025428	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JIP-4|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2264	chr13	104846362	104846562	+	1.44400	NA	intron (NM_029984, intron 2 of 2)	intron (NM_029984, intron 2 of 2)	17431	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Shisal2b	A930021C24Rik|Fam159b	shisa like 2B	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2900	chr15	44904259	44904459	+	1.44400	NA	Intergenic	Intergenic	22965	NR_033609	239410	Mm.352401	NR_033609	ENSMUSG00000060530	A930017M01Rik	Gm305	Smg-5 homolog, nonsense mediated mRNA decay factor pseudogene	pseudo	0.000000	0.313433			15(ATTTAAATGAGACAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8175	chrX	169335281	169335481	+	1.44400	NA	intron (NM_001361166, intron 4 of 5)	MER58A|DNA|hAT-Charlie	14986	NM_001361166	101055907		NM_001361166		Gm15246	-	predicted gene 15246	protein-coding	0.020000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7185	chr8	29978888	29979088	+	1.44400	NA	Intergenic	Intergenic	-589407	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	ncRNA	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7646	chr9	49073559	49073759	+	1.44400	NA	intron (NM_012039, intron 12 of 15)	intron (NM_012039, intron 12 of 15)	18078	NM_012039	26951	Mm.24791	NM_012039	ENSMUSG00000032264	Zw10	6330566F14Rik|MmZw10	zw10 kinetochore protein	protein-coding	0.005000	0.402985			-22(ATTTGTATGGCAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6342	chr6	19858309	19858509	+	1.44400	NA	Intergenic	Intergenic	303067	NR_105789	102465192		NR_105789	ENSMUSG00000099149	Mir6370	Gm27480|mmu-mir-6370	microRNA 6370	ncRNA	0.015000	0.353234			-1(TGATTATCATGCTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6059	chr5	82603170	82603370	+	1.44400	NA	Intergenic	Intergenic	195795	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mir-1187|mmu-mir-1187	microRNA 1187	ncRNA	0.000000	0.323383			-36(TATTTCTCATTCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8011	chrX	87031529	87031729	+	1.44400	NA	intron (NM_001160403, intron 6 of 10)	intron (NM_001160403, intron 6 of 10)	-676635	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo	0.010000	0.402985			47(ATTCGCATAACAAAGC,-,0.00),67(CTATTTCTATGTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4492	chr2	106688464	106688664	+	1.44400	NA	Intergenic	MER2|DNA|TcMar-Tigger	-4617	NM_001143683	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1061	chr10	115882022	115882222	+	1.44400	NA	Intergenic	Intergenic	64838	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2014	chr13	32704042	32704242	+	1.44400	NA	3' UTR (NM_001368880, exon 15 of 15)	3' UTR (NM_001368880, exon 15 of 15)	79822	NM_001368880	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding	0.010000	0.383085			-40(ATCTACATAGCAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3498	chr17	45607214	45607414	+	1.44400	NA	Intergenic	MER34A|LTR|ERV1	-5212	NM_001177469	653016	Mm.45676	NM_001177468	ENSMUSG00000079471	Mymx	EG653016|Esgp|Gm7325|minion|myomerger	myomixer, myoblast fusion factor	protein-coding	0.025000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4095	chr19	43552260	43552460	+	1.44400	NA	Intergenic	Intergenic	-27755	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding	0.000000	0.388060			-95(ATCTGCATGAATAGGG,-,0.00),3(GTCTTGCAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-11	chr1	6256006	6256206	+	1.44400	NA	intron (NM_009826, intron 15 of 23)	intron (NM_009826, intron 15 of 23)	41444	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7913	chrX	7306924	7307124	+	1.44400	NA	intron (NM_001243762, intron 2 of 13)	intron (NM_001243762, intron 2 of 13)	12334	NM_001243762	12728	Mm.486257	NM_016691	ENSMUSG00000004317	Clcn5	5430408K11Rik|ClC-5|Clc4-1|Clc5|Clcn4-1|D930009B12Rik|DXImx42e|Sfc13|T25545	chloride channel, voltage-sensitive 5	protein-coding	0.010000	0.402985		50(AATGCAAATTCATG,+,0.00),50(AATGCAAATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4727	chr2	150858125	150858325	+	1.44400	NA	intron (NM_024465, intron 2 of 12)	L1ME2z|LINE|L1	-15655	NM_001356550	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding	0.000000	0.417910			77(ATTAAAATAAAAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7821	chr9	93521532	93521732	+	1.44400	NA	Intergenic	PB1D7|SINE|Alu	-515899	NR_040756	78349	Mm.52612	NR_040756	ENSMUSG00000100294	1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1644	chr12	47777818	47778018	+	1.44400	NA	Intergenic	RMER6C|LTR|ERVK	-959151	NM_001364634	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6412	chr6	39819151	39819351	+	1.44400	NA	Intergenic	L1ME1|LINE|L1	-8315	NM_010270	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding	0.025000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7475	chr8	120828386	120828586	+	1.44400	NA	Intergenic	Intergenic	89847	NM_001301811	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding	0.025000	0.616915			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4488	chr2	104834738	104834938	+	1.44400	NA	intron (NM_178695, intron 5 of 5)	intron (NM_178695, intron 5 of 5)	15012	NM_178695	228413	Mm.259609	NM_178695	ENSMUSG00000027171	Prrg4	9930111I18Rik|TMG4	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3502	chr17	49182562	49182762	+	1.44400	NA	Intergenic	Intergenic	-69129	NR_038142	69311	Mm.46140	NR_038141	ENSMUSG00000101012	1700008K24Rik	-	RIKEN cDNA 1700008K24 gene	ncRNA	0.010000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3598	chr17	76162989	76163189	+	1.44400	NA	Intergenic	MER126|DNA|DNA	302066	NR_033456	100043885	Mm.127562	NR_033456	ENSMUSG00000117539	Gm4710	-	predicted gene 4710	ncRNA	0.000000	0.308458			-46(ATTTCCATAGGAATAC,-,0.00),-24(ATTTGCCAAACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4079	chr19	35804044	35804244	+	1.44400	NA	Intergenic	Intergenic	120434	NR_152130	329056	Mm.238105	NR_152130	ENSMUSG00000094707	A830019P07Rik	-	RIKEN cDNA A830019P07 gene	ncRNA	0.000000	0.313433			-36(ATTTGCATAATAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5679	chr4	107793771	107793971	+	1.44400	NA	Intergenic	L1MB3|LINE|L1	-8388	NM_053073	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding	0.000000	0.323383			43(TGTTTGTGGTGGAAAT,+,0.00),79(ATTAAAATGACAGTCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4369	chr2	67722134	67722334	+	1.44400	NA	Intergenic	Intergenic	46777	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA	0.015000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1795	chr12	87010537	87010737	+	1.44353	NA	Intergenic	Intergenic	-10703	NR_155207	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding	0.000000	0.348259			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-763	chr6	101617394	101617594	+	1.44284	NA	Intergenic	Intergenic	-156755	NR_027989	207157	Mm.57632	NM_177579	ENSMUSG00000052236	Gm9871	0610005I04|EG207157	predicted gene 9871	ncRNA	0.005000	0.442786			58(CTTTTGTTGTACAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-11	chr1	34197410	34197610	+	1.44284	NA	intron (NM_001276764, intron 44 of 102)	intron (NM_001276764, intron 44 of 102)	37250	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7681	chr9	61995150	61995350	+	1.44174	NA	intron (NM_028748, intron 1 of 7)	intron (NM_028748, intron 1 of 7)	31540	NM_028748	74090	Mm.273267	NM_028748	ENSMUSG00000032278	Paqr5	0610010I15Rik|AV002411|BB115488|mPRg	progestin and adipoQ receptor family member V	protein-coding	0.010000	0.427861			35(ATTTACAAAGCAAATC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-65	chr1	190586299	190586499	+	1.44174	NA	Intergenic	Intergenic	182751	NR_151624	433390	Mm.331295	NR_151624	ENSMUSG00000103644	Gm29678	-	predicted gene, 29678	ncRNA	0.025000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-368	chr1	128437349	128437549	+	1.44174	NA	Intergenic	MLTR25A|LTR|ERVK	-20033	NM_145507	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding	0.005000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-771	chr6	110003200	110003400	+	1.44093	NA	Intergenic	MER45B|DNA|hAT-Tip100	-642212	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding	0.005000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3041	chr15	95144244	95144444	+	1.44093	NA	intron (NR_015482, intron 2 of 2)	L4_C_Mam|LINE|RTE-X	4974	NR_015482	100043315	Mm.159041	NR_015482	ENSMUSG00000100603	LOC100043315	-	uncharacterized LOC100043315	ncRNA	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1286	chr11	49974033	49974233	+	1.44093	NA	intron (NM_029004, intron 11 of 13)	MER2|DNA|TcMar-Tigger	-51198	NM_001290749	59044	Mm.359004	NM_021540	ENSMUSG00000020376	Rnf130	2510042A13Rik|G1RZFP|G1rp|GOLIATH|GP	ring finger protein 130	protein-coding	0.010000	0.432836			-58(TATTTCTTATTTACAT,+,0.00),22(ATTTGCATAGCATTAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1459	chr11	109749736	109749936	+	1.43972	NA	Intergenic	MER2|DNA|TcMar-Tigger	-27598	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding	0.000000	0.333333			-34(ATTTGAATAAGAAACA,-,0.00),47(ATTTACATGGCATTTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7928	chrX	16651978	16652178	+	1.43970	NA	intron (NM_173740, intron 3 of 14)	L1MB7|LINE|L1	32380	NM_173740	17161	Mm.21108	NM_173740	ENSMUSG00000025037	Maoa	1110061B18Rik|AA407771	monoamine oxidase A	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2088	chr13	58257484	58257684	+	1.43970	NA	intron (NM_019832, intron 4 of 11)	B4A|SINE|B4	16604	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding	0.015000	0.482587			-41(TTAGTCTCATGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4595	chr2	126403152	126403352	+	1.43970	NA	exon (NM_001080944, exon 12 of 28)	exon (NM_001080944, exon 12 of 28)	88301	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	Im	ATPase, class I, type 8B, member 4	protein-coding	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5379	chr4	22653028	22653228	+	1.43970	NA	Intergenic	Intergenic	162580	NR_131335	105500046		NR_131335	ENSMUSG00000107859	Gm30731	Pnky|lnc-pou3f2	predicted gene, 30731	ncRNA	0.000000	0.313433	-60(TATGCATAATAAATA,-,0.00)		-61(CTATGCATAATAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7920	chrX	10692198	10692398	+	1.43970	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-25067	NM_026524	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding	0.000000	0.467662			-43(GTTTGAATAAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2108	chr13	63662542	63662742	+	1.43970	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	71656	NR_126476	75522	Mm.54259	NR_126476	ENSMUSG00000113825	1700024I08Rik	-	RIKEN cDNA 1700024I08 gene	ncRNA	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5619	chr4	96042120	96042320	+	1.43970	NA	TTS (NM_145548)	TTS (NM_145548)	35320	NM_145548	230459	Mm.268175	NM_145548	ENSMUSG00000028571	Cyp2j13	-	cytochrome P450, family 2, subfamily j, polypeptide 13	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5331	chr4	8589622	8589822	+	1.43970	NA	intron (NM_021518, intron 6 of 7)	ORR1C2|LTR|ERVL-MaLR	54078	NM_021518	59021	Mm.397471	NM_021518	ENSMUSG00000047187	Rab2a	9330148M11Rik|C80220|Rab2	RAB2A, member RAS oncogene family	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3731	chr18	20128350	20128550	+	1.43970	NA	Intergenic	Intergenic	-13677	NM_013504	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding	0.000000	0.363184		66(TATGCATATGTATG,+,0.00),66(TATGCATATGTATG,-,0.00),86(TATGTATATGTATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-994	chr10	105901347	105901547	+	1.43970	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	59968	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5965	chr5	54980275	54980475	+	1.43970	NA	Intergenic	Intergenic	630383	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13	predicted gene 10440	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7180	chr8	27527851	27528051	+	1.43970	NA	Intergenic	Intergenic	80281	NM_027618	70952	Mm.158160	NM_026256	ENSMUSG00000063932	Poteg	4921537P18Rik|4930456F22Rik|Gsarp1|Gsarp2	POTE ankyrin domain family, member G	protein-coding	0.000000	0.328358			-2(TTTTTATTATACAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2778	chr15	9585504	9585704	+	1.43970	NA	intron (NM_001305042, intron 34 of 36)	intron (NM_001305042, intron 34 of 36)	-55728	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding	0.000000	0.318408	-9(CATGCATAATGGAAT,+,0.00),-9(CATGCATAATGGAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4890	chr3	29774794	29774994	+	1.43970	NA	Intergenic	MER123|DNA|DNA	-116123	NR_110437	102636083		NR_110437	ENSMUSG00000102590	Mannr	Manr	Mecom adjacent non-protein coding RNA	ncRNA	0.005000	0.308458			-10(ATTAACATGAAAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6899	chr7	71471568	71471768	+	1.43970	NA	Intergenic	Intergenic	-438027	NR_130995	78156	Mm.243818	NR_130995	ENSMUSG00000108669	4930441H08Rik	-	RIKEN cDNA 4930441H08 gene	ncRNA	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-827	chr10	54037397	54037597	+	1.43970	NA	intron (NM_008548, intron 2 of 12)	intron (NM_008548, intron 2 of 12)	38240	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-965	chr10	97100398	97100598	+	1.43970	NA	Intergenic	Intergenic	64730	NR_045358	75301	Mm.108650	NR_045358	ENSMUSG00000111924	4930556N09Rik	-	RIKEN cDNA 4930556N09 gene	ncRNA	0.005000	0.343284			-21(CGTTTATCATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-66	chr1	22730198	22730398	+	1.43970	NA	intron (NM_001012624, intron 1 of 28)	intron (NM_001012624, intron 1 of 28)	75705	NM_053270	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1	regulating synaptic membrane exocytosis 1	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7906	chr9	120614137	120614337	+	1.43970	NA	Intergenic	Intergenic	36906	NR_073359	76100	Mm.48212	NR_073359	ENSMUSG00000052658	5830454E08Rik	-	RIKEN cDNA 5830454E08 gene	ncRNA	0.025000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4763	chr2	160622598	160622798	+	1.43970	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-23199	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6646	chr6	106520995	106521195	+	1.43970	NA	intron (NM_001109749, intron 11 of 25)	intron (NM_001109749, intron 11 of 25)	227942	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8176	chrY	897949	898149	+	1.43970	NA	exon (NM_011419, exon 1 of 26)	exon (NM_011419, exon 1 of 26)	261	NM_011419	20592	Mm.262676	NM_011419	ENSMUSG00000056673	Kdm5d	HY|Jarid1d|Smcy	lysine (K)-specific demethylase 5D	protein-coding	0.060000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5270	chr3	148538529	148538729	+	1.43970	NA	Intergenic	Intergenic	416006	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.005000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2702	chr14	115444967	115445167	+	1.43970	NA	intron (NM_175500, intron 5 of 7)	intron (NM_175500, intron 5 of 7)	-35515	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4215	chr2	23207297	23207497	+	1.43970	NA	promoter-TSS (NM_027635)	promoter-TSS (NM_027635)	-79	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding	0.040000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-130	chr1	44533480	44533680	+	1.43970	NA	Intergenic	Intergenic	-18091	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding	0.005000	0.388060			-53(GTTTTCTTATGCATAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1290	chr11	51984633	51984833	+	1.43970	NA	TTS (NM_009458)	TTS (NM_009458)	15758	NM_001362686	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	E2-14k|E214K|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding	0.010000	0.393035			-53(TTGTGCATGATAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1523	chr12	5477915	5478115	+	1.43970	NA	Intergenic	LTR79|LTR|ERVL	102295	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA	0.000000	0.462687			70(TTTTCAATGACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4267	chr2	42081001	42081201	+	1.43970	NA	intron (NM_053011, intron 2 of 90)	intron (NM_053011, intron 2 of 90)	366467	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA	0.000000	0.273632			63(TTTAGCATAACAGTAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5218	chr3	136864323	136864523	+	1.43970	NA	intron (NM_001293622, intron 2 of 12)	L1MA6|LINE|L1	194357	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding	0.000000	0.378109	33(AATGCATAATTCATT,+,0.00),33(AATGCATAATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7782	chr9	84503038	84503238	+	1.43970	NA	Intergenic	Intergenic	-271260	NR_040739	75253	Mm.401984	NR_040739	ENSMUSG00000099724	4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	ncRNA	0.000000	0.442786			-3(ATTTACATGACAGTAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3082	chr16	11607033	11607233	+	1.43970	NA	intron (NM_028964, intron 15 of 20)	L1VL2|LINE|L1	-172569	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2390	chr14	21428554	21428754	+	1.43970	NA	intron (NM_134079, intron 10 of 10)	intron (NM_134079, intron 10 of 10)	-71116	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3308	chr16	71515192	71515392	+	1.43970	NA	Intergenic	Intergenic	265388	NR_040576	78221	Mm.399298	NR_040576	ENSMUSG00000116982	4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	ncRNA	0.005000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6632	chr6	102372314	102372514	+	1.43970	NA	intron (NM_008779, intron 3 of 21)	intron (NM_008779, intron 3 of 21)	92253	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1891	chr12	111228706	111228906	+	1.43970	NA	intron (NM_001364364, intron 2 of 10)	L1M4|LINE|L1	-42290	NM_033603	93835	Mm.197639	NM_033603	ENSMUSG00000021278	Amn	-	amnionless	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7942	chrX	23997610	23997810	+	1.43970	NA	Intergenic	Intergenic	104947	NM_001034864	236749	Mm.296422	NM_001034864	ENSMUSG00000068113	Gm4907	EG236749	predicted gene 4907	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3037	chr15	94443696	94443896	+	1.43897	NA	Intergenic	Intergenic	-39446	NM_001164786	223838	Mm.214132	NM_177431	ENSMUSG00000022449	Adamts20	Adamst20|bt	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 20	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7215	chr8	39657069	39657269	+	1.43895	NA	Intergenic	Intergenic	-14491	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0.000000	0.348259			-100(CTTTTACTATGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7638	chr9	46493588	46493788	+	1.43895	NA	Intergenic	Intergenic	-173702	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-825	chr10	53943596	53943796	+	1.43895	NA	intron (NM_008548, intron 6 of 12)	intron (NM_008548, intron 6 of 12)	132041	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding	0.000000	0.398010			-76(CTCTACATAACAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6368	chr6	28491796	28491996	+	1.43895	NA	intron (NM_019776, intron 1 of 23)	intron (NM_019776, intron 1 of 23)	11548	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6486	chr6	63318910	63319110	+	1.43895	NA	intron (NM_001370966, intron 1 of 15)	intron (NM_001370966, intron 1 of 15)	63004	NM_001370966									0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-401	chr1	138174337	138174537	+	1.43895	NA	intron (NM_011210, intron 2 of 29)	intron (NM_011210, intron 2 of 29)	689	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding	0.020000	0.432836	11(AATGATTAATTCAAA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5468	chr4	53474452	53474652	+	1.43895	NA	intron (NM_133891, intron 1 of 15)	intron (NM_133891, intron 1 of 15)	34139	NM_133891	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2586	chr14	79773887	79774087	+	1.43895	NA	Intergenic	CpG	-2675	NM_001042726	18530	Mm.390715	NM_021543	ENSMUSG00000036422	Pcdh8	1700080P15Rik|Papc	protocadherin 8	protein-coding	0.070000	0.606965			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7631	chr9	44806896	44807096	+	1.43895	NA	3' UTR (NM_001357549, exon 36 of 36)	3' UTR (NM_001357549, exon 36 of 36)	-4045	NM_138951	192653	Mm.325487	NM_138951	ENSMUSG00000039438	Ttc36	-	tetratricopeptide repeat domain 36	protein-coding	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4093	chr19	43008984	43009184	+	1.43895	NA	intron (NM_001081257, intron 4 of 11)	intron (NM_001081257, intron 4 of 11)	-229106	NM_001346703	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Gm21361|Hps|ep	HPS1, biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1907	chr12	117345362	117345562	+	1.43745	NA	Intergenic	Intergenic	-8450	NR_044987	432713	Mm.459210	NR_044987	ENSMUSG00000101930	Gm5441	-	predicted gene 5441	ncRNA	0.015000	0.522388	-27(CATCCATAATTCATT,+,0.00),-27(CATCCATAATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5273	chr3	148663103	148663303	+	1.43682	NA	Intergenic	Intergenic	291432	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.025000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7624	chr9	42573313	42573513	+	1.43682	NA	intron (NM_175481, intron 13 of 20)	intron (NM_175481, intron 13 of 20)	-101155	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding	0.015000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4446	chr2	90566993	90567193	+	1.43682	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	13554	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding	0.005000	0.557214			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-21	chr1	86782670	86782870	+	1.43682	NA	intron (NM_153530, intron 5 of 20)	intron (NM_153530, intron 5 of 20)	78966	NM_001172157	208718	Mm.389152	NM_153530	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 like 3'-5' exoribonuclease 2	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6681	chr6	116056959	116057159	+	1.43682	NA	promoter-TSS (NM_001364577)	promoter-TSS (NM_001364577)	-48	NM_001364577	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding	0.030000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5115	chr3	109886414	109886614	+	1.43682	NA	intron (NM_030699, intron 3 of 7)	intron (NM_030699, intron 3 of 7)	256958	NM_001163348	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3669	chr17	91582088	91582288	+	1.43489	NA	Intergenic	Intergenic	-489386	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-963	chr10	96834576	96834776	+	1.43206	NA	Intergenic	RMER6A|LTR|ERVK	-201092	NR_045358	75301	Mm.108650	NR_045358	ENSMUSG00000111924	4930556N09Rik	-	RIKEN cDNA 4930556N09 gene	ncRNA	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7465	chr8	116144262	116144462	+	1.43206	NA	Intergenic	Intergenic	-360653	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding	0.020000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3957	chr18	81439817	81440017	+	1.43206	NA	Intergenic	Intergenic	-452896	NM_001369133	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	spalt like transcription factor 3	protein-coding	0.005000	0.288557			74(TCAATGTGATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4518	chr2	110020034	110020234	+	1.43206	NA	intron (NM_001355581, intron 1 of 7)	intron (NM_001355581, intron 1 of 7)	2317	NM_001355581	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1424	chr11	96720283	96720483	+	1.43200	NA	intron (NM_001177898, intron 9 of 10)	intron (NM_001177898, intron 9 of 10)	57172	NM_001163389	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding	0.025000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1423	chr11	96720007	96720207	+	1.43200	NA	intron (NM_001177898, intron 9 of 10)	intron (NM_001177898, intron 9 of 10)	57448	NM_001163389	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding	0.005000	0.343284	0(ACTGAATAATGCACA,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8167	chrX	167567292	167567492	+	1.43200	NA	intron (NM_001368936, intron 4 of 16)	ORR1B1|LTR|ERVL-MaLR	-184643	NM_001313758	110639	Mm.272955	NM_026662	ENSMUSG00000025742	Prps2	2610101M19Rik|AA589463|AI464149|Prps-2	phosphoribosyl pyrophosphate synthetase 2	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-687	chr10	8038618	8038818	+	1.43200	NA	Intergenic	Intergenic	-82595	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding	0.020000	0.427861	7(AATGAATAATTCGTA,+,0.00),7(AATGAATAATTCGTA,-,0.00),47(GATGCATAATTCAAA,+,0.00),47(GATGCATAATTCAAA,-,0.00)		22(CATTTGTAATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3504	chr17	49761183	49761383	+	1.43200	NA	intron (NM_177052, intron 13 of 22)	intron (NM_177052, intron 13 of 22)	146111	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-97	chr1	34197456	34197656	+	1.43198	NA	intron (NM_001276764, intron 44 of 102)	intron (NM_001276764, intron 44 of 102)	37296	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-67	chr1	23379546	23379746	+	1.43102	NA	intron (NM_001081079, intron 1 of 6)	intron (NM_001081079, intron 1 of 6)	3529	NM_001081079	70155	Mm.28013	NM_001081079	ENSMUSG00000026158	Ogfrl1	2210417C17Rik	opioid growth factor receptor-like 1	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6575	chr6	87567673	87567873	+	1.43102	NA	Intergenic	Intergenic	22970	NM_021381	58182	Mm.333226	NM_021381	ENSMUSG00000049409	Prokr1	EG-VEGFR1|Gpr73|Pk-r1|Pkr1	prokineticin receptor 1	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5866	chr5	25027824	25028024	+	1.43102	NA	intron (NM_145401, intron 2 of 15)	(CAGGG)n|Simple_repeat|Simple_repeat	-32171	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5691	chr4	111368404	111368604	+	1.43102	NA	intron (NM_001284190, intron 6 of 12)	intron (NM_001284190, intron 6 of 12)	-46502	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2663	chr14	103299404	103299604	+	1.43102	NA	intron (NM_207215, intron 4 of 84)	intron (NM_207215, intron 4 of 84)	47296	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2, E3 ubiquitin protein ligase	protein-coding	0.005000	0.402985			-27(ATTACCATAGCAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4795	chr2	171829224	171829424	+	1.43102	NA	Intergenic	Intergenic	133475	NR_040509	75655	Mm.396203	NR_040509	ENSMUSG00000086823	1700028P15Rik	-	RIKEN cDNA 1700028P15 gene	ncRNA	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3634	chr17	82869102	82869302	+	1.43102	NA	Intergenic	Intergenic	209023	NR_045094	100503434	Mm.187281	NR_045094	ENSMUSG00000117399	Gm19689	-	predicted gene, 19689	ncRNA	0.000000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5499	chr4	59963908	59964108	+	1.43102	NA	Intergenic	RLTR9A3A|LTR|ERVK	-3341	NM_008648	17843	Mm.457982	NM_008648	ENSMUSG00000041333	Mup4	Mup-4|Mup1	major urinary protein 4	protein-coding	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1593	chr12	34183357	34183557	+	1.43102	NA	intron (NM_001271386, intron 23 of 27)	intron (NM_001271386, intron 23 of 27)	225786	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding	0.005000	0.363184			2(AATTGAATAACAATGT,-,0.00),22(ATGAACAAGACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5784	chr4	145006343	145006543	+	1.43102	NA	intron (NM_001276465, intron 67 of 69)	intron (NM_001276465, intron 67 of 69)	113306	NM_001357274	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding	0.015000	0.402985			-48(ATCTCCATGAGAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1664	chr12	53769425	53769625	+	1.43102	NA	intron (NM_001370962, intron 4 of 11)	intron (NM_001370962, intron 4 of 11)	434349	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2737	chr14	121862610	121862810	+	1.43102	NA	Intergenic	Intergenic	15560	NR_131002	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7480	chr8	124012042	124012242	+	1.43102	NA	intron (NM_133966, intron 1 of 4)	ORR1A1-int|LTR|ERVL-MaLR	8914	NM_001357315	102162	Mm.291777	NM_133966	ENSMUSG00000038697	Taf5l	1110005N04Rik|AI849020	TATA-box binding protein associated factor 5 like	protein-coding	0.000000	0.398010			-19(ATCAAAATAACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1954	chr13	13778062	13778262	+	1.43102	NA	TTS (NM_010748)	TTS (NM_010748)	-5897	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding	0.010000	0.427861			42(CATTTGTTATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7170	chr8	22216917	22217117	+	1.43102	NA	intron (NM_027338, intron 11 of 13)	intron (NM_027338, intron 11 of 13)	-10286	NM_019576	56229	Mm.32067	NM_019576	ENSMUSG00000031480	Thsd1	4833423O18Rik|Tmtsp	thrombospondin, type I, domain 1	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-418	chr1	140661506	140661706	+	1.43094	NA	Intergenic	Intergenic	-5204	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3451	chr17	28096897	28097097	+	1.43094	NA	Intergenic	Intergenic	-16358	NM_001085555	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2973	chr15	67441323	67441523	+	1.43094	NA	Intergenic	MTD|LTR|ERVL-MaLR	214654	NR_045140	69334	Mm.63770	NR_045140	ENSMUSG00000102069	1700012I11Rik	-	RIKEN cDNA 1700012I11 gene	ncRNA	0.005000	0.422886		80(AATAATTATTCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4130	chr19	57765020	57765220	+	1.43094	NA	intron (NM_181415, intron 24 of 28)	RLTR12BD_Mm|LTR|ERVK	154086	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8039	chrX	101781042	101781242	+	1.43094	NA	Intergenic	RLTR14-int|LTR|ERV1	-13514	NM_001359671	382231	Mm.328112	NM_001359671	ENSMUSG00000046774	8030474K03Rik	Gm1142	RIKEN cDNA 8030474K03 gene	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7226	chr8	42242949	42243149	+	1.43094	NA	Intergenic	Lx7|LINE|L1	415782	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5625	chr4	97281411	97281611	+	1.43094	NA	Intergenic	Intergenic	-300432	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2777	chr15	9507458	9507658	+	1.43094	NA	3' UTR (NM_008372, exon 8 of 8)	3' UTR (NM_008372, exon 8 of 8)	22318	NM_001355680	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding	0.000000	0.348259			-50(ATTTGAATGATAGACC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2281	chr13	109100530	109100730	+	1.43094	NA	intron (NM_011056, intron 3 of 16)	L2|LINE|L2	-224114	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA	0.005000	0.417910			56(CTTTGAATAATAAGGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7319	chr8	77222789	77222989	+	1.43094	NA	intron (NM_001083906, intron 8 of 8)	intron (NM_001083906, intron 8 of 8)	229200	NM_001363420	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5742	chr4	127452709	127452909	+	1.43094	NA	Intergenic	Intergenic	-94645	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6993	chr7	99992445	99992645	+	1.43094	NA	Intergenic	Intergenic	-12087	NM_175388	108937	Mm.323087	NM_175388	ENSMUSG00000058761	Rnf169	2900057K09Rik	ring finger protein 169	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1065	chr10	116135743	116135943	+	1.43094	NA	intron (NM_011217, intron 2 of 13)	intron (NM_011217, intron 2 of 13)	-8055	NM_001161837	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding	0.010000	0.417910			7(GTTTGCATGACAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1770	chr12	82130417	82130617	+	1.43094	NA	Intergenic	Intergenic	-39499	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4574	chr2	124326597	124326797	+	1.43094	NA	intron (NM_001290997, intron 3 of 20)	intron (NM_001290997, intron 3 of 20)	-104339	NR_040612	75946	Mm.415059	NR_040612	ENSMUSG00000086954	4930583P06Rik	-	RIKEN cDNA 4930583P06 gene	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5822	chr5	9352288	9352488	+	1.43094	NA	intron (NR_153370, intron 1 of 19)	Tigger5b|DNA|TcMar-Tigger	-23316	NR_030537	100124492		NR_030537	ENSMUSG00000077896	Mir879	Mirn879|mir-879|mmu-mir-879	microRNA 879	ncRNA	0.020000	0.393035	48(AATACATATTGCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2199	chr13	91587087	91587287	+	1.43094	NA	intron (NM_001360776, intron 4 of 15)	intron (NM_001360776, intron 4 of 15)	126090	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding	0.015000	0.363184			45(TCATTTTTATTCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-961	chr10	96691050	96691250	+	1.43094	NA	Intergenic	Intergenic	74149	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6929	chr7	82087022	82087222	+	1.43094	NA	Intergenic	Intergenic	16735	NR_045744	434205	Mm.333986	NR_045744	ENSMUSG00000109145	Gm20744	-	predicted gene, 20744	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6270	chr5	150854765	150854965	+	1.43094	NA	Intergenic	Intergenic	-97742	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7547	chr9	17904843	17905043	+	1.43094	NA	Intergenic	L1_Mus3|LINE|L1	-387324	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding	0.005000	0.422886			44(TCTATGTTTTGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7143	chr8	9157051	9157251	+	1.43094	NA	Intergenic	Intergenic	12482	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1934	chr13	6118804	6119004	+	1.43094	NA	Intergenic	Intergenic	257415	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-448	chr1	150399605	150399805	+	1.43094	NA	intron (NM_133780, intron 4 of 51)	intron (NM_133780, intron 4 of 51)	-6625	NM_001357579	226499	Mm.222093	NM_145511	ENSMUSG00000006010	Odr4	1810053E15Rik|odr-4	odr4 GPCR localization factor homolog	protein-coding	0.005000	0.383085			-15(CCCTTATGATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6409	chr6	38787951	38788151	+	1.43094	NA	intron (NM_001294144, intron 2 of 14)	intron (NM_001294144, intron 2 of 14)	49260	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2109	chr13	64004221	64004421	+	1.43094	NA	Intergenic	MLTR14|LTR|ERV1	84880	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding	0.000000	0.402985			-86(ATTTAAAAAAGCAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7114	chr7	138144406	138144606	+	1.43094	NA	Intergenic	Intergenic	253224	NM_183289	70571	Mm.334297	NM_183289	ENSMUSG00000091002	Tcerg1l	5730476P14Rik	transcription elongation regulator 1-like	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-589	chr1	181149999	181150199	+	1.43061	NA	promoter-TSS (NM_030131)	promoter-TSS (NM_030131)	-832	NM_030131	98417	Mm.38229	NM_030131	ENSMUSG00000062169	Cnih4	AI647760|AW050376|CNIH-4|D530030D03Rik|E430023H19Rik|HSPC163	cornichon family AMPA receptor auxiliary protein 4	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-721	chr10	20182336	20182536	+	1.43024	NA	intron (NM_001358787, intron 1 of 17)	intron (NM_001358787, intron 1 of 17)	11414	NM_001358787	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding	0.010000	0.398010			-21(CTTAGCATAACCATGG,-,0.00),42(ATTTTGTTCTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8103	chrX	142962603	142962803	+	1.42873	NA	intron (NM_019496, intron 1 of 5)	MER5A|DNA|hAT-Charlie	4023	NM_019496	56068	Mm.143724	NM_019496	ENSMUSG00000042225	Ammecr1	6230420G18Rik	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3289	chr16	66968466	66968666	+	1.42873	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	311448	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2724	chr14	120268043	120268243	+	1.42873	NA	Intergenic	Lx7|LINE|L1	-7526	NM_001360377	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind like splicing factor 2	protein-coding	0.000000	0.353234	-58(AATAAATAATTAATT,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-35	chr1	131020841	131021041	+	1.42873	NA	intron (NM_010548, intron 1 of 4)	intron (NM_010548, intron 1 of 4)	1096	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-59	chr1	21702986	21703186	+	1.42651	NA	intron (NM_001160139, intron 1 of 14)	intron (NM_001160139, intron 1 of 14)	258856	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6832	chr7	40615362	40615562	+	1.42651	NA	Intergenic	Intergenic	-59275	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA	0.005000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-362	chr16	24030212	24030412	+	1.42651	NA	Intergenic	Intergenic	-41460	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7426	chr8	105233652	105233852	+	1.42651	NA	intron (NM_145604, intron 2 of 15)	intron (NM_145604, intron 2 of 15)	8564	NM_145604	234678	Mm.27186	NM_145604	ENSMUSG00000031889	D230025D16Rik	BC006874|Lin10	RIKEN cDNA D230025D16 gene	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7807	chr9	90711167	90711367	+	1.42651	NA	Intergenic	Intergenic	-440498	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding	0.015000	0.402985			83(ATTTAAAAAAAAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3120	chr16	24030186	24030386	+	1.42651	NA	Intergenic	Intergenic	-41434	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7056	chr7	122847370	122847570	+	1.42645	NA	Intergenic	Intergenic	122989	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA	0.010000	0.412935			-37(TAATTATCATGCTTAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5200	chr3	132982603	132982803	+	1.42645	NA	3' UTR (NM_026231, exon 12 of 12)	3' UTR (NM_026231, exon 12 of 12)	-32412	NM_033525	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding	0.000000	0.318408			-79(ATTTAAAAAAAAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1751	chr12	76958477	76958677	+	1.42561	NA	intron (NM_001146176, intron 1 of 3)	intron (NM_001146176, intron 1 of 3)	3671	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4965	chr3	60227504	60227704	+	1.42502	NA	Intergenic	Intergenic	145735	NM_032400	84112	Mm.125110	NM_032400	ENSMUSG00000027762	Sucnr1	Gpr91	succinate receptor 1	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2658	chr14	101788893	101789093	+	1.42502	NA	intron (NM_201529, intron 1 of 30)	intron (NM_201529, intron 1 of 30)	-51630	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding	0.005000	0.318408			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-222	chr12	120015322	120015522	+	1.42502	NA	intron (NM_001160385, intron 3 of 3)	intron (NM_001160385, intron 3 of 3)	69460	NM_001160385	217951	Mm.387395	NM_001160385	ENSMUSG00000048004	Tmem196	Gm528	transmembrane protein 196	protein-coding	0.005000	0.338308			-27(ATTTGATTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1923	chr12	120015332	120015532	+	1.42502	NA	intron (NM_001160385, intron 3 of 3)	intron (NM_001160385, intron 3 of 3)	69470	NM_001160385	217951	Mm.387395	NM_001160385	ENSMUSG00000048004	Tmem196	Gm528	transmembrane protein 196	protein-coding	0.005000	0.338308			-37(ATTTGATTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3631	chr17	82556462	82556662	+	1.42502	NA	Intergenic	Intergenic	521663	NR_045094	100503434	Mm.187281	NR_045094	ENSMUSG00000117399	Gm19689	-	predicted gene, 19689	ncRNA	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6618	chr6	101354556	101354756	+	1.42402	NA	intron (NM_018884, intron 2 of 9)	intron (NM_018884, intron 2 of 9)	23241	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-367	chr1	128437155	128437355	+	1.42402	NA	Intergenic	MLTR25A|LTR|ERVK	-19839	NM_145507	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1583	chr12	31459742	31459942	+	1.42136	NA	intron (NM_021353, intron 11 of 20)	intron (NM_021353, intron 11 of 20)	21623	NM_021353	13487	Mm.490454	NM_021353	ENSMUSG00000001225	Slc26a3	9030623B18Rik|9130013M11Rik|AV376035|Dra	solute carrier family 26, member 3	protein-coding	0.000000	0.383085		38(ACTGAATATGTATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2007	chr13	29995799	29995999	+	1.42136	NA	Intergenic	Intergenic	-9836	NM_010093	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding	0.015000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5505	chr4	62679335	62679535	+	1.42136	NA	intron (NM_001310706, intron 1 of 6)	L1ME3|LINE|L1	5461	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5370	chr4	20198091	20198291	+	1.42136	NA	intron (NM_001290410, intron 4 of 5)	intron (NM_001290410, intron 4 of 5)	156139	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding	0.000000	0.293532		2(AATAAATATGCAAA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7868	chr9	106230991	106231191	+	1.42136	NA	Intergenic	Intergenic	8493	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5916	chr5	42324555	42324755	+	1.42136	NA	Intergenic	Intergenic	256695	NR_131130	433882	Mm.319353	NR_131130	ENSMUSG00000067285	Gm16223	EG433882	predicted gene 16223	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2240	chr13	98587614	98587814	+	1.42136	NA	Intergenic	Intergenic	49696	NM_026685	68344	Mm.28766	NM_026685	ENSMUSG00000046082	Tmem174	0610009B10Rik|AA986094	transmembrane protein 174	protein-coding	0.040000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6807	chr7	29271447	29271647	+	1.42136	NA	intron (NM_011464, intron 1 of 6)	intron (NM_011464, intron 1 of 6)	10430	NM_001082548	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5094	chr3	103116924	103117124	+	1.42136	NA	Intergenic	Intergenic	-10532	NM_177857	329727	Mm.293641	NM_177857	ENSMUSG00000007379	Dennd2c	A930010I20Rik	DENN/MADD domain containing 2C	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3717	chr18	15289198	15289398	+	1.42136	NA	Intergenic	Intergenic	113701	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6118	chr5	102947912	102948112	+	1.42136	NA	intron (NM_001310685, intron 9 of 11)	intron (NM_001310685, intron 9 of 11)	103005	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding	0.000000	0.288557			27(ATATTGTTATTCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7715	chr9	70821999	70822199	+	1.42136	NA	intron (NM_001324472, intron 3 of 9)	RMER17C|LTR|ERVK	112709	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding	0.005000	0.507463			14(ATAAACACAACAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7689	chr9	63687492	63687692	+	1.42136	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	70402	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding	0.020000	0.537313		-25(CATAAATATTTATT,+,0.00),-25(CATAAATATTTATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-10	chr1	6034942	6035142	+	1.42136	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-117644	NM_010342	226304	Mm.291110	NM_010342	ENSMUSG00000033774	Npbwr1	Gpr7|Nbpwr1	neuropeptides B/W receptor 1	protein-coding	0.000000	0.442786			85(CTATTCTTATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7716	chr9	71284473	71284673	+	1.42136	NA	intron (NM_009022, intron 9 of 13)	intron (NM_009022, intron 9 of 13)	68784	NM_009022	19378	Mm.42016	NM_009022	ENSMUSG00000013584	Aldh1a2	AV116159|Aldh1a7|Raldh1|Raldh2	aldehyde dehydrogenase family 1, subfamily A2	protein-coding	0.000000	0.348259			-50(TTTTTGTCTTTTTAAT,+,0.00),-44(TCTTTTTAATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2442	chr14	34459012	34459212	+	1.42136	NA	intron (NM_009758, intron 2 of 12)	B3A|SINE|B2	43434	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK-3|ALK3|AU045487|BMPR-1A|BMPR-IA|Bmpr|SKR5	bone morphogenetic protein receptor, type 1A	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6983	chr7	96446623	96446823	+	1.42136	NA	intron (NM_001310760, intron 3 of 32)	MIRb|SINE|MIR	-104759	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	-	predicted gene 15412	ncRNA	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2459	chr14	40560389	40560589	+	1.42136	NA	Intergenic	Intergenic	332825	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding	0.005000	0.402985	-63(TATGAATAATGGAAA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2198	chr13	91236318	91236518	+	1.42136	NA	Intergenic	Intergenic	-12431	NM_025770	66795	Mm.235385	NM_025770	ENSMUSG00000021619	Atg10	5330424L23Rik|5430428K15Rik|AI852123|APG10|Agp10|Apg10l|Apg10p|Atg10l	autophagy related 10	protein-coding	0.000000	0.333333			-17(CTATTCATATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1959	chr13	15346956	15347156	+	1.42136	NA	Intergenic	Intergenic	-116667	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6124	chr5	103305827	103306027	+	1.42136	NA	Intergenic	L1ME2|LINE|L1	-6898	NR_040699	74624	Mm.389662	NR_040699	ENSMUSG00000104956	4930429D17Rik	-	RIKEN cDNA 4930429D17 gene	ncRNA	0.005000	0.353234		26(CATTAATTTGCATT,+,0.00)	55(CTTTTGTATTGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-255	chr1	88763832	88764032	+	1.42136	NA	Intergenic	RLTR26B_MM|LTR|ERVK	9042	NR_040493	78650	Mm.243767	NR_040493	ENSMUSG00000097398	Platr5	2410088K16Rik	pluripotency associated transcript 5	ncRNA	0.015000	0.621891			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5639	chr4	99373938	99374138	+	1.42136	NA	Intergenic	Intergenic	179891	NM_001145967	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding	0.035000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-152	chr1	52293349	52293549	+	1.42131	NA	Intergenic	Intergenic	-60217	NM_001113383	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-151	chr1	52293222	52293422	+	1.42131	NA	Intergenic	Intergenic	-60090	NM_001113383	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7406	chr8	100295641	100295841	+	1.42131	NA	Intergenic	Intergenic	879067	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.338308			-35(TTTTGAAAGAAAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7311	chr8	73135018	73135218	+	1.42080	NA	intron (NM_001317391, intron 3 of 15)	intron (NM_001317391, intron 3 of 15)	118606	NR_039551	100628574		NR_039551	ENSMUSG00000093140	Mir28b	mmu-mir-28b	microRNA 28b	ncRNA	0.005000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-842	chr8	79828807	79829007	+	1.42080	NA	Intergenic	L4_C_Mam|LINE|RTE-X	117058	NM_001357235	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6306	chr6	12318334	12318534	+	1.42080	NA	intron (NM_001164805, intron 25 of 26)	intron (NM_001164805, intron 25 of 26)	-208854	NR_003631	625347	Mm.389084	NM_001039041	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo	0.010000	0.373134			-74(ATTAGCAATGGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4866	chr3	19611191	19611391	+	1.42080	NA	TTS (NM_025489)	TTS (NM_025489)	-33169	NM_001081281	381485	Mm.35419	NM_001081281	ENSMUSG00000060913	Trim55	D830041C10Rik|Murf2|Rnf29	tripartite motif-containing 55	protein-coding	0.010000	0.412935			-94(TTTAAAATGACAAAAA,-,0.00),-36(ATCAGCATGAACATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1186	chr11	20927794	20927994	+	1.42080	NA	Intergenic	Intergenic	-96786	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding	0.010000	0.422886	48(AATGCATAATGGATG,+,0.00),48(AATGCATAATGGATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-676	chr10	5222034	5222234	+	1.42001	NA	intron (NM_001347711, intron 78 of 145)	intron (NM_001347711, intron 78 of 145)	-27427	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|KASH1|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding	0.005000	0.442786		-29(AATGAATTTACATG,-,0.00)	-24(ATTTACATGCCAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5187	chr3	130290220	130290420	+	1.42001	NA	intron (NM_029838, intron 2 of 37)	intron (NM_029838, intron 2 of 37)	109475	NM_001244952	77018	Mm.91728	NM_029838	ENSMUSG00000058897	Col25a1	2700062B08Rik|CLAC-P	collagen, type XXV, alpha 1	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5680	chr4	107919272	107919472	+	1.42001	NA	intron (NM_009949, intron 1 of 4)	MT2A|LTR|ERVL	4217	NM_009949	12896	Mm.307620	NM_009949	ENSMUSG00000028607	Cpt2	AI323697|CPTII	carnitine palmitoyltransferase 2	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5174	chr3	127249010	127249210	+	1.42001	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	87805	NR_105030	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1081	chr10	118469600	118469800	+	1.42001	NA	Intergenic	Intergenic	28654	NM_008337	15978	Mm.240327	NM_008337	ENSMUSG00000055170	Ifng	IFN-g|Ifg	interferon gamma	protein-coding	0.005000	0.353234		-77(CATGACTATTCATG,+,0.00),-77(CATGACTATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6398	chr6	36206783	36206983	+	1.42001	NA	Intergenic	Intergenic	-181201	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2295	chr13	110621698	110621898	+	1.42001	NA	Intergenic	Lx8|LINE|L1	226754	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo like kinase 2	protein-coding	0.000000	0.373134			29(ATTTACAAGGAAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3983	chr18	85523222	85523422	+	1.42001	NA	Intergenic	Intergenic	571206	NM_001367965	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding	0.000000	0.348259			66(TTTTTATGTTGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5936	chr5	48657420	48657620	+	1.42001	NA	intron (NM_001199244, intron 1 of 7)	Tigger17c|DNA|TcMar-Tigger	-57838	NM_001199245	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2259	chr13	103880004	103880204	+	1.41828	NA	intron (NM_001005868, intron 4 of 26)	intron (NM_001005868, intron 4 of 26)	40482	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding	0.000000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-379	chr16	72578204	72578404	+	1.41828	NA	Intergenic	Intergenic	-84845	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3311	chr16	72578188	72578388	+	1.41828	NA	Intergenic	Intergenic	-84861	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.010000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-408	chr17	71350396	71350596	+	1.41815	NA	intron (NM_028887, intron 45 of 47)	intron (NM_028887, intron 45 of 47)	-8692	NR_028023	100043644	Mm.362377	NR_028023	ENSMUSG00000117199	Gm4566	-	ubiquitin specific peptidase 16 pseudogene	pseudo	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5989	chr5	64279762	64279962	+	1.41683	NA	intron (NM_019636, intron 10 of 19)	intron (NM_019636, intron 10 of 19)	49505	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding	0.035000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-116	chr10	121056326	121056526	+	1.41682	NA	intron (NM_011915, intron 2 of 9)	intron (NM_011915, intron 2 of 9)	22422	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding	0.020000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-328	chr15	7684256	7684456	+	1.41600	NA	Intergenic	Intergenic	-125692	NM_001301332	14573	Mm.4679	NM_010275	ENSMUSG00000022144	Gdnf	AI385739|ATF	glial cell line derived neurotrophic factor	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6663	chr6	110003153	110003353	+	1.41600	NA	Intergenic	MER45B|DNA|hAT-Tip100	-642259	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-791	chr10	40444043	40444243	+	1.41600	NA	intron (NM_001291817, intron 4 of 11)	intron (NM_001291817, intron 4 of 11)	94835	NM_198164	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6623	chr6	101617473	101617673	+	1.41539	NA	Intergenic	Intergenic	-156676	NR_027989	207157	Mm.57632	NM_177579	ENSMUSG00000052236	Gm9871	0610005I04|EG207157	predicted gene 9871	ncRNA	0.005000	0.492537			-21(CTTTTGTTGTACAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-368	chr16	38073929	38074129	+	1.41491	NA	Intergenic	Intergenic	-14972	NM_001347232	56637	Mm.394930	NM_019827	ENSMUSG00000022812	Gsk3b	7330414F15Rik|8430431H08Rik|C86142|GSK-3|GSK-3beta|GSK3	glycogen synthase kinase 3 beta	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1309	chr11	61578043	61578243	+	1.41491	NA	intron (NM_001362587, intron 1 of 11)	intron (NM_001362587, intron 1 of 11)	1544	NM_001362585	13855	Mm.139695	NM_010148	ENSMUSG00000001036	Epn2	9530051D10Rik|AA536924|Ibp2	epsin 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4808	chr2	178664819	178665019	+	1.41451	NA	Intergenic	Intergenic	234404	NM_001291189	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding	0.010000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-851	chr8	122943326	122943526	+	1.41451	NA	intron (NM_001081379, intron 2 of 12)	intron (NM_001081379, intron 2 of 12)	95052	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5337	chr4	9595604	9595804	+	1.41384	NA	intron (NM_001177849, intron 9 of 22)	intron (NM_001177849, intron 9 of 22)	48013	NM_001177854	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7863	chr9	105406624	105406824	+	1.41384	NA	TTS (NM_025651)	TTS (NM_025651)	5936	NM_001164828	66595	Mm.84941	NM_025651	ENSMUSG00000032567	Aste1	1100001A21Rik|AV006403	asteroid homolog 1	protein-coding	0.000000	0.378109			30(TTTTTGTTGTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5384	chr4	25014289	25014489	+	1.41384	NA	Intergenic	Intergenic	40970	NM_030733	81006	Mm.160412	NM_030733	ENSMUSG00000040372	Gpr63	PSP24beta|Psp24-2	G protein-coupled receptor 63	protein-coding	0.010000	0.333333			-71(TTTTCCATGACAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5774	chr4	141823226	141823426	+	1.41384	NA	intron (NM_007919, intron 2 of 7)	intron (NM_007919, intron 2 of 7)	2679	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding	0.025000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8116	chrX	147014416	147014616	+	1.41384	NA	intron (NM_008312, intron 2 of 5)	intron (NM_008312, intron 2 of 5)	3915	NR_037205	100526460		NR_037205	ENSMUSG00000093122	Mir1264	mir-1264|mmu-mir-1264	microRNA 1264	ncRNA	0.015000	0.393035			65(TCTTTGACTTGCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2327	chr13	118805334	118805534	+	1.41384	NA	Intergenic	Intergenic	90735	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-979	chr10	101009505	101009705	+	1.41384	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-267970	NR_152765	102639396	Mm.404529	NR_152765		Gm35722	-	predicted gene, 35722	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5203	chr3	133481953	133482153	+	1.41384	NA	intron (NM_001040400, intron 4 of 10)	intron (NM_001040400, intron 4 of 10)	62337	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding	0.010000	0.333333			25(ATTTAAAAAAAAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-210	chr1	76090661	76090861	+	1.41384	NA	Intergenic	Intergenic	-398372	NR_038012	620079	Mm.378379	NR_038012	ENSMUSG00000100553	Gm17751	-	predicted gene, 17751	ncRNA	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3365	chr16	87207931	87208131	+	1.41384	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-79592	NR_153792	102635567	Mm.233725	NR_153792	ENSMUSG00000116979	Gm32865	-	predicted gene, 32865	ncRNA	0.005000	0.507463			35(ATCAGCATAAGAATCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-814	chr10	50488270	50488470	+	1.41384	NA	Intergenic	L1_Mur3|LINE|L1	-104299	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4347	chr2	62630590	62630790	+	1.41384	NA	intron (NM_001164477, intron 2 of 14)	intron (NM_001164477, intron 2 of 14)	15565	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6884	chr7	66377326	66377526	+	1.41384	NA	intron (NM_146191, intron 2 of 33)	intron (NM_146191, intron 2 of 33)	4298	NR_106024	102465640		NR_106024	ENSMUSG00000098353	Mir7057	Gm27550|mmu-mir-7057	microRNA 7057	ncRNA	0.020000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6430	chr6	46519534	46519734	+	1.41384	NA	intron (NM_001004357, intron 13 of 23)	intron (NM_001004357, intron 13 of 23)	-724762	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2634	chr14	93867298	93867498	+	1.41384	NA	intron (NM_001081377, intron 2 of 4)	intron (NM_001081377, intron 2 of 4)	23271	NM_001081377	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3965	chr18	83048715	83048915	+	1.41384	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-128255	NR_033307	75853	Mm.420737	NR_033307	ENSMUSG00000118339	4930592I03Rik	-	RIKEN cDNA 4930592I03 gene	ncRNA	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2239	chr13	98569793	98569993	+	1.41384	NA	Intergenic	L1MB8|LINE|L1	67517	NM_026685	68344	Mm.28766	NM_026685	ENSMUSG00000046082	Tmem174	0610009B10Rik|AA986094	transmembrane protein 174	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7363	chr8	85527363	85527563	+	1.41384	NA	3' UTR (NM_173866, exon 12 of 12)	3' UTR (NM_173866, exon 12 of 12)	27898	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding	0.010000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5211	chr3	135927472	135927672	+	1.41384	NA	Intergenic	Intergenic	-87303	NR_040540	71038	Mm.410798	NR_040540	ENSMUSG00000106306	4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	ncRNA	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5235	chr3	140862039	140862239	+	1.41384	NA	Intergenic	MTD|LTR|ERVL-MaLR	350216	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7781	chr9	84099453	84099653	+	1.41384	NA	intron (NM_199195, intron 9 of 10)	intron (NM_199195, intron 9 of 10)	150772	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding	0.005000	0.313433			-71(TTTTTGTTTTGTTGAT,+,0.00),-16(GCTTTATAATGTTAAT,+,0.00),30(CAGTGGTCATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6660	chr6	109012720	109012920	+	1.41384	NA	Intergenic	Intergenic	184179	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5129	chr3	114067758	114067958	+	1.41384	NA	intron (NM_007729, intron 4 of 66)	intron (NM_007729, intron 4 of 66)	37318	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding	0.005000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1993	chr13	27229798	27229998	+	1.41384	NA	Intergenic	Intergenic	-12532	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4026	chr19	17056041	17056241	+	1.41384	NA	intron (NM_181348, intron 6 of 19)	intron (NM_181348, intron 6 of 19)	100023	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding	0.010000	0.492537			-19(ATTTGCATTACTGAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4923	chr3	42496497	42496697	+	1.41384	NA	Intergenic	Intergenic	753979	NM_001099785	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4131	chr19	58041974	58042174	+	1.41384	NA	intron (NM_181415, intron 27 of 28)	intron (NM_181415, intron 27 of 28)	-9093	NR_049196	100885835		NR_049196	ENSMUSG00000093757	Mir5623	Gm26068|mir-5623|mmu-mir-5623	microRNA 5623	ncRNA	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-943	chr10	93129434	93129634	+	1.41384	NA	Intergenic	Intergenic	-31342	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2494	chr14	57753569	57753769	+	1.41384	NA	Intergenic	Intergenic	-7546	NM_015771	50523	Mm.347899	NM_015771	ENSMUSG00000021959	Lats2	4932411G09Rik|AV277261|AW228608	large tumor suppressor 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7486	chr8	125649430	125649630	+	1.41384	NA	Intergenic	Intergenic	-20288	NM_028908	74393	Mm.41709	NM_028908	ENSMUSG00000050930	Map10	4933403G14Rik|AI835009|mKIAA1383	microtubule-associated protein 10	protein-coding	0.005000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3532	chr17	54607880	54608080	+	1.41384	NA	Intergenic	L1Md_T|LINE|L1	-237906	NR_045825	69418	Mm.391004	NR_045825	ENSMUSG00000099747	1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	ncRNA	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2715	chr14	117772391	117772591	+	1.41384	NA	intron (NM_001079844, intron 4 of 9)	intron (NM_001079844, intron 4 of 9)	181356	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4555	chr2	119146992	119147192	+	1.41384	NA	intron (NM_001033136, intron 5 of 12)	intron (NM_001033136, intron 5 of 12)	9942	NM_001033136	67809	Mm.475909	NM_001033136	ENSMUSG00000070730	Rmdn3	1200015F23Rik|AI131757|Fam82a2|Ptpip51|RMD-3|Rmd3	regulator of microtubule dynamics 3	protein-coding	0.020000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5596	chr4	89840004	89840204	+	1.41384	NA	Intergenic	L1_Mus2|LINE|L1	151906	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4563	chr2	120960385	120960585	+	1.41236	NA	intron (NM_009461, intron 3 of 46)	intron (NM_009461, intron 3 of 46)	10230	NM_009461	22222	Mm.389330	NM_009461	ENSMUSG00000027272	Ubr1	AI504731	ubiquitin protein ligase E3 component n-recognin 1	protein-coding	0.000000	0.338308			17(TCTTTGTTATTCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2140	chr13	73020418	73020618	+	1.41236	NA	Intergenic	Intergenic	-203755	NR_046196	78446	Mm.244082	NR_046196	ENSMUSG00000113082	D730050B12Rik	-	RIKEN cDNA D730050B12 gene	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4064	chr19	29754276	29754476	+	1.41236	NA	exon (NM_172836, exon 3 of 8)	exon (NM_172836, exon 3 of 8)	51633	NM_172836	240613	Mm.313351	NM_172836	ENSMUSG00000046138	9930021J03Rik	Gm9832|mKIAA2026	RIKEN cDNA 9930021J03 gene	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7512	chr9	8911775	8911975	+	1.41236	NA	intron (NM_008829, intron 2 of 7)	Charlie7|DNA|hAT-Charlie	12042	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2790	chr15	11009893	11010093	+	1.41236	NA	intron (NM_053077, intron 2 of 6)	intron (NM_053077, intron 2 of 6)	9272	NM_053077	22293	Mm.138278	NM_053077	ENSMUSG00000022243	Slc45a2	Aim-1|Aim1|Dbr|Matp|Oca4|blanc-sale|bls|uw	solute carrier family 45, member 2	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7265	chr8	57362037	57362237	+	1.41236	NA	Intergenic	Intergenic	29702	NR_131041	75996	Mm.399754	NR_131041	ENSMUSG00000097910	5033428I22Rik	-	RIKEN cDNA 5033428I22 gene	ncRNA	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1965	chr13	16645885	16646085	+	1.41236	NA	Intergenic	Intergenic	-622562	NR_155430	100503142	Mm.359204	NR_155430		B230303A05Rik	B230303A05|EG328191	U1 small nuclear ribonucleoprotein 1C pseudogene	pseudo	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4030	chr19	17715462	17715662	+	1.41236	NA	intron (NM_001190483, intron 3 of 37)	intron (NM_001190483, intron 3 of 37)	122070	NM_001163144	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2745	chr14	122721077	122721277	+	1.41236	NA	intron (NM_144844, intron 18 of 23)	intron (NM_144844, intron 18 of 23)	186849	NM_144844	110821	Mm.23876	NM_144844	ENSMUSG00000041650	Pcca	C79630	propionyl-Coenzyme A carboxylase, alpha polypeptide	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7702	chr9	67390317	67390517	+	1.41236	NA	intron (NM_001081242, intron 6 of 57)	RLTR21|LTR|ERVK	-153691	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5003	chr3	69430864	69431064	+	1.41236	NA	intron (NM_178726, intron 1 of 3)	intron (NM_178726, intron 1 of 3)	114046	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6611	chr6	98952462	98952662	+	1.41236	NA	intron (NM_001197321, intron 11 of 17)	intron (NM_001197321, intron 11 of 17)	75736	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6102	chr5	97856943	97857143	+	1.41236	NA	Intergenic	Intergenic	173974	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6548	chr6	81223668	81223868	+	1.41197	NA	Intergenic	Intergenic	671895	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2178	chr13	83884978	83885178	+	1.41197	NA	Intergenic	Intergenic	-6130	NR_036594	72677	Mm.245636	NR_036594	ENSMUSG00000100891	2810049E08Rik	-	RIKEN cDNA 2810049E08 gene	ncRNA	0.010000	0.422886			82(CAAATGTGATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7118	chr7	138848350	138848550	+	1.41113	NA	intron (NM_026391, intron 2 of 8)	intron (NM_026391, intron 2 of 8)	2064	NM_026391	52432	Mm.258739	NM_026391	ENSMUSG00000041769	Ppp2r2d	1300017E19Rik|D7Ertd753e|MDS026	protein phosphatase 2, regulatory subunit B, delta	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4677	chr2	140330593	140330793	+	1.41049	NA	intron (NM_001033296, intron 2 of 19)	intron (NM_001033296, intron 2 of 19)	59017	NM_001033296	228684	Mm.486585	NM_001033296	ENSMUSG00000074764	Sel1l2	Gm118	sel-1 suppressor of lin-12-like 2 (C. elegans)	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5919	chr5	42881329	42881529	+	1.41049	NA	Intergenic	RMER13A|LTR|ERVK	-351824	NM_001368805	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6122	chr5	103220624	103220824	+	1.41049	NA	Intergenic	Intergenic	-9390	NM_001318102	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.000000	0.323383			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-405	chr17	66854425	66854625	+	1.41020	NA	intron (NM_008984, intron 14 of 30)	intron (NM_008984, intron 14 of 30)	140069	NR_151453	102639882	Mm.443262	NR_151453		1700016K05Rik	-	RIKEN cDNA 1700016K05 gene	ncRNA	0.010000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-639	chr4	98949405	98949605	+	1.41020	NA	intron (NM_001290636, intron 42 of 48)	intron (NM_001290636, intron 42 of 48)	25695	NM_001301414	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1568	chr12	25643073	25643273	+	1.40945	NA	Intergenic	B4|SINE|B4	513999	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2709	chr14	116916987	116917187	+	1.40945	NA	Intergenic	Intergenic	-8210	NM_001079844	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5065	chr3	93251503	93251703	+	1.40945	NA	Intergenic	L1ME3G|LINE|L1	54330	NM_001013804	229574	Mm.10755	NM_001013804		Flg2	EG229574	filaggrin family member 2	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3889	chr18	59406417	59406617	+	1.40945	NA	intron (NM_001081328, intron 2 of 2)	intron (NM_001081328, intron 2 of 2)	-173113	NR_105773	102465182		NR_105773	ENSMUSG00000098287	Mir6355	Gm27473|mmu-mir-6355	microRNA 6355	ncRNA	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2010	chr13	32022962	32023162	+	1.40945	NA	intron (NM_146041, intron 7 of 10)	intron (NM_146041, intron 7 of 10)	216416	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding	0.010000	0.248756			-61(ATTTGCATTACTAAAT,-,0.00),13(TATTTCTTATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3715	chr18	14671886	14672086	+	1.40945	NA	intron (NM_001161371, intron 2 of 8)	intron (NM_001161371, intron 2 of 8)	10928	NM_001161370	268996	Mm.31761	NM_009280	ENSMUSG00000037013	Ss18	D130059H17|Ssxt|Syt	SS18, nBAF chromatin remodeling complex subunit	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2926	chr15	53507410	53507610	+	1.40945	NA	intron (NM_177225, intron 4 of 4)	intron (NM_177225, intron 4 of 4)	106769	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5227	chr3	138112783	138112983	+	1.40945	NA	intron (NM_001163457, intron 10 of 19)	intron (NM_001163457, intron 10 of 19)	18770	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding	0.005000	0.303483			26(TTAATATTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-516	chr1	164780408	164780608	+	1.40945	NA	Intergenic	Intergenic	-16155	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding	0.000000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3151	chr16	31119134	31119334	+	1.40945	NA	intron (NM_030138, intron 11 of 22)	intron (NM_030138, intron 11 of 22)	-37802	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding	0.005000	0.343284			-71(TTTTTTTCTTTCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2575	chr14	78236208	78236408	+	1.40945	NA	Intergenic	Intergenic	-44830	NR_035499	100316715		NR_035499	ENSMUSG00000087932	Mir1971	mmu-mir-1971	microRNA 1971	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6830	chr7	40399484	40399684	+	1.40945	NA	Intergenic	Intergenic	-275153	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2632	chr14	93768983	93769183	+	1.40945	NA	intron (NM_001081377, intron 2 of 4)	intron (NM_001081377, intron 2 of 4)	121586	NM_001081377	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding	0.020000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1240	chr11	36553429	36553629	+	1.40945	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	390712	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding	0.015000	0.427861			-53(ATTTAAAAGACAACAC,-,0.00),41(TAATTGTTATGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7260	chr8	56286761	56286961	+	1.40945	NA	Intergenic	Intergenic	-7691	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5586	chr4	87234669	87234869	+	1.40945	NA	Intergenic	Intergenic	-4229	NM_172426	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding	0.015000	0.417910		-85(CATGCATAGGCAGG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2796	chr15	12677006	12677206	+	1.40945	NA	intron (NM_001081064, intron 2 of 25)	intron (NM_001081064, intron 2 of 25)	62786	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3	PDZ domain containing 2	protein-coding	0.035000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4781	chr2	166818588	166818788	+	1.40945	NA	intron (NM_001085495, intron 1 of 38)	intron (NM_001085495, intron 1 of 38)	13107	NM_001085495	99371	Mm.297192	NM_001085495	ENSMUSG00000074582	Arfgef2	AI463430|AW493672|BIG2|E230011G24Rik	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	protein-coding	0.015000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3074	chr16	9219877	9220077	+	1.40945	NA	Intergenic	Intergenic	389877	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2272	chr13	106838944	106839144	+	1.40945	NA	intron (NM_029665, intron 27 of 29)	intron (NM_029665, intron 27 of 29)	97914	NM_001360897	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7096	chr7	132765014	132765214	+	1.40945	NA	intron (NM_175268, intron 3 of 4)	intron (NM_175268, intron 3 of 4)	11802	NM_001347630	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-407	chr1	138507840	138508040	+	1.40945	NA	intron (NM_021605, intron 7 of 9)	intron (NM_021605, intron 7 of 9)	111817	NM_001311148	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding	0.020000	0.472637			4(CTTTGAAAGATAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1785	chr12	83864639	83864839	+	1.40945	NA	intron (NR_073563, intron 2 of 10)	ORR1C2|LTR|ERVL-MaLR	12073	NM_001272056	18222	Mm.4390	NM_010949	ENSMUSG00000021224	Numb	Nb	NUMB endocytic adaptor protein	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-914	chr10	86207063	86207263	+	1.40945	NA	intron (NM_013722, intron 6 of 13)	intron (NM_013722, intron 6 of 13)	-93249	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-637	chr1	190586241	190586441	+	1.40917	NA	Intergenic	Intergenic	182693	NR_151624	433390	Mm.331295	NR_151624	ENSMUSG00000103644	Gm29678	-	predicted gene, 29678	ncRNA	0.020000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6767	chr6	146298336	146298536	+	1.40908	NA	intron (NM_019923, intron 34 of 56)	HAL1ME|LINE|L1	203787	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding	0.015000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-752	chr6	72183086	72183286	+	1.40889	NA	Intergenic	MamRep1151|LTR?|LTR?	52391	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6224	chr5	138919438	138919638	+	1.40689	NA	Intergenic	Intergenic	74743	NR_156469	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	PDGF-1	platelet derived growth factor, alpha	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3336	chr16	79105744	79105944	+	1.40689	NA	Intergenic	Intergenic	-14747	NM_178855	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	transmembrane protease, serine 15	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4787	chr2	169033200	169033400	+	1.40689	NA	Intergenic	Intergenic	55031	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1604	chr12	36612408	36612608	+	1.40689	NA	intron (NM_178629, intron 9 of 9)	intron (NM_178629, intron 9 of 9)	196892	NR_037309	100499526		NR_037309	ENSMUSG00000092917	Mir3472	mmu-mir-3472	microRNA 3472	ncRNA	0.000000	0.338308	-75(GATGCAATATTCATT,+,0.00),-75(GATGCAATATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4335	chr2	59653770	59653970	+	1.40417	NA	intron (NM_198294, intron 2 of 26)	intron (NM_198294, intron 2 of 26)	7101	NM_001290659	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3341	chr16	79878846	79879046	+	1.40417	NA	Intergenic	Intergenic	-120430	NM_030146	78654		NM_030146		1700066C05Rik	-	RIKEN cDNA 1700066C05 gene	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4230	chr2	28222903	28223103	+	1.40417	NA	intron (NM_001038613, intron 5 of 5)	intron (NM_001038613, intron 5 of 5)	17314	NM_001038612	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding	0.025000	0.517413			2(CCTTTCTTGTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-221	chr1	81104062	81104262	+	1.40417	NA	intron (NM_001356399, intron 3 of 6)	intron (NM_001356399, intron 3 of 6)	26755	NM_001356397	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1852	chr12	101066446	101066646	+	1.40417	NA	intron (NM_211355, intron 2 of 14)	intron (NM_211355, intron 2 of 14)	-15905	NR_038047	319760	Mm.440198	NM_176997	ENSMUSG00000097121	D130020L05Rik	9430007L23Rik	RIKEN cDNA D130020L05 gene	ncRNA	0.005000	0.417910			-12(ATTTGCATTGTAAACA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-14	chr1	38530648	38530848	+	1.40417	NA	intron (NM_001290814, intron 4 of 21)	intron (NM_001290814, intron 4 of 21)	96496	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7449	chr8	111574274	111574474	+	1.40417	NA	intron (NM_001363489, intron 1 of 4)	intron (NM_001363489, intron 1 of 4)	36031	NM_001363489	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3808	chr18	40127973	40128173	+	1.40417	NA	Intergenic	Intergenic	91326	NM_023311	67180	Mm.270382	NM_023311	ENSMUSG00000024487	Yipf5	2610311I19Rik|AA408236|Yip1a	Yip1 domain family, member 5	protein-coding	0.010000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-437	chr18	40127937	40128137	+	1.40417	NA	Intergenic	Intergenic	91362	NM_023311	67180	Mm.270382	NM_023311	ENSMUSG00000024487	Yipf5	2610311I19Rik|AA408236|Yip1a	Yip1 domain family, member 5	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-238	chr1	84365414	84365614	+	1.40417	NA	Intergenic	Intergenic	-80869	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4|P-CLI1	phosphotyrosine interaction domain containing 1	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1253	chr11	40500085	40500285	+	1.40328	NA	Intergenic	Intergenic	192497	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-179	chr1	61530606	61530806	+	1.40328	NA	Intergenic	Intergenic	-108118	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1867	chr12	103645658	103645858	+	1.40328	NA	TTS (NM_007618)	TTS (NM_007618)	11460	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding	0.000000	0.263682			-29(ATTTATAAAAGAATGC,-,0.00),68(TCTTTGGCTTGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3637	chr17	84720757	84720957	+	1.40328	NA	intron (NM_028233, intron 30 of 37)	BGLII|LTR|ERVK	37736	NM_001347418	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP binding cassette subfamily G member 8	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1373	chr11	80413373	80413573	+	1.40328	NA	Intergenic	Intergenic	-15142	NM_178616	69077	Mm.260539	NM_178616	ENSMUSG00000017428	Psmd11	1700089D09Rik|1810019E17Rik|2610024G20Rik|2810055C24Rik|C78232|P44.5|S9	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-521	chr1	166151966	166152166	+	1.40328	NA	intron (NM_021610, intron 2 of 6)	intron (NM_021610, intron 2 of 6)	21845	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197|mA33	glycoprotein A33 (transmembrane)	protein-coding	0.015000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5372	chr4	20551192	20551392	+	1.40328	NA	intron (NM_172987, intron 1 of 4)	L1MA5|LINE|L1	227376	NM_001290410	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0.005000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5843	chr5	17707281	17707481	+	1.40328	NA	intron (NM_013657, intron 12 of 17)	L3|LINE|CR1	128515	NM_007643	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 molecule	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-414	chr1	140192159	140192359	+	1.40328	NA	Intergenic	Intergenic	-8848	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4400	chr2	75614419	75614619	+	1.40328	NA	Intergenic	Lx5|LINE|L1	-44740	NM_001359971	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5173	chr3	127248507	127248707	+	1.40328	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	87302	NR_105030	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-413	chr1	140192017	140192217	+	1.40328	NA	Intergenic	Intergenic	-8706	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-773	chr10	36649727	36649927	+	1.40265	NA	intron (NM_001081208, intron 2 of 3)	intron (NM_001081208, intron 2 of 3)	143020	NM_001081208	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0.005000	0.288557			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-848	chr8	100295624	100295824	+	1.40265	NA	Intergenic	Intergenic	879050	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.348259			-18(TTTTGAAAGAAAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2836	chr15	28041511	28041711	+	1.40265	NA	Intergenic	LTR88b|LTR|Gypsy?	-15763	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding	0.010000	0.457711			-93(CTTTAAATAACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1227	chr11	30224802	30225002	+	1.40265	NA	Intergenic	Intergenic	-5130	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding	0.000000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-201	chr12	87010367	87010567	+	1.40265	NA	Intergenic	Intergenic	-10873	NR_155207	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding	0.005000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3670	chr17	91582503	91582703	+	1.40265	NA	Intergenic	Intergenic	-489801	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6737	chr6	137541235	137541435	+	1.40265	NA	intron (NM_001271588, intron 1 of 20)	intron (NM_001271588, intron 1 of 20)	-21440	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0.010000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-88	chr10	36520743	36520943	+	1.40265	NA	intron (NM_001081208, intron 1 of 3)	intron (NM_001081208, intron 1 of 3)	14036	NM_001081208	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0.000000	0.363184			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-713	chr5	137796492	137796692	+	1.40265	NA	exon (NM_001360023, exon 3 of 17)	exon (NM_001360023, exon 3 of 17)	8790	NM_001005426	381678	Mm.332765	NM_001005426	ENSMUSG00000037108	Zcwpw1	Gm1053	zinc finger, CW type with PWWP domain 1	protein-coding	0.020000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-138	chr11	30224809	30225009	+	1.40265	NA	Intergenic	Intergenic	-5137	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4426	chr2	80517818	80518018	+	1.40212	NA	exon (NM_001290745, exon 25 of 32)	exon (NM_001290745, exon 25 of 32)	63264	NM_016965	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding	0.000000	0.343284			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-516	chr2	114239668	114239868	+	1.40212	NA	Intergenic	Intergenic	-38336	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding	0.005000	0.338308			-24(ATCTGAAAGAAAATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3880	chr18	57544076	57544276	+	1.40212	NA	intron (NM_001311063, intron 2 of 5)	intron (NM_001311063, intron 2 of 5)	7691	NR_027945	75084	Mm.243841	NR_015494	ENSMUSG00000086607	4930511M06Rik	-	RIKEN cDNA 4930511M06 gene	ncRNA	0.005000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-499	chr2	80517776	80517976	+	1.40212	NA	intron (NM_001355410, intron 25 of 31)	intron (NM_001355410, intron 25 of 31)	63306	NM_016965	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding	0.000000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-856	chr9	9645787	9645987	+	1.40108	NA	Intergenic	Intergenic	-248544	NR_105745	102466147		NR_105745	ENSMUSG00000098408	Mir6237	Gm27411|mmu-mir-6237	microRNA 6237	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2578	chr14	78747511	78747711	+	1.40061	NA	Intergenic	Intergenic	-14882	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding	0.005000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-399	chr17	51736293	51736493	+	1.39886	NA	3' UTR (NM_001163632, exon 11 of 11)	3' UTR (NM_001163632, exon 11 of 11)	75661	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4082	chr19	36199712	36199912	+	1.39886	NA	Intergenic	L1ME1|LINE|L1	-79968	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding	0.010000	0.258706			-20(TTTTGCATAACTATAT,-,0.00),49(ATTCTATCATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3140	chr16	28880519	28880719	+	1.39823	NA	intron (NM_177718, intron 1 of 1)	intron (NM_177718, intron 1 of 1)	49079	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding	0.030000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6525	chr6	72183096	72183296	+	1.39720	NA	Intergenic	MamRep1151|LTR?|LTR?	52381	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-232	chr1	83855658	83855858	+	1.39686	NA	Intergenic	Intergenic	363203	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-636	chr1	190138711	190138911	+	1.39686	NA	intron (NM_008937, intron 4 of 4)	intron (NM_008937, intron 4 of 4)	30704	NM_001360827	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik|PROX-1	prospero homeobox 1	protein-coding	0.020000	0.437811	73(CATGAAATATTCATA,+,0.00),73(CATGAAATATTCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2469	chr14	46416720	46416920	+	1.39686	NA	Intergenic	Intergenic	-26151	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding	0.000000	0.333333			-62(ATTTCCAAAGAAAAGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-488	chr2	65441754	65441954	+	1.39686	NA	Intergenic	Intergenic	-77454	NR_105755	102466151		NR_105755	ENSMUSG00000099184	Mir6337	Gm27877|mmu-mir-6337	microRNA 6337	ncRNA	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-301	chr1	105908448	105908648	+	1.39686	NA	Intergenic	Intergenic	81734	NR_151625	635504	Mm.359717	NR_151625		Gm7160	EG635504	predicted gene 7160	ncRNA	0.010000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4537	chr2	115500624	115500824	+	1.39686	NA	intron (NR_030712, intron 1 of 2)	L1Md_F2|LINE|L1	11477	NR_030712	100043232	Mm.240112	NR_030712	ENSMUSG00000085582	3110099E03Rik	-	RIKEN cDNA 3110099E03 gene	ncRNA	0.025000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5736	chr4	126266699	126266899	+	1.39686	NA	intron (NM_013718, intron 1 of 4)	intron (NM_013718, intron 1 of 4)	4394	NM_013718	27096	Mm.8392	NM_013718	ENSMUSG00000028847	Trappc3	1110058K12Rik|AI835942|AU019197|Bet3	trafficking protein particle complex 3	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2847	chr15	30401396	30401596	+	1.39686	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	228962	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3814	chr18	42549691	42549891	+	1.39686	NA	intron (NM_001360881, intron 9 of 20)	intron (NM_001360881, intron 9 of 20)	29861	NM_181543	240239	Mm.186779	NM_181543	ENSMUSG00000042816	Gpr151	C130082O03Rik|GalRL|PGR7|nGPCR-2037	G protein-coupled receptor 151	protein-coding	0.025000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-58	chr1	21702661	21702861	+	1.39686	NA	intron (NM_001160139, intron 1 of 14)	intron (NM_001160139, intron 1 of 14)	259181	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.010000	0.303483			13(TTTTAAATGATAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5236	chr3	141097784	141097984	+	1.39686	NA	Intergenic	Intergenic	114471	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7125	chr7	142595304	142595504	+	1.39686	NA	Intergenic	Intergenic	-17258	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191|EyeLinc6	H19, imprinted maternally expressed transcript	ncRNA	0.005000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6917	chr7	78099691	78099891	+	1.39686	NA	Intergenic	Intergenic	478047	NM_182809	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2761	chr15	6300621	6300821	+	1.39673	NA	intron (NM_001008702, intron 1 of 13)	intron (NM_001008702, intron 1 of 13)	932	NM_001008702	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1477	chr11	112783393	112783593	+	1.39673	NA	intron (NM_011448, intron 1 of 2)	intron (NM_011448, intron 1 of 2)	1283	NM_011448	20682	Mm.286407	NM_011448	ENSMUSG00000000567	Sox9	2010306G03Rik|AV220920|mKIAA4243	SRY (sex determining region Y)-box 9	protein-coding	0.035000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6283	chr6	4681522	4681722	+	1.39673	NA	intron (NM_001130188, intron 10 of 11)	intron (NM_001130188, intron 10 of 11)	65582	NM_011360	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7993	chrX	77427559	77427759	+	1.39673	NA	Intergenic	Intergenic	-83568	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding	0.010000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-351	chr15	90598116	90598316	+	1.39673	NA	intron (NM_001357979, intron 5 of 18)	intron (NM_001357979, intron 5 of 18)	81172	NM_001033851	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5392	chr4	25799590	25799790	+	1.39627	NA	5' UTR (NM_010243, exon 1 of 3)	5' UTR (NM_010243, exon 1 of 3)	313	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.120000	0.731343			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4451	chr2	91971913	91972113	+	1.39510	NA	Intergenic	Intergenic	-8450	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding	0.030000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5664	chr4	104308083	104308283	+	1.39510	NA	intron (NM_001369049, intron 4 of 19)	intron (NM_001369049, intron 4 of 19)	-59355	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.010000	0.348259			-76(TTATTCTCATGTAATT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-396	chr17	49761266	49761466	+	1.39464	NA	intron (NM_177052, intron 13 of 22)	intron (NM_177052, intron 13 of 22)	146194	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6419	chr6	43421824	43422024	+	1.39464	NA	intron (NM_001311111, intron 7 of 7)	intron (NM_001311111, intron 7 of 7)	-20505	NR_045988	319812	Mm.446393	NR_045988		9430018G01Rik	-	RIKEN cDNA 9430018G01 gene	ncRNA	0.000000	0.308458	-70(CATGCATTTTTCATT,+,0.00),-70(CATGCATTTTTCATT,-,0.00)		-98(CTCTGCATTACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1794	chr12	87010258	87010458	+	1.39464	NA	Intergenic	Intergenic	-10982	NR_155207	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding	0.005000	0.248756			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-739	chr6	43421835	43422035	+	1.39464	NA	intron (NM_001311111, intron 7 of 7)	intron (NM_001311111, intron 7 of 7)	-20494	NR_045988	319812	Mm.446393	NR_045988		9430018G01Rik	-	RIKEN cDNA 9430018G01 gene	ncRNA	0.000000	0.323383	-81(CATGCATTTTTCATT,+,0.00),-81(CATGCATTTTTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4022	chr19	16411363	16411563	+	1.39464	NA	Intergenic	MER58D|DNA|hAT-Charlie	-24204	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1035	chr10	111777671	111777871	+	1.39457	NA	Intergenic	Intergenic	96605	NR_046029	629206	Mm.391444	NR_046029	ENSMUSG00000112533	Gm20758	-	predicted gene, 20758	ncRNA	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1168	chr11	15390248	15390448	+	1.39457	NA	Intergenic	Intergenic	791108	NM_001164166	432536	Mm.33646	NM_001164166	ENSMUSG00000084135	Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding	0.000000	0.253731			-75(ATATACAATAAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3181	chr16	39551223	39551423	+	1.39457	NA	Intergenic	B3|SINE|B2	-362373	NR_153800	102640746		NR_153800	ENSMUSG00000116965	Gm36742	-	predicted gene, 36742	ncRNA	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1176	chr11	17940882	17941082	+	1.39457	NA	intron (NM_026576, intron 5 of 5)	intron (NM_026576, intron 5 of 5)	12893	NM_001362970	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing tumor-associated antigen 1	protein-coding	0.015000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2056	chr13	44924214	44924414	+	1.39457	NA	intron (NM_025772, intron 8 of 9)	intron (NM_025772, intron 8 of 9)	77782	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1885	chr12	109859438	109859638	+	1.39457	NA	Intergenic	L1M4b|LINE|L1	111660	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1306	chr11	60554686	60554886	+	1.39457	NA	3' UTR (NM_172943, exon 4 of 4)	3' UTR (NM_172943, exon 4 of 4)	17103	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4065	chr19	30642955	30643155	+	1.39457	NA	intron (NM_001013833, intron 9 of 17)	intron (NM_001013833, intron 9 of 17)	-93559	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1488	chr11	115506118	115506318	+	1.39457	NA	intron (NM_008258, intron 1 of 4)	B1_Mur3|SINE|Alu	8175	NM_008258	15374	Mm.1775	NM_008258	ENSMUSG00000020737	Jpt1	Hn1	Jupiter microtubule associated homolog 1	protein-coding	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1261	chr11	42611033	42611233	+	1.39457	NA	intron (NM_001347314, intron 9 of 9)	URR1B|DNA|hAT-Charlie	189932	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding	0.005000	0.383085			-42(CTATGAATAATAATGC,-,0.00),-38(GAATAATAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5004	chr3	70018229	70018429	+	1.39457	NA	intron (NM_001018031, intron 1 of 4)	intron (NM_001018031, intron 1 of 4)	10716	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-948	chr10	93370412	93370612	+	1.39457	NA	Intergenic	Intergenic	34301	NR_038014	432488	Mm.32833	NR_038014		Gm17745	Gm3546	predicted gene, 17745	ncRNA	0.025000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5084	chr3	100611480	100611680	+	1.39457	NA	intron (NM_010763, intron 8 of 12)	intron (NM_010763, intron 8 of 12)	73893	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-28	chr1	9615205	9615405	+	1.39457	NA	intron (NM_178399, intron 3 of 5)	intron (NM_178399, intron 3 of 5)	14038	NM_178399	76982	Mm.491098	NM_178399	ENSMUSG00000067879	Vxn	3110035E14Rik|AI415019|AV164974|R75066	vexin	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-415	chr1	140257199	140257399	+	1.39457	NA	intron (NM_001081027, intron 1 of 27)	intron (NM_001081027, intron 1 of 27)	11581	NM_001081027	240776	Mm.483845	NM_001081027	ENSMUSG00000052726	Kcnt2	E330038N15Rik|Slick	potassium channel, subfamily T, member 2	protein-coding	0.010000	0.308458			-96(TTATTATAATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6187	chr5	129430434	129430634	+	1.39457	NA	Intergenic	Intergenic	-70697	NM_172276	231769	Mm.288714	NM_172276	ENSMUSG00000029439	Sfswap	1190005N23Rik|6330437E22Rik|AI197402|AW212079|SWAP|Sfrs8|Srsf8	splicing factor SWAP	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4139	chr19	59625438	59625638	+	1.39457	NA	Intergenic	Intergenic	132402	NR_045308	72647	Mm.410849	NR_045308	ENSMUSG00000100119	2700089I24Rik	-	RIKEN cDNA 2700089I24 gene	ncRNA	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4337	chr2	60327335	60327535	+	1.39457	NA	intron (NM_013825, intron 23 of 34)	intron (NM_013825, intron 23 of 34)	-42951	NM_001290660	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding	0.000000	0.328358			39(TTATTGTTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7027	chr7	112563814	112564014	+	1.39457	NA	intron (NM_020606, intron 5 of 12)	L1_Rod|LINE|L1	-28231	NR_154467	102636183	Mm.446701	NR_154466		Parvaos	A230071N21Rik	parvin, alpha, opposite strand	ncRNA	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4009	chr19	12767477	12767677	+	1.39457	NA	3' UTR (NM_053009, exon 11 of 11)	3' UTR (NM_053009, exon 11 of 11)	-1945	NM_170786	12803	Mm.290924	NM_053007	ENSMUSG00000079415	Cntf	AI429687	ciliary neurotrophic factor	protein-coding	0.005000	0.338308			-21(ATTTTCAAAACTAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-454	chr1	151821526	151821726	+	1.39457	NA	3' UTR (NM_001311165, exon 21 of 21)	3' UTR (NM_001311165, exon 21 of 21)	66252	NM_001311166	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding	0.010000	0.383085			-53(CTTTTCTTATACAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1409	chr11	91121280	91121480	+	1.39457	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	316689	NR_045956	73922	Mm.233289	NR_045956	ENSMUSG00000085940	4930405D11Rik	-	RIKEN cDNA 4930405D11 gene	ncRNA	0.020000	0.378109			17(TTTTTTTTTTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-342	chr1	123946261	123946461	+	1.39457	NA	intron (NM_199021, intron 1 of 25)	intron (NM_199021, intron 1 of 25)	99198	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.005000	0.417910	-52(AATGAATAATTCATG,+,0.00),-52(AATGAATAATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6586	chr6	92229115	92229315	+	1.39457	NA	Intergenic	Intergenic	-14345	NM_030081	78287	Mm.290734	NM_030081	ENSMUSG00000014550	Rbsn	5330426D11Rik|Zfyve20	rabenosyn, RAB effector	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3977	chr18	84747011	84747211	+	1.39457	NA	intron (NR_155706, intron 2 of 2)	intron (NR_155706, intron 2 of 2)	3044	NR_155706	102641800		NR_155706		Gm38576	-	predicted gene, 38576	ncRNA	0.010000	0.447761			42(ATTAGAATATCAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6341	chr6	19857701	19857901	+	1.39457	NA	Intergenic	Intergenic	302459	NR_105789	102465192		NR_105789	ENSMUSG00000099149	Mir6370	Gm27480|mmu-mir-6370	microRNA 6370	ncRNA	0.005000	0.323383			-91(ATATACAAAAGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4106	chr19	48813945	48814145	+	1.39457	NA	Intergenic	Intergenic	608020	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5283	chr3	149553077	149553277	+	1.39457	NA	Intergenic	Intergenic	278440	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7693	chr9	65100980	65101180	+	1.39457	NA	promoter-TSS (NM_001290315)	promoter-TSS (NM_001290315)	-406	NM_001290315	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	DDM36|Nope	immunoglobulin superfamily, DCC subclass, member 4	protein-coding	0.010000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4319	chr2	56011242	56011442	+	1.39457	NA	Intergenic	Intergenic	575372	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding	0.000000	0.412935			-53(ATTTACAATGGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-175	chr1	61139465	61139665	+	1.39457	NA	Intergenic	Intergenic	161651	NM_017480	54167	Mm.42044	NM_017480	ENSMUSG00000026009	Icos	AILIM|CCLP|CRP-1|H4|Ly115	inducible T cell co-stimulator	protein-coding	0.025000	0.477612			-56(GATTTGTTTTTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1342	chr11	72014769	72014969	+	1.39457	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	22640	NM_053245	114230	Mm.95707	NM_053245	ENSMUSG00000040554	Aipl1	A930007I01Rik	aryl hydrocarbon receptor-interacting protein-like 1	protein-coding	0.015000	0.417910		0(GATCCATAGGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1988	chr13	24720010	24720210	+	1.39457	NA	intron (NM_029679, intron 19 of 22)	intron (NM_029679, intron 19 of 22)	-21111	NM_001370932	666145	Mm.390564	NM_001370932	ENSMUSG00000085861	Armh2	1700016G14Rik	armadillo-like helical domain containing 2	protein-coding	0.005000	0.363184			20(TTTTACATTACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3609	chr17	79932758	79932958	+	1.39457	NA	Intergenic	Intergenic	-36735	NM_019717	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8165	chrX	167319028	167319228	+	1.39457	NA	intron (NM_001290758, intron 2 of 3)	intron (NM_001290758, intron 2 of 3)	11443	NM_001290756	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3128	chr16	26567748	26567948	+	1.39457	NA	Intergenic	Intergenic	-13857	NM_001159317	16180	Mm.253424	NM_008364	ENSMUSG00000022514	Il1rap	6430709H04Rik|AI255955|AV239853|IL-1RAcP	interleukin 1 receptor accessory protein	protein-coding	0.010000	0.333333			30(TCATTATCATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4627	chr2	133245508	133245708	+	1.39457	NA	Intergenic	MTC|LTR|ERVL-MaLR	-299572	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4646	chr2	135634199	135634399	+	1.39457	NA	Intergenic	Intergenic	-25248	NM_001355153	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1121	chr10	125214444	125214644	+	1.39418	NA	Intergenic	MLTR25A|LTR|ERVK	94272	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5487	chr4	57167540	57167740	+	1.39243	NA	Intergenic	Intergenic	-4431	NR_040669	329851	Mm.392470	NR_040669	ENSMUSG00000085967	Gm12530	D730003B17	predicted gene 12530	ncRNA	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4671	chr2	139932964	139933164	+	1.39243	NA	intron (NR_110351, intron 10 of 13)	intron (NR_110351, intron 10 of 13)	133741	NM_001289611	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5143	chr3	117988679	117988879	+	1.39243	NA	Intergenic	Intergenic	-119843	NM_001190156	76561	Mm.33824	NM_029655	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1004	chr10	107094777	107094977	+	1.39243	NA	intron (NM_198636, intron 1 of 10)	intron (NM_198636, intron 1 of 10)	28760	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding	0.005000	0.437811			-92(CTTTGAAGGACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1547	chr12	13497928	13498128	+	1.39243	NA	intron (NM_027706, intron 44 of 51)	intron (NM_027706, intron 44 of 51)	129618	NR_136761	102639399	Mm.122052	NR_136761	ENSMUSG00000113666	Gm35725	-	predicted gene, 35725	ncRNA	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3095	chr16	15478831	15479031	+	1.39243	NA	Intergenic	ORR1G|LTR|ERVL-MaLR	115587	NM_023585	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8140	chrX	161198245	161198445	+	1.39243	NA	intron (NM_001290651, intron 6 of 25)	intron (NM_001290651, intron 6 of 25)	35595	NM_001290651	107815	Mm.159173	NM_133194	ENSMUSG00000000037	Scml2	4932420G07Rik	Scm polycomb group protein like 2	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1558	chr12	16913440	16913640	+	1.39243	NA	intron (NM_009072, intron 1 of 32)	intron (NM_009072, intron 1 of 32)	18562	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding	0.000000	0.333333	43(AATGCTTTATTCATT,+,0.00),43(AATGCTTTATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5091	chr3	102525639	102525839	+	1.39243	NA	Intergenic	Intergenic	55820	NM_013609	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb|beta-NGF	nerve growth factor	protein-coding	0.005000	0.383085			-11(CTGTTGTCTTGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-535	chr1	169507754	169507954	+	1.39243	NA	intron (NM_001355159, intron 11 of 14)	intron (NM_001355159, intron 11 of 14)	23610	NM_001355159	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	NUF2, NDC80 kinetochore complex component	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7747	chr9	77924949	77925149	+	1.39243	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	7684	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding	0.005000	0.323383		-4(TTTGAATATTCAAG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-515	chr1	164396687	164396887	+	1.39243	NA	intron (NM_138314, intron 12 of 13)	intron (NM_138314, intron 12 of 13)	61568	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2062	chr13	46943510	46943710	+	1.39243	NA	Intergenic	Intergenic	-13892	NM_010617	16553	Mm.342703	NM_010617	ENSMUSG00000021375	Kif13a	4930505I07Rik|mKIAA4109	kinesin family member 13A	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-651	chr1	194194456	194194656	+	1.39243	NA	Intergenic	Intergenic	28203	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.000000	0.422886			-73(ATGTGCAAAACAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6033	chr5	74868201	74868401	+	1.39243	NA	Intergenic	Intergenic	-80893	NR_045866	619945	Mm.359372	NM_001037908	ENSMUSG00000072874	Gm6116	EG619945	predicted gene 6116	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6876	chr7	64321687	64321887	+	1.39243	NA	intron (NM_172742, intron 12 of 15)	intron (NM_172742, intron 12 of 15)	34117	NM_172742	233315	Mm.214959	NM_172742	ENSMUSG00000030522	Mtmr10	BB128963|C79734	myotubularin related protein 10	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2223	chr13	95829528	95829728	+	1.39243	NA	intron (NM_027711, intron 2 of 35)	intron (NM_027711, intron 2 of 35)	62294	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding	0.015000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5411	chr4	31873657	31873857	+	1.39243	NA	Intergenic	Intergenic	-90350	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3927	chr18	70559323	70559523	+	1.39243	NA	Intergenic	MIRb|SINE|MIR	-8869	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3694	chr18	7526148	7526348	+	1.39243	NA	intron (NM_001081287, intron 2 of 16)	intron (NM_001081287, intron 2 of 16)	81906	NM_001360860	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3494	chr17	44788970	44789170	+	1.39243	NA	intron (NR_158206, intron 2 of 11)	intron (NR_158206, intron 2 of 11)	11904	NM_178652	109115	Mm.431327	NM_178652	ENSMUSG00000038954	Supt3	2310066G22Rik|AI315192|SPT3|SPT3L|Supt3h	suppressor of Ty 3	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3061	chr15	100794652	100794852	+	1.39243	NA	intron (NM_021530, intron 11 of 24)	intron (NM_021530, intron 11 of 24)	13498	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding	0.020000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6839	chr7	47160490	47160690	+	1.39243	NA	Intergenic	Intergenic	-26906	NM_013643	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2856	chr15	33856465	33856665	+	1.39091	NA	Intergenic	Lx|LINE|L1	-168682	NM_001085421	239364	Mm.60794	NM_001085421	ENSMUSG00000038984	Tspyl5	6330530B20|E130308C19Rik	testis-specific protein, Y-encoded-like 5	protein-coding	0.000000	0.323383			-24(TTTAGAATAACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6321	chr6	15489322	15489522	+	1.39091	NA	Intergenic	Intergenic	-231239	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding	0.005000	0.388060			-58(CCATTCTCATGCTTAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1300	chr11	58110410	58110610	+	1.39091	NA	intron (NM_001363084, intron 3 of 7)	intron (NM_001363084, intron 3 of 7)	6201	NM_001363086	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding	0.010000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7257	chr8	53877724	53877924	+	1.39091	NA	Intergenic	Intergenic	-199708	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding	0.000000	0.253731		-92(TATAAATATTTATG,+,0.00),-92(TATAAATATTTATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8110	chrX	145089635	145089835	+	1.39091	NA	intron (NM_001033795, intron 2 of 6)	intron (NM_001033795, intron 2 of 6)	50391	NR_037309	100499526		NR_037309	ENSMUSG00000092917	Mir3472	mmu-mir-3472	microRNA 3472	ncRNA	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3608	chr17	79231576	79231776	+	1.39091	NA	Intergenic	Intergenic	123415	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5528	chr4	69824480	69824680	+	1.39091	NA	Intergenic	Intergenic	585855	NM_145990	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding	0.015000	0.383085	33(TTTAAATAATTCATC,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4853	chr3	13787105	13787305	+	1.39091	NA	intron (NM_001357034, intron 2 of 7)	intron (NM_001357034, intron 2 of 7)	-134340	NR_040598	75203	Mm.490940	NR_040598		4930539N22Rik	-	RIKEN cDNA 4930539N22 gene	ncRNA	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1749	chr12	76118109	76118309	+	1.39091	NA	Intergenic	Intergenic	59050	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7791	chr9	85524788	85524988	+	1.39091	NA	Intergenic	Intergenic	-197738	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Tent5a	BAP014|D930050G01Rik|Fam46a	terminal nucleotidyltransferase 5A	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5744	chr4	128222755	128222955	+	1.39091	NA	intron (NM_001281955, intron 5 of 70)	MTC|LTR|ERVL-MaLR	38040	NM_027036	69317	Mm.331893	NM_027036	ENSMUSG00000048686	Hmgb4	1700001F22Rik|AI326135	high-mobility group box 4	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1772	chr12	82305437	82305637	+	1.39091	NA	intron (NM_001167983, intron 3 of 23)	RLTR25B|LTR|ERVK	-5812	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding	0.000000	0.373134			-16(ATTTACATATCAATTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4413	chr2	77502121	77502321	+	1.39091	NA	intron (NR_156434, intron 2 of 7)	intron (NR_156434, intron 2 of 7)	17445	NR_156434	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding	0.000000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8097	chrX	139678631	139678831	+	1.39091	NA	Intergenic	BGLII|LTR|ERVK	-6265	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding	0.015000	0.442786			21(CCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3236	chr16	54927439	54927639	+	1.39091	NA	Intergenic	Intergenic	355698	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0.005000	0.278607		-88(ATTGAATATGCATT,+,0.00),-88(ATTGAATATGCATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4924	chr3	42532155	42532355	+	1.39091	NA	Intergenic	Intergenic	789637	NM_001099785	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6688	chr6	118535385	118535585	+	1.39091	NA	intron (NM_001081112, intron 15 of 33)	intron (NM_001081112, intron 15 of 33)	26786	NM_001081112	232339	Mm.276116	NM_001081112	ENSMUSG00000007827	Ankrd26	5730521P14Rik|BC008111|mKIAA1074	ankyrin repeat domain 26	protein-coding	0.040000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6565	chr6	84654495	84654695	+	1.39091	NA	intron (NM_177077, intron 20 of 21)	intron (NM_177077, intron 20 of 21)	-60687	NM_001177713	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding	0.005000	0.393035			-4(TCTTTCTCATTCTAAT,+,0.00),10(ATTTGTAAAACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-75	chr1	24236495	24236695	+	1.39091	NA	intron (NM_001290691, intron 27 of 31)	URR1A|DNA|hAT-Charlie	41392	NM_001290691	12839	Mm.154662	NM_007740	ENSMUSG00000026147	Col9a1	Col9a-1	collagen, type IX, alpha 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3740	chr18	22476315	22476515	+	1.39091	NA	intron (NM_001167777, intron 9 of 12)	intron (NM_001167777, intron 9 of 12)	131326	NM_001167777	211961	Mm.392310	NM_001167777	ENSMUSG00000045215	Asxl3	C230079D11Rik|D430002O22Rik|D930044O18Rik|Gm329|Gm945	additional sex combs like 3, transcriptional regulator	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4322	chr2	56694495	56694695	+	1.39091	NA	Intergenic	Lx7|LINE|L1	-91216	NR_105751	102465169		NR_105751	ENSMUSG00000098437	Mir195b	Gm27491|mmu-mir-195b	microRNA 195b	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3269	chr16	62413368	62413568	+	1.39091	NA	Intergenic	MLTR14|LTR|ERV1	373248	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-929	chr10	89196792	89196992	+	1.39091	NA	intron (NR_102339, intron 1 of 26)	intron (NR_102339, intron 1 of 26)	60898	NR_102339	320091	Mm.236464	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1202	chr11	25674273	25674473	+	1.39091	NA	intron (NR_027973, intron 2 of 5)	intron (NR_027973, intron 2 of 5)	348266	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	ncRNA	0.000000	0.407960			-44(ATTTAAAAGACAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-250	chr1	87103945	87104145	+	1.39091	NA	Intergenic	Intergenic	-2439	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding	0.005000	0.422886			59(TTTTAAATGAAAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7078	chr7	128966491	128966691	+	1.39091	NA	Intergenic	Intergenic	221721	NM_001029982	207352	Mm.297105	NM_001029982	ENSMUSG00000055319	Sec23ip	D7Ertd373e|p125	Sec23 interacting protein	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6045	chr5	79326962	79327162	+	1.39091	NA	Intergenic	Lx7|LINE|L1	-1693509	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5265	chr3	147927417	147927617	+	1.39091	NA	Intergenic	Intergenic	1027118	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.005000	0.437811			-38(ATTTGCATCACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8135	chrX	159027203	159027403	+	1.39091	NA	Intergenic	MER5A1|DNA|hAT-Charlie	-228479	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7317	chr8	75458840	75459040	+	1.39091	NA	intron (NM_027944, intron 1 of 12)	intron (NM_027944, intron 1 of 12)	10246	NM_001164235	71831	Mm.443238	NM_027944	ENSMUSG00000031620	Iqcm	1700007B14Rik	IQ motif containing M	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1723	chr12	71600323	71600523	+	1.39091	NA	Intergenic	Intergenic	59816	NR_045941	73815	Mm.416916	NR_045941	ENSMUSG00000113630	4930404H11Rik	-	RIKEN cDNA 4930404H11 gene	ncRNA	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1419	chr11	95566392	95566592	+	1.39091	NA	Intergenic	MER33|DNA|hAT-Charlie	21206	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3534	chr17	55187775	55187975	+	1.39091	NA	Intergenic	RMER13A|LTR|ERVK	-257507	NM_001347403	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	beta galactoside alpha 2,6 sialyltransferase 2	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4199	chr2	20283822	20284022	+	1.39091	NA	Intergenic	Intergenic	-5991	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.015000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4219	chr2	24512774	24512974	+	1.39091	NA	Intergenic	Intergenic	-37275	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding	0.010000	0.378109			-33(CCTTACACATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1403	chr11	89074628	89074828	+	1.39091	NA	intron (NM_001033266, intron 1 of 3)	intron (NM_001033266, intron 1 of 3)	887	NM_001033266	217071	Mm.342127	NM_001033266	ENSMUSG00000072553	Gm525	-	predicted gene 525	protein-coding	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2820	chr15	22833345	22833545	+	1.39091	NA	Intergenic	Intergenic	-118461	NM_001165971	545091	Mm.475598	NM_001165971		Hnrnpa1l2-ps2	EG545091|Gm5803	heterogeneous nuclear ribonucleoprotein A1-like 2, pseudogene 2	protein-coding	0.000000	0.283582			58(CTTAACAAGATAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2356	chr14	11531878	11532078	+	1.39091	NA	Intergenic	Intergenic	-21575	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding	0.030000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6231	chr5	141435957	141436157	+	1.39091	NA	intron (NM_177879, intron 1 of 44)	L1MEg|LINE|L1	194523	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding	0.005000	0.303483			-95(GCTTAGTGATTTTAAT,+,0.00),-49(ATTTTGACTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2532	chr14	69867216	69867416	+	1.39091	NA	intron (NM_028560, intron 3 of 6)	intron (NM_028560, intron 3 of 6)	26909	NM_028526	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4006	chr19	11902513	11902713	+	1.39091	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	6590	NM_146410	258405	Mm.358933	NM_146410	ENSMUSG00000060878	Olfr1420	MOR266-4	olfactory receptor 1420	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2257	chr13	102916116	102916316	+	1.39091	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	155961	NR_130318	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1204	chr11	25951567	25951767	+	1.39091	NA	intron (NR_027973, intron 2 of 5)	intron (NR_027973, intron 2 of 5)	-250573	NR_105791	102466154		NR_105791	ENSMUSG00000099015	Mir6372	Gm27358|mmu-mir-6372	microRNA 6372	ncRNA	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7688	chr9	63687045	63687245	+	1.39091	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	70849	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2633	chr14	93860281	93860481	+	1.39091	NA	intron (NM_001081377, intron 2 of 4)	intron (NM_001081377, intron 2 of 4)	30288	NM_001081377	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding	0.000000	0.293532			-29(ATTTGAATGTGAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6608	chr6	98307982	98308182	+	1.39091	NA	intron (NM_001128092, intron 2 of 3)	intron (NM_001128092, intron 2 of 3)	34672	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1787	chr12	85103604	85103804	+	1.39091	NA	intron (NM_175198, intron 1 of 4)	intron (NM_175198, intron 1 of 4)	2727	NM_175198	73422	Mm.311944	NM_175198	ENSMUSG00000042320	Prox2	1700058C01Rik	prospero homeobox 2	protein-coding	0.000000	0.303483			-4(ATCTACATGACACTAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-166	chr1	56946269	56946469	+	1.39091	NA	intron (NM_139146, intron 3 of 10)	intron (NM_139146, intron 3 of 10)	24965	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	BAP002|mKIAA1034	special AT-rich sequence binding protein 2	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4869	chr3	21795365	21795565	+	1.39091	NA	Intergenic	BLACKJACK|DNA|hAT-Blackjack	-281187	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.000000	0.268657			-36(CTCTGCATGAAAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2024	chr13	36317254	36317454	+	1.39062	NA	intron (NM_001039189, intron 3 of 5)	intron (NM_001039189, intron 3 of 5)	199711	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1130	chr10	126680524	126680724	+	1.39062	NA	Intergenic	Intergenic	29767	NR_105841	102465224		NR_105841	ENSMUSG00000098756	Mir378d	Gm27650|mmu-mir-378d	microRNA 378d	ncRNA	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7113	chr7	138121283	138121483	+	1.38995	NA	Intergenic	Intergenic	276347	NM_183289	70571	Mm.334297	NM_183289	ENSMUSG00000091002	Tcerg1l	5730476P14Rik	transcription elongation regulator 1-like	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-587	chr3	137880135	137880335	+	1.38995	NA	intron (NM_001033155, intron 1 of 7)	intron (NM_001033155, intron 1 of 7)	12560	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding	0.015000	0.412935			63(TTTTTTTTTTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4990	chr3	67885314	67885514	+	1.38995	NA	Intergenic	Intergenic	-6806	NM_001113419	100505386	Mm.331064	NM_001113419	ENSMUSG00000102422	Iqschfp	Gm21949|Iqcj-schip1|Schip-1-iqcj|Schip1	Iqcj and Schip1 fusion protein	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3716	chr18	15012524	15012724	+	1.38836	NA	intron (NM_134112, intron 1 of 4)	intron (NM_134112, intron 1 of 4)	23629	NR_045372	74456	Mm.391075	NR_045372	ENSMUSG00000117450	4933424G05Rik	-	RIKEN cDNA 4933424G05 gene	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4471	chr2	101585044	101585244	+	1.38836	NA	intron (NM_001362687, intron 4 of 6)	ORR1D2|LTR|ERVL-MaLR	35902	NM_001362687	68170	Mm.31263	NM_026592	ENSMUSG00000027165	B230118H07Rik	NWC	RIKEN cDNA B230118H07 gene	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3518	chr17	51766056	51766256	+	1.38836	NA	intron (NM_001357640, intron 8 of 10)	intron (NM_001357640, intron 8 of 10)	45898	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1887	chr12	110349769	110349969	+	1.38836	NA	Intergenic	ORR1A2-int|LTR|ERVL-MaLR	70639	NM_172119	107585	Mm.154427	NM_172119	ENSMUSG00000075707	Dio3	-	deiodinase, iodothyronine type III	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5141	chr3	117664582	117664782	+	1.38836	NA	intron (NM_029425, intron 4 of 5)	intron (NM_029425, intron 4 of 5)	89455	NM_029425	75769	Mm.72187	NM_029425	ENSMUSG00000033342	Plppr5	4833424O15Rik|Lppr5|PRG-5|Pap2d	phospholipid phosphatase related 5	protein-coding	0.005000	0.383085			9(AAACTTTGATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-633	chr1	189754891	189755091	+	1.38836	NA	intron (NM_008976, intron 1 of 18)	B4A|SINE|B4	26723	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding	0.015000	0.512438			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-308	chr14	89225182	89225382	+	1.38836	NA	Intergenic	Intergenic	-670942	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	poly(A)-binding protein, cytoplasmic pseudogene	pseudo	0.010000	0.298507			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-360	chr16	12780566	12780766	+	1.38836	NA	Intergenic	RLTR41B|LTR|ERV1	-30724	NR_040507	75493	Mm.396146	NR_040507	ENSMUSG00000101565	1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	ncRNA	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-372	chr1	128566643	128566843	+	1.38836	NA	Intergenic	Intergenic	25556	NM_001356509	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|CXC-R4|CXCR-4|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4017	chr19	15883222	15883422	+	1.38836	NA	Intergenic	Intergenic	41300	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding	0.025000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4241	chr2	29747564	29747764	+	1.38836	NA	intron (NM_001370924, intron 1 of 3)	intron (NM_001370924, intron 1 of 3)	3993	NM_001370923	433415	Mm.359309	NM_001370923	ENSMUSG00000079497	Gm13420	Dspd2	predicted gene 13420	protein-coding	0.060000	0.601990			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1991	chr13	25933002	25933202	+	1.38836	NA	intron (NR_045062, intron 1 of 3)	intron (NR_045062, intron 1 of 3)	33214	NR_045062	100503530	Mm.86763	NR_045062	ENSMUSG00000086531	Gm11351	-	predicted gene 11351	ncRNA	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7985	chrX	70881591	70881791	+	1.38836	NA	Intergenic	Intergenic	-168565	NM_001081354	333639	Mm.371730	NM_001081354	ENSMUSG00000059401	Mamld1	G630014P10Rik	mastermind-like domain containing 1	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3325	chr16	76596052	76596252	+	1.38836	NA	Intergenic	RLTR13B1|LTR|ERVK	47357	NR_155449	102632730		NR_155449		Gm30726	-	predicted gene, 30726	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5156	chr3	121401507	121401707	+	1.38836	NA	Intergenic	MER47A|DNA|TcMar-Tigger	-24934	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-332	chr15	12921985	12922185	+	1.38836	NA	intron (NM_026799, intron 29 of 34)	intron (NM_026799, intron 29 of 34)	97270	NM_026799	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding	0.015000	0.562189			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-67	chr1	191438497	191438697	+	1.38836	NA	intron (NR_151615, intron 5 of 5)	intron (NR_151615, intron 5 of 5)	26451	NR_151615	102634668		NR_151615		Gm32200	-	predicted gene, 32200	ncRNA	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3423	chr17	13926039	13926239	+	1.38836	NA	Intergenic	L1_Mur3|LINE|L1	-22234	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding	0.010000	0.432836			-55(TCATCATTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2619	chr14	89225089	89225289	+	1.38836	NA	Intergenic	Intergenic	-671035	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	poly(A)-binding protein, cytoplasmic pseudogene	pseudo	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-461	chr1	152954257	152954457	+	1.38593	NA	promoter-TSS (NM_175460)	promoter-TSS (NM_175460)	-744	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.010000	0.422886			52(AATTTCCCATTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4702	chr2	144174403	144174603	+	1.38517	NA	intron (NR_136884, intron 3 of 3)	intron (NR_136884, intron 3 of 3)	14787	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA	0.005000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-60	chr1	184918427	184918627	+	1.38478	NA	intron (NM_145515, intron 9 of 17)	intron (NM_145515, intron 9 of 17)	-35491	NM_178692	226777	Mm.169542	NM_178692	ENSMUSG00000039349	C130074G19Rik	-	RIKEN cDNA C130074G19 gene	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8034	chrX	98774752	98774952	+	1.38471	NA	intron (NM_001313754, intron 5 of 25)	intron (NM_001313754, intron 5 of 25)	116173	NM_001313756	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding	0.000000	0.402985			70(GGTTTGTTATCCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-630	chr4	76459511	76459711	+	1.38471	NA	intron (NR_160919, intron 10 of 39)	intron (NR_160919, intron 10 of 39)	-115368	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-462	chr1	152954474	152954674	+	1.38442	NA	promoter-TSS (NM_175460)	promoter-TSS (NM_175460)	-527	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.010000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5246	chr3	143864323	143864523	+	1.38374	NA	Intergenic	Intergenic	-152280	NR_040405	621809	Mm.360134	NR_040405	ENSMUSG00000105279	Gm6260	EG621809	predicted gene 6260	ncRNA	0.010000	0.402985			-33(ATTTGCATGAGAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6218	chr5	137796530	137796730	+	1.38374	NA	exon (NM_001360023, exon 3 of 17)	exon (NM_001360023, exon 3 of 17)	8828	NM_001005426	381678	Mm.332765	NM_001005426	ENSMUSG00000037108	Zcwpw1	Gm1053	zinc finger, CW type with PWWP domain 1	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4083	chr19	36199836	36200036	+	1.38374	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-80092	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding	0.005000	0.368159			-75(ATTCTATCATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4754	chr2	159239364	159239564	+	1.38374	NA	Intergenic	L1MA6|LINE|L1	444657	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding	0.005000	0.338308		8(CATGAATATGTACA,+,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-153	chr11	65684747	65684947	+	1.38366	NA	Intergenic	Intergenic	49985	NR_030417	791070		NR_030417	ENSMUSG00000076460	Mir744	Mirn744|mir-744|mmu-mir-744	microRNA 744	ncRNA	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5644	chr4	100534955	100535155	+	1.38366	NA	intron (NM_001033773, intron 8 of 9)	intron (NM_001033773, intron 8 of 9)	56188	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6954	chr7	89166754	89166954	+	1.38366	NA	intron (NM_001360745, intron 5 of 13)	intron (NM_001360745, intron 5 of 13)	171933	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding	0.005000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-171	chr11	114320316	114320516	+	1.38366	NA	Intergenic	Intergenic	122158	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1594	chr12	34406145	34406345	+	1.38366	NA	intron (NM_024124, intron 7 of 11)	intron (NM_024124, intron 7 of 11)	122644	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6946	chr7	87319373	87319573	+	1.38366	NA	intron (NM_001285833, intron 8 of 19)	intron (NM_001285833, intron 8 of 19)	72824	NM_001285835	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding	0.005000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1400	chr11	88620268	88620468	+	1.38212	NA	intron (NR_131025, intron 1 of 2)	intron (NR_131025, intron 1 of 2)	1117	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA	0.025000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7506	chr9	6845233	6845433	+	1.38212	NA	Intergenic	RLTR13D3|LTR|ERVK	-331257	NM_001357484	76863	Mm.27293	NM_029775	ENSMUSG00000032002	Dcun1d5	3110001A18Rik|4833420K19Rik|AW060460|D430047L21Rik	DCN1, defective in cullin neddylation 1, domain containing 5 (S. cerevisiae)	protein-coding	0.010000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-645	chr4	104308113	104308313	+	1.38175	NA	intron (NM_001369049, intron 4 of 19)	intron (NM_001369049, intron 4 of 19)	-59325	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.010000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8162	chrX	166767255	166767455	+	1.38175	NA	Intergenic	Intergenic	105330	NR_046015	382255	Mm.336320	NR_046015	ENSMUSG00000086860	Gm1720	-	predicted gene 1720	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1059	chr10	115759702	115759902	+	1.38175	NA	Intergenic	Intergenic	-57482	NM_146010	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8074	chrX	129478854	129479054	+	1.37930	NA	Intergenic	Intergenic	-270788	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8109	chrX	144308268	144308468	+	1.37930	NA	Intergenic	Lx5c|LINE|L1	-9598	NR_037145	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031	asparagine-linked glycosylation 13	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4930	chr3	46324631	46324831	+	1.37930	NA	Intergenic	Intergenic	123210	NM_001101479	241989	Mm.119234	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	poly(A) binding protein, cytoplasmic 4-like	protein-coding	0.005000	0.253731			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2635	chr14	94895324	94895524	+	1.37930	NA	Intergenic	RMER17B|LTR|ERVK	-985830	NM_001358241	66732	Mm.75060	NM_025733	ENSMUSG00000034689	Spertl	4921530L21Rik	spermatid associated like	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1414	chr11	93333029	93333229	+	1.37930	NA	intron (NM_001361707, intron 4 of 9)	intron (NM_001361707, intron 4 of 9)	233839	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0.020000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2857	chr15	34029480	34029680	+	1.37930	NA	Intergenic	RLTR13D2|LTR|ERVK	-53139	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6040	chr5	77303841	77304041	+	1.37930	NA	intron (NM_019836, intron 4 of 6)	B3A|SINE|B2	6145	NM_019836	56412	Mm.129136	NM_019836	ENSMUSG00000036285	Noa1	2610024G14Rik|AU022345|AtNOS1|mAtNOS1	nitric oxide associated 1	protein-coding	0.005000	0.407960		-38(CATTCATATGGATG,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1256	chr11	40593108	40593308	+	1.37930	NA	Intergenic	MER33|DNA|hAT-Charlie	99474	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5279	chr3	149117327	149117527	+	1.37930	NA	Intergenic	Intergenic	-157310	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6628	chr6	101918923	101919123	+	1.37930	NA	Intergenic	L1MB7|LINE|L1	144774	NR_027989	207157	Mm.57632	NM_177579	ENSMUSG00000052236	Gm9871	0610005I04|EG207157	predicted gene 9871	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4547	chr2	117328700	117328900	+	1.37930	NA	intron (NM_011246, intron 2 of 16)	intron (NM_011246, intron 2 of 16)	14077	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp|calDAG-GEFII	RAS guanyl releasing protein 1	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5876	chr5	27243705	27243905	+	1.37930	NA	intron (NM_207282, intron 1 of 25)	intron (NM_207282, intron 1 of 25)	-18130	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4382	chr2	70793698	70793898	+	1.37930	NA	intron (NR_156421, intron 1 of 6)	Lx9|LINE|L1	31006	NM_001362963	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1147	chr11	6840531	6840731	+	1.37930	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-120594	NR_046025	626419	Mm.390334	NR_046025	ENSMUSG00000086808	Gm11981	-	predicted gene 11981	ncRNA	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1410	chr11	92153425	92153625	+	1.37930	NA	Intergenic	Intergenic	-575970	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1106	chr10	123139508	123139708	+	1.37930	NA	intron (NM_001301628, intron 7 of 20)	Lx|LINE|L1	57411	NM_001301628	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding	0.015000	0.462687			-58(GTTTTTTTATTTAGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-376	chr16	66374775	66374975	+	1.37930	NA	Intergenic	Intergenic	-282243	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA	0.005000	0.318408			-95(TTTTTGTCTTTCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7076	chr7	128331813	128332013	+	1.37930	NA	Intergenic	Intergenic	-33782	NM_145590	233913	Mm.220880	NM_145590	ENSMUSG00000030780	BC017158	-	cDNA sequence BC017158	protein-coding	0.025000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5350	chr4	13340412	13340612	+	1.37930	NA	Intergenic	Intergenic	-402790	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	RUNX1 translocation partner 1	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6481	chr6	61627023	61627223	+	1.37930	NA	intron (NM_183310, intron 6 of 10)	intron (NM_183310, intron 6 of 10)	-446313	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2871	chr15	39362168	39362368	+	1.37930	NA	intron (NM_053271, intron 5 of 26)	intron (NM_053271, intron 5 of 26)	163982	NM_001256382	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1374	chr11	81604788	81604988	+	1.37930	NA	intron (NM_001034013, intron 1 of 9)	L1M4b|LINE|L1	-31349	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4701	chr2	144174035	144174235	+	1.37923	NA	non-coding (NR_136884, exon 4 of 4)	non-coding (NR_136884, exon 4 of 4)	15155	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA	0.005000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-805	chr7	109104254	109104454	+	1.37923	NA	Intergenic	RLTR11B|LTR|ERVK	-21023	NM_001311161	320360	Mm.71007	NM_178780	ENSMUSG00000048330	Ric3	E130307J04Rik	RIC3 acetylcholine receptor chaperone	protein-coding	0.000000	0.363184			-49(GTTTGCACAACAAAGG,-,0.00),-30(ATATACATGAGAATTT,-,0.00),22(TTTAGCATTACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5628	chr4	97818452	97818652	+	1.37923	NA	intron (NM_001122953, intron 2 of 9)	intron (NM_001122953, intron 2 of 9)	40926	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2292	chr13	109926704	109926904	+	1.37923	NA	intron (NM_011056, intron 8 of 16)	intron (NM_011056, intron 8 of 16)	22995	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.030000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7016	chr7	109104269	109104469	+	1.37923	NA	Intergenic	RLTR11B|LTR|ERVK	-21038	NM_001311161	320360	Mm.71007	NM_178780	ENSMUSG00000048330	Ric3	E130307J04Rik	RIC3 acetylcholine receptor chaperone	protein-coding	0.005000	0.363184			-64(GTTTGCACAACAAAGG,-,0.00),-45(ATATACATGAGAATTT,-,0.00),7(TTTAGCATTACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5930	chr5	47776083	47776283	+	1.37915	NA	Intergenic	Intergenic	-206972	NM_001291227	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|b2b1200.1Clo|mKIAA4141|slit-2	slit guidance ligand 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-557	chr1	175723001	175723201	+	1.37893	NA	intron (NM_029453, intron 4 of 27)	intron (NM_029453, intron 4 of 27)	24508	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3925	chr18	69973129	69973329	+	1.37883	NA	Intergenic	Intergenic	47670	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-745	chr10	27125810	27126010	+	1.37883	NA	intron (NM_008481, intron 34 of 63)	intron (NM_008481, intron 34 of 63)	-263956	NR_131034	75855	Mm.402080	NR_131034	ENSMUSG00000101636	4930579H20Rik	-	RIKEN cDNA 4930579H20 gene	ncRNA	0.000000	0.358209		-86(TATGAATATACAAG,-,0.00)	-68(CTTTAAATAACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1908	chr12	117472802	117473002	+	1.37883	NA	Intergenic	Intergenic	-43577	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding	0.015000	0.388060			-59(AATTTGCTATTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-600	chr1	184675493	184675693	+	1.37883	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-36904	NR_040627	74971	Mm.410816	NR_040627	ENSMUSG00000092578	4930488B22Rik	-	RIKEN cDNA 4930488B22 gene	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4527	chr2	114239721	114239921	+	1.37883	NA	Intergenic	Intergenic	-38389	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding	0.000000	0.328358			-77(ATCTGAAAGAAAATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4148	chr2	3518657	3518857	+	1.37842	NA	intron (NM_177647, intron 1 of 3)	intron (NM_177647, intron 1 of 3)	5692	NM_177647	227526	Mm.211455	NM_177647	ENSMUSG00000039496	Cdnf	9330140G23|Armetl1	cerebral dopamine neurotrophic factor	protein-coding	0.000000	0.353234			-65(TTGTGCATGATAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2861	chr15	35911485	35911685	+	1.37842	NA	intron (NM_177151, intron 56 of 61)	intron (NM_177151, intron 56 of 61)	26661	NM_053071	12864	Mm.548	NM_053071	ENSMUSG00000014313	Cox6c	-	cytochrome c oxidase subunit 6C	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8122	chrX	152097769	152097969	+	1.37842	NA	Intergenic	MER2|DNA|TcMar-Tigger	-46399	NM_001114664	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2406	chr14	25857185	25857385	+	1.37842	NA	intron (NM_013469, intron 1 of 14)	MIR3|SINE|MIR	15130	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding	0.000000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6906	chr7	73893111	73893311	+	1.37842	NA	Intergenic	Intergenic	67287	NR_102375	100861851		NR_102375		Gm21269	-	predicted gene, 21269	ncRNA	0.010000	0.388060		-49(CATTTATATTCATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3698	chr18	9147567	9147767	+	1.37842	NA	Intergenic	Intergenic	-65189	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled class receptor 8	protein-coding	0.005000	0.398010		-70(CATACATTTGCATG,+,0.00),-70(CATACATTTGCATG,-,0.00)	-89(AAATTCTTATGCTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-917	chr10	87081543	87081743	+	1.37842	NA	intron (NM_029685, intron 2 of 5)	intron (NM_029685, intron 2 of 5)	23597	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding	0.000000	0.363184			32(CTTTCCAAGGCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1164	chr11	13970685	13970885	+	1.37842	NA	Intergenic	Intergenic	208256	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3653	chr17	87424490	87424690	+	1.37842	NA	intron (NM_029298, intron 2 of 6)	intron (NM_029298, intron 2 of 6)	3151	NM_029298	75467	Mm.50108	NM_029298	ENSMUSG00000036557	Stpg4	1700011E24Rik|GSE	sperm tail PG rich repeat containing 4	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1323	chr11	66314540	66314740	+	1.37842	NA	intron (NM_001034874, intron 2 of 4)	intron (NM_001034874, intron 2 of 4)	-146089	NM_001099633	237806	Mm.264210	NM_001099633	ENSMUSG00000056752	Dnah9	9030022M04|A230091C01|C230051G16|D11Ertd686e|Dnahc9|mKIAA0357	dynein, axonemal, heavy chain 9	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3824	chr18	44632220	44632420	+	1.37842	NA	intron (NM_001085373, intron 3 of 18)	MER58B|DNA|hAT-Charlie	-29345	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6701	chr6	119826292	119826492	+	1.37842	NA	intron (NR_104484, intron 1 of 20)	B3A|SINE|B2	21758	NR_155458	111173	Mm.288860	NM_053204	ENSMUSG00000030172	Erc1	4930404L01Rik|5033405M01Rik|9630025C19Rik|B430107L16Rik|CAST2|ELKS|Elks1|RAB6IP2A|RAB6IP2B|Rab6ip2|mKIAA1081	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.010000	0.383085			10(ATTAGAATAATAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8134	chrX	158924835	158925035	+	1.37842	NA	Intergenic	Intergenic	-330847	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding	0.005000	0.388060	-71(CATGAATTATTCAGA,+,0.00),-71(CATGAATTATTCAGA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4876	chr3	25031028	25031228	+	1.37842	NA	Intergenic	Intergenic	-247122	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding	0.000000	0.258706			-5(ATTTAAAATATAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3232	chr16	53038756	53038956	+	1.37842	NA	Intergenic	L1_Mur1|LINE|L1	-223112	NR_040495	73820	Mm.60493	NR_040495	ENSMUSG00000116611	4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7259	chr8	56199386	56199586	+	1.37842	NA	Intergenic	Intergenic	-95066	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding	0.010000	0.333333			-10(ATTTTACTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7477	chr8	122943456	122943656	+	1.37803	NA	intron (NM_001081379, intron 2 of 12)	intron (NM_001081379, intron 2 of 12)	95182	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6604	chr6	97808690	97808890	+	1.37571	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	1732	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	melanogenesis associated transcription factor	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5473	chr4	53656635	53656835	+	1.37571	NA	intron (NM_001195284, intron 5 of 12)	intron (NM_001195284, intron 5 of 12)	25264	NM_001355377	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl	fibronectin type III and SPRY domain containing 1-like	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3013	chr15	89379703	89379903	+	1.37571	NA	promoter-TSS (NM_001013022)	promoter-TSS (NM_001013022)	-549	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding	0.025000	0.462687			78(ATTTGCAAAACTAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6918	chr7	78099905	78100105	+	1.37571	NA	Intergenic	Intergenic	477833	NM_182809	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8079	chrX	130473192	130473392	+	1.37569	NA	Intergenic	Intergenic	723550	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7268	chr8	57596047	57596247	+	1.37569	NA	intron (NM_001167981, intron 1 of 11)	intron (NM_001167981, intron 1 of 11)	-55606	NR_040698	100502619	Mm.393851	NR_040698		AW046200	-	expressed sequence AW046200	ncRNA	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1246	chr11	37877034	37877234	+	1.37569	NA	Intergenic	Intergenic	218145	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA	0.005000	0.427861			-9(ATTTGAAAATGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-841	chr10	57696240	57696440	+	1.37569	NA	intron (NM_001039052, intron 3 of 4)	intron (NM_001039052, intron 3 of 4)	45359	NM_001190402	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2238	chr13	98275741	98275941	+	1.37569	NA	Intergenic	Intergenic	12765	NM_001271388	68558	Mm.209642	NM_023472	ENSMUSG00000021661	Ankra2	1110004M18Rik|Ankra	ankyrin repeat, family A (RFXANK-like), 2	protein-coding	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4389	chr2	72859452	72859652	+	1.37569	NA	Intergenic	Intergenic	-45835	NR_102349	76218	Mm.75260	NR_102348	ENSMUSG00000085427	6430710C18Rik	5033406J01Rik	RIKEN cDNA 6430710C18 gene	ncRNA	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1602	chr12	36109941	36110141	+	1.37569	NA	intron (NM_025840, intron 7 of 11)	intron (NM_025840, intron 7 of 11)	19662	NR_003649	432649	Mm.347860	NM_001014396	ENSMUSG00000059301	Gm5434	EG432649	ubiquitin-conjugating enzyme E2F (putative) pseudogene	pseudo	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4589	chr2	125598470	125598670	+	1.37569	NA	intron (NM_001081091, intron 12 of 27)	intron (NM_001081091, intron 12 of 27)	26543	NM_001081091	99100	Mm.330545	NM_001081091	ENSMUSG00000068394	Cep152	AI851464|mKIAA0912	centrosomal protein 152	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8087	chrX	133600809	133601009	+	1.37569	NA	intron (NM_001105246, intron 4 of 4)	AT_rich|Low_complexity|Low_complexity	-86871	NR_153117	102632590	Mm.403836	NR_153117	ENSMUSG00000096978	Gm26851	-	predicted gene, 26851	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7908	chr9	122472915	122473115	+	1.37569	NA	Intergenic	Intergenic	-74214	NR_045967	654800	Mm.393956	NR_045967		A730085K08Rik	-	RIKEN cDNA A730085K08 gene	ncRNA	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5367	chr4	19626666	19626866	+	1.37569	NA	intron (NM_177327, intron 20 of 24)	B1_Mus2|SINE|Alu	51700	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-599	chr1	184411228	184411428	+	1.37569	NA	Intergenic	Intergenic	146363	NR_040472	73590	Mm.82792	NR_040472	ENSMUSG00000101574	1700112H15Rik	-	RIKEN cDNA 1700112H15 gene	ncRNA	0.010000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-575	chr1	177785874	177786074	+	1.37569	NA	intron (NM_007422, intron 1 of 12)	intron (NM_007422, intron 1 of 12)	10535	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding	0.005000	0.358209		-79(AATACATATTTATT,+,0.00),-79(AATACATATTTATT,-,0.00)	-91(TTTTGCATAAAAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7964	chrX	51372642	51372842	+	1.37569	NA	Intergenic	Intergenic	-166752	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind like splicing factor 3	protein-coding	0.020000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3257	chr16	57690674	57690874	+	1.37569	NA	intron (NM_007739, intron 1 of 3)	X6B_LINE|LINE|CR1	63963	NM_007739	12837	Mm.130388	NM_007739	ENSMUSG00000068196	Col8a1	Col8a-1	collagen, type VIII, alpha 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4127	chr19	56562451	56562651	+	1.37569	NA	intron (NM_025811, intron 2 of 10)	MLTR18A_MM|LTR|ERVK	14290	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7546	chr9	17586256	17586456	+	1.37569	NA	Intergenic	Intergenic	-705911	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6487	chr6	63374740	63374940	+	1.37569	NA	intron (NM_001370966, intron 1 of 15)	intron (NM_001370966, intron 1 of 15)	118834	NM_001370966									0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3520	chr17	51856209	51856409	+	1.37569	NA	Intergenic	Intergenic	-23019	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3561	chr17	66070009	66070209	+	1.37569	NA	intron (NM_001025572, intron 1 of 12)	intron (NM_001025572, intron 1 of 12)	6937	NM_001025572	106585	Mm.34706	NM_001025572	ENSMUSG00000034647	Ankrd12	2900001A12Rik|AI447928|ANCO-2|AV347965|GAC-1|mKIAA0874	ankyrin repeat domain 12	protein-coding	0.005000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3801	chr18	39169628	39169828	+	1.37569	NA	intron (NM_175164, intron 11 of 22)	intron (NM_175164, intron 11 of 22)	176583	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4749	chr2	158186967	158187167	+	1.37569	NA	intron (NM_001131021, intron 14 of 15)	intron (NM_001131021, intron 14 of 15)	-4941	NR_036606	73399	Mm.416861	NR_036606	ENSMUSG00000078957	1700060C20Rik	-	RIKEN cDNA 1700060C20 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2515	chr14	62718214	62718414	+	1.37569	NA	intron (NM_008715, intron 4 of 18)	L1M5|LINE|L1	-42187	NR_045503	71000	Mm.399410	NR_045503	ENSMUSG00000097775	4931440J10Rik	-	RIKEN cDNA 4931440J10 gene	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3170	chr16	37495155	37495355	+	1.37569	NA	Intergenic	Intergenic	44534	NM_001355727	74197	Mm.287795	NM_028812	ENSMUSG00000022828	Gtf2e1	2610024P03Rik|56kDa|AI303800|FE|TFIIE-A	general transcription factor II E, polypeptide 1 (alpha subunit)	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2068	chr13	51001602	51001802	+	1.37569	NA	Intergenic	Intergenic	99025	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2927	chr15	53784042	53784242	+	1.37569	NA	intron (NM_177225, intron 2 of 4)	Charlie15b|DNA|hAT-Charlie	118294	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding	0.010000	0.363184			32(ATATTGTTTTGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1077	chr10	117870098	117870298	+	1.37569	NA	Intergenic	Intergenic	-24224	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding	0.015000	0.457711			37(TTTAAAATGATAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6250	chr5	146940264	146940464	+	1.37569	NA	Intergenic	Intergenic	-8293	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5617	chr4	95143191	95143391	+	1.37569	NA	Intergenic	Intergenic	-91069	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1516	chr12	3854485	3854685	+	1.37569	NA	intron (NM_001271753, intron 3 of 22)	intron (NM_001271753, intron 3 of 22)	7659	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5587	chr4	87844828	87845028	+	1.37569	NA	intron (NM_027326, intron 4 of 10)	intron (NM_027326, intron 4 of 10)	-38605	NM_001286158	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6	chr1	3920816	3921016	+	1.37569	NA	Intergenic	Intergenic	-249418	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding	0.000000	0.373134			-11(CTTTTCTTATTCATAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3876	chr18	57051291	57051491	+	1.37569	NA	Intergenic	Intergenic	-76012	NM_029909	77422	Mm.256874	NM_029909	ENSMUSG00000024592	C330018D20Rik	AU018666	RIKEN cDNA C330018D20 gene	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4904	chr3	32644714	32644914	+	1.37569	NA	Intergenic	RMER15|LTR|ERVL	-28224	NM_001348105	14696	Mm.139192	NM_013531	ENSMUSG00000027669	Gnb4	6720453A21Rik|G(beta)4	guanine nucleotide binding protein (G protein), beta 4	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6877	chr7	64345511	64345711	+	1.37569	NA	3' UTR (NM_177893, exon 14 of 14)	3' UTR (NM_177893, exon 14 of 14)	28445	NM_177893	330554	Mm.236510	NM_177893	ENSMUSG00000033458	Fan1	6030441H18Rik|Mtmr15|mFAN1	FANCD2/FANCI-associated nuclease 1	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3174	chr16	38074048	38074248	+	1.37408	NA	Intergenic	Intergenic	-14853	NM_001347232	56637	Mm.394930	NM_019827	ENSMUSG00000022812	Gsk3b	7330414F15Rik|8430431H08Rik|C86142|GSK-3|GSK-3beta|GSK3	glycogen synthase kinase 3 beta	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-211	chr12	99907523	99907723	+	1.37408	NA	intron (NM_028354, intron 7 of 15)	intron (NM_028354, intron 7 of 15)	23108	NM_028354	104884	Mm.312323	NM_028354	ENSMUSG00000021177	Tdp1	2810481F14Rik|4921509N21Rik|AI838772|AW493413|E430034L06Rik|MLZ-501|SCAN1	tyrosyl-DNA phosphodiesterase 1	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-19	chr1	7497500	7497700	+	1.37408	NA	Intergenic	LTRIS2|LTR|ERV1	408680	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.005000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-726	chr6	14504872	14505072	+	1.37395	NA	Intergenic	Intergenic	250302	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory subunit 3A	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-604	chr1	184918334	184918534	+	1.37377	NA	intron (NM_145515, intron 9 of 17)	intron (NM_145515, intron 9 of 17)	-35398	NM_178692	226777	Mm.169542	NM_178692	ENSMUSG00000039349	C130074G19Rik	-	RIKEN cDNA C130074G19 gene	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1215	chr11	28048867	28049067	+	1.37274	NA	Intergenic	Intergenic	535357	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5816	chr5	5291296	5291496	+	1.37274	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	-25328	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4115	chr19	49835152	49835352	+	1.37223	NA	Intergenic	Intergenic	843394	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.000000	0.288557			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-593	chr3	148663184	148663384	+	1.37223	NA	Intergenic	Intergenic	291351	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7448	chr8	111574158	111574358	+	1.37223	NA	intron (NM_001363489, intron 1 of 4)	PB1D10|SINE|Alu	35915	NM_001363489	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6789	chr7	12933632	12933832	+	1.37223	NA	Intergenic	B1_Mur3|SINE|Alu	6316	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-872	chr10	68525741	68525941	+	1.37223	NA	intron (NM_028491, intron 2 of 7)	intron (NM_028491, intron 2 of 7)	16034	NM_028491	73287	Mm.141830	NM_028491	ENSMUSG00000019945	Cabcoco1	1700040L02Rik	ciliary associated calcium binding coiled-coil 1	protein-coding	0.015000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-56	chr1	177078680	177078880	+	1.36948	NA	exon (NM_011785, exon 7 of 13)	exon (NM_011785, exon 7 of 13)	169987	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-571	chr1	177078668	177078868	+	1.36948	NA	intron (NM_011785, intron 7 of 12)	intron (NM_011785, intron 7 of 12)	169999	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1882	chr12	108176642	108176842	+	1.36907	NA	intron (NM_001364266, intron 1 of 13)	MER2|DNA|TcMar-Tigger	2499	NM_001364267	52690	Mm.159185	NM_028262	ENSMUSG00000056770	Setd3	2610102I01Rik|2610305M23Rik|6030490B17Rik|D12Ertd771e	SET domain containing 3	protein-coding	0.010000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-537	chr2	144174412	144174612	+	1.36907	NA	intron (NR_136884, intron 3 of 3)	intron (NR_136884, intron 3 of 3)	14778	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA	0.005000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-912	chrX	166767164	166767364	+	1.36907	NA	Intergenic	Intergenic	105239	NR_046015	382255	Mm.336320	NR_046015	ENSMUSG00000086860	Gm1720	-	predicted gene 1720	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-113	chr1	39239911	39240111	+	1.36844	NA	intron (NM_008719, intron 1 of 20)	intron (NM_008719, intron 1 of 20)	45739	NM_008719	18143	Mm.2380	NM_008719	ENSMUSG00000026077	Npas2	MOP4|bHLHe9	neuronal PAS domain protein 2	protein-coding	0.000000	0.457711			-38(ATTAGCATGCCAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-243	chr1	85814821	85815021	+	1.36844	NA	intron (NM_001355047, intron 2 of 9)	intron (NM_001355047, intron 2 of 9)	20904	NM_001355047	12283	Mm.26135	NM_133781	ENSMUSG00000036707	Cab39	AA408805|AA960512|C78372|MO25|MO25alpha	calcium binding protein 39	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-203	chr1	71301629	71301829	+	1.36670	NA	intron (NM_175210, intron 22 of 52)	intron (NM_175210, intron 22 of 52)	113181	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	ATP-binding cassette, sub-family A (ABC1), member 12	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1946	chr13	11466701	11466901	+	1.36670	NA	Intergenic	Intergenic	-55251	NR_027813	664793	Mm.410565	NR_027813	ENSMUSG00000113593	Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1949	chr13	12072942	12073142	+	1.36670	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	33903	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding	0.010000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7758	chr9	79971143	79971343	+	1.36670	NA	intron (NM_001357352, intron 1 of 5)	intron (NM_001357352, intron 1 of 5)	6639	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding	0.010000	0.368159			30(TGATTGTCTTGGTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1051	chr10	115162535	115162735	+	1.36670	NA	intron (NM_173391, intron 5 of 10)	intron (NM_173391, intron 5 of 10)	22387	NM_173391	216343	Mm.31597	NM_173391	ENSMUSG00000006764	Tph2	AU043594|Ntph	tryptophan hydroxylase 2	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6798	chr7	24561901	24562101	+	1.36670	NA	intron (NM_001360169, intron 2 of 15)	intron (NM_001360169, intron 2 of 15)	10514	NM_001360169	22594	Mm.4347	NM_009532	ENSMUSG00000051768	Xrcc1	Xrcc-1	X-ray repair complementing defective repair in Chinese hamster cells 1	protein-coding	0.015000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5294	chr3	153203564	153203764	+	1.36670	NA	3' UTR (NM_011372, exon 5 of 5)	3' UTR (NM_011372, exon 5 of 5)	-51556	NR_108044	75001		NR_108044		4930482G09Rik	-	RIKEN cDNA 4930482G09 gene	ncRNA	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2541	chr14	73495867	73496067	+	1.36670	NA	Intergenic	Intergenic	-14082	NM_026119	67381	Mm.282888	NM_026119	ENSMUSG00000022109	Med4	2410046H15Rik|DRIP36|HSPC126|TRAP36|Vdirp|Vdrip	mediator complex subunit 4	protein-coding	0.020000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4498	chr2	106895969	106896169	+	1.36670	NA	Intergenic	Intergenic	74322	NM_173750	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6294	chr6	7903781	7903981	+	1.36670	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	58657	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding	0.000000	0.313433			51(GTTTGAAAGAGAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6889	chr7	68154591	68154791	+	1.36670	NA	intron (NM_010513, intron 2 of 20)	L1MB8|LINE|L1	109542	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5868	chr5	25184608	25184808	+	1.36670	NA	intron (NM_026449, intron 1 of 8)	intron (NM_026449, intron 1 of 8)	3228	NM_026449	67909	Mm.141471	NM_026449	ENSMUSG00000028938	Galntl5	1700021B12Rik|Galnt15	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-377	chr1	130027491	130027691	+	1.36670	NA	intron (NM_172485, intron 15 of 27)	intron (NM_172485, intron 15 of 27)	-395233	NR_151525	102640368		NR_151525	ENSMUSG00000087691	Gm15674	-	predicted gene 15674	ncRNA	0.005000	0.388060		-37(CATGAAAATGTATC,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6653	chr6	108145983	108146183	+	1.36670	NA	intron (NM_145937, intron 6 of 8)	intron (NM_145937, intron 6 of 8)	39500	NM_145937	58911	Mm.439876	NM_145937	ENSMUSG00000030101	Sumf1	AA543204|AI463102|AI851573|FGE	sulfatase modifying factor 1	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2325	chr13	117511540	117511740	+	1.36670	NA	Intergenic	Intergenic	-90680	NM_010408	15165	Mm.343429	NM_010408	ENSMUSG00000021730	Hcn1	Bcng1|C630013B14Rik|HAC2	hyperpolarization activated cyclic nucleotide gated potassium channel 1	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1450	chr11	107683951	107684151	+	1.36670	NA	intron (NM_001368755, intron 31 of 32)	intron (NM_001368755, intron 31 of 32)	32425	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1029	chr10	111082147	111082347	+	1.36670	NA	Intergenic	Intergenic	-72181	NM_001359624	320150	Mm.339281	NM_172554	ENSMUSG00000035798	Zdhhc17	A230053P19Rik|BB187739|D130071N24Rik|DHHC-17|Hip14	zinc finger, DHHC domain containing 17	protein-coding	0.010000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3575	chr17	69720888	69721088	+	1.36670	NA	Intergenic	Intergenic	-248085	NM_001360665	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	DLG associated protein 1	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6901	chr7	72376018	72376218	+	1.36670	NA	Intergenic	L1M5|LINE|L1	-69523	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8094	chrX	138065291	138065491	+	1.36670	NA	intron (NM_030688, intron 2 of 10)	intron (NM_030688, intron 2 of 10)	144189	NM_026469	67944	Mm.443280	NM_026469	ENSMUSG00000071686	Tex13a	1700025D03Rik	testis expressed 13A	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7536	chr9	15021303	15021503	+	1.36656	NA	exon (NM_019482, exon 2 of 5)	exon (NM_019482, exon 2 of 5)	24075	NM_019482	55991	Mm.142253	NM_019482	ENSMUSG00000031934	Panx1	AI847747	pannexin 1	protein-coding	0.025000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-857	chr10	66250972	66251172	+	1.36656	NA	Intergenic	Intergenic	105776	NR_131070	77198	Mm.107617	NR_131070	ENSMUSG00000112210	4930407I19Rik	-	RIKEN cDNA 4930407I19 gene	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2249	chr13	101453948	101454148	+	1.36656	NA	Intergenic	Intergenic	-56468	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	ncRNA	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3393	chr16	94718325	94718525	+	1.36656	NA	Intergenic	Intergenic	107006	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding	0.010000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2996	chr15	75901539	75901739	+	1.36656	NA	intron (NM_001285429, intron 1 of 7)	intron (NM_001285429, intron 1 of 7)	-7158	NM_172607	223646	Mm.288368	NM_172607	ENSMUSG00000022574	Naprt	9130210N20Rik|Naprt1	nicotinate phosphoribosyltransferase	protein-coding	0.015000	0.462687			48(TTTTCCATAAAAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-640	chr1	191438610	191438810	+	1.36656	NA	intron (NR_151615, intron 5 of 5)	intron (NR_151615, intron 5 of 5)	26338	NR_151615	102634668		NR_151615		Gm32200	-	predicted gene, 32200	ncRNA	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7425	chr8	105233453	105233653	+	1.36656	NA	intron (NM_145604, intron 2 of 15)	intron (NM_145604, intron 2 of 15)	8365	NM_145604	234678	Mm.27186	NM_145604	ENSMUSG00000031889	D230025D16Rik	BC006874|Lin10	RIKEN cDNA D230025D16 gene	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5093	chr3	103081173	103081373	+	1.36656	NA	intron (NM_001033303, intron 4 of 15)	intron (NM_001033303, intron 4 of 15)	7259	NM_001033303	229665	Mm.331272	NM_001033303	ENSMUSG00000070385	Ampd1	AI553520|Ampd-1	adenosine monophosphate deaminase 1	protein-coding	0.025000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3974	chr18	84301155	84301355	+	1.36656	NA	intron (NM_001033341, intron 8 of 8)	intron (NM_001033341, intron 8 of 8)	213097	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding	0.005000	0.328358			-25(TAATTCTCTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-218	chr1	80169921	80170121	+	1.36656	NA	Intergenic	Intergenic	43923	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding	0.000000	0.333333		-42(CATACATATACATT,+,0.00),-42(CATACATATACATT,-,0.00)	-97(ATTTGCAAAATAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6693	chr6	118833590	118833790	+	1.36656	NA	intron (NM_001256000, intron 3 of 46)	MER63D|DNA|hAT-Blackjack	-46468	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA	0.015000	0.407960			-92(ATTTGCATCACCATCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4405	chr2	76805384	76805584	+	1.36606	NA	intron (NM_028004, intron 68 of 191)	intron (NM_028004, intron 68 of 191)	130169	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding	0.000000	0.303483			-28(TTTTGCATTAGAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3036	chr15	94443378	94443578	+	1.36606	NA	Intergenic	Intergenic	-39128	NM_001164786	223838	Mm.214132	NM_177431	ENSMUSG00000022449	Adamts20	Adamst20|bt	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 20	protein-coding	0.010000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-494	chr2	76805337	76805537	+	1.36606	NA	intron (NM_028004, intron 68 of 191)	intron (NM_028004, intron 68 of 191)	130122	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding	0.005000	0.348259			19(TTTTGCATTAGAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5663	chr4	104307960	104308160	+	1.36508	NA	intron (NM_001369049, intron 4 of 19)	intron (NM_001369049, intron 4 of 19)	-59478	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.010000	0.412935			47(TTATTCTCATGTAATT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-249	chr1	86782643	86782843	+	1.36477	NA	intron (NM_153530, intron 5 of 20)	intron (NM_153530, intron 5 of 20)	78939	NM_001172157	208718	Mm.389152	NM_153530	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 like 3'-5' exoribonuclease 2	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4287	chr2	47330778	47330978	+	1.36477	NA	Intergenic	Intergenic	-1483231	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2806	chr15	13455656	13455856	+	1.36477	NA	Intergenic	Intergenic	-282081	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4289	chr2	47960900	47961100	+	1.36477	NA	Intergenic	Lx10|LINE|L1	-853109	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0.000000	0.318408			-33(CCATTGTTGTGTTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2463	chr14	43979900	43980100	+	1.36458	NA	Intergenic	Lx5|LINE|L1	22931	NM_007448	503844	Mm.24663	NM_007448	ENSMUSG00000053961	Ang5	-	angiogenin, ribonuclease A family, member 5	protein-coding	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2083	chr13	57877118	57877318	+	1.36326	NA	intron (NM_001166466, intron 2 of 11)	intron (NM_001166466, intron 2 of 11)	31114	NM_009262	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2244	chr13	99676913	99677113	+	1.36326	NA	Intergenic	L1MD3|LINE|L1	-160411	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding	0.005000	0.318408			-26(TTATTCTCAAACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-529	chr1	168351131	168351331	+	1.36326	NA	intron (NM_001291508, intron 2 of 7)	intron (NM_001291508, intron 2 of 7)	80938	NM_183355	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding	0.005000	0.427861			55(GCTTACACATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8076	chrX	129788920	129789120	+	1.36326	NA	intron (NM_172493, intron 1 of 26)	MIRb|SINE|MIR	39278	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding	0.015000	0.417910			-63(GCATTCTTATGGAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4740	chr2	155115538	155115738	+	1.36326	NA	Intergenic	Intergenic	-15559	NR_040634	100504268	Mm.410858	NR_040634	ENSMUSG00000087254	2310005A03Rik	-	RIKEN cDNA 2310005A03 gene	ncRNA	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5914	chr5	41324684	41324884	+	1.36326	NA	Intergenic	Intergenic	382907	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2158	chr13	77985938	77986138	+	1.36326	NA	intron (NM_001163419, intron 7 of 9)	intron (NM_001163419, intron 7 of 9)	-38864	NM_029315	75507	Mm.443255	NM_029315	ENSMUSG00000093668	Pou5f2	1700013G10Rik|SPRM-1|Sprm1	POU domain class 5, transcription factor 2	protein-coding	0.015000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4909	chr3	38860817	38861017	+	1.36326	NA	Intergenic	Intergenic	-26023	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5553	chr4	77512852	77513052	+	1.36326	NA	intron (NR_160919, intron 4 of 39)	intron (NR_160919, intron 4 of 39)	698790	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5841	chr5	17624312	17624512	+	1.36326	NA	intron (NM_013657, intron 2 of 17)	intron (NM_013657, intron 2 of 17)	49596	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3785	chr18	34551783	34551983	+	1.36326	NA	Intergenic	Intergenic	9556	NM_009290	20890	Mm.558	NM_009290	ENSMUSG00000012282	Wnt8a	Stra11|Wnt-8A|Wnt-8D|Wnt8d	wingless-type MMTV integration site family, member 8A	protein-coding	0.020000	0.467662		-48(CATTCATATGCAGT,+,0.00)	44(CTTTTGACTTGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1653	chr12	51217001	51217201	+	1.36326	NA	Intergenic	MER34|LTR|ERV1	-131129	NM_001167963	217558	Mm.253264	NM_001015099	ENSMUSG00000035293	G2e3	6030408C04Rik|9030416F18|AW046379|D930034K21Rik|mKIAA1333	G2/M-phase specific E3 ubiquitin ligase	protein-coding	0.000000	0.348259			32(CTTTTTCCTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1370	chr11	78785456	78785656	+	1.36326	NA	Intergenic	Intergenic	-33827	NM_197989	69109	Mm.341420	NM_197989	ENSMUSG00000049489	Ccnq	1810009O10Rik|Fam58a|Fam58b	cyclin Q	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4951	chr3	54456668	54456868	+	1.36326	NA	Intergenic	Intergenic	95661	NM_015784	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding	0.000000	0.358209			57(ATTTGCAAGAATACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1748	chr12	75983435	75983635	+	1.36326	NA	intron (NM_001005510, intron 53 of 115)	intron (NM_001005510, intron 53 of 115)	74432	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA	0.030000	0.452736			17(TCATTATGATGATAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6794	chr7	16437586	16437786	+	1.36326	NA	TTS (NM_198631)	TTS (NM_198631)	-15093	NM_026938	69094	Mm.29633	NM_026938	ENSMUSG00000019158	Tmem160	1810008O21Rik	transmembrane protein 160	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2905	chr15	46232315	46232515	+	1.36326	NA	Intergenic	L1_Mus3|LINE|L1	-92170	NR_045509	71120	Mm.158571	NR_045509	ENSMUSG00000099751	1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	ncRNA	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2967	chr15	66285765	66285965	+	1.36326	NA	exon (NM_152923, exon 1 of 15)	exon (NM_152923, exon 1 of 15)	764	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding	0.070000	0.651741			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3027	chr15	92434703	92434903	+	1.36326	NA	intron (NM_001164593, intron 3 of 9)	intron (NM_001164593, intron 3 of 9)	37993	NM_001164593	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding	0.020000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7192	chr8	32451937	32452137	+	1.36326	NA	Intergenic	Intergenic	300142	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	ncRNA	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4316	chr2	55446416	55446616	+	1.36326	NA	intron (NM_001304810, intron 2 of 2)	intron (NM_001304810, intron 2 of 2)	10546	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4119	chr19	52193257	52193457	+	1.36326	NA	Intergenic	Intergenic	-70940	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6667	chr6	111511256	111511456	+	1.36326	NA	intron (NM_001346640, intron 10 of 10)	intron (NM_001346640, intron 10 of 10)	-699352	NR_027865	67336	Mm.378014	NR_027865	ENSMUSG00000100219	1700054K19Rik	-	RIKEN cDNA 1700054K19 gene	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5886	chr5	29713029	29713229	+	1.36326	NA	Intergenic	RMER10A|LTR|ERVL	-22769	NM_001037940	23950	Mm.290110	NM_011847	ENSMUSG00000029131	Dnajb6	HSJ-2|Mrj|mDj4	DnaJ heat shock protein family (Hsp40) member B6	protein-coding	0.000000	0.412935			-35(CCTTTGACATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4687	chr2	142194692	142194892	+	1.36326	NA	intron (NM_001013802, intron 9 of 18)	intron (NM_001013802, intron 9 of 18)	706672	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6786	chr7	5103620	5103820	+	1.36326	NA	Intergenic	(TATATG)n|Simple_repeat|Simple_repeat	13191	NM_001145013	192658	Mm.28764	NM_138954	ENSMUSG00000035191	Rfpl4	D7Ertd486e|Rfpl4a	ret finger protein-like 4	protein-coding	0.005000	0.283582		-48(TATACATATGTATA,+,0.00),-48(TATACATATGTATA,-,0.00),5(TATGTATATGTATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7605	chr9	34384237	34384437	+	1.36326	NA	Intergenic	Intergenic	-104394	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kirre like nephrin family adhesion molecule 3	protein-coding	0.005000	0.358209	70(AATAAATTAGGCATA,+,0.00),70(AATAAATTAGGCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8038	chrX	101746723	101746923	+	1.36326	NA	Intergenic	RLTR40|LTR|ERVK	-12676	NM_009910	12766	Mm.12876	NM_009910	ENSMUSG00000050232	Cxcr3	Cd183|Cmkar3	chemokine (C-X-C motif) receptor 3	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3045	chr15	96029118	96029318	+	1.36217	NA	Intergenic	L1_Mur3|LINE|L1	50335	NR_126493	402773	Mm.210567	NM_001033483	ENSMUSG00000078925	D030018L15Rik	-	nuclear receptor coactivator 2 pseudogene	pseudo	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7579	chr9	29013667	29013867	+	1.36217	NA	intron (NM_001357597, intron 5 of 8)	intron (NM_001357597, intron 5 of 8)	398918	NM_001357602	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5542	chr4	76459693	76459893	+	1.36217	NA	intron (NR_160919, intron 10 of 39)	intron (NR_160919, intron 10 of 39)	-115550	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-658	chr1	194320510	194320710	+	1.36089	NA	Intergenic	L1M5|LINE|L1	-97851	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.005000	0.323383			-45(TCATTGTGATTTTAAT,+,0.00),1(ATATTTTCATGTTTAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-913	chrX	167131146	167131346	+	1.36074	NA	Intergenic	Intergenic	-60876	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding	0.010000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-45	chr1	152954789	152954989	+	1.36044	NA	promoter-TSS (NM_175460)	promoter-TSS (NM_175460)	-212	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.040000	0.527363			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-701	chr5	107448935	107449135	+	1.36016	NA	intron (NM_001255991, intron 2 of 8)	intron (NM_001255991, intron 2 of 8)	11038	NM_001255991	100503185	Mm.366650	NM_001255991	ENSMUSG00000111375	Btbd8	EG627196|Gm16115	BTB (POZ) domain containing 8	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1428	chr11	97223593	97223793	+	1.35917	NA	intron (NM_008942, intron 16 of 22)	intron (NM_008942, intron 16 of 22)	-35801	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding	0.010000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-164	chr11	97223597	97223797	+	1.35917	NA	intron (NM_008942, intron 16 of 22)	intron (NM_008942, intron 16 of 22)	-35805	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1280	chr11	48114531	48114731	+	1.35890	NA	Intergenic	Intergenic	-685729	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3580	chr17	71350300	71350500	+	1.35890	NA	intron (NM_028887, intron 45 of 47)	intron (NM_028887, intron 45 of 47)	-8596	NR_028023	100043644	Mm.362377	NR_028023	ENSMUSG00000117199	Gm4566	-	ubiquitin specific peptidase 16 pseudogene	pseudo	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2579	chr14	78747747	78747947	+	1.35730	NA	Intergenic	Intergenic	-15118	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding	0.010000	0.308458			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-783	chr6	146298482	146298682	+	1.35713	NA	intron (NM_019923, intron 34 of 56)	HAL1ME|LINE|L1	203641	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding	0.005000	0.323383			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-160	chr11	88620207	88620407	+	1.35689	NA	intron (NR_131025, intron 1 of 2)	intron (NR_131025, intron 1 of 2)	1056	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA	0.025000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5241	chr3	142331865	142332065	+	1.35631	NA	intron (NM_001190856, intron 3 of 14)	intron (NM_001190856, intron 3 of 14)	59885	NM_001190857	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding	0.005000	0.333333			-1(TTAATTTTATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6216	chr5	136952384	136952584	+	1.35631	NA	promoter-TSS (NM_001163243)	promoter-TSS (NM_001163243)	-791	NM_001163243	66437	Mm.25849	NM_025562	ENSMUSG00000019054	Fis1	2010003O14Rik|Ttc11	fission, mitochondrial 1	protein-coding	0.010000	0.427861			60(ATTTGTAAAATAAAGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-640	chr4	100534913	100535113	+	1.35631	NA	intron (NM_001033773, intron 8 of 9)	intron (NM_001033773, intron 8 of 9)	56146	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5995	chr5	65560965	65561165	+	1.35631	NA	intron (NM_001310618, intron 1 of 4)	intron (NM_001310618, intron 1 of 4)	23820	NM_001310618	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1480	chr11	114320444	114320644	+	1.35631	NA	Intergenic	Intergenic	122286	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6238	chr5	142806315	142806515	+	1.35631	NA	intron (NM_178242, intron 2 of 15)	MIR|SINE|MIR	11247	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding	0.025000	0.383085		73(CGTGTATATGCATG,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7587	chr9	30600735	30600935	+	1.35598	NA	Intergenic	Intergenic	173506	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding	0.010000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5207	chr3	135565512	135565712	+	1.35598	NA	intron (NM_027288, intron 14 of 16)	ORR1E|LTR|ERVL-MaLR	80001	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4894	chr3	30466284	30466484	+	1.35598	NA	intron (NM_001361034, intron 1 of 16)	intron (NM_001361034, intron 1 of 16)	43291	NM_021442	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0.025000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-958	chr10	96332677	96332877	+	1.35598	NA	Intergenic	Intergenic	106570	NR_110448	74881	Mm.410819	NR_110448	ENSMUSG00000112762	4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4229	chr2	28213413	28213613	+	1.35598	NA	intron (NM_001038613, intron 3 of 5)	intron (NM_001038613, intron 3 of 5)	7824	NM_001038612	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding	0.030000	0.432836			-47(TTCCTCTCATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7881	chr9	111721317	111721517	+	1.35598	NA	Intergenic	Intergenic	-31069	NM_016853	20840	Mm.1414	NM_016853	ENSMUSG00000032502	Stac	-	src homology three (SH3) and cysteine rich domain	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4421	chr2	79716081	79716281	+	1.35598	NA	intron (NR_110980, intron 2 of 2)	intron (NR_110980, intron 2 of 2)	8401	NR_110979	75276	Mm.257373	NM_172420	ENSMUSG00000034683	Ppp1r1c	4930565M23Rik|4930579P15Rik	protein phosphatase 1, regulatory inhibitor subunit 1C	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2026	chr13	36345040	36345240	+	1.35598	NA	intron (NM_001039189, intron 4 of 5)	intron (NM_001039189, intron 4 of 5)	227497	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.000000	0.467662			-35(CCATGGTCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3292	chr16	67072722	67072922	+	1.35598	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	415704	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA	0.000000	0.308458			54(TTTAGCATCAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4371	chr2	68162550	68162750	+	1.35598	NA	Intergenic	Intergenic	57978	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4019	chr19	16140420	16140620	+	1.35516	NA	intron (NM_008139, intron 1 of 6)	intron (NM_008139, intron 1 of 6)	7836	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2767	chr15	7149009	7149209	+	1.35516	NA	intron (NM_013584, intron 1 of 19)	intron (NM_013584, intron 1 of 19)	8567	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	LIF receptor alpha	protein-coding	0.005000	0.427861			33(ACATTCTTATTTTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1122	chr10	125214697	125214897	+	1.35330	NA	Intergenic	MLTR25A|LTR|ERVK	94019	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.005000	0.417910			-10(ATTTGCAAGAGAAAAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-124	chr10	125214696	125214896	+	1.35330	NA	Intergenic	MLTR25A|LTR|ERVK	94020	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.005000	0.417910			-9(ATTTGCAAGAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1742	chr12	74934483	74934683	+	1.35321	NA	intron (NM_172805, intron 10 of 10)	Lx9|LINE|L1	242749	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2291	chr13	109926433	109926633	+	1.35308	NA	intron (NM_011056, intron 8 of 16)	intron (NM_011056, intron 8 of 16)	22724	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.025000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1740	chr12	73831413	73831613	+	1.35279	NA	Intergenic	Intergenic	-69811	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7640	chr9	47024883	47025083	+	1.35274	NA	Intergenic	L1M3a|LINE|L1	26242	NM_001243258	215467	Mm.246572	NM_001243258	ENSMUSG00000094893	Gm4791	D930036J05	predicted gene 4791	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1085	chr10	119687104	119687304	+	1.35274	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	74495	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	Grip1os2	4930564G21Rik	glutamate receptor interacting protein 1, opposite strand 2	ncRNA	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4151	chr2	4734706	4734906	+	1.35274	NA	intron (NM_178663, intron 2 of 8)	intron (NM_178663, intron 2 of 8)	16975	NM_001190400	209645	Mm.149539	NM_178663	ENSMUSG00000048186	Bend7	1110017O21Rik|E130319B15Rik	BEN domain containing 7	protein-coding	0.005000	0.353234	-46(TATGAATATTTCATC,+,0.00),-46(TATGAATATTTCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-842	chr10	57799584	57799784	+	1.35274	NA	intron (NM_020561, intron 1 of 7)	ORR1D2|LTR|ERVL-MaLR	5140	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding	0.000000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5630	chr4	97825883	97826083	+	1.35274	NA	intron (NM_001122953, intron 2 of 9)	intron (NM_001122953, intron 2 of 9)	48357	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1299	chr11	57805173	57805373	+	1.35274	NA	intron (NM_001081168, intron 1 of 3)	intron (NM_001081168, intron 1 of 3)	3636	NM_001081168	50724	Mm.340083	NM_001081168	ENSMUSG00000020519	Sap30l	2310079P12Rik|AF006998|L55	SAP30-like	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7738	chr9	76196836	76197036	+	1.35274	NA	intron (NM_205844, intron 5 of 8)	intron (NM_205844, intron 5 of 8)	16721	NR_153419	404194	Mm.213862	NM_205844	ENSMUSG00000059383	Gfral	AY457637|Gral	GDNF family receptor alpha like	protein-coding	0.010000	0.383085			-96(ATTTGAATTTCAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5893	chr5	32442316	32442516	+	1.35274	NA	Intergenic	Intergenic	-16554	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1 catalytic subunit beta	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3226	chr16	50896207	50896407	+	1.35274	NA	Intergenic	Intergenic	112898	NR_131006	78639	Mm.160109	NR_131005	ENSMUSG00000092276	1700116B05Rik	-	RIKEN cDNA 1700116B05 gene	ncRNA	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1135	chr10	128518903	128519103	+	1.35274	NA	exon (NM_011843, exon 15 of 31)	exon (NM_011843, exon 15 of 31)	6856	NM_011843	23943	Mm.66056	NM_011843	ENSMUSG00000025366	Esyt1	Fam62a|Mbc2|vp115	extended synaptotagmin-like protein 1	protein-coding	0.025000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3567	chr17	67263654	67263854	+	1.35274	NA	intron (NM_008984, intron 1 of 30)	intron (NM_008984, intron 1 of 30)	90705	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding	0.020000	0.442786			35(TTTTTAACATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6206	chr5	132652242	132652442	+	1.35274	NA	Intergenic	Intergenic	-109122	NM_001363480	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0.000000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2437	chr14	33722644	33722844	+	1.35274	NA	Intergenic	Intergenic	88539	NR_131114	218902	Mm.107791	NR_131113	ENSMUSG00000115751	4930503F20Rik	4930453C15	RIKEN cDNA 4930503F20 gene	ncRNA	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-94	chr1	33328592	33328792	+	1.35274	NA	Intergenic	Intergenic	341102	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding	0.005000	0.398010			-60(CTTCTTTTTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4975	chr3	63665320	63665520	+	1.35274	NA	Intergenic	Intergenic	-181514	NM_001369305	102637511		NM_001369305	ENSMUSG00000103476	Strit1	DWORF|Gm34302	small transmembrane regulator of ion transport 1	protein-coding	0.005000	0.398010	-31(CATGAATCATTCATG,+,0.00),-31(CATGAATCATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3570	chr17	68518364	68518564	+	1.35274	NA	intron (NM_177278, intron 12 of 20)	intron (NM_177278, intron 12 of 20)	244667	NM_177278	320858	Mm.137356	NM_177278	ENSMUSG00000041565	L3mbtl4	A730037L19Rik|D930040M24Rik	L3MBTL4 histone methyl-lysine binding protein	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7611	chr9	37090343	37090543	+	1.35274	NA	intron (NM_001029838, intron 1 of 12)	intron (NM_001029838, intron 1 of 12)	56879	NM_148950	208076	Mm.260335	NM_148950	ENSMUSG00000035934	Pknox2	D230005H23Rik|Prep2	Pbx/knotted 1 homeobox 2	protein-coding	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6077	chr5	89260005	89260205	+	1.35274	NA	Intergenic	ID_B1|SINE|B4	197793	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	vitamin D binding protein	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7093	chr7	131805677	131805877	+	1.35274	NA	Intergenic	Intergenic	-160683	NM_173410	233919	Mm.208740	NM_173410	ENSMUSG00000040125	Gpr26	9630036A11Rik|A730021D22	G protein-coupled receptor 26	protein-coding	0.025000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2953	chr15	60097891	60098091	+	1.35274	NA	Intergenic	Intergenic	-81373	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6866	chr7	56519842	56520042	+	1.35274	NA	intron (NR_157031, intron 22 of 22)	intron (NR_157031, intron 22 of 22)	280183	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p|p<cas>	oculocutaneous albinism II	protein-coding	0.010000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7665	chr9	56254928	56255128	+	1.35274	NA	intron (NM_172924, intron 4 of 6)	intron (NM_172924, intron 4 of 6)	-93958	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding	0.005000	0.293532		-6(TATACATATTCATG,+,0.00),-6(TATACATATTCATG,-,0.00)	-70(ATATCAATGACAATCC,-,0.00),-37(ATTTAAAAAGCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4173	chr2	11257734	11257934	+	1.35123	NA	intron (NM_008859, intron 11 of 17)	intron (NM_008859, intron 11 of 17)	-81655	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	-	predicted gene 13293	ncRNA	0.005000	0.388060			24(TCTCTGCCCTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5558	chr4	79741158	79741358	+	1.35123	NA	Intergenic	Intergenic	-1092955	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3650	chr17	86733768	86733968	+	1.35123	NA	Intergenic	Intergenic	-19996	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.010000	0.601990			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8063	chrX	113069397	113069597	+	1.35123	NA	intron (NM_001370788, intron 11 of 14)	L1MA9|LINE|L1	5396	NR_029849	723850		NR_029849	ENSMUSG00000065510	Mir361	Mirn361|mir-361|mmu-mir-361	microRNA 361	ncRNA	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8174	chrX	169062591	169062791	+	1.35123	NA	intron (NM_178754, intron 1 of 12)	intron (NM_178754, intron 1 of 12)	26080	NR_109847	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7795	chr9	86555638	86555838	+	1.35123	NA	TTS (NM_177208)	TTS (NM_177208)	16104	NM_028352	109785	Mm.390201	NM_028352	ENSMUSG00000056131	Pgm3	2810473H05Rik|Agm1|BB187688|C77933|PAGM|Pgm-3	phosphoglucomutase 3	protein-coding	0.005000	0.303483			-85(ATTTACATCACATAGT,-,0.00),-70(TCATTGCCATGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-54	chr1	19758168	19758368	+	1.35123	NA	Intergenic	Intergenic	546214	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4711	chr2	146919333	146919533	+	1.35123	NA	intron (NM_001033298, intron 6 of 13)	PB1D10|SINE|Alu	63553	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Kiz	Gm114|Ncrna00153|Plk1s1	kizuna centrosomal protein	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7189	chr8	30811701	30811901	+	1.35123	NA	Intergenic	Intergenic	243406	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4533	chr2	115429917	115430117	+	1.35123	NA	Intergenic	MTD|LTR|ERVL-MaLR	82184	NR_030712	100043232	Mm.240112	NR_030712	ENSMUSG00000085582	3110099E03Rik	-	RIKEN cDNA 3110099E03 gene	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3671	chr17	91849691	91849891	+	1.35123	NA	Intergenic	Lx9|LINE|L1	-756989	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.010000	0.402985			3(CAATTGGTATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4193	chr2	17939922	17940122	+	1.35123	NA	Intergenic	Intergenic	56936	NM_026627	68231	Mm.23887	NM_026627	ENSMUSG00000062651	H2al2a	1700113O17Rik|H2A.Bbd|H2A.L.2|H2afb1|H2al2|TSEG-1|Tseg1	H2A histone family member L2A	protein-coding	0.010000	0.388060			-88(ATTTACATAAAAGATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-296	chr1	104784687	104784887	+	1.35123	NA	intron (NM_011800, intron 1 of 11)	intron (NM_011800, intron 1 of 11)	16267	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.005000	0.417910			19(TGATTGTTTTGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-890	chr10	73822148	73822348	+	1.35123	NA	5' UTR (NM_001142737, exon 1 of 31)	5' UTR (NM_001142737, exon 1 of 31)	381	NM_001142742	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-265	chr1	91547684	91547884	+	1.35123	NA	intron (NM_001039126, intron 3 of 4)	intron (NM_001039126, intron 3 of 4)	6704	NM_023046	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6635	chr6	103086094	103086294	+	1.35123	NA	Intergenic	MamRep605|LTR?|LTR?	291810	NR_105792	102466636		NR_105792	ENSMUSG00000098533	Mir6373	Gm27870|mmu-mir-6373	microRNA 6373	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1302	chr11	59693270	59693470	+	1.35123	NA	intron (NM_001368931, intron 1 of 23)	Lx9|LINE|L1	30863	NM_001368931	26936	Mm.2402	NM_012027	ENSMUSG00000005417	Mprip	9530046C02|AA536749|AI647711|C76423|Gm34094|RIP3|Rhoip3|mKIAA0864|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.000000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6413	chr6	39848847	39849047	+	1.35123	NA	Intergenic	RMER1B|Other|Other	-22489	NM_001360978	434008	Mm.53915	NM_001004182	ENSMUSG00000057716	Tmem178b	A930009E05Rik|EG434008|Gm5567	transmembrane protein 178B	protein-coding	0.010000	0.582090			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5165	chr3	125746175	125746375	+	1.35123	NA	Intergenic	Intergenic	192377	NR_149311	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding	0.000000	0.343284	24(TGTACATAATGCATT,+,0.00),24(TGTACATAATGCATT,-,0.00)		-11(TCTTTGCAATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2813	chr15	19995101	19995301	+	1.35123	NA	Intergenic	RLTR13G|LTR|ERVK	671549	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5786	chr4	145377425	145377625	+	1.35123	NA	Intergenic	RLTR13B1|LTR|ERVK	-62361	NM_009401	21941	Mm.12810	NM_009401	ENSMUSG00000028602	Tnfrsf8	Cd30|D1S166E|Ki|Ki-1	tumor necrosis factor receptor superfamily, member 8	protein-coding	0.035000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1082	chr10	118678908	118679108	+	1.35123	NA	Intergenic	Intergenic	36718	NR_155867	102636202	Mm.407006	NR_155867		Gm33337	-	predicted gene, 33337	ncRNA	0.030000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5532	chr4	70912716	70912916	+	1.35123	NA	Intergenic	Intergenic	-377888	NM_172694	230316	Mm.251188	NM_172694	ENSMUSG00000039270	Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding	0.000000	0.243781			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7541	chr9	16518650	16518850	+	1.35123	NA	Intergenic	Intergenic	-16696	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6182	chr5	127661016	127661216	+	1.35123	NA	intron (NM_177005, intron 4 of 11)	ID_B1|SINE|B4	28854	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7996	chrX	78482988	78483188	+	1.35123	NA	intron (NM_001289683, intron 4 of 4)	intron (NM_001289683, intron 4 of 4)	100717	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4567	chr2	122682960	122683160	+	1.35123	NA	3' UTR (NM_001290993, exon 6 of 6)	3' UTR (NM_001290993, exon 6 of 6)	19603	NM_001290993	22785	Mm.27801	NM_011774	ENSMUSG00000005802	Slc30a4	Znt4|lm|znT-4	solute carrier family 30 (zinc transporter), member 4	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6422	chr6	43619431	43619631	+	1.35123	NA	intron (NM_001311111, intron 2 of 7)	intron (NM_001311111, intron 2 of 7)	46747	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-474	chr1	154812743	154812943	+	1.35123	NA	Intergenic	Intergenic	-86923	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6292	chr6	7578129	7578329	+	1.35123	NA	Intergenic	Intergenic	23168	NM_001311060	21333	Mm.1440	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6457	chr6	54082529	54082729	+	1.35123	NA	intron (NM_001163640, intron 1 of 12)	intron (NM_001163640, intron 1 of 12)	42697	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3406	chr17	3730545	3730745	+	1.35123	NA	Intergenic	MIR|SINE|MIR	-34384	NM_198958	224480	Mm.328756	NM_198958	ENSMUSG00000023802	Nox3	GP91-3|het|nmf250	NADPH oxidase 3	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-874	chr10	68684165	68684365	+	1.35123	NA	Intergenic	Intergenic	-39481	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-789	chr10	40363103	40363303	+	1.35123	NA	intron (NM_001291816, intron 1 of 11)	RMER10A|LTR|ERVL	13895	NM_198164	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding	0.005000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8156	chrX	165524538	165524738	+	1.35123	NA	Intergenic	Lx9|LINE|L1	-196771	NM_001357099	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	glycine receptor, alpha 2 subunit	protein-coding	0.000000	0.373134			-57(CTGTGCATAAAAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7794	chr9	86518363	86518563	+	1.35123	NA	intron (NM_177208, intron 20 of 38)	intron (NM_177208, intron 20 of 38)	51309	NM_177208	320615	Mm.245500	NM_177208	ENSMUSG00000034973	Dop1a	B130005I07Rik|BC035275|C130028L17|D9Ertd809e|Dopey1	DOP1 leucine zipper like protein A	protein-coding	0.000000	0.323383			10(ATTTCCATAACAGTAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8144	chrX	162541919	162542119	+	1.35123	NA	intron (NM_178256, intron 5 of 17)	intron (NM_178256, intron 5 of 17)	23497	NM_001359104	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1698	chr12	65456958	65457158	+	1.35123	NA	Intergenic	Intergenic	231541	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20rt	4921538B03Rik|4930427E19Rik|Wdr20|Wdr20b	WD repeat domain 20, retrogene	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1574	chr12	27745517	27745717	+	1.35123	NA	Intergenic	B4|SINE|B4	-402899	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-993	chr10	105867957	105868157	+	1.35123	NA	Intergenic	Intergenic	26578	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5398	chr4	28095027	28095227	+	1.35123	NA	Intergenic	Intergenic	-718004	NM_001290434	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2991	chr15	73305039	73305239	+	1.35123	NA	intron (NM_001358045, intron 9 of 33)	intron (NM_001358045, intron 9 of 33)	-50257	NR_029561	387169		NR_029561	ENSMUSG00000065612	Mir151	Mirn151|mir-151|mmu-mir-151	microRNA 151	ncRNA	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-110	chr1	38470766	38470966	+	1.35123	NA	intron (NM_001290814, intron 4 of 21)	intron (NM_001290814, intron 4 of 21)	156378	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding	0.035000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4345	chr2	62465987	62466187	+	1.35123	NA	Intergenic	L1ME3|LINE|L1	17566	NM_008100	14526	Mm.45494	NM_008100	ENSMUSG00000000394	Gcg	GLP-1|Glu|PPG	glucagon	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1662	chr12	53401726	53401926	+	1.35123	NA	intron (NM_001370962, intron 2 of 11)	intron (NM_001370962, intron 2 of 11)	153394	NM_001370960	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2716	chr14	117851682	117851882	+	1.35123	NA	intron (NM_001079844, intron 4 of 9)	intron (NM_001079844, intron 4 of 9)	102065	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7871	chr9	106359395	106359595	+	1.35083	NA	Intergenic	Intergenic	-9137	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding	0.020000	0.611940			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-533	chr1	169341144	169341344	+	1.35083	NA	Intergenic	LTR88c|LTR|Gypsy?	190220	NM_001355159	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	NUF2, NDC80 kinetochore complex component	protein-coding	0.005000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-330	chr15	10277080	10277280	+	1.34953	NA	intron (NM_001253781, intron 1 of 9)	intron (NM_001253781, intron 1 of 9)	-16471	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0.000000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-547	chr2	178665045	178665245	+	1.34821	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	234630	NM_001291189	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4809	chr2	178665024	178665224	+	1.34821	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	234609	NM_001291189	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2958	chr15	62216152	62216352	+	1.34821	NA	intron (NR_132747, intron 2 of 4)	intron (NR_132747, intron 2 of 4)	3199	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo	0.015000	0.492537			-65(TATCTGCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3149	chr16	29799709	29799909	+	1.34821	NA	Intergenic	Intergenic	179315	NR_037689	328657	Mm.425982	NM_001033403	ENSMUSG00000075286	Gm1968	-	predicted gene 1968	ncRNA	0.005000	0.338308			66(ATTAGCATTAGAATTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2328	chr13	118886673	118886873	+	1.34730	NA	Intergenic	Intergenic	172074	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding	0.010000	0.447761			12(CTATTGTCATACAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2762	chr15	6300761	6300961	+	1.34730	NA	intron (NM_001008702, intron 1 of 13)	B1_Mus1|SINE|Alu	1072	NM_001008702	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding	0.005000	0.407960			57(TCAGACTTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1928	chr13	5160113	5160313	+	1.34730	NA	Intergenic	Intergenic	-551049	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4676	chr2	140275250	140275450	+	1.34730	NA	intron (NM_001033296, intron 5 of 19)	intron (NM_001033296, intron 5 of 19)	104704	NM_027093	69487	Mm.287921	NM_027093	ENSMUSG00000027384	Ndufaf5	2310003L22Rik	NADH:ubiquinone oxidoreductase complex assembly factor 5	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4245	chr2	31057884	31058084	+	1.34730	NA	intron (NM_001038700, intron 7 of 14)	intron (NM_001038700, intron 7 of 14)	38516	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding	0.005000	0.432836			13(ATTTTAAAAAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-986	chr10	103827806	103828006	+	1.34730	NA	Intergenic	L1MC4|LINE|L1	-315081	NM_001270899	627488	Mm.441727	NM_001270899	ENSMUSG00000097427	Gm6763	EG627488|Gm21293	predicted gene 6763	protein-coding	0.005000	0.263682			33(ATCTGTATAAGAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4134	chr19	58369953	58370153	+	1.34730	NA	intron (NM_001285457, intron 4 of 9)	intron (NM_001285457, intron 4 of 9)	73849	NR_040449	791347	Mm.452208	NR_040449		Gm10007	-	predicted gene 10007	ncRNA	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1322	chr11	65684922	65685122	+	1.34730	NA	Intergenic	L1M4a1|LINE|L1	49810	NR_030417	791070		NR_030417	ENSMUSG00000076460	Mir744	Mirn744|mir-744|mmu-mir-744	microRNA 744	ncRNA	0.005000	0.353234		3(ATTTAATATGCATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2824	chr15	24527525	24527725	+	1.34730	NA	Intergenic	B2_Mm2|SINE|B2	886139	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5274	chr3	148663406	148663606	+	1.34730	NA	Intergenic	Intergenic	291129	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.000000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3550	chr17	62861379	62861579	+	1.34730	NA	intron (NM_207654, intron 1 of 4)	intron (NM_207654, intron 1 of 4)	19838	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0.025000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-837	chr10	57595333	57595533	+	1.34667	NA	Intergenic	Lx4A|LINE|L1	-36548	NM_008863	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5923	chr5	44627831	44628031	+	1.34667	NA	intron (NM_001077398, intron 2 of 8)	MIR|SINE|MIR	171815	NM_001359070	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2405	chr14	25690000	25690200	+	1.34667	NA	Intergenic	Intergenic	-4070	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4195	chr2	18149015	18149215	+	1.34667	NA	intron (NR_045539, intron 11 of 24)	intron (NR_045539, intron 11 of 24)	84530	NR_045538	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding	0.000000	0.293532			-1(ATTTGCAAGTGAAGGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7457	chr8	115201614	115201814	+	1.34667	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	505180	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5472	chr4	53656271	53656471	+	1.34667	NA	intron (NM_001195284, intron 5 of 12)	intron (NM_001195284, intron 5 of 12)	24900	NM_001355377	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl	fibronectin type III and SPRY domain containing 1-like	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6139	chr5	107379653	107379853	+	1.34667	NA	intron (NM_054054, intron 18 of 18)	L1MA4|LINE|L1	-23760	NM_001001804	384214	Mm.489863	NM_001001804	ENSMUSG00000033805	Ephx4	Abhd7|Ephxrp|Gm1382	epoxide hydrolase 4	protein-coding	0.005000	0.402985			-93(ATATACATGACAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3909	chr18	65661360	65661560	+	1.34667	NA	intron (NM_001361052, intron 6 of 8)	intron (NM_001361052, intron 6 of 8)	-36808	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-588	chr3	138841292	138841492	+	1.34667	NA	intron (NR_121195, intron 1 of 7)	intron (NR_121195, intron 1 of 7)	99184	NR_121195	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3958	chr18	81439992	81440192	+	1.34667	NA	Intergenic	Intergenic	-453071	NM_001369133	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	spalt like transcription factor 3	protein-coding	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-380	chr1	131020687	131020887	+	1.34660	NA	intron (NM_010548, intron 1 of 4)	intron (NM_010548, intron 1 of 4)	942	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2957	chr15	62113026	62113226	+	1.34660	NA	intron (NR_132746, intron 2 of 6)	RLTR11A2|LTR|ERVK	73869	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	Pvt1 oncogene	ncRNA	0.015000	0.447761			0(CTTTTGTTGTGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6335	chr6	17941941	17942141	+	1.34660	NA	intron (NM_001083315, intron 14 of 14)	intron (NM_001083315, intron 14 of 14)	88404	NM_023653	22413	Mm.33653	NM_023653	ENSMUSG00000010797	Wnt2	2610510E18Rik|Int1l1|Irp|Mirp|Wnt-2|Wnt2a	wingless-type MMTV integration site family, member 2	protein-coding	0.010000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-671	chr5	49989877	49990077	+	1.34649	NA	intron (NM_133911, intron 11 of 18)	intron (NM_133911, intron 11 of 18)	69019	NM_133911	70693	Mm.272974	NM_133911	ENSMUSG00000029090	Adgra3	3830613O22Rik|AU044632|Gpr125|Tem5-like	adhesion G protein-coupled receptor A3	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5942	chr5	49989879	49990079	+	1.34649	NA	intron (NM_133911, intron 11 of 18)	intron (NM_133911, intron 11 of 18)	69017	NM_133911	70693	Mm.272974	NM_133911	ENSMUSG00000029090	Adgra3	3830613O22Rik|AU044632|Gpr125|Tem5-like	adhesion G protein-coupled receptor A3	protein-coding	0.015000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-679	chr5	64280125	64280325	+	1.34598	NA	intron (NM_019636, intron 10 of 19)	intron (NM_019636, intron 10 of 19)	49868	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2577	chr14	78747365	78747565	+	1.34549	NA	Intergenic	Intergenic	-14736	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding	0.005000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-590	chr3	143864392	143864592	+	1.34515	NA	Intergenic	Intergenic	-152349	NR_040405	621809	Mm.360134	NR_040405	ENSMUSG00000105279	Gm6260	EG621809	predicted gene 6260	ncRNA	0.025000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5671	chr4	105323206	105323406	+	1.34515	NA	Intergenic	Intergenic	165959	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|PRG-2|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding	0.025000	0.497512			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-541	chr2	159239409	159239609	+	1.34515	NA	Intergenic	L1MA6|LINE|L1	444702	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding	0.005000	0.353234		-37(CATGAATATGTACA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8020	chrX	93301946	93302146	+	1.34364	NA	Intergenic	Intergenic	15539	NM_007492	11878	Mm.275547	NM_007492	ENSMUSG00000035277	Arx	Arx1	aristaless related homeobox	protein-coding	0.025000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8139	chrX	160618976	160619176	+	1.34364	NA	Intergenic	L1MEd|LINE|L1	100896	NM_011147	237178	Mm.296779	NM_011147	ENSMUSG00000062168	Ppef1	PPEF-1	protein phosphatase with EF hand calcium-binding domain 1	protein-coding	0.020000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7534	chr9	14839562	14839762	+	1.34364	NA	Intergenic	Intergenic	-20548	NM_010287	14608	Mm.4672	NM_010287	ENSMUSG00000031932	Gpr83	AW045253|Gir|Gpr72|RP105|RP39|RP82	G protein-coupled receptor 83	protein-coding	0.025000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6702	chr6	119826496	119826696	+	1.34364	NA	intron (NR_104484, intron 1 of 20)	MER46C|DNA|TcMar-Tigger	21554	NR_155458	111173	Mm.288860	NM_053204	ENSMUSG00000030172	Erc1	4930404L01Rik|5033405M01Rik|9630025C19Rik|B430107L16Rik|CAST2|ELKS|Elks1|RAB6IP2A|RAB6IP2B|Rab6ip2|mKIAA1081	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.015000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8118	chrX	151859146	151859346	+	1.34364	NA	promoter-TSS (NR_130340)	promoter-TSS (NR_130340)	-316	NR_130340	100526542		NR_130340	ENSMUSG00000093219	Mir3113	mmu-mir-3113	microRNA 3113	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6595	chr6	94327407	94327607	+	1.34364	NA	Intergenic	Intergenic	-43590	NM_001286784	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4693	chr2	142724313	142724513	+	1.34364	NA	intron (NM_001355123, intron 17 of 26)	intron (NM_001355123, intron 17 of 26)	177051	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3092	chr16	13707396	13707596	+	1.34364	NA	Intergenic	BGLII_A|LTR|ERVK	-22340	NR_040574	76684	Mm.491043	NR_040574	ENSMUSG00000086550	Pla2g10os	1810007I06Rik	phospholipase A2, group X, opposite strand	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5408	chr4	31686257	31686457	+	1.34364	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-277750	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.000000	0.422886			-29(GTTTAAATAAGAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2202	chr13	92454104	92454304	+	1.34364	NA	intron (NM_001163627, intron 5 of 5)	intron (NM_001163627, intron 5 of 5)	28235	NM_175455	218440	Mm.213623	NM_175455	ENSMUSG00000045034	Ankrd34b	6430502M16Rik|DP58	ankyrin repeat domain 34B	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5931	chr5	47979513	47979713	+	1.34364	NA	Intergenic	Intergenic	-3542	NM_001291227	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|b2b1200.1Clo|mKIAA4141|slit-2	slit guidance ligand 2	protein-coding	0.015000	0.457711			-2(CCTTTTTCATGTTTAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6634	chr6	102833226	102833426	+	1.34335	NA	Intergenic	Intergenic	38942	NR_105792	102466636		NR_105792	ENSMUSG00000098533	Mir6373	Gm27870|mmu-mir-6373	microRNA 6373	ncRNA	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4198	chr2	20068579	20068779	+	1.34335	NA	Intergenic	L1MB8|LINE|L1	-221234	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.000000	0.323383		16(TGTGAATATTCATG,+,0.00),16(TGTGAATATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2205	chr13	92880220	92880420	+	1.34335	NA	Intergenic	Intergenic	35552	NM_001162945	382793	Mm.296770	NM_001162945	ENSMUSG00000021704	Mtx3	4930470O13Rik|AA409304|AI853833|AU067765|EG624619|Gm1194|Gm6514	metaxin 3	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1569	chr12	25729782	25729982	+	1.34335	NA	Intergenic	Intergenic	480623	NR_131149	629481	Mm.390460	NR_131149	ENSMUSG00000113550	Gm29687	-	predicted gene, 29687	ncRNA	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8002	chrX	84708827	84709027	+	1.34335	NA	intron (NM_007868, intron 55 of 78)	GA-rich|Low_complexity|Low_complexity	-339368	NM_001314037	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-828	chr10	54376612	54376812	+	1.34335	NA	Intergenic	Intergenic	300790	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6385	chr6	33884650	33884850	+	1.34335	NA	intron (NM_009148, intron 14 of 17)	intron (NM_009148, intron 14 of 17)	-144698	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7328	chr8	77510592	77510792	+	1.34335	NA	intron (NM_001363418, intron 1 of 21)	intron (NM_001363418, intron 1 of 21)	-6364	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA	0.010000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7277	chr8	60113362	60113562	+	1.34335	NA	Intergenic	Intergenic	287813	NR_126087	75017	Mm.60775	NR_126087	ENSMUSG00000110406	4930470O06Rik	-	RIKEN cDNA 4930470O06 gene	ncRNA	0.005000	0.383085			41(AAACTGTTATGAAAAT,+,0.00),49(ATGAAAATGAAAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5571	chr4	83058699	83058899	+	1.34335	NA	Intergenic	L1MA5|LINE|L1	-6633	NM_001198811	329872	Mm.242337	NM_177863	ENSMUSG00000059049	Frem1	BC037594|D430009N09|D630008K06|crf11|eye<m02Jus>|eyes2|heb|qbrick	Fras1 related extracellular matrix protein 1	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1436	chr11	102145378	102145578	+	1.34335	NA	promoter-TSS (NM_145829)	promoter-TSS (NM_145829)	-35	NM_145829	217214	Mm.31686	NM_145829	ENSMUSG00000048217	Nags	1700120E20Rik|argA	N-acetylglutamate synthase	protein-coding	0.055000	0.631841			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-772	chr10	36625399	36625599	+	1.34335	NA	intron (NM_001253355, intron 2 of 5)	intron (NM_001253355, intron 2 of 5)	118692	NM_001081208	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7438	chr8	108220551	108220751	+	1.34335	NA	Intergenic	RMER1A|Other|Other	364026	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA	0.010000	0.492537			-47(ATTTTCACTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2373	chr14	16313997	16314197	+	1.34335	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-51109	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3083	chr16	11619831	11620031	+	1.34335	NA	intron (NM_028964, intron 15 of 20)	intron (NM_028964, intron 15 of 20)	-159771	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA	0.005000	0.323383			-84(ACATTGTTATGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4679	chr2	140635542	140635742	+	1.34335	NA	intron (NM_001013802, intron 3 of 18)	intron (NM_001013802, intron 3 of 18)	35834	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0.010000	0.378109		-78(ACTTAATATGCATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6305	chr6	12038173	12038373	+	1.34335	NA	intron (NM_001362122, intron 15 of 16)	intron (NM_001362122, intron 15 of 16)	71307	NR_003631	625347	Mm.389084	NM_001039041	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-159	chr1	55162792	55162992	+	1.34335	NA	Intergenic	Intergenic	31647	NM_025283	19070	Mm.291037	NM_025283	ENSMUSG00000025979	Mob4	2610109B12Rik|Mobkl3|Phocn|Prei3	MOB family member 4, phocein	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2118	chr13	68905923	68906123	+	1.34335	NA	intron (NM_153534, intron 2 of 24)	intron (NM_153534, intron 2 of 24)	93518	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5763	chr4	136636316	136636516	+	1.34335	NA	intron (NM_001243262, intron 7 of 7)	intron (NM_001243262, intron 7 of 7)	13795	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5851	chr5	19951048	19951248	+	1.34335	NA	intron (NM_015823, intron 1 of 21)	intron (NM_015823, intron 1 of 21)	43630	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7021	chr7	110247931	110248131	+	1.34335	NA	intron (NM_009302, intron 2 of 11)	L1MB8|LINE|L1	26328	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-346	chr1	124653360	124653560	+	1.34335	NA	Intergenic	Intergenic	-607901	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.000000	0.383085			-55(ATGTCCATGACTAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2395	chr14	22233183	22233383	+	1.34335	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	213571	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	Lrmda	1700112E06Rik|2700009F18Rik	leucine rich melanocyte differentiation associated	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5089	chr3	101291354	101291554	+	1.34335	NA	Intergenic	MER34A1|LTR|ERV1	-3515	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4814	chr2	180521565	180521765	+	1.34335	NA	intron (NM_018766, intron 1 of 3)	intron (NM_018766, intron 1 of 3)	21689	NM_018766	18216	Mm.301712	NM_018766	ENSMUSG00000027568	Ntsr1	NT-1R|NTR-1|NTR1	neurotensin receptor 1	protein-coding	0.020000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7954	chrX	42803591	42803791	+	1.34335	NA	intron (NM_011855, intron 12 of 32)	ORR1D1-int|LTR|ERVL-MaLR	298369	NM_001313691	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1596	chr12	34894889	34895089	+	1.34335	NA	intron (NM_001271386, intron 2 of 27)	intron (NM_001271386, intron 2 of 27)	22106	NM_001271386	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3966	chr18	83427626	83427826	+	1.34335	NA	Intergenic	MER44D|DNA|TcMar-Tigger	-101842	NR_045361	70960	Mm.410834	NR_045361	ENSMUSG00000118333	4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA	0.020000	0.343284			-63(TCAATGTGATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-247	chr1	86691176	86691376	+	1.34335	NA	Intergenic	L1MA8|LINE|L1	-12528	NM_153530	208718	Mm.389152	NM_153530	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 like 3'-5' exoribonuclease 2	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7979	chrX	68366473	68366673	+	1.34335	NA	Intergenic	Intergenic	311826	NR_033481	100038638	Mm.368431	NR_033481	ENSMUSG00000096946	Fmr1os	Asfmr1|Gm10474	fragile X mental retardation 1, opposite strand	ncRNA	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5425	chr4	35571802	35572002	+	1.34335	NA	Intergenic	Intergenic	273302	NM_175516	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5014	chr3	75388185	75388385	+	1.34335	NA	intron (NM_001370850, intron 3 of 13)	intron (NM_001370850, intron 3 of 13)	42952	NM_001370850	213248	Mm.245572	NM_001370850	ENSMUSG00000104301	Wdr49	EG213248	WD repeat domain 49	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5443	chr4	44949025	44949225	+	1.34335	NA	Intergenic	Intergenic	-32269	NM_080289	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik|Glxr	glyoxylate reductase/hydroxypyruvate reductase	protein-coding	0.020000	0.457711			21(ATTTAAATGGCTAAGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-280	chr14	21507498	21507698	+	1.34324	NA	intron (NM_017479, intron 1 of 16)	intron (NM_017479, intron 1 of 16)	7813	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding	0.000000	0.293532			-13(TCATTTTCATGGTGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-855	chr9	6845221	6845421	+	1.34273	NA	Intergenic	RLTR13D3|LTR|ERVK	-331269	NM_001357484	76863	Mm.27293	NM_029775	ENSMUSG00000032002	Dcun1d5	3110001A18Rik|4833420K19Rik|AW060460|D430047L21Rik	DCN1, defective in cullin neddylation 1, domain containing 5 (S. cerevisiae)	protein-coding	0.015000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-42	chr1	143853264	143853464	+	1.34273	NA	Intergenic	Intergenic	76086	NM_001159866	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding	0.000000	0.407960			7(CTTAGCAAAAGAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5635	chr4	98948947	98949147	+	1.34108	NA	intron (NM_001290636, intron 42 of 48)	L2a|LINE|L2	25237	NM_001301414	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5815	chr5	5291025	5291225	+	1.34108	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	-25057	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding	0.020000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7097	chr7	133441425	133441625	+	1.33926	NA	Intergenic	Intergenic	160590	NM_028654	73808	Mm.159067	NM_028654	ENSMUSG00000030976	Tex36	4930404H21Rik	testis expressed 36	protein-coding	0.010000	0.427861			-76(ATTTACATGCTAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3618	chr17	80736297	80736497	+	1.33926	NA	Intergenic	B1F2|SINE|Alu	-8372	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2421	chr14	30516221	30516421	+	1.33926	NA	intron (NM_133761, intron 6 of 9)	intron (NM_133761, intron 6 of 9)	-25165	NM_028981	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding	0.000000	0.303483			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-610	chr4	21922696	21922896	+	1.33926	NA	Intergenic	Intergenic	-8530	NM_175234	76132	Mm.159689	NM_175234	ENSMUSG00000028246	Faxc	6230409E13Rik|AW742931	failed axon connections homolog	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1940	chr13	9346252	9346452	+	1.33926	NA	intron (NM_001081426, intron 1 of 36)	intron (NM_001081426, intron 1 of 36)	69827	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding	0.005000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-219	chr12	117472723	117472923	+	1.33926	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-43656	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding	0.005000	0.417910			20(AATTTGCTATTCTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-557	chr3	56159187	56159387	+	1.33926	NA	intron (NM_030595, intron 1 of 57)	intron (NM_030595, intron 1 of 57)	24414	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding	0.015000	0.343284			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-282	chr14	30516320	30516520	+	1.33926	NA	intron (NM_133761, intron 6 of 9)	intron (NM_133761, intron 6 of 9)	-25264	NM_028981	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7488	chr8	126883916	126884116	+	1.33926	NA	Intergenic	Intergenic	34996	NR_151740	414091	Mm.240068	NM_001033546		A630001O12Rik	Gm45803	RIKEN cDNA A630001O12 gene	ncRNA	0.005000	0.462687			-61(CTTTAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1762	chr12	79535499	79535699	+	1.33891	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	238248	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6769	chr6	146413594	146413794	+	1.33891	NA	intron (NM_019923, intron 9 of 56)	intron (NM_019923, intron 9 of 56)	88529	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding	0.005000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-669	chr5	47775930	47776130	+	1.33891	NA	Intergenic	L2b|LINE|L2	-207125	NM_001291227	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|b2b1200.1Clo|mKIAA4141|slit-2	slit guidance ligand 2	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2335	chr14	7928507	7928707	+	1.33844	NA	intron (NM_001081427, intron 34 of 45)	intron (NM_001081427, intron 34 of 45)	-28693	NM_001371278									0.005000	0.343284			13(TTGTTTTCTTGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1901	chr12	116959300	116959500	+	1.33844	NA	intron (NM_011215, intron 11 of 22)	RLTR30E_MM|LTR|ERV1	191869	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.005000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6272	chr5	151056227	151056427	+	1.33844	NA	intron (NR_153382, intron 7 of 13)	intron (NR_153382, intron 7 of 13)	103720	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding	0.025000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5900	chr5	33922893	33923093	+	1.33844	NA	intron (NM_011914, intron 1 of 10)	intron (NM_011914, intron 1 of 10)	13278	NM_011914	24116	Mm.332320	NM_011914	ENSMUSG00000029111	Nelfa	Whsc2|Whsc2h	negative elongation factor complex member A, Whsc2	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3176	chr16	38285925	38286125	+	1.33844	NA	intron (NM_001098404, intron 1 of 8)	L1MB2|LINE|L1	8799	NM_001098404	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding	0.025000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6208	chr5	133823917	133824117	+	1.33844	NA	Intergenic	Intergenic	-275731	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Castor2	7530428J21Rik|AW742413|Gats|Gatsl1|Gatsl2	cytosolic arginine sensor for mTORC1 subunit 2	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5076	chr3	98429797	98429997	+	1.33844	NA	3' UTR (NM_172863, exon 3 of 3)	3' UTR (NM_172863, exon 3 of 3)	27134	NM_001111336	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding	0.015000	0.482587			70(ATTTATATCATAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7577	chr9	28983144	28983344	+	1.33844	NA	Intergenic	Intergenic	429441	NM_001357602	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5899	chr5	33922659	33922859	+	1.33844	NA	intron (NM_011914, intron 1 of 10)	intron (NM_011914, intron 1 of 10)	13512	NM_011914	24116	Mm.332320	NM_011914	ENSMUSG00000029111	Nelfa	Whsc2|Whsc2h	negative elongation factor complex member A, Whsc2	protein-coding	0.005000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-262	chr13	96615205	96615405	+	1.33844	NA	intron (NM_023420, intron 9 of 17)	intron (NM_023420, intron 9 of 17)	55631	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1868	chr12	104396967	104397167	+	1.33596	NA	Intergenic	RLTR13D3A|LTR|ERVK	-9641	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2164	chr13	80293450	80293650	+	1.33596	NA	Intergenic	Intergenic	-589834	NR_153410	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6935	chr7	83500762	83500962	+	1.33596	NA	Intergenic	Intergenic	-84069	NM_177695	233424	Mm.486619	NM_177695	ENSMUSG00000038540	Tmc3	9030203A06	transmembrane channel-like gene family 3	protein-coding	0.000000	0.388060			45(ATTTGAATAATACAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6068	chr5	85937572	85937772	+	1.33596	NA	Intergenic	Intergenic	127911	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding	0.030000	0.402985			69(ATTTGTATAGCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6834	chr7	41582158	41582358	+	1.33596	NA	Intergenic	MLTR18B_MM|LTR|ERVK	-51273	NM_001360677	67607	Mm.384626	NM_023363	ENSMUSG00000074165	Zfp788	2810426N06Rik|AI256342|AI605193	zinc finger protein 788	protein-coding	0.000000	0.383085			-33(CCATTCTTATGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3849	chr18	51612059	51612259	+	1.33596	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	494261	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6873	chr7	62486249	62486449	+	1.33596	NA	Intergenic	Intergenic	-21839	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1213	chr11	27481908	27482108	+	1.33596	NA	Intergenic	Intergenic	696900	NR_002890	654472	Mm.347777	NR_002890		Gm12070	-	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-505	chr1	162336737	162336937	+	1.33596	NA	intron (NM_001038619, intron 4 of 20)	intron (NM_001038619, intron 4 of 20)	113469	NR_029796	387210		NR_029796	ENSMUSG00000065516	Mir214	Mirn214|mir-214|mmu-mir-214	microRNA 214	ncRNA	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1212	chr11	27481793	27481993	+	1.33596	NA	Intergenic	Intergenic	696785	NR_002890	654472	Mm.347777	NR_002890		Gm12070	-	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4907	chr3	35173870	35174070	+	1.33596	NA	Intergenic	Intergenic	-251319	NR_105799	102466155		NR_105799	ENSMUSG00000098862	Mir6378	Gm27706|mmu-mir-6378	microRNA 6378	ncRNA	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4088	chr19	38356442	38356642	+	1.33596	NA	Intergenic	Intergenic	-39438	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-638	chr1	190852480	190852680	+	1.33596	NA	intron (NM_178775, intron 6 of 14)	intron (NM_178775, intron 6 of 14)	59190	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4261	chr2	38380556	38380756	+	1.33596	NA	Intergenic	L1ME4b|LINE|L1	29348	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5226	chr3	138112621	138112821	+	1.33596	NA	intron (NM_001163457, intron 10 of 19)	intron (NM_001163457, intron 10 of 19)	18932	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3831	chr18	46381059	46381259	+	1.33596	NA	Intergenic	Intergenic	-69231	NM_001160399	240261	Mm.329416	NM_001160399	ENSMUSG00000071855	Ccdc112	8430438M01Rik|AW108467	coiled-coil domain containing 112	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3224	chr16	50537987	50538187	+	1.33596	NA	intron (NR_040380, intron 2 of 4)	intron (NR_040380, intron 2 of 4)	9585	NR_040379	619312	Mm.427671	NR_040379	ENSMUSG00000097694	G730013B05Rik	linc-Cblb|linc1610	RIKEN cDNA G730013B05 gene	ncRNA	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-307	chr1	106612600	106612800	+	1.33560	NA	intron (NM_009741, intron 1 of 1)	intron (NM_009741, intron 1 of 1)	-66069	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA	0.010000	0.432836			18(CAATTAGTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1493	chr11	117814152	117814352	+	1.33560	NA	TTS (NM_009304)	TTS (NM_009304)	4585	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding	0.020000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3593	chr17	75278286	75278486	+	1.33560	NA	intron (NM_206958, intron 8 of 29)	intron (NM_206958, intron 8 of 29)	99605	NM_206958	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding	0.005000	0.333333			82(GTTAGCATGACAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3088	chr16	12780661	12780861	+	1.33560	NA	Intergenic	Intergenic	-30629	NR_040507	75493	Mm.396146	NR_040507	ENSMUSG00000101565	1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	ncRNA	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6013	chr5	69450141	69450341	+	1.33560	NA	Intergenic	Intergenic	92406	NM_023784	75581	Mm.154776	NM_023784	ENSMUSG00000029158	Yipf7	2310016N21Rik|Yip1b	Yip1 domain family, member 7	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4581	chr2	124912352	124912552	+	1.33560	NA	Intergenic	Intergenic	-155675	NM_175034	317750	Mm.330538	NM_175034	ENSMUSG00000035183	Slc24a5	F630045L20Rik|JSX|NCKX5|NCX5|Oca6	solute carrier family 24, member 5	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5974	chr5	58660055	58660255	+	1.33560	NA	Intergenic	Intergenic	-207157	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA	0.005000	0.358209			0(CCACTGGCATGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5545	chr4	76812111	76812311	+	1.33560	NA	intron (NR_160919, intron 8 of 39)	Eulor6B|DNA?|DNA?	-467968	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.000000	0.358209	-52(TATGATTATTTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2355	chr14	11503801	11504001	+	1.33560	NA	Intergenic	Intergenic	-49652	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7453	chr8	114384233	114384433	+	1.33560	NA	Intergenic	Intergenic	-32855	NR_045831	71122	Mm.437539	NR_045831		4933408N05Rik	-	RIKEN cDNA 4933408N05 gene	ncRNA	0.005000	0.502488			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-638	chr4	98811888	98812088	+	1.33560	NA	intron (NM_172872, intron 1 of 9)	intron (NM_172872, intron 1 of 9)	5549	NM_172872	242553	Mm.440211	NM_172872	ENSMUSG00000035407	Kank4	AU021071|Ankrd38|BC060737|C130031J23	KN motif and ankyrin repeat domains 4	protein-coding	0.040000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7136	chr8	4466490	4466690	+	1.33560	NA	Intergenic	Lx9|LINE|L1	-26815	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6359	chr6	24169432	24169632	+	1.33560	NA	Intergenic	Intergenic	-1440	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding	0.000000	0.298507			29(ATCTGAATAACAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2038	chr13	40575592	40575792	+	1.33203	NA	Intergenic	Intergenic	-152116	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA	0.010000	0.432836			-8(GTTTTGTTTTTAAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-449	chr18	78731540	78731740	+	1.33203	NA	Intergenic	Intergenic	-134690	NM_207651	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding	0.010000	0.527363			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-561	chr3	67885248	67885448	+	1.33203	NA	Intergenic	Intergenic	-6872	NM_001113419	100505386	Mm.331064	NM_001113419	ENSMUSG00000102422	Iqschfp	Gm21949|Iqcj-schip1|Schip-1-iqcj|Schip1	Iqcj and Schip1 fusion protein	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3972	chr18	84267428	84267628	+	1.33203	NA	intron (NM_001033341, intron 8 of 8)	L1M5|LINE|L1	179370	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3242	chr16	55536783	55536983	+	1.33192	NA	Intergenic	Intergenic	42152	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2491	chr14	55078031	55078231	+	1.33192	NA	intron (NM_001039198, intron 1 of 9)	intron (NM_001039198, intron 1 of 9)	5040	NR_004444	432855	Mm.490799	NR_004444		Zfhx2os	Zfhx2as	zinc finger homeobox 2, opposite strand	ncRNA	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3440	chr17	22355920	22356120	+	1.33192	NA	intron (NM_001355280, intron 3 of 6)	intron (NM_001355280, intron 3 of 6)	5380	NM_001355280	319615	Mm.442162	NM_176962	ENSMUSG00000033972	Zfp944	6330416L07Rik	zinc finger protein 944	protein-coding	0.000000	0.313433			5(TTTTTTTTTTTTAAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-801	chr7	95774480	95774680	+	1.33192	NA	Intergenic	Intergenic	-396664	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-165	chr11	99427769	99427969	+	1.33108	NA	TTS (NM_023256)	TTS (NM_023256)	-5610	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding	0.000000	0.343284			20(ATTAGCATGAGAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-661	chr1	194852608	194852808	+	1.33108	NA	Intergenic	L1MA5|LINE|L1	30707	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA	0.005000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1431	chr11	99427734	99427934	+	1.33108	NA	TTS (NM_023256)	TTS (NM_023256)	-5575	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding	0.000000	0.333333			55(ATTAGCATGAGAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5720	chr4	123036867	123037067	+	1.33108	NA	intron (NR_151450, intron 1 of 9)	intron (NR_151450, intron 1 of 9)	20374	NR_151450	66966	Mm.235030	NM_025873	ENSMUSG00000028653	Trit1	2310075G14Rik|AI314189|AI314635|AV099619|IPPT|IPT|MOD5	tRNA isopentenyltransferase 1	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1203	chr11	25855229	25855429	+	1.33108	NA	intron (NR_027973, intron 2 of 5)	intron (NR_027973, intron 2 of 5)	-346911	NR_105791	102466154		NR_105791	ENSMUSG00000099015	Mir6372	Gm27358|mmu-mir-6372	microRNA 6372	ncRNA	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6334	chr6	17629673	17629873	+	1.32916	NA	Intergenic	Intergenic	-7237	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding	0.020000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6407	chr6	38764317	38764517	+	1.32913	NA	intron (NM_001294144, intron 2 of 14)	intron (NM_001294144, intron 2 of 14)	72894	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1640	chr12	45833298	45833498	+	1.32913	NA	Intergenic	Intergenic	-758915	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1462	chr11	110284817	110285017	+	1.32913	NA	intron (NM_147219, intron 28 of 38)	intron (NM_147219, intron 28 of 38)	-33141	NM_147218	76184	Mm.159704	NM_147218	ENSMUSG00000044749	Abca6	6330565N06Rik	ATP-binding cassette, sub-family A (ABC1), member 6	protein-coding	0.025000	0.412935			-87(ATTAAAATGACAACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2607	chr14	86968546	86968746	+	1.32913	NA	intron (NM_019670, intron 15 of 27)	intron (NM_019670, intron 15 of 27)	172578	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.000000	0.383085			-47(ACTGTGTCTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5297	chr3	153504800	153505000	+	1.32913	NA	intron (NM_011372, intron 2 of 4)	intron (NM_011372, intron 2 of 4)	-206251	NR_126464	75489	Mm.443252	NR_126464	ENSMUSG00000105023	1700012D16Rik	-	RIKEN cDNA 1700012D16 gene	ncRNA	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4836	chr3	9817670	9817870	+	1.32913	NA	intron (NM_001195031, intron 1 of 8)	intron (NM_001195031, intron 1 of 8)	15909	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-629	chr1	189177992	189178192	+	1.32913	NA	Intergenic	Intergenic	165261	NM_001357119	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1570	chr12	25742421	25742621	+	1.32913	NA	Intergenic	Intergenic	467984	NR_131149	629481	Mm.390460	NR_131149	ENSMUSG00000113550	Gm29687	-	predicted gene, 29687	ncRNA	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6719	chr6	133976740	133976940	+	1.32913	NA	Intergenic	Intergenic	-58860	NM_001303102	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1326	chr11	66652446	66652646	+	1.32913	NA	Intergenic	Intergenic	-126420	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-394	chr1	136305219	136305419	+	1.32913	NA	intron (NM_001347110, intron 2 of 16)	intron (NM_001347110, intron 2 of 16)	40785	NM_001347110	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4188	chr2	16603489	16603689	+	1.32913	NA	intron (NM_026162, intron 4 of 13)	intron (NM_026162, intron 4 of 13)	247285	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6955	chr7	89606237	89606437	+	1.32913	NA	Intergenic	Intergenic	-26481	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5550	chr4	77235627	77235827	+	1.32913	NA	intron (NR_160919, intron 6 of 39)	intron (NR_160919, intron 6 of 39)	-891484	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.005000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-688	chr10	8475664	8475864	+	1.32913	NA	intron (NM_177387, intron 1 of 7)	intron (NM_177387, intron 1 of 7)	43061	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding	0.015000	0.412935			-66(ATTTACAACATAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3746	chr18	23913298	23913498	+	1.32913	NA	Intergenic	B4|SINE|B4	-41290	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding	0.005000	0.432836			-21(TGTTTGCCATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7318	chr8	77150954	77151154	+	1.32913	NA	intron (NM_001083906, intron 3 of 8)	(TTTTG)n|Simple_repeat|Simple_repeat	248724	NM_001083906	110784	Mm.324393	NM_001083906	ENSMUSG00000031618	Nr3c2	MR|Mlr	nuclear receptor subfamily 3, group C, member 2	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7440	chr8	108535534	108535734	+	1.32913	NA	Intergenic	Intergenic	49043	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1451	chr11	107684110	107684310	+	1.32913	NA	intron (NM_001368755, intron 31 of 32)	intron (NM_001368755, intron 31 of 32)	32266	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding	0.040000	0.587065			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-381	chr16	73342050	73342250	+	1.32843	NA	Intergenic	Intergenic	679001	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5747	chr4	128787556	128787756	+	1.32842	NA	intron (NM_001081098, intron 4 of 8)	intron (NM_001081098, intron 4 of 8)	18456	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding	0.025000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2289	chr13	109881320	109881520	+	1.32842	NA	intron (NM_011056, intron 7 of 16)	intron (NM_011056, intron 7 of 16)	-22389	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7660	chr9	54051675	54051875	+	1.32842	NA	intron (NM_001033535, intron 1 of 1)	HAL1|LINE|L1	16636	NM_001033535	244882	Mm.325589	NM_001033535	ENSMUSG00000074345	Tnfaip8l3	9930029P06Rik|Gm517	tumor necrosis factor, alpha-induced protein 8-like 3	protein-coding	0.010000	0.388060			-55(GTTTCCATGACTAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5495	chr4	59154288	59154488	+	1.32842	NA	Intergenic	Intergenic	-15405	NM_001370843	100155	Mm.331636	NM_001033200	ENSMUSG00000038598	Shoc1	AI481877|Gm426|Mzip2	shortage in chiasmata 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2194	chr13	90512982	90513182	+	1.32842	NA	Intergenic	Intergenic	392273	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	ATPase, H+ transporting, lysosomal accessory protein 1-like	protein-coding	0.000000	0.313433	-95(TTTGAATTATTCATG,+,0.00),-95(TTTGAATTATTCATG,-,0.00)		-21(CATTAGTAATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5147	chr3	119320802	119321002	+	1.32842	NA	intron (NM_170778, intron 20 of 22)	intron (NM_170778, intron 20 of 22)	462486	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.253731			-38(CCTTATTCATTCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5460	chr4	51288515	51288715	+	1.32842	NA	Intergenic	Intergenic	71937	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	cylicin, basic protein of sperm head cytoskeleton 2	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4113	chr19	49734446	49734646	+	1.32842	NA	Intergenic	Intergenic	944100	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-222	chr1	81104235	81104435	+	1.32842	NA	intron (NM_001356399, intron 3 of 6)	intron (NM_001356399, intron 3 of 6)	26928	NM_001356397	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-858	chr10	66295004	66295204	+	1.32842	NA	Intergenic	Intergenic	149808	NR_131070	77198	Mm.107617	NR_131070	ENSMUSG00000112210	4930407I19Rik	-	RIKEN cDNA 4930407I19 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-652	chr1	194236541	194236741	+	1.32553	NA	Intergenic	L2|LINE|L2	-13882	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.000000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-192	chr12	71923012	71923212	+	1.32545	NA	intron (NM_026102, intron 3 of 25)	intron (NM_026102, intron 3 of 25)	33569	NM_001286452	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-627	chr1	188785038	188785238	+	1.32498	NA	intron (NM_021408, intron 48 of 70)	MTEa|LTR|ERVL-MaLR	222702	NM_001359577	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding	0.035000	0.487562			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-64	chr1	188785137	188785337	+	1.32498	NA	intron (NM_021408, intron 48 of 70)	MTEa|LTR|ERVL-MaLR	222603	NM_001359577	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding	0.020000	0.502488			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-147	chr11	48114597	48114797	+	1.32495	NA	Intergenic	Intergenic	-685663	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1407	chr11	90391650	90391850	+	1.32442	NA	promoter-TSS (NM_172563)	promoter-TSS (NM_172563)	-833	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6210	chr5	134571816	134572016	+	1.32442	NA	promoter-TSS (NR_106087)	promoter-TSS (NR_106087)	-160	NR_106087	102465708		NR_106087	ENSMUSG00000106323	Mir7228	mmu-mir-7228	microRNA 7228	ncRNA	0.010000	0.462687			-12(TTTTATTCATGAAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-710	chr5	134571829	134572029	+	1.32442	NA	promoter-TSS (NR_106087)	promoter-TSS (NR_106087)	-147	NR_106087	102465708		NR_106087	ENSMUSG00000106323	Mir7228	mmu-mir-7228	microRNA 7228	ncRNA	0.015000	0.477612			-25(TTTTATTCATGAAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-728	chr6	17941991	17942191	+	1.32442	NA	intron (NM_001083315, intron 14 of 14)	intron (NM_001083315, intron 14 of 14)	88354	NM_023653	22413	Mm.33653	NM_023653	ENSMUSG00000010797	Wnt2	2610510E18Rik|Int1l1|Irp|Mirp|Wnt-2|Wnt2a	wingless-type MMTV integration site family, member 2	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1095	chr10	121701486	121701686	+	1.32442	NA	Intergenic	Intergenic	-38344	NM_001359720	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding	0.010000	0.328358			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-69	chr1	192779297	192779497	+	1.32402	NA	Intergenic	Intergenic	-8178	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6555	chr6	82755064	82755264	+	1.32283	NA	intron (NM_013820, intron 2 of 17)	intron (NM_013820, intron 2 of 17)	19290	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7446	chr8	110407631	110407831	+	1.32283	NA	intron (NM_172916, intron 14 of 86)	intron (NM_172916, intron 14 of 86)	94625	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5921	chr5	44000963	44001163	+	1.32283	NA	TTS (NM_001163582)	TTS (NM_001163582)	-19264	NM_001271616	14181	Mm.46053	NM_008009	ENSMUSG00000048373	Fgfbp1	FGF-BP|FGF-BP1|FGFBP-1	fibroblast growth factor binding protein 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6079	chr5	89355007	89355207	+	1.32283	NA	Intergenic	BGLII|LTR|ERVK	102791	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	vitamin D binding protein	protein-coding	0.005000	0.437811			36(ATTTGTAAAATAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5748	chr4	129488046	129488246	+	1.32283	NA	TTS (NM_080442)	TTS (NM_080442)	2624	NM_080442	58864	Mm.143802	NM_080442	ENSMUSG00000000411	Tssk3	1700014N07Rik|4930594I21Rik|Stk22c|Stk22d|Tsk-3|Tssk-3|Tssk3b	testis-specific serine kinase 3	protein-coding	0.015000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1956	chr13	14321086	14321286	+	1.32283	NA	intron (NM_001081348, intron 8 of 28)	intron (NM_001081348, intron 8 of 28)	202040	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1165	chr11	13970900	13971100	+	1.32283	NA	Intergenic	Intergenic	208041	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4554	chr2	119033059	119033259	+	1.32283	NA	Intergenic	Intergenic	-1631	NM_173450	271842	Mm.33617	NM_173450	ENSMUSG00000027324	Rpusd2	4921503C21Rik|9630001E10|BB231107	RNA pseudouridylate synthase domain containing 2	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-263	chr1	90218661	90218861	+	1.32283	NA	Intergenic	Intergenic	14781	NM_001271607	12778	Mm.6522	NM_007722	ENSMUSG00000044337	Ackr3	AW541270|CXC-R7|CXCR-7|Cmkor1|Cxcr7|RDC-1|Rdc1	atypical chemokine receptor 3	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1089	chr10	120044693	120044893	+	1.32283	NA	intron (NM_001358811, intron 18 of 23)	RMER17C|LTR|ERVK	51871	NR_102387	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7067	chr7	125727917	125728117	+	1.32283	NA	intron (NM_001358287, intron 1 of 26)	intron (NM_001358287, intron 1 of 26)	20147	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2129	chr13	70448386	70448586	+	1.32283	NA	Intergenic	Intergenic	-124755	NR_045934	73584	Mm.442491	NR_045934	ENSMUSG00000101051	1700100L14Rik	-	RIKEN cDNA 1700100L14 gene	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7073	chr7	127645315	127645515	+	1.32192	NA	Intergenic	Intergenic	-30143	NR_155450	320683	Mm.156718	NM_177226	ENSMUSG00000045639	Zfp629	9330199A09Rik|Znf629	zinc finger protein 629	protein-coding	0.015000	0.442786			22(CTTCTGTCATGGTGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-648	chr4	109703676	109703876	+	1.32192	NA	intron (NM_007983, intron 1 of 18)	intron (NM_007983, intron 1 of 18)	27149	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7847	chr9	100096946	100097146	+	1.32192	NA	Intergenic	Intergenic	74746	NR_040763	108970	Mm.390215	NR_040763	ENSMUSG00000101584	4930519F24Rik	-	RIKEN cDNA 4930519F24 gene	ncRNA	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3132	chr16	26787299	26787499	+	1.32192	NA	Intergenic	Intergenic	-31897	NR_105063	100504628	Mm.393275	NR_105063	ENSMUSG00000092545	Gm20319	-	predicted gene, 20319	ncRNA	0.010000	0.422886			-54(TTATTGTCTTGCAATC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3969	chr18	83924841	83925041	+	1.32192	NA	Intergenic	Intergenic	161524	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|teashirt1	teashirt zinc finger family member 1	protein-coding	0.005000	0.457711			-56(GCATTGCCATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3430	chr17	15247832	15248032	+	1.32192	NA	Intergenic	Intergenic	-7149	NR_046164	328747	Mm.256835	NR_046164	ENSMUSG00000097624	Gm5091	C330048F19	predicted gene 5091	ncRNA	0.015000	0.587065			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5685	chr4	109703659	109703859	+	1.32192	NA	intron (NM_007983, intron 1 of 18)	intron (NM_007983, intron 1 of 18)	27132	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-985	chr10	103827753	103827953	+	1.32192	NA	Intergenic	L1MC4|LINE|L1	-315134	NM_001270899	627488	Mm.441727	NM_001270899	ENSMUSG00000097427	Gm6763	EG627488|Gm21293	predicted gene 6763	protein-coding	0.010000	0.323383			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-73	chr1	194852684	194852884	+	1.32192	NA	Intergenic	L1MA5|LINE|L1	30783	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3614	chr17	80708860	80709060	+	1.31964	NA	intron (NM_001290345, intron 1 of 33)	intron (NM_001290345, intron 1 of 33)	19065	NM_001360278	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.020000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3529	chr17	53672758	53672958	+	1.31942	NA	TTS (NM_020005)	TTS (NM_020005)	16457	NM_028232	72415	Mm.153202	NM_028232	ENSMUSG00000023940	Sgo1	3300001M08Rik|C81037|Sgol1	shugoshin 1	protein-coding	0.010000	0.402985			7(ATAAACAAAAGAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5204	chr3	133506627	133506827	+	1.31928	NA	intron (NM_001040400, intron 2 of 10)	MER21B|LTR|ERVL	37663	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding	0.030000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5192	chr3	131139454	131139654	+	1.31928	NA	intron (NM_010703, intron 3 of 11)	intron (NM_010703, intron 3 of 11)	26763	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding	0.010000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-71	chr1	194320480	194320680	+	1.31928	NA	Intergenic	L1M5|LINE|L1	-97821	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.000000	0.348259			-15(TCATTGTGATTTTAAT,+,0.00),31(ATATTTTCATGTTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5637	chr4	98949802	98950002	+	1.31928	NA	intron (NM_001290636, intron 42 of 48)	PB1D11|SINE|Alu	26092	NM_001301414	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1092	chr10	121056358	121056558	+	1.31928	NA	intron (NM_011915, intron 2 of 9)	intron (NM_011915, intron 2 of 9)	22454	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2783	chr15	10277101	10277301	+	1.31923	NA	intron (NM_001253781, intron 1 of 9)	intron (NM_001253781, intron 1 of 9)	-16450	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7698	chr9	65810669	65810869	+	1.31866	NA	intron (NM_172536, intron 1 of 9)	Lx10|LINE|L1	16795	NM_172536	214812	Mm.139231	NM_172536	ENSMUSG00000040524	Zfp609	9830165N24|BC016271|Znf609|mKIAA0295	zinc finger protein 609	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4867	chr3	20730593	20730793	+	1.31866	NA	Intergenic	Intergenic	-363516	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	angiotensin II receptor, type 1b	protein-coding	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4540	chr2	116103597	116103797	+	1.31866	NA	Intergenic	Intergenic	-27601	NR_033447	69974	Mm.440293	NR_033447		2810405F15Rik	-	RIKEN cDNA 2810405F15 gene	ncRNA	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1297	chr11	56786077	56786277	+	1.31866	NA	Intergenic	Intergenic	-225441	NM_001113325	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-357	chr1	127125239	127125439	+	1.31866	NA	Intergenic	Intergenic	-79647	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2993	chr15	74021626	74021826	+	1.31866	NA	Intergenic	Intergenic	-182055	NM_001368162	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4051	chr19	22349797	22349997	+	1.31866	NA	intron (NM_001035239, intron 1 of 24)	intron (NM_001035239, intron 1 of 24)	-98311	NM_001362507	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding	0.025000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4543	chr2	116789640	116789840	+	1.31866	NA	Intergenic	Intergenic	-88951	NM_026104	67356	Mm.131623	NM_026104	ENSMUSG00000027355	Tmco5	1700095F04Rik|Tmco5a	transmembrane and coiled-coil domains 5	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1295	chr11	56157780	56157980	+	1.31866	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-116893	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4980	chr3	65071648	65071848	+	1.31866	NA	intron (NM_001357358, intron 1 of 13)	HAL1|LINE|L1	-37266	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7274	chr8	58518926	58519126	+	1.31866	NA	intron (NM_175032, intron 2 of 11)	intron (NM_175032, intron 2 of 11)	181770	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	-	predicted gene 15881	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2582	chr14	79442793	79442993	+	1.31866	NA	Intergenic	Intergenic	-8942	NM_001034882	432879	Mm.308666	NM_001034882	ENSMUSG00000075502	Kbtbd6	EG432879|Gm5465|Zbtbd6	kelch repeat and BTB (POZ) domain containing 6	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6415	chr6	41124950	41125150	+	1.31866	NA	Intergenic	Intergenic	-89541	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5368	chr4	19628563	19628763	+	1.31866	NA	intron (NM_177327, intron 18 of 24)	intron (NM_177327, intron 18 of 24)	53597	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7991	chrX	75775963	75776163	+	1.31866	NA	Intergenic	Intergenic	-11364	NR_029443	74396	Mm.162493	NR_029443	ENSMUSG00000087396	4933407K13Rik	A130080L05Rik|Dxz4	RIKEN cDNA 4933407K13 gene	ncRNA	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1532	chr12	8571815	8572015	+	1.31866	NA	intron (NM_177802, intron 1 of 6)	ERVB7_2-LTR_MM|LTR|ERVK	27151	NM_177802	328059	Mm.46326	NM_177802	ENSMUSG00000020600	Slc7a15	Arpat	solute carrier family 7 (cationic amino acid transporter, y+ system), member 15	protein-coding	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7598	chr9	32425070	32425270	+	1.31866	NA	intron (NM_008026, intron 8 of 8)	intron (NM_008026, intron 8 of 8)	31185	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-809	chr10	47482541	47482741	+	1.31866	NA	Intergenic	BGLII|LTR|ERVK	1237893	NR_028274	100302593		NR_028274	ENSMUSG00000095118	Snord14d	Gm23710	small nucleolar RNA, C/D box 14D	snoRNA	0.000000	0.398010			-9(ATTTGTAAAATAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-96	chr1	34132948	34133148	+	1.31866	NA	intron (NM_001276764, intron 8 of 102)	intron (NM_001276764, intron 8 of 102)	15689	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA	0.045000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6925	chr7	80502071	80502271	+	1.31866	NA	intron (NM_001042527, intron 7 of 21)	intron (NM_001042527, intron 7 of 21)	32827	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ like helicase	protein-coding	0.010000	0.328358			-31(GATTTGTAATTCATAT,+,0.00),-4(ATTTGCATGGAAACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-532	chr1	168913708	168913908	+	1.31866	NA	Intergenic	Intergenic	105281	NR_105772	102466632		NR_105772	ENSMUSG00000098829	Mir6354	Gm27282|mmu-mir-6354	microRNA 6354	ncRNA	0.005000	0.328358			-59(ATCTGAATGAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7816	chr9	93049023	93049223	+	1.31866	NA	Intergenic	Lx8|LINE|L1	-43390	NR_040756	78349	Mm.52612	NR_040756	ENSMUSG00000100294	1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	ncRNA	0.000000	0.308458			-81(TTTTTATTATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6757	chr6	142798808	142799008	+	1.31866	NA	intron (NM_001145390, intron 2 of 5)	intron (NM_001145390, intron 2 of 5)	5558	NM_001145390	330440	Mm.484618	NM_001033417	ENSMUSG00000048473	Sult6b2	Gm766	sulfotransferase family 6B, member 2	protein-coding	0.030000	0.437811		63(GATCCATATGAATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3553	chr17	63204388	63204588	+	1.31866	NA	intron (NM_015794, intron 7 of 8)	intron (NM_015794, intron 7 of 8)	108485	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5490	chr4	58511608	58511808	+	1.31866	NA	intron (NM_010336, intron 1 of 3)	intron (NM_010336, intron 1 of 3)	-12305	NM_001290486	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1255	chr11	40573382	40573582	+	1.31866	NA	Intergenic	Intergenic	119200	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding	0.015000	0.442786		28(ACTGAATATGCATG,+,0.00),28(ACTGAATATGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1285	chr11	49803606	49803806	+	1.31866	NA	intron (NM_013529, intron 1 of 18)	intron (NM_013529, intron 1 of 18)	9551	NM_013529	14584	Mm.24402	NM_013529	ENSMUSG00000020363	Gfpt2	AI480523|GFAT2	glutamine fructose-6-phosphate transaminase 2	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1676	chr12	57243937	57244137	+	1.31866	NA	intron (NM_001164370, intron 1 of 9)	RMER15|LTR|ERVL	13612	NM_001164370	73490	Mm.268180	NM_001164370	ENSMUSG00000047022	Mipol1	1700081O04Rik|6030439O22Rik|AU021838|AW536152|D12Ertd19e	mirror-image polydactyly 1	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5714	chr4	119305136	119305336	+	1.31866	NA	intron (NM_028677, intron 9 of 9)	ID_B1|SINE|B4	-10723	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4052	chr19	23351118	23351318	+	1.31866	NA	intron (NM_174857, intron 8 of 13)	intron (NM_174857, intron 8 of 13)	-77321	NM_001252684	226026	Mm.23267	NM_153808	ENSMUSG00000024943	Smc5	MLZ-453|SMC-5|Smc5l1|mKIAA0594|mSMC5	structural maintenance of chromosomes 5	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-808	chr10	46665327	46665527	+	1.31866	NA	Intergenic	RLTR19A|LTR|ERVK	420679	NR_028274	100302593		NR_028274	ENSMUSG00000095118	Snord14d	Gm23710	small nucleolar RNA, C/D box 14D	snoRNA	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1708	chr12	68790618	68790818	+	1.31866	NA	Intergenic	L1MB7|LINE|L1	368468	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-840	chr10	57666210	57666410	+	1.31866	NA	intron (NM_001039052, intron 2 of 4)	ERVL-B4-int|LTR|ERVL	15329	NM_001190402	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1818	chr12	92737115	92737315	+	1.31866	NA	Intergenic	Intergenic	707608	NR_126436	75295	Mm.243878	NR_126436	ENSMUSG00000113164	4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7994	chrX	77452142	77452342	+	1.31866	NA	Intergenic	Intergenic	-58985	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding	0.000000	0.412935			26(ATTTCCATGACACCAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3385	chr16	92596150	92596350	+	1.31866	NA	Intergenic	Intergenic	98103	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding	0.015000	0.462687			-8(CCTTTCCTTTTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1012	chr10	108280593	108280793	+	1.31866	NA	TTS (NM_001368736)	TTS (NM_001368736)	-51496	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6920	chr7	79630059	79630259	+	1.31866	NA	Intergenic	MER5B|DNA|hAT-Charlie	-12502	NM_019799	56315	Mm.10909	NM_019799	ENSMUSG00000030549	Rhcg	BB065800	Rhesus blood group-associated C glycoprotein	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6271	chr5	150936126	150936326	+	1.31866	NA	Intergenic	Intergenic	-16381	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6758	chr6	143337171	143337371	+	1.31866	NA	Intergenic	MLTR25A|LTR|ERVK	91383	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2410	chr14	27701915	27702115	+	1.31866	NA	intron (NM_177814, intron 2 of 15)	intron (NM_177814, intron 2 of 15)	79608	NM_001347497	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7329	chr8	77534192	77534392	+	1.31866	NA	Intergenic	Intergenic	-15105	NM_001081240	102182	Mm.197630	NM_178903	ENSMUSG00000037134	Prmt9	AI931714|Prmt10	protein arginine methyltransferase 9	protein-coding	0.020000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1087	chr10	119837677	119837877	+	1.31866	NA	intron (NR_131760, intron 4 of 4)	intron (NR_131760, intron 4 of 4)	14613	NR_131760	78105	Mm.399086	NR_131760	ENSMUSG00000085418	Grip1os1	4930404E01Rik|4930483C13Rik	glutamate receptor interacting protein 1, opposite strand 1	ncRNA	0.015000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7639	chr9	46642792	46642992	+	1.31866	NA	Intergenic	Intergenic	-270711	NR_015605	73040	Mm.265384	NR_015605	ENSMUSG00000099696	2900052N01Rik	AU067665	RIKEN cDNA 2900052N01 gene	ncRNA	0.040000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2965	chr15	66182399	66182599	+	1.31866	NA	intron (NM_152923, intron 1 of 14)	intron (NM_152923, intron 1 of 14)	104130	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding	0.000000	0.288557			21(ATTAACATAACCATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1275	chr11	45753909	45754109	+	1.31866	NA	Intergenic	Intergenic	-54074	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7960	chrX	48802272	48802472	+	1.31866	NA	Intergenic	Intergenic	75341	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1734	chr12	72828878	72829078	+	1.31866	NA	Intergenic	Intergenic	67767	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2766	chr15	7070863	7071063	+	1.31866	NA	Intergenic	Intergenic	-58609	NM_001358593	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	LIF receptor alpha	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6711	chr6	126313447	126313647	+	1.31866	NA	intron (NR_045480, intron 3 of 3)	L1_Mus3|LINE|L1	15139	NR_045480	100038574	Mm.399353	NR_045480	ENSMUSG00000107623	Gm10415	-	predicted gene 10415	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3703	chr18	10536478	10536678	+	1.31866	NA	intron (NM_001083628, intron 19 of 32)	intron (NM_001083628, intron 19 of 32)	73774	NM_001081222	77805	Mm.210996	NM_144542	ENSMUSG00000024293	Esco1	A930014I12Rik	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1843	chr12	99907650	99907850	+	1.31834	NA	intron (NM_028354, intron 7 of 15)	intron (NM_028354, intron 7 of 15)	23235	NM_028354	104884	Mm.312323	NM_028354	ENSMUSG00000021177	Tdp1	2810481F14Rik|4921509N21Rik|AI838772|AW493413|E430034L06Rik|MLZ-501|SCAN1	tyrosyl-DNA phosphodiesterase 1	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3517	chr17	51736061	51736261	+	1.31834	NA	TTS (NM_001163632)	TTS (NM_001163632)	75893	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5595	chr4	89839842	89840042	+	1.31819	NA	Intergenic	L1_Mus2|LINE|L1	151744	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4565	chr2	121626942	121627142	+	1.31819	NA	intron (NM_001360084, intron 1 of 13)	intron (NM_001360084, intron 1 of 13)	118549	NM_001369185	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7048	chr7	120818444	120818644	+	1.31819	NA	intron (NM_001370881, intron 6 of 11)	intron (NM_001370881, intron 6 of 11)	8914	NM_001370881	436008		NM_001370881		Gm5737	EG436008	predicted gene 5737	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1839	chr12	99474203	99474403	+	1.31819	NA	Intergenic	Intergenic	-24229	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-455	chr1	151923986	151924186	+	1.31819	NA	intron (NM_197990, intron 3 of 5)	intron (NM_197990, intron 3 of 5)	166234	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik	RIKEN cDNA 1700025G04 gene	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6520	chr6	71376198	71376398	+	1.31819	NA	intron (NM_001081110, intron 4 of 4)	intron (NM_001081110, intron 4 of 4)	2871	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding	0.010000	0.452736			-75(TTCTGCAAGACAATTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-201	chr1	70881304	70881504	+	1.31819	NA	intron (NM_177164, intron 3 of 3)	intron (NM_177164, intron 3 of 3)	155689	NM_001310658	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding	0.010000	0.398010	-25(CATGAATAAATCATC,+,0.00),-25(CATGAATAAATCATC,-,0.00),-6(CATGAATTATTCATT,+,0.00),-6(CATGAATTATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1832	chr12	96959092	96959292	+	1.31819	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	-911970	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo	0.000000	0.348259			70(TAAGTATTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1478	chr11	113406684	113406884	+	1.31819	NA	intron (NM_027216, intron 5 of 9)	L1MA4|LINE|L1	159031	NM_027216	69806	Mm.341021	NM_027216	ENSMUSG00000041654	Slc39a11	1810074D23Rik|ZIP-11	solute carrier family 39 (metal ion transporter), member 11	protein-coding	0.030000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8007	chrX	86330905	86331105	+	1.31819	NA	Intergenic	Intergenic	23989	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3043	chr15	95778957	95779157	+	1.31819	NA	Intergenic	Intergenic	-11786	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-234	chr1	83909778	83909978	+	1.31819	NA	Intergenic	MER58A|DNA|hAT-Charlie	309083	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA	0.010000	0.313433		-32(AATGAATAGTCATG,+,0.00),-32(AATGAATAGTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-85	chr1	28831069	28831269	+	1.31819	NA	Intergenic	Lx8b|LINE|L1	-50917	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5649	chr4	101053743	101053943	+	1.31819	NA	Intergenic	Intergenic	-15195	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5099	chr3	104877309	104877509	+	1.31819	NA	intron (NM_001253703, intron 5 of 11)	intron (NM_001253703, intron 5 of 11)	12903	NM_001253702	229681	Mm.206379	NM_153091	ENSMUSG00000045576	St7l	St7r	suppression of tumorigenicity 7-like	protein-coding	0.015000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1369	chr11	78229606	78229806	+	1.31819	NA	intron (NM_009297, intron 8 of 36)	intron (NM_009297, intron 8 of 36)	15997	NM_009297	20926	Mm.20755	NM_009297	ENSMUSG00000002052	Supt6	5131400N11Rik|AI132449|SPT6|Supt6h|mKIAA0162	suppressor of Ty 6	protein-coding	0.010000	0.412935			-7(ATTTGCATTGGAATTC,-,0.00),54(TTCCTTTCATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7997	chrX	80220914	80221114	+	1.31819	NA	Intergenic	Intergenic	-549579	NM_028025	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5555	chr4	77574289	77574489	+	1.31819	NA	intron (NR_160919, intron 3 of 39)	intron (NR_160919, intron 3 of 39)	637353	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.000000	0.308458			6(ATATACAATACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2401	chr14	24134729	24134929	+	1.31819	NA	3' UTR (NM_001163513, exon 32 of 32)	3' UTR (NM_001163513, exon 32 of 32)	45952	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3683	chr18	5524524	5524724	+	1.31819	NA	intron (NR_033552, intron 5 of 6)	intron (NR_033552, intron 5 of 6)	-67236	NM_011546	21417	Mm.3929	NM_011546	ENSMUSG00000024238	Zeb1	3110032K11Rik|AREB6|BZP|MEB1|Nil2|TCF-8|Tcf18|Tcf8|Tw|ZEB|Zfhep|Zfhx1a|Zfx1a|Zfx1ha|[delta]EF1	zinc finger E-box binding homeobox 1	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-78	chr1	25181890	25182090	+	1.31819	NA	intron (NM_175642, intron 19 of 30)	intron (NM_175642, intron 19 of 30)	95964	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding	0.000000	0.412935			14(ATTTGTAACACAAAAC,-,0.00),41(ATTTGTAACACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-292	chr1	99625393	99625593	+	1.31819	NA	Intergenic	B4A|SINE|B4	-146908	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0.000000	0.358209			-52(TTTTGCATGAGTATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6299	chr6	8575283	8575483	+	1.31819	NA	intron (NM_001286729, intron 4 of 7)	intron (NM_001286729, intron 4 of 7)	55325	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding	0.010000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6562	chr6	83542120	83542320	+	1.31819	NA	TTS (NM_024239)	TTS (NM_024239)	-5969	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-796	chr10	43103513	43103713	+	1.31819	NA	intron (NM_175407, intron 4 of 6)	L2a|LINE|L2	70917	NM_175407	109205	Mm.153750	NM_175407	ENSMUSG00000038248	Sobp	2900009C16Rik|5330439J01Rik|JXC1|jc	sine oculis binding protein	protein-coding	0.020000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4099	chr19	45736858	45737058	+	1.31819	NA	3' UTR (NM_010205, exon 5 of 5)	3' UTR (NM_010205, exon 5 of 5)	5926	NM_001166362	14179	Mm.4012	NM_010205	ENSMUSG00000025219	Fgf8	Aigf|Fgf-8	fibroblast growth factor 8	protein-coding	0.070000	0.641791			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4933	chr3	48769898	48770098	+	1.31819	NA	Intergenic	Intergenic	-160898	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-495	chr1	160880438	160880638	+	1.31819	NA	Intergenic	Intergenic	-25873	NM_001024952	381305	Mm.329667	NM_001024952	ENSMUSG00000040423	Rc3h1	5730557L09Rik|Gm551|N28103|mKIAA2025	RING CCCH (C3H) domains 1	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3981	chr18	85430579	85430779	+	1.31819	NA	Intergenic	RLTR48A|LTR|ERV1	478563	NM_001367965	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3434	chr17	16166587	16166787	+	1.31819	NA	Intergenic	Intergenic	-340101	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding	0.005000	0.343284			75(TTTTTTTCATGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-686	chr10	7908193	7908393	+	1.31819	NA	intron (NM_001359534, intron 6 of 6)	intron (NM_001359534, intron 6 of 6)	44772	NM_001359534	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding	0.000000	0.378109	3(TATGCATTTTGTATA,-,0.00)	26(CATGAGTATGCATG,+,0.00),26(CATGAGTATGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3195	chr16	43548788	43548988	+	1.31819	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-91767	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6705	chr6	120444373	120444573	+	1.31819	NA	3' UTR (NM_145997, exon 28 of 28)	3' UTR (NM_145997, exon 28 of 28)	-18724	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6180	chr5	126256499	126256699	+	1.31819	NA	Intergenic	Intergenic	-406698	NM_001370875	231736		NM_001370875		Gm4868	EG231736	predicted gene 4868	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4559	chr2	120761778	120761978	+	1.31819	NA	intron (NM_001024857, intron 9 of 14)	intron (NM_001024857, intron 9 of 14)	-30361	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4529	chr2	115035947	115036147	+	1.31819	NA	Intergenic	B4A|SINE|B4	308233	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4392	chr2	73127910	73128110	+	1.31819	NA	intron (NM_025942, intron 7 of 10)	intron (NM_025942, intron 7 of 10)	86437	NM_030091	67059	Mm.22661	NM_025942	ENSMUSG00000027108	Ola1	2510025G09Rik|2810405J23Rik|2810409H07Rik|Gtpbp9|PTD004	Obg-like ATPase 1	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6062	chr5	83005056	83005256	+	1.31819	NA	Intergenic	Intergenic	-206091	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mir-1187|mmu-mir-1187	microRNA 1187	ncRNA	0.015000	0.318408			-11(CTATTATGTTGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-24	chr1	8915450	8915650	+	1.31819	NA	intron (NM_027671, intron 3 of 20)	intron (NM_027671, intron 3 of 20)	384327	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding	0.010000	0.437811			-17(ATCTGTATGAAAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5159	chr3	122308013	122308213	+	1.31819	NA	Intergenic	Intergenic	-14410	NR_030439	791077		NR_030439	ENSMUSG00000076456	Mir760	Mirn760|mir-760|mmu-mir-760	microRNA 760	ncRNA	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2254	chr13	101913002	101913202	+	1.31819	NA	Intergenic	MER2|DNA|TcMar-Tigger	-144885	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.000000	0.412935			-25(AAAATGCCATGCAAAT,+,0.00),8(GTTTGAAGAACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6865	chr7	56402423	56402623	+	1.31819	NA	intron (NR_157031, intron 18 of 22)	intron (NR_157031, intron 18 of 22)	162764	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p|p<cas>	oculocutaneous albinism II	protein-coding	0.000000	0.368159			-1(ATCTCCATGAGAAGAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7418	chr8	102857952	102858152	+	1.31819	NA	Intergenic	MER5A1|DNA|hAT-Charlie	-72941	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4344	chr2	61765406	61765606	+	1.31819	NA	intron (NM_021526, intron 7 of 11)	intron (NM_021526, intron 7 of 11)	-38947	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5765	chr4	138102603	138102803	+	1.31819	NA	intron (NM_001355699, intron 6 of 32)	intron (NM_001355699, intron 6 of 32)	35815	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA	0.010000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-613	chr1	185956090	185956290	+	1.31819	NA	intron (NR_030555, intron 5 of 6)	RLTR13D6|LTR|ERVK	161120	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-817	chr10	51926897	51927097	+	1.31819	NA	Intergenic	Intergenic	-95505	NM_153786	215031	Mm.87237	NM_153786	ENSMUSG00000049641	Vgll2	C130057C21Rik|VITO-1|Vito1|vgl-2	vestigial like family member 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2580	chr14	78747922	78748122	+	1.31749	NA	Intergenic	Intergenic	-15293	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4399	chr2	75591041	75591241	+	1.31701	NA	Intergenic	Lx7|LINE|L1	-68118	NM_001359971	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7613	chr9	37761866	37762066	+	1.31701	NA	Intergenic	RMER10A|LTR|ERVL	-10671	NM_146749	258744	Mm.347661	NM_146749	ENSMUSG00000058628	Olfr875	MOR161-4	olfactory receptor 875	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2468	chr14	46416519	46416719	+	1.31701	NA	Intergenic	Intergenic	-25950	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5201	chr3	133081665	133081865	+	1.31701	NA	intron (NM_001356309, intron 3 of 11)	ORR1F|LTR|ERVL-MaLR	10060	NM_026231	67553	Mm.304899	NM_026231	ENSMUSG00000028018	Gstcd	4933434L15Rik	glutathione S-transferase, C-terminal domain containing	protein-coding	0.015000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7352	chr8	81471947	81472147	+	1.31701	NA	intron (NM_001297593, intron 1 of 23)	intron (NM_001297593, intron 1 of 23)	129485	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-725	chr10	21056985	21057185	+	1.31701	NA	intron (NM_001358561, intron 19 of 22)	intron (NM_001358561, intron 19 of 22)	16265	NM_001177776	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7158	chr8	12786056	12786256	+	1.31701	NA	intron (NR_121603, intron 1 of 29)	intron (NR_121603, intron 1 of 29)	29140	NM_001293667	50770	Mm.257837	NM_015804	ENSMUSG00000031441	Atp11a	4930558F19Rik|AU040868|Atpc1h|Ih	ATPase, class VI, type 11A	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3506	chr17	49863178	49863378	+	1.31701	NA	intron (NM_177052, intron 15 of 22)	intron (NM_177052, intron 15 of 22)	248106	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding	0.000000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-518	chr2	115500560	115500760	+	1.31701	NA	intron (NR_030712, intron 1 of 2)	L1Md_F2|LINE|L1	11541	NR_030712	100043232	Mm.240112	NR_030712	ENSMUSG00000085582	3110099E03Rik	-	RIKEN cDNA 3110099E03 gene	ncRNA	0.025000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3290	chr16	67043509	67043709	+	1.31701	NA	intron (NM_178721, intron 1 of 9)	RSINE1|SINE|B4	386491	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2215	chr13	94449784	94449984	+	1.31701	NA	intron (NM_009680, intron 12 of 26)	intron (NM_009680, intron 12 of 26)	90924	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding	0.020000	0.477612			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-769	chr6	108549865	108550065	+	1.31598	NA	3' UTR (NM_010585, exon 62 of 62)	3' UTR (NM_010585, exon 62 of 62)	60222	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-469	chr1	153321639	153321839	+	1.31598	NA	intron (NM_010683, intron 1 of 27)	intron (NM_010683, intron 1 of 27)	11047	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding	0.030000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1194	chr11	23378529	23378729	+	1.31598	NA	intron (NM_001190401, intron 21 of 79)	intron (NM_001190401, intron 21 of 79)	71734	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4114	chr19	49734735	49734935	+	1.31598	NA	Intergenic	Lx6|LINE|L1	943811	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4880	chr3	26796310	26796510	+	1.31598	NA	intron (NM_027583, intron 4 of 9)	intron (NM_027583, intron 4 of 9)	158779	NM_029150	70862	Mm.330943	NM_027583	ENSMUSG00000039335	Spata16	4921511F01Rik|4930503K02Rik|Nyd-sp12	spermatogenesis associated 16	protein-coding	0.010000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-134	chr11	23378556	23378756	+	1.31598	NA	intron (NM_001190401, intron 21 of 79)	intron (NM_001190401, intron 21 of 79)	71761	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-523	chr1	167805034	167805234	+	1.31598	NA	intron (NM_033652, intron 3 of 7)	intron (NM_033652, intron 3 of 7)	115576	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding	0.025000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3933	chr18	71525212	71525412	+	1.31551	NA	intron (NM_007831, intron 12 of 28)	intron (NM_007831, intron 12 of 28)	825757	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-649	chr1	194041466	194041666	+	1.31551	NA	Intergenic	Intergenic	181193	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-60	chr1	21745425	21745625	+	1.31551	NA	intron (NM_001160139, intron 1 of 14)	intron (NM_001160139, intron 1 of 14)	216417	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.005000	0.313433	22(CTTAAATTATTTATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7653	chr9	51935035	51935235	+	1.31551	NA	Intergenic	Intergenic	20706	NR_040731	74072	Mm.84915	NR_040731	ENSMUSG00000111836	4933407I05Rik	-	RIKEN cDNA 4933407I05 gene	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1599	chr12	35371607	35371807	+	1.31551	NA	Intergenic	Intergenic	163282	NM_013464	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4605	chr2	129420837	129421037	+	1.31551	NA	Intergenic	RLTR9B|LTR|ERVK	-49798	NM_008361	16176	Mm.222830	NM_008361	ENSMUSG00000027398	Il1b	IL-1beta|Il-1b	interleukin 1 beta	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8032	chrX	97086837	97087037	+	1.31551	NA	Intergenic	RMER15-int|LTR|ERVL	14341	NM_001033361	245526	Mm.336164	NM_001033361	ENSMUSG00000031212	Pgr15l	-	G protein-coupled receptor 15-like	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5606	chr4	94177763	94177963	+	1.31551	NA	Intergenic	Intergenic	378933	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1442	chr11	104333776	104333976	+	1.31551	NA	3' UTR (NM_001081045, exon 14 of 14)	3' UTR (NM_001081045, exon 14 of 14)	102440	NM_010838	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6932	chr7	83141350	83141550	+	1.31551	NA	Intergenic	Intergenic	-7020	NM_177895	330578	Mm.5796	NM_177895	ENSMUSG00000053528	A530021J07Rik	-	Riken cDNA A530021J07 gene	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3819	chr18	44007415	44007615	+	1.31551	NA	intron (NM_001081180, intron 20 of 31)	intron (NM_001081180, intron 20 of 31)	-20354	NM_001039218	433178	Mm.120009	NM_001039218	ENSMUSG00000051050	Spink14	EG433178|Gm5505	serine peptidase inhibitor, Kazal type 14	protein-coding	0.000000	0.363184			4(ATTTACAAGAGTGAAA,-,0.00),28(TGTTTCTGATGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2885	chr15	41860138	41860338	+	1.31551	NA	non-coding (NR_152565, exon 18 of 18)	non-coding (NR_152565, exon 18 of 18)	9482	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2408	chr14	26620523	26620723	+	1.31551	NA	intron (NM_145969, intron 15 of 17)	intron (NM_145969, intron 15 of 17)	-17511	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding	0.005000	0.432836			25(GCCTTGTATTGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2649	chr14	99802271	99802471	+	1.31551	NA	Intergenic	L1_Mur3|LINE|L1	347425	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0.010000	0.313433			0(ATCAGCAAGATAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6323	chr6	15640157	15640357	+	1.31551	NA	Intergenic	Intergenic	-80404	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-82	chr1	27547569	27547769	+	1.31551	NA	Intergenic	L1M2|LINE|L1	-336377	NR_151583	433281	Mm.329306	NR_151583	ENSMUSG00000101514	Gm5524	AI875557|EG433281	predicted gene 5524	ncRNA	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3239	chr16	55329078	55329278	+	1.31551	NA	Intergenic	Intergenic	-45941	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1185	chr11	20822705	20822905	+	1.31551	NA	TTS (NM_173752)	TTS (NM_173752)	8303	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-496	chr1	161005170	161005370	+	1.31551	NA	Intergenic	Intergenic	26664	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-22	chr1	8914013	8914213	+	1.31551	NA	intron (NM_027671, intron 3 of 20)	intron (NM_027671, intron 3 of 20)	385764	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4902	chr3	32340593	32340793	+	1.31551	NA	3' UTR (NM_009517, exon 6 of 6)	3' UTR (NM_009517, exon 6 of 6)	-24796	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4961	chr3	58245802	58246002	+	1.31551	NA	Intergenic	Intergenic	-82095	NR_040538	67850	Mm.416968	NR_040538	ENSMUSG00000100666	1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	ncRNA	0.010000	0.402985			85(ATCAAAATAAAAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1008	chr10	107822958	107823158	+	1.31551	NA	intron (NM_001177567, intron 26 of 57)	intron (NM_001177567, intron 26 of 57)	89321	NM_001370989									0.000000	0.353234			-70(ATCTAAATGAAAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3526	chr17	52712444	52712644	+	1.31551	NA	intron (NM_001031811, intron 1 of 15)	intron (NM_001031811, intron 1 of 15)	109835	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding	0.005000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6111	chr5	100723002	100723202	+	1.31551	NA	Intergenic	MTB_Mm-int|LTR|ERVL-MaLR	-3386	NM_152803	15442	Mm.265786	NM_152803	ENSMUSG00000035273	Hpse	HSE1|Hpa|Hpr1	heparanase	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2514	chr14	62712735	62712935	+	1.31551	NA	intron (NM_008715, intron 7 of 18)	RLTR11A2|LTR|ERVK	-47666	NR_045503	71000	Mm.399410	NR_045503	ENSMUSG00000097775	4931440J10Rik	-	RIKEN cDNA 4931440J10 gene	ncRNA	0.010000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7713	chr9	69768737	69768937	+	1.31551	NA	intron (NR_040765, intron 1 of 4)	intron (NR_040765, intron 1 of 4)	7691	NR_040765	319970	Mm.186434	NR_040765	ENSMUSG00000097623	B230323A14Rik	-	RIKEN cDNA B230323A14 gene	ncRNA	0.050000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1711	chr12	69649410	69649610	+	1.31551	NA	intron (NM_001135559, intron 3 of 22)	(TG)n|Simple_repeat|Simple_repeat	32342	NM_001135559	20663	Mm.3770	NM_001135559	ENSMUSG00000034801	Sos2	SOS-2|mSOS-2	SOS Ras/Rho guanine nucleotide exchange factor 2	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6482	chr6	62382379	62382579	+	1.31551	NA	3' UTR (NM_001164316, exon 11 of 11)	3' UTR (NM_001164316, exon 11 of 11)	-873527	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4257	chr2	36029148	36029348	+	1.31551	NA	Intergenic	Intergenic	20090	NM_026703	68375	Mm.19834	NM_026703	ENSMUSG00000026895	Ndufa8	0610033L03Rik|AW261656|CI-19kD|CI-PGIV	NADH:ubiquinone oxidoreductase subunit A8	protein-coding	0.010000	0.378109			-97(TCATTTTCTTTTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7175	chr8	24437850	24438050	+	1.31551	NA	3' UTR (NM_026931, exon 1 of 1)	3' UTR (NM_026931, exon 1 of 1)	996	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	Tcim	1110065B09Rik|1810011O10Rik|AW121743|AW321058	transcriptional and immune response regulator	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-343	chr15	58367405	58367605	+	1.31489	NA	intron (NM_027211, intron 1 of 8)	ORR1C2|LTR|ERVL-MaLR	21769	NM_027211	69787	Mm.237985	NM_027211		Anxa13	1810034H17Rik|AV055219	annexin A13	protein-coding	0.005000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-764	chr6	102192685	102192885	+	1.31466	NA	intron (NM_008779, intron 18 of 21)	intron (NM_008779, intron 18 of 21)	-73315	NR_131018	75893	Mm.2968	NR_131017	ENSMUSG00000107563	4930587E11Rik	4930523E13Rik|Gm44188	RIKEN cDNA 4930587E11 gene	ncRNA	0.005000	0.432836			45(ATTTGCATTATACAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5050	chr3	85618704	85618904	+	1.31419	NA	intron (NM_144896, intron 8 of 12)	intron (NM_144896, intron 8 of 12)	44675	NM_144896	229487	Mm.52275	NM_144896	ENSMUSG00000028085	Gatb	9430026F02Rik|Pet112|Pet112l	glutamyl-tRNA(Gln) amidotransferase, subunit B	protein-coding	0.015000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-200	chr12	83624388	83624588	+	1.31419	NA	Intergenic	L2a|LINE|L2	-7755	NM_001364416	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding	0.000000	0.383085			85(ATTAGAATAAGACAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6361	chr6	25033130	25033330	+	1.31419	NA	Intergenic	Intergenic	-77105	NM_177013	319832	Mm.127446	NM_177013	ENSMUSG00000048022	Tmem229a	6332401O19Rik	transmembrane protein 229A	protein-coding	0.000000	0.437811			8(ATTTGCTTAACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1781	chr12	83624377	83624577	+	1.31419	NA	Intergenic	L2a|LINE|L2	-7766	NM_001364416	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8163	chrX	167131088	167131288	+	1.31386	NA	Intergenic	Intergenic	-60818	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding	0.000000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-339	chr15	28166573	28166773	+	1.31386	NA	Intergenic	Intergenic	-37093	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b3491Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding	0.000000	0.447761			-41(TTTAACATGAGAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-977	chr10	99385623	99385823	+	1.31340	NA	Intergenic	Intergenic	122492	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.015000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-352	chr15	94443308	94443508	+	1.31340	NA	Intergenic	Intergenic	-39058	NM_001164786	223838	Mm.214132	NM_177431	ENSMUSG00000022449	Adamts20	Adamst20|bt	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 20	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6980	chr7	95774365	95774565	+	1.31275	NA	Intergenic	MIRb|SINE|MIR	-396779	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7322	chr8	77272653	77272853	+	1.31275	NA	intron (NR_156496, intron 20 of 22)	RMER10B|LTR|ERVL	179336	NM_001363420	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3261	chr16	58637618	58637818	+	1.31275	NA	exon (NM_175011, exon 2 of 4)	exon (NM_175011, exon 2 of 4)	685	NM_175011	224247	Mm.26145	NM_175011	ENSMUSG00000055789	E330017A01Rik	-	RIKEN cDNA E330017A01 gene	protein-coding	0.020000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-215	chr12	117028664	117028864	+	1.31275	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	122505	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.015000	0.417910			19(ATCTGCATGAAATTGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5519	chr4	65238760	65238960	+	1.31191	NA	intron (NM_021362, intron 9 of 21)	intron (NM_021362, intron 9 of 21)	114686	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding	0.030000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2195	chr13	90643916	90644116	+	1.31191	NA	Intergenic	Intergenic	261339	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	ATPase, H+ transporting, lysosomal accessory protein 1-like	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6649	chr6	107012942	107013142	+	1.31191	NA	Intergenic	Intergenic	-212955	NM_175357	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-507	chr1	163537642	163537842	+	1.31191	NA	Intergenic	Intergenic	-134073	NM_001313738	98376	Mm.32901	NM_178883	ENSMUSG00000040124	Gorab	NTKL-BP1|SCYL1-BP1|Scyl1bp1	golgin, RAB6-interacting	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6928	chr7	81652982	81653182	+	1.31191	NA	intron (NM_001164086, intron 1 of 8)	MIRb|SINE|MIR	-39714	NR_162810	114482937		NR_162810		Mir12203	mmu-mir-12203	microRNA mir-12203	ncRNA	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3835	chr18	47852506	47852706	+	1.31191	NA	Intergenic	Intergenic	-63073	NR_152200	100042982	Mm.125235	NR_152200		Gm4146	Gm45939	predicted gene 4146	ncRNA	0.005000	0.368159	-18(CATGAATAATGCAGA,+,0.00),-18(CATGAATAATGCAGA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4546	chr2	117282719	117282919	+	1.31191	NA	intron (NM_011246, intron 16 of 16)	intron (NM_011246, intron 16 of 16)	33080	NM_026620	68215	Mm.219389	NM_026620	ENSMUSG00000027349	Fam98b	2610510H03Rik	family with sequence similarity 98, member B	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3330	chr16	77331879	77332079	+	1.31191	NA	intron (NR_015543, intron 1 of 4)	intron (NR_015543, intron 1 of 4)	2651	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA	0.010000	0.313433			41(TATTTCTTATTTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3437	chr17	17393004	17393204	+	1.31191	NA	intron (NM_025934, intron 9 of 9)	intron (NM_025934, intron 9 of 9)	-9582	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding	0.020000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3477	chr17	36981549	36981749	+	1.31191	NA	promoter-TSS (NM_029747)	promoter-TSS (NM_029747)	-412	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding	0.035000	0.587065			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2241	chr13	98842689	98842889	+	1.31191	NA	3' UTR (NM_178716, exon 24 of 24)	3' UTR (NM_178716, exon 24 of 24)	-27340	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding	0.005000	0.343284			25(ACTTTTTTTTGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6875	chr7	63970669	63970869	+	1.31191	NA	Intergenic	Intergenic	-31854	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2696	chr14	112658801	112659001	+	1.31191	NA	Intergenic	BGLII_Mus|LTR|ERVK	983786	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding	0.000000	0.452736			-43(CCTTTATCTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7313	chr8	73383194	73383394	+	1.31191	NA	Intergenic	LTRIS4|LTR|ERV1	-29754	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5155	chr3	121204050	121204250	+	1.31191	NA	3' UTR (NM_001355678, exon 8 of 8)	3' UTR (NM_001355678, exon 8 of 8)	-32455	NM_028456	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|Rsume|X2CR1	RWD domain containing 3	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2229	chr13	96615197	96615397	+	1.31161	NA	intron (NM_023420, intron 9 of 17)	intron (NM_023420, intron 9 of 17)	55639	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-570	chr1	176991638	176991838	+	1.31161	NA	intron (NM_029756, intron 16 of 17)	intron (NM_029756, intron 16 of 17)	-155605	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo	0.020000	0.398010			-8(AACTTCCCTTGCAAAT,+,0.00),57(CTATTCTCATGGAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5693	chr4	111782608	111782808	+	1.31161	NA	intron (NM_026470, intron 8 of 12)	intron (NM_026470, intron 8 of 12)	5111	NM_001357231	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7803	chr9	89335040	89335240	+	1.31161	NA	Intergenic	L1MA8|LINE|L1	123756	NM_001359993	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5071	chr3	95665125	95665325	+	1.31161	NA	Intergenic	Intergenic	6504	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-899	chr10	78787008	78787208	+	1.31161	NA	intron (NM_009200, intron 1 of 9)	intron (NM_009200, intron 1 of 9)	6612	NM_009200	20513	Mm.6257	NM_009200	ENSMUSG00000005357	Slc1a6	EAAT4	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1806	chr12	89273049	89273249	+	1.31161	NA	intron (NM_172544, intron 6 of 19)	intron (NM_172544, intron 6 of 19)	319759	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0.000000	0.457711			-93(ATCAAAATGACAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4535	chr2	115500374	115500574	+	1.31161	NA	intron (NR_030712, intron 1 of 2)	intron (NR_030712, intron 1 of 2)	11727	NR_030712	100043232	Mm.240112	NR_030712	ENSMUSG00000085582	3110099E03Rik	-	RIKEN cDNA 3110099E03 gene	ncRNA	0.020000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2391	chr14	21507590	21507790	+	1.31148	NA	intron (NM_017479, intron 1 of 16)	intron (NM_017479, intron 1 of 16)	7905	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding	0.010000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-670	chr5	48657992	48658192	+	1.31052	NA	intron (NM_001199244, intron 1 of 7)	MER5A1|DNA|hAT-Charlie	-58410	NM_001199245	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.005000	0.398010			76(CTTTGAATAACAAAAT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-750	chr6	67486855	67487055	+	1.31052	NA	intron (NM_144548, intron 2 of 10)	intron (NM_144548, intron 2 of 10)	4900	NM_144548	209590	Mm.221227	NM_144548	ENSMUSG00000049093	Il23r	IL-23R	interleukin 23 receptor	protein-coding	0.000000	0.243781	-52(GATGCATTATTGAAT,-,0.00)		66(TAATTTCCATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2720	chr14	119122928	119123128	+	1.31052	NA	Intergenic	Intergenic	-15237	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding	0.000000	0.328358			-8(ATTTGAAAGACATAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3310	chr16	72577838	72578038	+	1.31052	NA	Intergenic	Intergenic	-85211	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.005000	0.328358			74(GTATTGTGATGTTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-725	chr6	13295255	13295455	+	1.31029	NA	Intergenic	Intergenic	-70390	NM_001013757	232585	Mm.389082	NM_001013757	ENSMUSG00000079679	Vwde	Gm467	von Willebrand factor D and EGF domains	protein-coding	0.010000	0.422886			-63(ACTCAGCCATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-303	chr1	106058267	106058467	+	1.30912	NA	Intergenic	RLTR23|LTR|ERV1	67961	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding	0.015000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-29	chr1	106058229	106058429	+	1.30912	NA	Intergenic	RLTR23|LTR|ERV1	67923	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4225	chr2	26531936	26532136	+	1.30797	NA	Intergenic	Intergenic	28109	NR_132655	102639736		NR_132655		Gm35978	-	predicted gene, 35978	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-702	chr10	13116052	13116252	+	1.30797	NA	intron (NM_001364643, intron 5 of 8)	(CAAAA)n|Simple_repeat|Simple_repeat	25307	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA	0.005000	0.363184			-10(ATTAACAAAACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3954	chr18	80500236	80500436	+	1.30797	NA	Intergenic	Intergenic	-30644	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding	0.010000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3813	chr18	42059818	42060018	+	1.30797	NA	intron (NM_172966, intron 1 of 7)	intron (NM_172966, intron 1 of 7)	6208	NM_001146299	269016	Mm.45472	NM_172966	ENSMUSG00000057719	Sh3rf2	2310046K19|9130023G24Rik|AI452083|Ppp1r39|RNF158	SH3 domain containing ring finger 2	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4599	chr2	127867060	127867260	+	1.30797	NA	intron (NM_028765, intron 1 of 17)	intron (NM_028765, intron 1 of 17)	12532	NM_028765	74121	Mm.244835	NM_028765	ENSMUSG00000027380	Acoxl	1200014P05Rik|AV025673	acyl-Coenzyme A oxidase-like	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-826	chr10	53943838	53944038	+	1.30797	NA	intron (NM_008548, intron 6 of 12)	MTE-int|LTR|ERVL-MaLR	131799	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3208	chr16	46131302	46131502	+	1.30797	NA	Intergenic	L1MA5|LINE|L1	-11154	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding	0.000000	0.353234			44(CCATGGACTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5038	chr3	82994267	82994467	+	1.30797	NA	Intergenic	Intergenic	-13357	NM_133862	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding	0.025000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-240	chr13	42679511	42679711	+	1.30788	NA	Intergenic	Intergenic	-1188	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8164	chrX	167131262	167131462	+	1.30758	NA	Intergenic	Intergenic	-60992	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5984	chr5	62672834	62673034	+	1.30658	NA	intron (NM_178407, intron 15 of 32)	intron (NM_178407, intron 15 of 32)	93243	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-30	chr1	11748530	11748730	+	1.30658	NA	intron (NM_001160369, intron 8 of 13)	intron (NM_001160369, intron 8 of 13)	334525	NM_001310451	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5097	chr3	103333048	103333248	+	1.30658	NA	intron (NM_053170, intron 11 of 19)	intron (NM_053170, intron 11 of 19)	53855	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1303	chr11	59991854	59992054	+	1.30658	NA	intron (NM_001290012, intron 2 of 6)	intron (NM_001290012, intron 2 of 6)	-27010	NM_009026	19416	Mm.3903	NM_009026	ENSMUSG00000049892	Rasd1	Dexras1	RAS, dexamethasone-induced 1	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5739	chr4	126779884	126780084	+	1.30658	NA	intron (NM_001035526, intron 2 of 23)	intron (NM_001035526, intron 2 of 23)	26214	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4003	chr19	10845597	10845797	+	1.30658	NA	intron (NM_023044, intron 1 of 7)	intron (NM_023044, intron 1 of 7)	3153	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding	0.010000	0.417910			-31(TATTAACTATGCAAAT,+,0.00),-16(TGAGAGTTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1731	chr12	71923081	71923281	+	1.30547	NA	intron (NM_026102, intron 3 of 25)	intron (NM_026102, intron 3 of 25)	33638	NM_001286452	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3921	chr18	69394224	69394424	+	1.30547	NA	intron (NM_001361127, intron 3 of 19)	intron (NM_001361127, intron 3 of 19)	48164	NM_001361128	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding	0.000000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-181	chr12	25609012	25609212	+	1.30437	NA	Intergenic	Intergenic	479938	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA	0.010000	0.383085			49(TTTTTCCATTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6324	chr6	15756300	15756500	+	1.30437	NA	intron (NM_175088, intron 3 of 4)	intron (NM_175088, intron 3 of 4)	35739	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding	0.005000	0.383085			11(ATGTAAAAGAGAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-720	chr10	20181996	20182196	+	1.30406	NA	intron (NM_001358787, intron 1 of 17)	intron (NM_001358787, intron 1 of 17)	11074	NM_001358787	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding	0.000000	0.398010	-25(TTTCCATTATTCATG,+,0.00),-25(TTTCCATTATTCATG,-,0.00),49(CATGAATAATTAAAA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3255	chr16	57465328	57465528	+	1.30395	NA	intron (NM_001040397, intron 1 of 4)	intron (NM_001040397, intron 1 of 4)	-83814	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-73	chr1	23963372	23963572	+	1.30395	NA	Intergenic	Intergenic	-41091	NM_001357395	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding	0.000000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-817	chr8	4466410	4466610	+	1.30395	NA	Intergenic	Lx9|LINE|L1	-26895	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4893	chr3	30466102	30466302	+	1.30395	NA	intron (NM_001361034, intron 1 of 16)	intron (NM_001361034, intron 1 of 16)	43473	NM_021442	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0.025000	0.422886			-9(GCTTTGTTTTTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4057	chr19	28134823	28135023	+	1.30395	NA	Intergenic	Intergenic	-123757	NM_001166414	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2400	chr14	24061622	24061822	+	1.30395	NA	Intergenic	Intergenic	-27155	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2563	chr14	77263736	77263936	+	1.30395	NA	intron (NM_172813, intron 1 of 18)	intron (NM_172813, intron 1 of 18)	107073	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7271	chr8	57914631	57914831	+	1.30395	NA	intron (NM_175032, intron 6 of 11)	intron (NM_175032, intron 6 of 11)	-261676	NM_001167981	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.000000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-150	chr11	61132753	61132953	+	1.30395	NA	intron (NM_021349, intron 1 of 4)	intron (NM_021349, intron 1 of 4)	6098	NM_021349	57916	Mm.265915	NM_021349	ENSMUSG00000010142	Tnfrsf13b	1200009E08Rik|Taci	tumor necrosis factor receptor superfamily, member 13b	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1305	chr11	60444999	60445199	+	1.30395	NA	3' UTR (NM_025757, exon 6 of 6)	3' UTR (NM_025757, exon 6 of 6)	-9492	NM_021354	13495	Mm.41803	NM_021354	ENSMUSG00000020537	Drg2	AI255295|AI461605|DRG-2	developmentally regulated GTP binding protein 2	protein-coding	0.010000	0.288557			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-459	chr19	28134902	28135102	+	1.30395	NA	Intergenic	Intergenic	-123836	NM_001166414	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1308	chr11	61132776	61132976	+	1.30395	NA	intron (NM_021349, intron 1 of 4)	intron (NM_021349, intron 1 of 4)	6121	NM_021349	57916	Mm.265915	NM_021349	ENSMUSG00000010142	Tnfrsf13b	1200009E08Rik|Taci	tumor necrosis factor receptor superfamily, member 13b	protein-coding	0.005000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-692	chr5	97427501	97427701	+	1.30389	NA	intron (NR_045981, intron 2 of 7)	intron (NR_045981, intron 2 of 7)	29422	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6765	chr6	146231087	146231287	+	1.30389	NA	intron (NM_019923, intron 41 of 56)	intron (NM_019923, intron 41 of 56)	271036	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding	0.020000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-255	chr13	83885083	83885283	+	1.30277	NA	Intergenic	Intergenic	-6025	NR_036594	72677	Mm.245636	NR_036594	ENSMUSG00000100891	2810049E08Rik	-	RIKEN cDNA 2810049E08 gene	ncRNA	0.020000	0.363184			-23(CAAATGTGATGTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-90	chr10	43982952	43983152	+	1.30277	NA	intron (NM_001368306, intron 7 of 20)	intron (NM_001368306, intron 7 of 20)	21794	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Crybg1	Aim1	crystallin beta-gamma domain containing 1	protein-coding	0.015000	0.427861			-23(ATTTGAAAAGCAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-800	chr10	43982966	43983166	+	1.30277	NA	intron (NM_001368306, intron 7 of 20)	intron (NM_001368306, intron 7 of 20)	21780	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Crybg1	Aim1	crystallin beta-gamma domain containing 1	protein-coding	0.015000	0.412935			-37(ATTTGAAAAGCAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6281	chr6	4600132	4600332	+	1.30271	NA	promoter-TSS (NM_145398)	promoter-TSS (NM_145398)	-679	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1|SOAT	CAS1 domain containing 1	protein-coding	0.000000	0.407960			-71(GTATGAATAAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1834	chr12	97977928	97978128	+	1.30188	NA	Intergenic	Intergenic	281431	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2843	chr15	29507287	29507487	+	1.30188	NA	Intergenic	Lx10|LINE|L1	206017	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7145	chr8	9962676	9962876	+	1.30188	NA	Intergenic	Intergenic	13547	NM_176953	319583	Mm.80584	NM_176953	ENSMUSG00000049717	Lig4	5830471N16Rik|tiny	ligase IV, DNA, ATP-dependent	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3135	chr16	27391563	27391763	+	1.30188	NA	intron (NM_001025615, intron 1 of 9)	intron (NM_001025615, intron 1 of 9)	2707	NM_026202	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding	0.000000	0.328358			-71(TAAATGTCATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4243	chr2	30474168	30474368	+	1.30076	NA	promoter-TSS (NM_030244)	promoter-TSS (NM_030244)	-69	NM_030244	72500	Mm.295464	NM_030244	ENSMUSG00000089762	Ier5l	2610524G09Rik	immediate early response 5-like	protein-coding	0.080000	0.651741			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3439	chr17	22355573	22355773	+	1.30076	NA	intron (NM_001355280, intron 3 of 6)	L1_Mur3|LINE|L1	5727	NM_001355280	319615	Mm.442162	NM_176962	ENSMUSG00000033972	Zfp944	6330416L07Rik	zinc finger protein 944	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7066	chr7	124628149	124628349	+	1.30002	NA	intron (NR_045907, intron 2 of 3)	intron (NR_045907, intron 2 of 3)	80686	NR_045907	73076	Mm.417827	NR_045907	ENSMUSG00000086254	3100003L05Rik	-	RIKEN cDNA 3100003L05 gene	ncRNA	0.020000	0.437811			-57(ATTTTCATGGGAATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4004	chr19	11880232	11880432	+	1.29996	NA	Intergenic	Intergenic	-9027	NM_001011775	257938	Mm.377309	NM_001011775	ENSMUSG00000067545	Olfr1419	MOR266-10	olfactory receptor 1419	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7069	chr7	125837822	125838022	+	1.29996	NA	intron (NM_001358287, intron 13 of 26)	MER2|DNA|TcMar-Tigger	130052	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7923	chrX	11907353	11907553	+	1.29996	NA	Intergenic	Intergenic	173100	NM_029510	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1064	chr10	116052715	116052915	+	1.29996	NA	intron (NM_011217, intron 2 of 13)	L1_Mur3|LINE|L1	34452	NM_011217	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4536	chr2	115500485	115500685	+	1.29996	NA	intron (NR_030712, intron 1 of 2)	L1Md_F2|LINE|L1	11616	NR_030712	100043232	Mm.240112	NR_030712	ENSMUSG00000085582	3110099E03Rik	-	RIKEN cDNA 3110099E03 gene	ncRNA	0.030000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4296	chr2	50550352	50550552	+	1.29996	NA	Intergenic	RMER17B|LTR|ERVK	195427	NR_154590	102634280		NR_154590		Gm48908	-	predicted gene 48908	ncRNA	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3291	chr16	67043680	67043880	+	1.29996	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	386662	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA	0.005000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-377	chr16	67043663	67043863	+	1.29996	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	386645	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA	0.005000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-485	chr2	59653655	59653855	+	1.29996	NA	intron (NM_198294, intron 2 of 26)	intron (NM_198294, intron 2 of 26)	6986	NM_001290659	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6310	chr6	13295277	13295477	+	1.29933	NA	Intergenic	Intergenic	-70412	NM_001013757	232585	Mm.389082	NM_001013757	ENSMUSG00000079679	Vwde	Gm467	von Willebrand factor D and EGF domains	protein-coding	0.010000	0.388060			-85(ACTCAGCCATGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-914	chrX	167567328	167567528	+	1.29747	NA	intron (NM_001368936, intron 4 of 16)	ORR1B1|LTR|ERVL-MaLR	-184679	NM_001313758	110639	Mm.272955	NM_026662	ENSMUSG00000025742	Prps2	2610101M19Rik|AA589463|AI464149|Prps-2	phosphoribosyl pyrophosphate synthetase 2	protein-coding	0.005000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-435	chr18	36404842	36405042	+	1.29747	NA	intron (NM_026027, intron 3 of 3)	intron (NM_026027, intron 3 of 3)	49553	NM_026027	67199	Mm.30184	NM_026027	ENSMUSG00000024346	Pfdn1	2700086I23Rik|AA408327|AU044714	prefoldin 1	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5536	chr4	72441975	72442175	+	1.29747	NA	Intergenic	Intergenic	240831	NR_027923	68285	Mm.37541	NR_027923		C630043F03Rik	AI851307	RIKEN cDNA C630043F03 gene	ncRNA	0.005000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-329	chr15	10053333	10053533	+	1.29747	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-123805	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0.005000	0.402985			-92(GTTTGAATAAGAATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6756	chr6	142770354	142770554	+	1.29747	NA	intron (NM_009908, intron 4 of 7)	intron (NM_009908, intron 4 of 7)	13768	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding	0.025000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2302	chr13	111424093	111424293	+	1.29747	NA	Intergenic	Intergenic	65934	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding	0.005000	0.288557			-29(ATTTAAAAAAAAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3793	chr18	36404778	36404978	+	1.29747	NA	intron (NM_026027, intron 3 of 3)	intron (NM_026027, intron 3 of 3)	49617	NM_026027	67199	Mm.30184	NM_026027	ENSMUSG00000024346	Pfdn1	2700086I23Rik|AA408327|AU044714	prefoldin 1	protein-coding	0.010000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-973	chr10	99046542	99046742	+	1.29747	NA	Intergenic	Intergenic	-60440	NR_153333	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding	0.015000	0.333333			-32(ATTTACATCAAAGTGT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-627	chr4	72299798	72299998	+	1.29636	NA	Intergenic	Intergenic	98654	NR_027923	68285	Mm.37541	NR_027923		C630043F03Rik	AI851307	RIKEN cDNA C630043F03 gene	ncRNA	0.000000	0.388060			-36(TATTTGTAATGCATAT,+,0.00),-7(GTTTTGCATTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4149	chr2	3890869	3891069	+	1.29636	NA	Intergenic	Intergenic	-126714	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|mKIAA1294	FERM domain containing 4A	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5719	chr4	123001091	123001291	+	1.29636	NA	3' UTR (NM_001303121, exon 3 of 3)	3' UTR (NM_001303121, exon 3 of 3)	5260	NM_008506	16918	Mm.1055	NM_008506	ENSMUSG00000028654	Mycl	AW536278|L-myc|Lmyc-1|Lmyc1|Mycl1|bHLHe38	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived	protein-coding	0.005000	0.482587			74(CCTTTGTTATGCAATG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5533	chr4	72299819	72300019	+	1.29636	NA	Intergenic	Intergenic	98675	NR_027923	68285	Mm.37541	NR_027923		C630043F03Rik	AI851307	RIKEN cDNA C630043F03 gene	ncRNA	0.000000	0.368159			-57(TATTTGTAATGCATAT,+,0.00),-28(GTTTTGCATTTCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-742	chr6	46737644	46737844	+	1.29636	NA	intron (NM_001004357, intron 13 of 23)	URR1A|DNA|hAT-Charlie	-506652	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.005000	0.368159	62(CATGAATAATGTAAG,+,0.00),62(CATGAATAATGTAAG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6431	chr6	46737648	46737848	+	1.29636	NA	intron (NM_001004357, intron 13 of 23)	URR1A|DNA|hAT-Charlie	-506648	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.005000	0.363184	58(CATGAATAATGTAAG,+,0.00),58(CATGAATAATGTAAG,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-191	chr12	71704659	71704859	+	1.29607	NA	Intergenic	Intergenic	-126309	NM_026102	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.020000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7159	chr8	13194872	13195072	+	1.29607	NA	intron (NM_001368858, intron 2 of 8)	intron (NM_001368858, intron 2 of 8)	5652	NM_001368858	66790	Mm.34901	NM_025768	ENSMUSG00000038515	Grtp1	5430401C05Rik|C81211|Tbc1d6	GH regulated TBC protein 1	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6172	chr5	123955341	123955541	+	1.29607	NA	intron (NM_001134767, intron 9 of 12)	intron (NM_001134767, intron 9 of 12)	-18187	NM_145070	29816	Mm.149954	NM_145070	ENSMUSG00000000915	Hip1r	AA410023|mKIAA0655	huntingtin interacting protein 1 related	protein-coding	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3592	chr17	75233252	75233452	+	1.29607	NA	intron (NM_206958, intron 3 of 29)	intron (NM_206958, intron 3 of 29)	54571	NM_206958	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding	0.000000	0.447761			27(GTTAGAATCACAATAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-454	chr19	11880499	11880699	+	1.29607	NA	Intergenic	Intergenic	-9294	NM_001011775	257938	Mm.377309	NM_001011775	ENSMUSG00000067545	Olfr1419	MOR266-10	olfactory receptor 1419	protein-coding	0.010000	0.393035			-3(CCATTGTGATGTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3064	chr15	102392611	102392811	+	1.29607	NA	Intergenic	B1_Mus1|SINE|Alu	-13605	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding	0.005000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-128	chr10	126680370	126680570	+	1.29607	NA	Intergenic	Intergenic	29921	NR_105841	102465224		NR_105841	ENSMUSG00000098756	Mir378d	Gm27650|mmu-mir-378d	microRNA 378d	ncRNA	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6041	chr5	77828216	77828416	+	1.29607	NA	Intergenic	MLTR18B_MM|LTR|ERVK	362828	NR_131050	69370	Mm.426881	NR_131050	ENSMUSG00000107232	1700017L05Rik	-	RIKEN cDNA 1700017L05 gene	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5534	chr4	72441333	72441533	+	1.29607	NA	Intergenic	Intergenic	240189	NR_027923	68285	Mm.37541	NR_027923		C630043F03Rik	AI851307	RIKEN cDNA C630043F03 gene	ncRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-248	chr1	86782497	86782697	+	1.29607	NA	intron (NM_153530, intron 5 of 20)	MER5A1|DNA|hAT-Charlie	78793	NM_001172157	208718	Mm.389152	NM_153530	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 like 3'-5' exoribonuclease 2	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6947	chr7	87319632	87319832	+	1.29607	NA	intron (NM_001285833, intron 8 of 19)	intron (NM_001285833, intron 8 of 19)	73083	NM_001285835	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding	0.000000	0.318408			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-410	chr17	75233310	75233510	+	1.29607	NA	intron (NM_206958, intron 3 of 29)	intron (NM_206958, intron 3 of 29)	54629	NM_206958	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding	0.005000	0.452736			-31(GTTAGAATCACAATAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-667	chr5	33922766	33922966	+	1.29607	NA	intron (NM_011914, intron 1 of 10)	intron (NM_011914, intron 1 of 10)	13405	NM_011914	24116	Mm.332320	NM_011914	ENSMUSG00000029111	Nelfa	Whsc2|Whsc2h	negative elongation factor complex member A, Whsc2	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6622	chr6	101617123	101617323	+	1.29589	NA	Intergenic	Intergenic	-157026	NR_027989	207157	Mm.57632	NM_177579	ENSMUSG00000052236	Gm9871	0610005I04|EG207157	predicted gene 9871	ncRNA	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5990	chr5	64280076	64280276	+	1.29575	NA	intron (NM_019636, intron 10 of 19)	intron (NM_019636, intron 10 of 19)	49819	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3761	chr18	28308309	28308509	+	1.29515	NA	Intergenic	Intergenic	-251755	NR_045398	320624	Mm.50107	NR_045398	ENSMUSG00000117473	4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA	0.005000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-428	chr18	28308248	28308448	+	1.29515	NA	Intergenic	Intergenic	-251816	NR_045398	320624	Mm.50107	NR_045398	ENSMUSG00000117473	4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA	0.005000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-81	chr10	12383683	12383883	+	1.29405	NA	3' UTR (NM_011682, exon 74 of 74)	3' UTR (NM_011682, exon 74 of 74)	477952	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding	0.000000	0.298507			26(TAATTCTTATGCAATT,+,0.00),41(TTTTTCTCTTGGTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2803	chr15	13062206	13062406	+	1.29333	NA	intron (NM_007666, intron 3 of 11)	MIRb|SINE|MIR	111369	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.010000	0.368159			-95(ATTTGCATTAATATAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-400	chr17	53672656	53672856	+	1.29333	NA	TTS (NM_020005)	TTS (NM_020005)	16559	NM_028232	72415	Mm.153202	NM_028232	ENSMUSG00000023940	Sgo1	3300001M08Rik|C81037|Sgol1	shugoshin 1	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4804	chr2	174924572	174924772	+	1.29333	NA	Intergenic	Intergenic	143097	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	-	predicted gene 14393	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4284	chr2	45496911	45497111	+	1.29231	NA	Intergenic	L1_Rod|LINE|L1	-199594	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA	0.000000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-554	chr3	19611073	19611273	+	1.29231	NA	TTS (NM_025489)	TTS (NM_025489)	-33287	NM_001081281	381485	Mm.35419	NM_001081281	ENSMUSG00000060913	Trim55	D830041C10Rik|Murf2|Rnf29	tripartite motif-containing 55	protein-coding	0.010000	0.363184			24(TTTAAAATGACAAAAA,-,0.00),82(ATCAGCATGAACATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4023	chr19	16486845	16487045	+	1.29231	NA	intron (NM_008137, intron 1 of 6)	MLT1E2|LTR|ERVL-MaLR	51278	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding	0.015000	0.477612			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-721	chr6	4866049	4866249	+	1.29231	NA	Intergenic	L1M2|LINE|L1	-36826	NM_001363809	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|neurabin-I	protein phosphatase 1, regulatory subunit 9A	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7590	chr9	31203211	31203411	+	1.29231	NA	intron (NM_001102456, intron 1 of 16)	L1ME3B|LINE|L1	8537	NM_001102455	11804	Mm.19133	NM_009691	ENSMUSG00000031996	Aplp2	AI790698|APLP-2|CDEBP	amyloid beta (A4) precursor-like protein 2	protein-coding	0.025000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6658	chr6	108549878	108550078	+	1.29231	NA	3' UTR (NM_010585, exon 62 of 62)	3' UTR (NM_010585, exon 62 of 62)	60235	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-797	chr10	43117674	43117874	+	1.29231	NA	intron (NM_175407, intron 4 of 6)	intron (NM_175407, intron 4 of 6)	56756	NM_175407	109205	Mm.153750	NM_175407	ENSMUSG00000038248	Sobp	2900009C16Rik|5330439J01Rik|JXC1|jc	sine oculis binding protein	protein-coding	0.005000	0.507463	78(AATGAATAATTCAGC,+,0.00),78(AATGAATAATTCAGC,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-660	chr5	9993498	9993698	+	1.29231	NA	Intergenic	Intergenic	-268246	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding	0.005000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-720	chr6	4600048	4600248	+	1.29192	NA	promoter-TSS (NM_145398)	promoter-TSS (NM_145398)	-763	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1|SOAT	CAS1 domain containing 1	protein-coding	0.000000	0.388060			13(GTATGAATAAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1324	chr11	66573947	66574147	+	1.29124	NA	Intergenic	Intergenic	-47921	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-423	chr1	141795333	141795533	+	1.29124	NA	Intergenic	Lx3_Mus|LINE|L1	-1139031	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA	0.000000	0.437811		-8(GATGAATATGCATA,+,0.00),-8(GATGAATATGCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3301	chr16	69938769	69938969	+	1.29124	NA	Intergenic	Intergenic	-75125	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5840	chr5	17623273	17623473	+	1.29124	NA	intron (NM_013657, intron 2 of 17)	intron (NM_013657, intron 2 of 17)	48557	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1479	chr11	114198357	114198557	+	1.29124	NA	intron (NR_045930, intron 1 of 2)	intron (NR_045930, intron 1 of 2)	199	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA	0.020000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4278	chr2	44316865	44317065	+	1.29124	NA	intron (NM_001364029, intron 11 of 12)	intron (NM_001364029, intron 11 of 12)	-251641	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2226	chr13	96393061	96393261	+	1.29124	NA	intron (NM_026173, intron 3 of 12)	intron (NM_026173, intron 3 of 12)	4867	NM_026173	67463	Mm.86472	NM_026173	ENSMUSG00000021671	Poc5	1200014M14Rik|AV144706	POC5 centriolar protein	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2728	chr14	120567971	120568171	+	1.29124	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	89610	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2072	chr13	51777054	51777254	+	1.29124	NA	intron (NM_001281880, intron 1 of 16)	intron (NM_001281880, intron 1 of 16)	16593	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1557	chr12	16912867	16913067	+	1.29124	NA	intron (NM_009072, intron 1 of 32)	intron (NM_009072, intron 1 of 32)	17989	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding	0.005000	0.323383		-37(CATCCATTTGCATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1328	chr11	67756006	67756206	+	1.29124	NA	intron (NM_175681, intron 4 of 12)	intron (NM_175681, intron 4 of 12)	15047	NM_175681	93896	Mm.118883	NM_175681	ENSMUSG00000049928	Glp2r	9530092J08Rik|GLP-2	glucagon-like peptide 2 receptor	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7269	chr8	57638841	57639041	+	1.29124	NA	intron (NM_001167981, intron 1 of 11)	intron (NM_001167981, intron 1 of 11)	-12812	NR_040698	100502619	Mm.393851	NR_040698		AW046200	-	expressed sequence AW046200	ncRNA	0.015000	0.442786			-57(ATGTAAATCAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5537	chr4	73037435	73037635	+	1.29124	NA	Intergenic	Intergenic	-184901	NM_001199270	353204	Mm.317892	NM_001199270	ENSMUSG00000059343	Aldoart1	4921524E03Rik|Aldo1-ps|Aldo1-ps2|Aldoa-ps2	aldolase 1 A, retrogene 1	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-69	chr1	23394439	23394639	+	1.29124	NA	Intergenic	Intergenic	-11364	NM_001081079	70155	Mm.28013	NM_001081079	ENSMUSG00000026158	Ogfrl1	2210417C17Rik	opioid growth factor receptor-like 1	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7826	chr9	94643772	94643972	+	1.29124	NA	Intergenic	Intergenic	-26020	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3062	chr15	101529280	101529480	+	1.29124	NA	intron (NM_008474, intron 4 of 8)	intron (NM_008474, intron 4 of 8)	3440	NM_008474	16680	Mm.25292	NM_008474	ENSMUSG00000044294	Krt84	AV235125|HRb-1|Krt2-16|Krt2-3	keratin 84	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2606	chr14	86823611	86823811	+	1.29124	NA	intron (NM_019670, intron 24 of 27)	intron (NM_019670, intron 24 of 27)	317513	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4564	chr2	121363698	121363898	+	1.29124	NA	TTS (NM_001355069)	TTS (NM_001355069)	5188	NM_009897	12716	Mm.252145	NM_009897	ENSMUSG00000000308	Ckmt1	Mt-CK|ScCKmit|U-MtCK|UbCKmit|mi-CK|mia-CK	creatine kinase, mitochondrial 1, ubiquitous	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-284	chr1	96929933	96930133	+	1.29124	NA	intron (NR_120500, intron 9 of 14)	Lx9|LINE|L1	-57862	NM_172658	227394	Mm.11662	NM_172658	ENSMUSG00000040693	Slco4c1	9530051F04|C330017E21Rik|OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20|oatp-R	solute carrier organic anion transporter family, member 4C1	protein-coding	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2805	chr15	13441851	13442051	+	1.29124	NA	Intergenic	Lx5c|LINE|L1	-268276	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5610	chr4	94374794	94374994	+	1.29124	NA	Intergenic	Lx5|LINE|L1	181902	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.000000	0.422886			-13(ATTTAAATAAGAAGGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3555	chr17	64185418	64185618	+	1.29124	NA	Intergenic	Intergenic	-134846	NR_130982	68771	Mm.443351	NR_130982		1110058D11Rik	-	RIKEN cDNA 1110058D11 gene	ncRNA	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5806	chr5	3260837	3261037	+	1.29124	NA	Intergenic	Intergenic	-82956	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding	0.000000	0.338308			-36(TATTTGTCATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1490	chr11	115881093	115881293	+	1.29124	NA	Intergenic	Intergenic	-18946	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding	0.020000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3656	chr17	88779716	88779916	+	1.29124	NA	intron (NM_001364898, intron 1 of 10)	intron (NM_001364898, intron 1 of 10)	12198	NM_013582	16867	Mm.1644	NM_013582	ENSMUSG00000024107	Lhcgr	Gpcr19-rs1|LH-R|LH/CG-R|LSH-R|Lhr	luteinizing hormone/choriogonadotropin receptor	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3223	chr16	50193699	50193899	+	1.29124	NA	3' UTR (NM_001347240, exon 17 of 17)	3' UTR (NM_001347240, exon 17 of 17)	-120947	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1173	chr11	16497567	16497767	+	1.29124	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	10817	NM_011343	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding	0.000000	0.412935			57(CCATTCTTATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1457	chr11	109393659	109393859	+	1.29054	NA	intron (NM_010303, intron 3 of 3)	B3|SINE|B2	-30105	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	-	predicted gene 11696	ncRNA	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7732	chr9	75536452	75536652	+	1.29054	NA	intron (NM_001357828, intron 1 of 10)	MER58A|DNA|hAT-Charlie	23105	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3094	chr16	15478658	15478858	+	1.29054	NA	Intergenic	Intergenic	115760	NM_023585	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7133	chr8	4267399	4267599	+	1.29054	NA	intron (NM_011592, intron 6 of 12)	intron (NM_011592, intron 6 of 12)	-8225	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding	0.010000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2518	chr14	62893067	62893267	+	1.29054	NA	intron (NM_175546, intron 2 of 11)	intron (NM_175546, intron 2 of 11)	27625	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-473	chr1	154216501	154216701	+	1.29054	NA	Intergenic	MTC|LTR|ERVL-MaLR	15414	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	Gm10178|Gm203	zinc finger protein 648	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4843	chr3	11261139	11261339	+	1.29054	NA	Intergenic	Intergenic	583120	NR_040751	100038545	Mm.388494	NR_040751	ENSMUSG00000104015	Gm10745	-	predicted gene 10745	ncRNA	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4762	chr2	160544280	160544480	+	1.29054	NA	Intergenic	Intergenic	-101517	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2730	chr14	120584509	120584709	+	1.29054	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	106148	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding	0.010000	0.462687			14(TGGTTCTCATTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2324	chr13	117511292	117511492	+	1.29054	NA	Intergenic	Intergenic	-90928	NM_010408	15165	Mm.343429	NM_010408	ENSMUSG00000021730	Hcn1	Bcng1|C630013B14Rik|HAC2	hyperpolarization activated cyclic nucleotide gated potassium channel 1	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7019	chr7	110190737	110190937	+	1.29054	NA	Intergenic	Intergenic	-30866	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4699	chr2	144082396	144082596	+	1.29054	NA	Intergenic	L1ME1|LINE|L1	49394	NM_001044750	403171	Mm.389362	NM_207275	ENSMUSG00000037307	Banf2	4930517K23Rik|Baf-L|Baf-like|Gm115	barrier to autointegration factor 2	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-465	chr1	152966124	152966324	+	1.29054	NA	intron (NM_175460, intron 1 of 10)	L2a|LINE|L2	11123	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.025000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2950	chr15	59585819	59586019	+	1.29054	NA	intron (NM_026746, intron 4 of 6)	L2a|LINE|L2	-62735	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8124	chrX	153666477	153666677	+	1.29054	NA	Intergenic	RLTR28|LTR|ERVL	29703	NM_175429	207474	Mm.271572	NM_175429	ENSMUSG00000041633	Kctd12b	9530071H11Rik|B430319H24Rik	potassium channel tetramerisation domain containing 12b	protein-coding	0.000000	0.402985			-71(CTTCTGTCATGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2148	chr13	75859564	75859764	+	1.29019	NA	Intergenic	Intergenic	19778	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1389	chr11	86701244	86701444	+	1.29019	NA	intron (NM_001356393, intron 30 of 32)	intron (NM_001356393, intron 30 of 32)	17270	NM_175004	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147|PTH 2	peptidyl-tRNA hydrolase 2	protein-coding	0.000000	0.442786	23(CATTCATTATGCATA,+,0.00),23(CATTCATTATGCATA,-,0.00)		29(TTATGCATAAGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6797	chr7	24022614	24022814	+	1.29019	NA	Intergenic	Lx8b|LINE|L1	19603	NM_207619	404287	Mm.377931	NM_207619	ENSMUSG00000092456	V1rd19	Vmn1r182	vomeronasal 1 receptor, D19	protein-coding	0.000000	0.363184		-35(CATGCATATACATA,+,0.00),-35(CATGCATATACATA,-,0.00)	10(ATATTGTTATGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1603	chr12	36425476	36425676	+	1.29019	NA	intron (NR_037309, intron 1 of 2)	intron (NR_037309, intron 1 of 2)	9960	NR_037309	100499526		NR_037309	ENSMUSG00000092917	Mir3472	mmu-mir-3472	microRNA 3472	ncRNA	0.030000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5070	chr3	95598825	95599025	+	1.29019	NA	intron (NM_146133, intron 2 of 4)	intron (NM_146133, intron 2 of 4)	9991	NM_146133	229593	Mm.245830	NM_146133	ENSMUSG00000046519	Golph3l	2010204I15Rik|AU015439|AW549227|C77637|Gpp34r	golgi phosphoprotein 3-like	protein-coding	0.000000	0.343284			-69(ACTTTGTCTTGTTCAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4047	chr19	22126367	22126567	+	1.29019	NA	Intergenic	Intergenic	-12579	NM_001035240	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4340	chr2	61043109	61043309	+	1.29019	NA	Intergenic	Intergenic	-68058	NR_045335	100038493	Mm.388076	NR_045335	ENSMUSG00000075325	Gm13582	-	predicted gene 13582	ncRNA	0.005000	0.383085			11(GCATTGTCAGGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4085	chr19	37155923	37156123	+	1.29019	NA	intron (NM_198300, intron 2 of 10)	Tigger10|DNA|TcMar-Tigger	-17820	NR_045329	319931	Mm.446730	NR_045329	ENSMUSG00000097591	A330032B11Rik	-	RIKEN cDNA A330032B11 gene	ncRNA	0.000000	0.358209			35(ATTTTAAAAAGAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2970	chr15	66572598	66572798	+	1.29019	NA	Intergenic	Intergenic	-4874	NM_001081409	239510	Mm.267473	NM_178718	ENSMUSG00000072501	Phf20l1	CGI-72|E130113K22Rik	PHD finger protein 20-like 1	protein-coding	0.005000	0.358209			-68(ATTTGAATACAAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-744	chr10	26837985	26838185	+	1.29019	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	65573	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4784	chr2	167865611	167865811	+	1.29019	NA	Intergenic	Intergenic	-66616	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2536	chr14	71521174	71521374	+	1.29019	NA	Intergenic	Intergenic	270001	NR_046076	100043132	Mm.399336	NR_046075	ENSMUSG00000115139	Gm4251	-	predicted gene 4251	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-351	chr1	125974920	125975120	+	1.29019	NA	intron (NM_176957, intron 12 of 12)	intron (NM_176957, intron 12 of 12)	-62092	NM_001311089	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3810	chr18	40301818	40302018	+	1.29019	NA	intron (NM_026135, intron 2 of 2)	MTD|LTR|ERVL-MaLR	44919	NM_001371039									0.000000	0.457711	-51(CATTCATTAAGCATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1860	chr12	102900002	102900202	+	1.29019	NA	intron (NM_001039049, intron 1 of 1)	intron (NM_001039049, intron 1 of 1)	796	NM_001039049	75483	Mm.660	NM_001039049	ENSMUSG00000043319	Cox8c	1700007F21Rik|COX8-3|COXVIII-3	cytochrome c oxidase subunit 8C	protein-coding	0.020000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-724	chr10	21025862	21026062	+	1.29019	NA	intron (NM_001358561, intron 17 of 22)	intron (NM_001358561, intron 17 of 22)	-14858	NM_001177776	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1034	chr10	111723949	111724149	+	1.29019	NA	Intergenic	Intergenic	-129776	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA	0.005000	0.457711			-28(TCATTATTATGTACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2686	chr14	107040583	107040783	+	1.29019	NA	Intergenic	Intergenic	-554163	NR_045938	73631	Mm.48862	NR_045938	ENSMUSG00000099794	1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	ncRNA	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5548	chr4	76849352	76849552	+	1.29019	NA	intron (NR_160919, intron 8 of 39)	intron (NR_160919, intron 8 of 39)	-505209	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.005000	0.427861			-65(CTTTGCATGAGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2815	chr15	20971652	20971852	+	1.29019	NA	Intergenic	Intergenic	-139700	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4306	chr2	52772321	52772521	+	1.29019	NA	Intergenic	L1_Mur3|LINE|L1	-30272	NM_019667	56324	Mm.263639	NM_019667	ENSMUSG00000055371	Stam2	1200004O12Rik|5730456G07Rik|BB145015|Hbp	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	protein-coding	0.010000	0.333333			61(TTTTTTTTTTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2172	chr13	82360776	82360976	+	1.29019	NA	Intergenic	Intergenic	337457	NR_039537	100628621		NR_039537	ENSMUSG00000106655	Mir3961	mmu-mir-3961	microRNA 3961	ncRNA	0.005000	0.412935			15(ATTTCCATGAGAAACG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3987	chr18	86304087	86304287	+	1.29019	NA	Intergenic	Lx7|LINE|L1	-90765	NM_001360910	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-815	chr10	50993761	50993961	+	1.29019	NA	Intergenic	L1_Mus3|LINE|L1	98210	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded family bHLH transcription factor 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2826	chr15	24989895	24990095	+	1.29019	NA	Intergenic	Intergenic	423769	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4090	chr19	40819017	40819217	+	1.29019	NA	Intergenic	Intergenic	-12162	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3019	chr15	90685447	90685647	+	1.29019	NA	Intergenic	Intergenic	-6159	NM_001357979	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6018	chr5	70986335	70986535	+	1.29019	NA	intron (NM_008066, intron 8 of 9)	intron (NM_008066, intron 8 of 9)	109414	NM_008066	14395	Mm.5304	NM_008066	ENSMUSG00000000560	Gabra2	C630048P16Rik|Gabra-2	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 2	protein-coding	0.015000	0.333333			-82(AATTTCTTTTTTAAAT,+,0.00),-27(CAATTTTCTTTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5568	chr4	82866978	82867178	+	1.29019	NA	Intergenic	Intergenic	-7405	NR_149737	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7917	chrX	8270510	8270710	+	1.29019	NA	promoter-TSS (NM_172479)	promoter-TSS (NM_172479)	-771	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4460	chr2	95992651	95992851	+	1.29019	NA	Intergenic	Intergenic	-325418	NM_001363048	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6254	chr5	148006194	148006394	+	1.29019	NA	intron (NM_029920, intron 1 of 14)	ORR1D2|LTR|ERVL-MaLR	48974	NM_029920	77521	Mm.244177	NM_029920	ENSMUSG00000029651	Mtus2	5730592G18Rik|A730013O20Rik|AU067634|C130038G02Rik|Cazip|Gm763|mKIAA0774	microtubule associated tumor suppressor candidate 2	protein-coding	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6312	chr6	13478537	13478737	+	1.29019	NA	Intergenic	Intergenic	65300	NR_038149	69413	Mm.177847	NR_038149	ENSMUSG00000101894	1700016P04Rik	-	RIKEN cDNA 1700016P04 gene	ncRNA	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7004	chr7	102485031	102485231	+	1.29019	NA	5' UTR (NM_020289, exon 2 of 2)	5' UTR (NM_020289, exon 2 of 2)	3176	NM_020289	257926	Mm.103733	NM_020289	ENSMUSG00000043925	Olfr544	MOR42-3|Ors6	olfactory receptor 544	protein-coding	0.010000	0.641791			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5119	chr3	110383137	110383337	+	1.29019	NA	Intergenic	Intergenic	-132238	NM_178891	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1902	chr12	117018091	117018291	+	1.29019	NA	intron (NM_011215, intron 11 of 22)	intron (NM_011215, intron 11 of 22)	133078	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-896	chr10	76190133	76190333	+	1.29019	NA	TTS (NM_133184)	TTS (NM_133184)	17176	NR_030443	751554		NR_030443	ENSMUSG00000076068	Mir678	Mirn678|mmu-mir-678	microRNA 678	ncRNA	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2445	chr14	36907804	36908004	+	1.29019	NA	intron (NM_001347503, intron 3 of 7)	intron (NM_001347503, intron 3 of 7)	11631	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding	0.020000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3147	chr16	29693392	29693592	+	1.29019	NA	Intergenic	Intergenic	114158	NM_133752	74143	Mm.274285	NM_133752	ENSMUSG00000038084	Opa1	1200011N24Rik|AI225888|AI847218|lilr3|mKIAA0567	OPA1, mitochondrial dynamin like GTPase	protein-coding	0.010000	0.467662			-24(GGCTTGGCATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4388	chr2	72242250	72242450	+	1.29019	NA	intron (NM_019688, intron 27 of 29)	intron (NM_019688, intron 27 of 29)	-43287	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|HCCS-4|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding	0.015000	0.631841			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7830	chr9	95056443	95056643	+	1.29019	NA	intron (NM_177909, intron 12 of 15)	intron (NM_177909, intron 12 of 15)	304714	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA	0.000000	0.323383	-66(AATGAATAAATTATT,+,0.00),-62(AATAAATTATTCATG,+,0.00),-62(AATAAATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1249	chr11	39678655	39678855	+	1.29019	NA	Intergenic	Intergenic	-288530	NR_126439	75315	Mm.461295	NR_126439		4930553C11Rik	-	RIKEN cDNA 4930553C11 gene	ncRNA	0.000000	0.437811			-32(CTCTAAATGACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1615	chr12	38994141	38994341	+	1.29019	NA	Intergenic	L1_Mus4|LINE|L1	210530	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding	0.000000	0.358209			-35(AAATTCTTAGGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2956	chr15	62026996	62027196	+	1.29019	NA	Intergenic	L1ME4a|LINE|L1	-10890	NR_003368	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	Pvt1 oncogene	ncRNA	0.015000	0.388060	66(TATAAATAATGTATA,+,0.00),66(TATAAATAATGTATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2610	chr14	87226722	87226922	+	1.29019	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-85598	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.005000	0.412935			-16(CCATTTTCATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-302	chr1	106007693	106007893	+	1.29019	NA	intron (NM_001122676, intron 4 of 13)	intron (NM_001122676, intron 4 of 13)	17387	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7677	chr9	60972362	60972562	+	1.29019	NA	Intergenic	LTR68|LTR|ERV1	-44607	NR_040767	330956	Mm.207985	NR_040767	ENSMUSG00000111290	Gm5122	A430102L10	predicted gene 5122	ncRNA	0.000000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1567	chr12	25609106	25609306	+	1.29007	NA	Intergenic	Intergenic	480032	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA	0.005000	0.457711			-45(TTTTTCCATTGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-310	chr14	98414345	98414545	+	1.28941	NA	Intergenic	Intergenic	-244680	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund family transcription factor 1	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3514	chr17	51357777	51357977	+	1.28889	NA	intron (NR_037264, intron 3 of 4)	intron (NR_037264, intron 3 of 4)	79889	NR_037260	100526491		NR_037260	ENSMUSG00000105182	Mir669a-9	mmu-mir-669a-9	microRNA 4669a-9	ncRNA	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4354	chr2	65043925	65044125	+	1.28889	NA	Intergenic	Intergenic	-21259	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding	0.005000	0.348259			56(ATTAGCAAGTCAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5853	chr5	20791078	20791278	+	1.28889	NA	intron (NM_172992, intron 8 of 17)	L1_Rod|LINE|L1	90946	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding	0.005000	0.407960			16(TTTTTGGTTTGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7932	chrX	18923139	18923339	+	1.28889	NA	Intergenic	Intergenic	223149	NR_029806	723827		NR_029806	ENSMUSG00000065422	Mir221	Mirn221|mir-221|mmu-mir-221	microRNA 221	ncRNA	0.005000	0.388060			14(ATATTGTCATTGTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-719	chr6	3539629	3539829	+	1.28889	NA	intron (NM_001167751, intron 12 of 26)	intron (NM_001167751, intron 12 of 26)	41336	NM_001167751	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3369	chr16	87747956	87748156	+	1.28889	NA	Intergenic	Intergenic	49102	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding	0.010000	0.402985			-18(ATCTATATGACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1356	chr11	75034323	75034523	+	1.28889	NA	intron (NM_001002764, intron 10 of 18)	intron (NM_001002764, intron 10 of 18)	31568	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2844	chr15	30343289	30343489	+	1.28889	NA	intron (NM_008729, intron 2 of 22)	PB1D7|SINE|Alu	170855	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding	0.005000	0.378109			-47(CCTTTATAATGAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-402	chr1	138174552	138174752	+	1.28889	NA	intron (NM_011210, intron 2 of 29)	intron (NM_011210, intron 2 of 29)	474	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5002	chr3	69430654	69430854	+	1.28889	NA	intron (NM_178726, intron 1 of 3)	intron (NM_178726, intron 1 of 3)	113836	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1158	chr11	11216449	11216649	+	1.28889	NA	intron (NM_177033, intron 3 of 3)	URR1B|DNA|hAT-Charlie	102533	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4664	chr2	138514479	138514679	+	1.28889	NA	Intergenic	Intergenic	236086	NM_145534	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding	0.000000	0.363184			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-490	chr2	68162456	68162656	+	1.28889	NA	Intergenic	Intergenic	57884	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding	0.005000	0.402985			-31(TCCTTGTCTTTCTAAT,+,0.00),-25(TCTTTCTAATGAAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6340	chr6	19135323	19135523	+	1.28889	NA	Intergenic	RLTR13B1|LTR|ERVK	143420	NR_126084	74725	Mm.387798	NR_126084	ENSMUSG00000107217	4930524B17Rik	-	RIKEN cDNA 4930524B17 gene	ncRNA	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5180	chr3	127544870	127545070	+	1.28868	NA	promoter-TSS (NR_146435)	promoter-TSS (NR_146435)	-119	NR_146435	110008574		NR_146435		LOC110008574	-	miR-302 host gene	ncRNA	0.000000	0.363184			16(ATTAAAATAACAAAGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-580	chr3	127544865	127545065	+	1.28868	NA	promoter-TSS (NR_146435)	promoter-TSS (NR_146435)	-124	NR_146435	110008574		NR_146435		LOC110008574	-	miR-302 host gene	ncRNA	0.000000	0.358209			21(ATTAAAATAACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5301	chr3	154612008	154612208	+	1.28868	NA	intron (NM_001357673, intron 4 of 8)	ORR1C2|LTR|ERVL-MaLR	14911	NM_001357674	12972	Mm.374855	NM_009968	ENSMUSG00000028199	Cryz	Sez9	crystallin, zeta	protein-coding	0.005000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-659	chr5	5291086	5291286	+	1.28833	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	-25118	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7080	chr7	129048301	129048501	+	1.28827	NA	Intergenic	Intergenic	-208693	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1849	chr12	100773337	100773537	+	1.28672	NA	Intergenic	Intergenic	-5620	NM_001361017	217830	Mm.218590	NM_145448	ENSMUSG00000021185	Dglucy	9030617O03Rik	D-glutamate cyclase	protein-coding	0.025000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7838	chr9	98295647	98295847	+	1.28672	NA	promoter-TSS (NM_144533)	promoter-TSS (NM_144533)	-823	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2670	chr14	105023049	105023249	+	1.28672	NA	Intergenic	Intergenic	154165	NM_134077	74213	Mm.124957	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5197	chr3	132778285	132778485	+	1.28672	NA	intron (NM_001163455, intron 23 of 25)	intron (NM_001163455, intron 23 of 25)	-93995	NM_001368626	13722	Mm.235137	NM_007926	ENSMUSG00000028029	Aimp1	9830137A06Rik|AIMP1/p43|EMAPII|Emap2|Scye1|p43	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1	protein-coding	0.005000	0.407960			82(TCATTATTATTGATAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-315	chr14	105023089	105023289	+	1.28672	NA	Intergenic	Intergenic	154125	NM_134077	74213	Mm.124957	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2794	chr15	12625528	12625728	+	1.28672	NA	intron (NM_001081064, intron 2 of 25)	intron (NM_001081064, intron 2 of 25)	114264	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3	PDZ domain containing 2	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3199	chr16	44178671	44178871	+	1.28672	NA	intron (NM_001029889, intron 1 of 7)	intron (NM_001029889, intron 1 of 7)	5374	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Usf3	5530400K22Rik|Gm1779|Gm608|mKIAA2018	upstream transcription factor family member 3	protein-coding	0.005000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3955	chr18	80770249	80770449	+	1.28672	NA	intron (NM_001201569, intron 15 of 29)	L1MC3|LINE|L1	-57278	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1793	chr12	86931434	86931634	+	1.28672	NA	Intergenic	Intergenic	-15507	NM_001289431	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744	CLOCK interacting protein, circadian	protein-coding	0.010000	0.582090			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-305	chr14	80055860	80056060	+	1.28631	NA	Intergenic	Intergenic	55658	NM_001351947	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.015000	0.442786			75(ATTTAAATAGCAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3194	chr16	43486473	43486673	+	1.28570	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-66377	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	-	predicted gene 15713	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1744	chr12	75886303	75886503	+	1.28570	NA	intron (NM_001005510, intron 6 of 115)	intron (NM_001005510, intron 6 of 115)	-22700	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3604	chr17	78753039	78753239	+	1.28570	NA	exon (NM_001081179, exon 36 of 36)	exon (NM_001081179, exon 36 of 36)	-16578	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding	0.035000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3503	chr17	49373526	49373726	+	1.28570	NA	Intergenic	Intergenic	-54738	NM_028464	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding	0.000000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5939	chr5	49611040	49611240	+	1.28570	NA	Intergenic	Intergenic	-325481	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5044	chr3	83601692	83601892	+	1.28570	NA	Intergenic	Intergenic	-27674	NR_036591	69460	Mm.389464	NR_036591	ENSMUSG00000101334	1700028M03Rik	-	RIKEN cDNA 1700028M03 gene	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6885	chr7	66545220	66545420	+	1.28570	NA	Intergenic	Intergenic	-117843	NM_053080	56847	Mm.140988	NM_053080	ENSMUSG00000015134	Aldh1a3	ALDH6|RALDH3|V1	aldehyde dehydrogenase family 1, subfamily A3	protein-coding	0.015000	0.532338			-52(GCTTTGTGATGCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4327	chr2	57722070	57722270	+	1.28570	NA	Intergenic	MLT2C2|LTR|ERVL	-275985	NM_172855	241391	Mm.484118	NM_172855	ENSMUSG00000026828	Galnt5	4832424J23	polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0.000000	0.303483			64(GCATTCTCATATACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7000	chr7	101736080	101736280	+	1.28570	NA	intron (NM_001363991, intron 5 of 16)	L1MC4a|LINE|L1	72429	NM_009191	20480	Mm.3990	NM_009191	ENSMUSG00000001829	Clpb	AL118244|Skd3	ClpB caseinolytic peptidase B	protein-coding	0.005000	0.363184	-91(TATTCATTATTCATT,+,0.00),-91(TATTCATTATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6620	chr6	101415480	101415680	+	1.28570	NA	Intergenic	MER33|DNA|hAT-Charlie	-37683	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5638	chr4	98990003	98990203	+	1.28570	NA	intron (NM_001369285, intron 24 of 48)	B1_Mur1|SINE|Alu	-40851	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding	0.005000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3851	chr18	52471566	52471766	+	1.28570	NA	intron (NM_026040, intron 1 of 7)	intron (NM_026040, intron 1 of 7)	5973	NM_026040	67222	Mm.100617	NM_026040	ENSMUSG00000024528	Srfbp1	2810036K01Rik|p49/STRAP	serum response factor binding protein 1	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7686	chr9	63198312	63198512	+	1.28570	NA	intron (NM_001364493, intron 18 of 20)	intron (NM_001364493, intron 18 of 20)	-49451	NM_001163758	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding	0.020000	0.442786			-22(ATTAACAAAGGAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1473	chr11	112259469	112259669	+	1.28570	NA	Intergenic	Intergenic	451787	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6492	chr6	63899613	63899813	+	1.28570	NA	intron (NM_001370966, intron 2 of 15)	intron (NM_001370966, intron 2 of 15)	643707	NM_001370966									0.005000	0.293532			-35(CTTACCATTACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2923	chr15	52757050	52757250	+	1.28570	NA	Intergenic	LTR82A|LTR|ERVL	44705	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5406	chr4	30181034	30181234	+	1.28570	NA	Intergenic	L1_Mur3|LINE|L1	-483462	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	ncRNA	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3234	chr16	53549148	53549348	+	1.28570	NA	Intergenic	Intergenic	-733504	NR_040495	73820	Mm.60493	NR_040495	ENSMUSG00000116611	4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA	0.000000	0.368159			-28(ATTTTAATGACAGACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4440	chr2	86298537	86298737	+	1.28570	NA	exon (NM_147010, exon 1 of 1)	exon (NM_147010, exon 1 of 1)	819	NM_147010	259012	Mm.377788	NM_147010	ENSMUSG00000047149	Olfr1052	MOR172-1	olfactory receptor 1052	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1266	chr11	44463380	44463580	+	1.28570	NA	intron (NM_024475, intron 6 of 10)	intron (NM_024475, intron 6 of 10)	7068	NM_024475	79560	Mm.338784	NM_024475	ENSMUSG00000041231	Ublcp1	4930527B16Rik|8430435I17Rik|BC002236	ubiquitin-like domain containing CTD phosphatase 1	protein-coding	0.000000	0.283582			60(CTTAAAAAGAGAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7089	chr7	130535939	130536139	+	1.28570	NA	intron (NM_001162855, intron 7 of 10)	intron (NM_001162855, intron 7 of 10)	11342	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6694	chr6	118971888	118972088	+	1.28570	NA	intron (NM_001256000, intron 3 of 46)	L1MB3|LINE|L1	91830	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA	0.015000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3600	chr17	78091220	78091420	+	1.28570	NA	Intergenic	Intergenic	-108928	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6358	chr6	23934554	23934754	+	1.28570	NA	Intergenic	Intergenic	35406	NM_207022	387347	Mm.377909	NM_207022	ENSMUSG00000043865	Tas2r118	Gm465|T2R16|T2R18|Tas2r16|Tas2r18|mGR18|mt2r40	taste receptor, type 2, member 118	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-978	chr10	100522477	100522677	+	1.28570	NA	intron (NM_146009, intron 25 of 53)	ORR1G|LTR|ERVL-MaLR	34995	NM_146009	216274	Mm.229114	NM_146009	ENSMUSG00000019971	Cep290	BC004690|Nphp6|b2b1454Clo|b2b1752Clo	centrosomal protein 290	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6242	chr5	144033946	144034146	+	1.28570	NA	intron (NM_033039, intron 1 of 4)	L1M5|LINE|L1	16563	NM_033039	18261	Mm.270533	NM_033039	ENSMUSG00000029618	Ocm	-	oncomodulin	protein-coding	0.020000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3312	chr16	72939248	72939448	+	1.28570	NA	intron (NM_019413, intron 6 of 28)	intron (NM_019413, intron 6 of 28)	276199	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1500	chr11	119593086	119593286	+	1.28570	NA	Intergenic	Intergenic	-9719	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	regulatory associated protein of MTOR, complex 1	protein-coding	0.025000	0.552239	-24(CGTGAATAATTCATG,+,0.00),-24(CGTGAATAATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6700	chr6	119634278	119634478	+	1.28570	NA	intron (NR_155458, intron 14 of 18)	intron (NR_155458, intron 14 of 18)	-90031	NM_009525	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7212	chr8	38792819	38793019	+	1.28570	NA	Intergenic	L2c|LINE|L2	-131411	NM_145841	244431	Mm.210388	NM_145841	ENSMUSG00000039539	Sgcz	C230085N17Rik	sarcoglycan zeta	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4434	chr2	84481816	84482016	+	1.28570	NA	Intergenic	MLTR18B_MM|LTR|ERVK	-5141	NM_001355271	21788	Mm.124316	NM_011576	ENSMUSG00000027082	Tfpi	A630013F22Rik|AW552122|EPI|LACI	tissue factor pathway inhibitor	protein-coding	0.025000	0.398010			-37(GCTTTGTTGTGATAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7210	chr8	37964679	37964879	+	1.28570	NA	intron (NM_145841, intron 1 of 7)	intron (NM_145841, intron 1 of 7)	287423	NR_029884	723860		NR_029884	ENSMUSG00000065457	Mir383	Mirn383|mir-383|mmu-mir-383	microRNA 383	ncRNA	0.000000	0.402985			52(ATTTGCAGGACAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7969	chrX	53001031	53001231	+	1.28570	NA	intron (NM_013556, intron 2 of 8)	B2_Mm2|SINE|B2	13053	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding	0.005000	0.437811			-23(ATCTGCATGCCAGAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4172	chr2	11162848	11163048	+	1.28570	NA	Intergenic	Intergenic	-9434	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5825	chr5	9823440	9823640	+	1.28570	NA	Intergenic	RLTR48A|LTR|ERV1	-98188	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7967	chrX	52354894	52355094	+	1.28570	NA	intron (NM_016697, intron 6 of 7)	intron (NM_016697, intron 6 of 7)	23187	NR_105805	102465202		NR_105805	ENSMUSG00000105738	Mir6384	mmu-mir-6384	microRNA 6384	ncRNA	0.005000	0.363184			-50(TCTGTGTTGTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4839	chr3	10466019	10466219	+	1.28570	NA	Intergenic	Intergenic	-25989	NM_029068	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5280	chr3	149184134	149184334	+	1.28570	NA	Intergenic	Intergenic	-90503	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.015000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5645	chr4	100842978	100843178	+	1.28570	NA	intron (NM_198037, intron 1 of 26)	intron (NM_198037, intron 1 of 26)	66399	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1443	chr11	104510726	104510926	+	1.28570	NA	intron (NM_145436, intron 15 of 18)	RLTR20A3_MM|LTR|ERVK	39794	NM_145436	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5139	chr3	117190570	117190770	+	1.28570	NA	Intergenic	MER58A|DNA|hAT-Charlie	-112905	NR_038029	433646	Mm.158997	NR_038029	ENSMUSG00000028009	1700061I17Rik	-	RIKEN cDNA 1700061I17 gene	ncRNA	0.000000	0.358209		82(GTTGCATATTCAAG,-,0.00)	75(CACTTGTGTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-920	chr10	87886615	87886815	+	1.28570	NA	intron (NM_010512, intron 2 of 4)	intron (NM_010512, intron 2 of 4)	25604	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1706	chr12	68132462	68132662	+	1.28570	NA	Intergenic	Intergenic	-910013	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1|Tg(Prnp-PFN1*G118V)838Kiaei	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6959	chr7	90120641	90120841	+	1.28570	NA	Intergenic	B4A|SINE|B4	8733	NR_046006	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5031	chr3	80550656	80550856	+	1.28570	NA	Intergenic	Intergenic	252079	NR_152147	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2|gluR-K2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding	0.000000	0.383085			10(ATTTACATCTGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3748	chr18	24567305	24567505	+	1.28570	NA	Intergenic	B3|SINE|B2	36412	NM_139143	106957	Mm.21688	NM_139143	ENSMUSG00000024270	Slc39a6	Ermelin|Zip6	solute carrier family 39 (metal ion transporter), member 6	protein-coding	0.000000	0.363184			-34(TTTTTTTTATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5527	chr4	69677176	69677376	+	1.28570	NA	Intergenic	Intergenic	-722879	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2318	chr13	116201644	116201844	+	1.28570	NA	Intergenic	G-rich|Low_complexity|Low_complexity	107944	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	ISL1 transcription factor, LIM/homeodomain	protein-coding	0.015000	0.582090			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2200	chr13	92132995	92133195	+	1.28570	NA	Intergenic	Intergenic	-1267	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4521	chr2	112397369	112397569	+	1.28570	NA	intron (NM_024254, intron 1 of 9)	L1MA6|LINE|L1	18258	NM_024254	72425	Mm.425091	NM_024254	ENSMUSG00000027132	Katnbl1	2410042D21Rik|AA166487|AA473307|AI467442	katanin p80 subunit B like 1	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4501	chr2	107181165	107181365	+	1.28570	NA	Intergenic	Intergenic	-109324	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6336	chr6	17951791	17951991	+	1.28570	NA	Intergenic	Intergenic	78554	NM_023653	22413	Mm.33653	NM_023653	ENSMUSG00000010797	Wnt2	2610510E18Rik|Int1l1|Irp|Mirp|Wnt-2|Wnt2a	wingless-type MMTV integration site family, member 2	protein-coding	0.030000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2047	chr13	41874393	41874593	+	1.28570	NA	intron (NR_033545, intron 1 of 6)	intron (NR_033545, intron 1 of 6)	8578	NR_033545	100038577	Mm.387093	NR_033545	ENSMUSG00000113856	Gm10790	-	predicted gene 10790	ncRNA	0.005000	0.348259			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-808	chr7	118472856	118473056	+	1.28520	NA	Intergenic	Intergenic	19019	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7043	chr7	118472890	118473090	+	1.28520	NA	Intergenic	Intergenic	18985	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7042	chr7	118472752	118472952	+	1.28520	NA	Intergenic	Intergenic	19123	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5937	chr5	48657942	48658142	+	1.28520	NA	intron (NM_001199244, intron 1 of 7)	MER5A1|DNA|hAT-Charlie	-58360	NM_001199245	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2049	chr13	42679388	42679588	+	1.28444	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-1311	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-579	chr1	178441568	178441768	+	1.28426	NA	intron (NM_026626, intron 2 of 6)	Charlie26a|DNA|hAT-Charlie	35650	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4697	chr2	142969166	142969366	+	1.28426	NA	Intergenic	Intergenic	66301	NR_131921	75053	Mm.72638	NR_131921	ENSMUSG00000086504	Kif16bos	4930511F01Rik	kinesin family member 16B, opposite strand	ncRNA	0.000000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-197	chr12	79482165	79482365	+	1.28426	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	184914	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-665	chr10	3359642	3359842	+	1.28426	NA	Intergenic	Intergenic	-6408	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory inhibitor subunit 14C	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3055	chr15	99664857	99665057	+	1.28426	NA	Intergenic	Intergenic	-5420	NM_009597	11419	Mm.440107	NM_009597	ENSMUSG00000023017	Asic1	AI843610|ASIC|ASIC1a|Accn2|B530003N02Rik|BNaC2	acid-sensing (proton-gated) ion channel 1	protein-coding	0.075000	0.676617	9(TATGAATTATTCACC,+,0.00),9(TATGAATTATTCACC,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-254	chr13	81476724	81476924	+	1.28426	NA	intron (NM_054053, intron 53 of 89)	intron (NM_054053, intron 53 of 89)	156320	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Adgrv1	Frings|Gpr98|Mass1|Mgr1|VLGR1	adhesion G protein-coupled receptor V1	protein-coding	0.005000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3172	chr16	37839151	37839351	+	1.28426	NA	Intergenic	L1M2|LINE|L1	21939	NM_001370898	102639802		NM_001370898	ENSMUSG00000108763	Gm36028	-	predicted gene, 36028	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4431	chr2	83733734	83733934	+	1.28426	NA	intron (NM_008402, intron 1 of 29)	intron (NM_008402, intron 1 of 29)	9437	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-662	chr1	194852839	194853039	+	1.28426	NA	Intergenic	Intergenic	30938	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA	0.005000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-650	chr4	111782705	111782905	+	1.28426	NA	intron (NM_026470, intron 8 of 12)	MLT1A|LTR|ERVL-MaLR	5208	NM_001357231	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding	0.000000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-479	chr2	47330759	47330959	+	1.28426	NA	Intergenic	Intergenic	-1483250	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3259	chr16	58080946	58081146	+	1.28165	NA	Intergenic	Intergenic	-326309	NM_007739	12837	Mm.130388	NM_007739	ENSMUSG00000068196	Col8a1	Col8a-1	collagen, type VIII, alpha 1	protein-coding	0.000000	0.253731			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7905	chr9	119315648	119315848	+	1.28165	NA	intron (NR_045693, intron 1 of 18)	intron (NR_045693, intron 1 of 18)	6679	NM_133985	108737	Mm.293565	NM_133985	ENSMUSG00000036737	Oxsr1	2210022N24Rik|2810422B09Rik|AI462649|AW209236|Osr1|mKIAA1101	oxidative-stress responsive 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4862	chr3	16086621	16086821	+	1.28165	NA	Intergenic	Intergenic	-80389	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6566	chr6	84796844	84797044	+	1.28165	NA	intron (NM_177077, intron 18 of 21)	intron (NM_177077, intron 18 of 21)	-203036	NM_001177713	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6096	chr5	93176744	93176944	+	1.28165	NA	3' UTR (NM_001310671, exon 10 of 10)	3' UTR (NM_001310671, exon 10 of 10)	29651	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding	0.015000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-751	chr6	70103919	70104119	+	1.28165	NA	Intergenic	RLTR13G|LTR|ERVK	688156	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2809	chr15	14266579	14266779	+	1.28165	NA	Intergenic	Intergenic	-1093004	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5057	chr3	87661064	87661264	+	1.28165	NA	intron (NM_001003912, intron 1 of 39)	intron (NM_001003912, intron 1 of 39)	18861	NM_001370863	625281		NM_001370863		Gm6570	EG625281	predicted gene 6570	protein-coding	0.000000	0.363184			-2(CATTTCTCATGGTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4962	chr3	59079410	59079610	+	1.28165	NA	intron (NM_177855, intron 10 of 43)	intron (NM_177855, intron 10 of 43)	22311	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding	0.005000	0.447761		39(TTTGAATATTGATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-88	chr1	29339914	29340114	+	1.28165	NA	Intergenic	Intergenic	-81474	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5992	chr5	64646972	64647172	+	1.28165	NA	Intergenic	Intergenic	-36373	NR_045078	100042198	Mm.25191	NR_045078	ENSMUSG00000105402	Gm3716	Gm1683	predicted gene 3716	ncRNA	0.000000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-464	chr19	58370038	58370238	+	1.28165	NA	intron (NM_001285457, intron 4 of 9)	intron (NM_001285457, intron 4 of 9)	73934	NR_040449	791347	Mm.452208	NR_040449		Gm10007	-	predicted gene 10007	ncRNA	0.020000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1128	chr10	125902093	125902293	+	1.28165	NA	Intergenic	Intergenic	-64026	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding	0.005000	0.323383	43(CATGAAATATTTATG,+,0.00),43(CATGAAATATTTATG,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-46	chr1	153321676	153321876	+	1.27898	NA	intron (NM_010683, intron 1 of 27)	intron (NM_010683, intron 1 of 27)	11010	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding	0.030000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-126	chr10	125403317	125403517	+	1.27898	NA	Intergenic	Intergenic	-74454	NM_001358496	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1126	chr10	125403333	125403533	+	1.27898	NA	Intergenic	Intergenic	-74470	NM_001358496	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3540	chr17	57286949	57287149	+	1.27898	NA	intron (NM_011691, intron 1 of 26)	intron (NM_011691, intron 1 of 26)	7949	NM_001163816	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding	0.010000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-327	chr15	7149129	7149329	+	1.27898	NA	intron (NM_013584, intron 1 of 19)	intron (NM_013584, intron 1 of 19)	8687	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	LIF receptor alpha	protein-coding	0.005000	0.308458			-87(ACATTCTTATTTTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2768	chr15	7149289	7149489	+	1.27898	NA	intron (NM_013584, intron 1 of 19)	intron (NM_013584, intron 1 of 19)	8847	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	LIF receptor alpha	protein-coding	0.005000	0.368159			18(TTTAAAATAACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1060	chr10	115759804	115760004	+	1.27864	NA	Intergenic	Intergenic	-57380	NM_146010	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding	0.000000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-814	chr7	129048330	129048530	+	1.27780	NA	Intergenic	Intergenic	-208664	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding	0.015000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-847	chr8	100224623	100224823	+	1.27629	NA	Intergenic	Intergenic	808049	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2780	chr15	10053247	10053447	+	1.27629	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-123891	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0.000000	0.358209			-6(GTTTGAATAAGAATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1805	chr12	89127387	89127587	+	1.27629	NA	intron (NM_172544, intron 2 of 19)	intron (NM_172544, intron 2 of 19)	174097	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0.020000	0.437811			-7(ATTTCCATGACATTTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3947	chr18	78731524	78731724	+	1.27629	NA	Intergenic	Intergenic	-134674	NM_207651	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3177	chr16	38286219	38286419	+	1.27629	NA	intron (NM_001098404, intron 1 of 8)	Lx8|LINE|L1	8505	NM_001098404	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2681	chr14	105390576	105390776	+	1.27562	NA	Intergenic	Intergenic	-36883	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.010000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-393	chr1	135715186	135715386	+	1.27555	NA	Intergenic	Intergenic	-4777	NM_001360782	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4856	chr3	14390980	14391180	+	1.27362	NA	Intergenic	Intergenic	27963	NR_033591	622229	Mm.486084	NR_033591		Gm6300	EG622229	solute carrier family 7 (cationic amino acid transporter, y+ system), member pseudogene	pseudo	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3931	chr18	70629106	70629306	+	1.27362	NA	Intergenic	Intergenic	60914	NM_001311071	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1491	chr11	116755020	116755220	+	1.27362	NA	intron (NR_003364, intron 3 of 3)	RLTR4_MM-int|LTR|ERV1	2953	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA	0.000000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-258	chr13	87928779	87928979	+	1.27362	NA	Intergenic	Intergenic	-892593	NM_010103	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1|Sox2-cre|Sox2Cre|Tg(Sox2-cre)1Amc	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.005000	0.323383			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-731	chr6	25033124	25033324	+	1.27259	NA	Intergenic	Intergenic	-77099	NM_177013	319832	Mm.127446	NM_177013	ENSMUSG00000048022	Tmem229a	6332401O19Rik	transmembrane protein 229A	protein-coding	0.000000	0.437811			14(ATTTGCTTAACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6549	chr6	81223848	81224048	+	1.27259	NA	Intergenic	Intergenic	671715	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA	0.000000	0.283582			-30(TTTTGAAGGACAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1454	chr11	108263296	108263496	+	1.27259	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	80492	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding	0.010000	0.422886		-16(ATTGCATAAGCATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6480	chr6	61492542	61492742	+	1.27259	NA	intron (NM_183310, intron 5 of 10)	intron (NM_183310, intron 5 of 10)	-311832	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2589	chr14	80055879	80056079	+	1.27257	NA	Intergenic	Intergenic	55677	NM_001351947	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.015000	0.437811			56(ATTTAAATAGCAATGC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-380	chr16	73341833	73342033	+	1.27257	NA	Intergenic	Intergenic	678784	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5901	chr5	34162117	34162317	+	1.27157	NA	intron (NM_146159, intron 4 of 4)	intron (NM_146159, intron 4 of 4)	7207	NM_146159	231123	Mm.319286	NM_146159	ENSMUSG00000079555	Haus3	D4S43h|D5H4S43|D5H4S43E	HAUS augmin-like complex, subunit 3	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-146	chr1	51490365	51490565	+	1.27157	NA	Intergenic	Intergenic	-12066	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6440	chr6	49654948	49655148	+	1.27157	NA	Intergenic	Intergenic	-167662	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-242	chr1	85762561	85762761	+	1.27157	NA	Intergenic	Intergenic	10713	NR_106172	102466882		NR_106172	ENSMUSG00000098634	Mir8096	Gm27479|mmu-mir-8096	microRNA 8096	ncRNA	0.015000	0.373134			-24(ATTTGAATTAAAAAAA,-,0.00),-18(ATTAAAAAAACAAAAA,-,0.00),38(CTTTGCATGACTAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1626	chr12	43696023	43696223	+	1.27157	NA	Intergenic	RLTR13D6|LTR|ERVK	513945	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-923	chr10	88287359	88287559	+	1.27157	NA	Intergenic	Intergenic	69616	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding	0.030000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-588	chr1	180548837	180549037	+	1.27157	NA	Intergenic	Intergenic	-19954	NM_007415	11545	Mm.277779	NM_007415	ENSMUSG00000026496	Parp1	5830444G22Rik|AI893648|ARTD1|Adprp|Adprt1|C80510|PARP|PPOL|msPARP|parp-1|sPARP-1	poly (ADP-ribose) polymerase family, member 1	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3830	chr18	46301579	46301779	+	1.27139	NA	intron (NM_001160399, intron 1 of 9)	RLTR16C_MM|LTR|ERVK	10249	NM_001160399	240261	Mm.329416	NM_001160399	ENSMUSG00000071855	Ccdc112	8430438M01Rik|AW108467	coiled-coil domain containing 112	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3587	chr17	72557250	72557450	+	1.27139	NA	intron (NM_007439, intron 1 of 28)	intron (NM_007439, intron 1 of 28)	46957	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5450	chr4	49191549	49191749	+	1.27139	NA	intron (NM_178756, intron 1 of 7)	MTC-int|LTR|ERVL-MaLR	132187	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	Plppr1	E130309F12Rik|Lppr1|PRG-3|mKIAA4247	phospholipid phosphatase related 1	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1047	chr10	114667221	114667421	+	1.27139	NA	intron (NM_146241, intron 3 of 18)	intron (NM_146241, intron 3 of 18)	134049	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5911	chr5	39364843	39365043	+	1.27139	NA	Intergenic	Intergenic	238631	NR_045416	75095	Mm.332354	NR_045416	ENSMUSG00000106741	4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2964	chr15	66171227	66171427	+	1.27139	NA	intron (NM_152923, intron 1 of 14)	intron (NM_152923, intron 1 of 14)	115302	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding	0.005000	0.452736			-83(ATTTGCATGAGAATCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3327	chr16	76843821	76844021	+	1.27139	NA	Intergenic	BGLII|LTR|ERVK	-64829	NR_155453	102632814		NR_155453	ENSMUSG00000109333	Gm30790	Gm45028	predicted gene, 30790	ncRNA	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8064	chrX	113184435	113184635	+	1.27139	NA	intron (NM_001370788, intron 1 of 14)	intron (NM_001370788, intron 1 of 14)	980	NM_001370789	12662	Mm.257316	NM_018818	ENSMUSG00000025531	Chm	Rep-1	choroidermia (RAB escort protein 1)	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4779	chr2	166552034	166552234	+	1.27139	NA	Intergenic	Intergenic	-12388	NR_152154	433503	Mm.491336	NR_152154		Gm29679	-	predicted gene, 29679	ncRNA	0.020000	0.462687			68(CTCTTGTGTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3934	chr18	71837381	71837581	+	1.27139	NA	intron (NM_007831, intron 2 of 28)	intron (NM_007831, intron 2 of 28)	513588	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6391	chr6	35223739	35223939	+	1.27139	NA	intron (NM_027513, intron 24 of 42)	intron (NM_027513, intron 24 of 42)	-28860	NR_015608	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA	0.010000	0.358209			-45(ATTTGCCATACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2233	chr13	97235117	97235317	+	1.27139	NA	Intergenic	Intergenic	-5888	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding	0.030000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-410	chr1	139079636	139079836	+	1.27139	NA	intron (NM_001166501, intron 9 of 21)	intron (NM_001166501, intron 9 of 21)	102079	NR_108103	78229	Mm.437838	NR_108103	ENSMUSG00000104900	4930596I21Rik	-	RIKEN cDNA 4930596I21 gene	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-586	chr1	179756890	179757090	+	1.27139	NA	intron (NM_026375, intron 31 of 35)	B1_Mur2|SINE|Alu	-11790	NM_001370897	383592		NM_001370897	ENSMUSG00000087236	Kif28	Gm1305|Kif28p	kinesin family member 28	protein-coding	0.000000	0.368159			-25(GAGTTGTCATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6965	chr7	91091345	91091545	+	1.27139	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	659	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs large MAGUK scaffold protein 2	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2474	chr14	47785903	47786103	+	1.27139	NA	Intergenic	Intergenic	-112861	NR_045959	73961	Mm.390702	NR_045959	ENSMUSG00000115609	4930447J18Rik	4930425M13Rik	RIKEN cDNA 4930447J18 gene	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7288	chr8	63760042	63760242	+	1.27139	NA	Intergenic	RLTR13D6|LTR|ERVK	192028	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgo2b	EG244495|Gm4975|Sgol2b	shugoshin 2B	protein-coding	0.015000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-390	chr17	22355834	22356034	+	1.27099	NA	intron (NM_001355280, intron 3 of 6)	L1_Mur3|LINE|L1	5466	NM_001355280	319615	Mm.442162	NM_176962	ENSMUSG00000033972	Zfp944	6330416L07Rik	zinc finger protein 944	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3771	chr18	31525797	31525997	+	1.27099	NA	Intergenic	Intergenic	-78482	NM_009308	20983	Mm.233846	NM_009308	ENSMUSG00000024261	Syt4	SytIV	synaptotagmin IV	protein-coding	0.015000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-430	chr18	31525821	31526021	+	1.27099	NA	Intergenic	Intergenic	-78506	NM_009308	20983	Mm.233846	NM_009308	ENSMUSG00000024261	Syt4	SytIV	synaptotagmin IV	protein-coding	0.010000	0.348259			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-404	chr17	65026891	65027091	+	1.27092	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-190920	NM_030031	78057	Mm.109380	NM_030031	ENSMUSG00000024088	4930583I09Rik	-	RIKEN cDNA 4930583I09 gene	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7064	chr7	124376904	124377104	+	1.27092	NA	intron (NM_001252072, intron 1 of 1)	RLTR31D_MM|LTR|ERVK	331931	NR_045907	73076	Mm.417827	NR_045907	ENSMUSG00000086254	3100003L05Rik	-	RIKEN cDNA 3100003L05 gene	ncRNA	0.010000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-474	chr2	38221369	38221569	+	1.27092	NA	intron (NM_001362973, intron 2 of 22)	intron (NM_001362973, intron 2 of 22)	65915	NM_001362977	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6515	chr6	70171674	70171874	+	1.27092	NA	Intergenic	Intergenic	620401	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1483	chr11	114465690	114465890	+	1.27092	NA	Intergenic	Intergenic	-16930	NR_027643	319819	Mm.50754	NM_177008	ENSMUSG00000062391	4932435O22Rik	-	RIKEN cDNA 4932435O22 gene	ncRNA	0.010000	0.442786			-50(ATTAGCAAGGCAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1327	chr11	67011754	67011954	+	1.27092	NA	Intergenic	RLTR9A3B|LTR|ERVK	-13300	NM_001291042	338369	Mm.128138	NM_177392	ENSMUSG00000050270	Tmem220	-	transmembrane protein 220	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6944	chr7	84672385	84672585	+	1.27092	NA	intron (NM_001360577, intron 1 of 7)	L1M5|LINE|L1	6911	NM_022985	65098	Mm.209349	NM_022985	ENSMUSG00000030629	Zfand6	3110005P07Rik|Awp1|Za20d3	zinc finger, AN1-type domain 6	protein-coding	0.000000	0.333333			12(ATTAGCATCACAGTGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4260	chr2	38221338	38221538	+	1.27092	NA	intron (NM_001362973, intron 2 of 22)	intron (NM_001362973, intron 2 of 22)	65946	NM_001362977	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2472	chr14	47654920	47655120	+	1.26986	NA	intron (NM_001293636, intron 2 of 39)	intron (NM_001293636, intron 2 of 39)	5709	NM_001347528	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1967	chr13	17706581	17706781	+	1.26986	NA	Intergenic	Intergenic	11268	NM_025479	66308	Mm.291109	NM_025479	ENSMUSG00000012429	Mplkip	2810021B07Rik|C330007M08Rik|Ttdn1	M-phase specific PLK1 intereacting protein	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5167	chr3	126565242	126565442	+	1.26986	NA	Intergenic	Intergenic	-31609	NM_001293666	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5017	chr3	75647712	75647912	+	1.26986	NA	non-coding (NR_040539, exon 3 of 3)	non-coding (NR_040539, exon 3 of 3)	7919	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3815	chr18	42868012	42868212	+	1.26986	NA	intron (NM_028392, intron 1 of 8)	intron (NM_028392, intron 1 of 8)	31394	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding	0.000000	0.318408			-48(CATTTGTGATGGAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4132	chr19	58243773	58243973	+	1.26986	NA	intron (NM_010279, intron 9 of 10)	intron (NM_010279, intron 9 of 10)	-52331	NR_040449	791347	Mm.452208	NR_040449		Gm10007	-	predicted gene 10007	ncRNA	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7487	chr8	125995445	125995645	+	1.26986	NA	exon (NM_008430, exon 1 of 3)	exon (NM_008430, exon 1 of 3)	443	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding	0.100000	0.691542			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-737	chr10	24634700	24634900	+	1.26986	NA	Intergenic	Intergenic	-38997	NR_163910									0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3858	chr18	53961467	53961667	+	1.26986	NA	Intergenic	Cheshire|DNA|hAT-Charlie	99454	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding	0.000000	0.328358		8(GATGAATATGCACT,+,0.00),8(GATGAATATGCACT,-,0.00)	-80(GCTTTGCCATGTAACT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4817	chr2	181357008	181357208	+	1.26986	NA	TTS (NM_001166668)	TTS (NM_001166668)	-7823	NM_144894	229007	Mm.87720	NM_144894	ENSMUSG00000027582	Zgpat	1500006I01Rik|BC021513	zinc finger, CCCH-type with G patch domain	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6697	chr6	119522228	119522428	+	1.26986	NA	intron (NM_009525, intron 1 of 4)	intron (NM_009525, intron 1 of 4)	22019	NM_009525	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding	0.000000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-424	chr1	143009972	143010172	+	1.26986	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-630625	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding	0.000000	0.378109			68(CCATTTTCATTTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6215	chr5	136679020	136679220	+	1.26986	NA	Intergenic	Intergenic	-14026	NM_001303019	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding	0.015000	0.587065			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1072	chr10	117648481	117648681	+	1.26986	NA	intron (NM_027468, intron 2 of 8)	ORR1A2|LTR|ERVL-MaLR	19081	NM_027468	70574	Mm.339332	NM_027468	ENSMUSG00000020183	Cpm	1110060I01Rik|5730456K23Rik|AA589379|E030045M14Rik	carboxypeptidase M	protein-coding	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1440	chr11	104027908	104028108	+	1.26986	NA	Intergenic	RLTR14|LTR|ERV1	61137	NM_007477	11841	Mm.5061	NM_007477	ENSMUSG00000062421	Arf2	-	ADP-ribosylation factor 2	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2925	chr15	53308411	53308611	+	1.26986	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	37672	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2946	chr15	58854791	58854991	+	1.26986	NA	Intergenic	L1M5|LINE|L1	-17758	NM_026642	68260	Mm.278805	NM_026642	ENSMUSG00000037085	Trmt12	4632406N01Rik|AI449275|Tyw2	tRNA methyltranferase 12	protein-coding	0.015000	0.338308			-35(ATTTGCATGACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3881	chr18	57646858	57647058	+	1.26986	NA	intron (NM_001311063, intron 5 of 5)	intron (NM_001311063, intron 5 of 5)	-8373	NR_045360	70157	Mm.490532	NR_045360	ENSMUSG00000118322	2210409D07Rik	-	RIKEN cDNA 2210409D07 gene	ncRNA	0.000000	0.323383			49(CATTGTTTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1005	chr10	107094954	107095154	+	1.26986	NA	intron (NM_198636, intron 1 of 10)	intron (NM_198636, intron 1 of 10)	28583	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1609	chr12	37595686	37595886	+	1.26986	NA	Intergenic	Intergenic	-284388	NM_001361688	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3538	chr17	56552146	56552346	+	1.26986	NA	intron (NR_130128, intron 3 of 3)	intron (NR_130128, intron 3 of 3)	2141	NR_130128	100504425	Mm.384143	NR_130128	ENSMUSG00000110218	Gm20219	Tincr	predicted gene, 20219	ncRNA	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7401	chr8	99358056	99358256	+	1.26986	NA	intron (NM_001039154, intron 2 of 12)	intron (NM_001039154, intron 2 of 12)	58315	NM_001285913	12564	Mm.441131	NM_007667	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2478	chr14	48192097	48192297	+	1.26986	NA	intron (NM_033602, intron 2 of 5)	intron (NM_033602, intron 2 of 5)	-6519	NR_003630	624367	Mm.445185	NM_001037921	ENSMUSG00000021846	Gm6498	EG624367	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.005000	0.457711		79(AATGAATATTGAAG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1505	chr11	121768518	121768718	+	1.26986	NA	Intergenic	Intergenic	-61600	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding	0.015000	0.457711			41(CCATAGTGATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1524	chr12	5764502	5764702	+	1.26986	NA	Intergenic	Intergenic	388882	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA	0.000000	0.452736			-90(ATTAAAAAAAAAAAAA,-,0.00),41(ATGTGCATGGCAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3857	chr18	53881021	53881221	+	1.26986	NA	intron (NM_152809, intron 1 of 12)	Tigger20a|DNA|TcMar-Tigger	19008	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding	0.000000	0.447761			-43(TTTTACATGATAATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5340	chr4	10625298	10625498	+	1.26986	NA	intron (NR_045185, intron 4 of 4)	intron (NR_045185, intron 4 of 4)	172404	NR_045185	73624	Mm.67392	NR_045185	ENSMUSG00000086080	1700123O12Rik	-	RIKEN cDNA 1700123O12 gene	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3855	chr18	53286450	53286650	+	1.26986	NA	intron (NM_029394, intron 1 of 6)	L1MC5a|LINE|L1	40925	NM_001370761	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6116	chr5	102547928	102548128	+	1.26986	NA	intron (NM_146161, intron 1 of 8)	L2|LINE|L2	66637	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding	0.000000	0.407960			-30(ATTTGCAAAACACAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6500	chr6	65726946	65727146	+	1.26986	NA	Intergenic	Intergenic	-51916	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4438	chr2	85233812	85234012	+	1.26986	NA	Intergenic	Intergenic	-35162	NM_001033346	241528	Mm.291095	NM_001033346	ENSMUSG00000075224	Lrrc55	A330097E02Rik|Gm351	leucine rich repeat containing 55	protein-coding	0.000000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1578	chr12	29682168	29682368	+	1.26986	NA	intron (NR_046080, intron 2 of 3)	intron (NR_046080, intron 2 of 3)	4177	NR_046080	328075	Mm.447832	NR_046080	ENSMUSG00000112663	C630031E19Rik	C630031E19	RIKEN cDNA C630031E19 gene	ncRNA	0.000000	0.318408			-96(TTATTCTCTTTGAAAG,+,0.00),44(ATTTGCAACTCAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6851	chr7	51927936	51928136	+	1.26986	NA	intron (NM_001330607, intron 4 of 7)	intron (NM_001330607, intron 4 of 7)	49069	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding	0.000000	0.363184			-66(CTATAGTCAGTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2467	chr14	46088482	46088682	+	1.26986	NA	Intergenic	Intergenic	4555	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7129	chr7	143368341	143368541	+	1.26974	NA	intron (NM_008434, intron 15 of 15)	L1M4|LINE|L1	-37791	NR_045842	71153	Mm.398340	NR_045842	ENSMUSG00000101360	4933417O13Rik	-	RIKEN cDNA 4933417O13 gene	ncRNA	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1725	chr12	71704879	71705079	+	1.26974	NA	Intergenic	Intergenic	-126089	NM_026102	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.010000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-455	chr19	14499981	14500181	+	1.26974	NA	intron (NM_001302947, intron 8 of 19)	intron (NM_001302947, intron 8 of 19)	-61575	NR_003027	19862		NR_003027	ENSMUSG00000095132	Rnu6	-	U6 small nuclear RNA	snRNA	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2022	chr13	36236377	36236577	+	1.26974	NA	intron (NM_001039189, intron 2 of 5)	intron (NM_001039189, intron 2 of 5)	118834	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.005000	0.442786			-17(TATTAGTTATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1161	chr11	12371011	12371211	+	1.26974	NA	intron (NM_001282993, intron 4 of 13)	intron (NM_001282993, intron 4 of 13)	41029	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3130	chr16	26786828	26787028	+	1.26974	NA	Intergenic	Intergenic	-31426	NR_105063	100504628	Mm.393275	NR_105063	ENSMUSG00000092545	Gm20319	-	predicted gene, 20319	ncRNA	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1724	chr12	71704658	71704858	+	1.26974	NA	Intergenic	Intergenic	-126310	NM_026102	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.020000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6636	chr6	103810597	103810797	+	1.26974	NA	Intergenic	Intergenic	153987	NR_144494	100846987		NR_144494		Pou5f1-rs5	Gm21054|Oct4P5|Otf3-rs5|Otf3e	POU domain, class 5, transcription factor 1, related sequence 5	pseudo	0.020000	0.407960			-11(CCTTTCTTATTCTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-234	chr13	36236392	36236592	+	1.26974	NA	intron (NM_001039189, intron 2 of 5)	intron (NM_001039189, intron 2 of 5)	118849	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.005000	0.427861			-32(TATTAGTTATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4418	chr2	79047801	79048001	+	1.26974	NA	Intergenic	L3|LINE|CR1	178223	NM_001356395	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding	0.005000	0.358209			-81(TGATTCTTATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5393	chr4	25799819	25800019	+	1.26973	NA	promoter-TSS (NM_010243)	promoter-TSS (NM_010243)	84	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.030000	0.626866			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5134	chr3	115950121	115950321	+	1.26823	NA	intron (NM_023214, intron 10 of 10)	intron (NM_023214, intron 10 of 10)	-29681	NR_130332	100316705		NR_130332	ENSMUSG00000089261	Mir669n	mmu-mir-669n	microRNA 669n	ncRNA	0.010000	0.398010			-34(TCATTGTTGTGTAAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-251	chr13	76069090	76069290	+	1.26823	NA	intron (NM_029847, intron 5 of 7)	intron (NM_029847, intron 5 of 7)	-12194	NM_175495	238725	Mm.167172	NM_175495	ENSMUSG00000045509	Gpr150	C030001A19Rik|PGR11	G protein-coupled receptor 150	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2394	chr14	22075035	22075235	+	1.26823	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	55423	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	Lrmda	1700112E06Rik|2700009F18Rik	leucine rich melanocyte differentiation associated	protein-coding	0.030000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8170	chrX	167973110	167973310	+	1.26823	NA	intron (NM_001033330, intron 3 of 19)	intron (NM_001033330, intron 3 of 19)	-118133	NM_001290428	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6087	chr5	91571682	91571882	+	1.26823	NA	intron (NM_145562, intron 1 of 3)	intron (NM_145562, intron 1 of 3)	54082	NM_145562	231440	Mm.5002	NM_145562	ENSMUSG00000034981	Parm1	2210012L08Rik|9130213B05Rik|W91666	prostate androgen-regulated mucin-like protein 1	protein-coding	0.005000	0.343284			32(ATTTGCATGACTGTGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-571	chr3	115950099	115950299	+	1.26823	NA	intron (NM_023214, intron 10 of 10)	intron (NM_023214, intron 10 of 10)	-29703	NR_130332	100316705		NR_130332	ENSMUSG00000089261	Mir669n	mmu-mir-669n	microRNA 669n	ncRNA	0.005000	0.398010			-12(TCATTGTTGTGTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1268	chr11	44805139	44805339	+	1.26823	NA	intron (NM_001362579, intron 7 of 16)	intron (NM_001362579, intron 7 of 16)	185011	NM_001362569	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding	0.010000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-478	chr2	45496888	45497088	+	1.26823	NA	Intergenic	L1_Rod|LINE|L1	-199617	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2422	chr14	30561792	30561992	+	1.26821	NA	intron (NM_009388, intron 4 of 13)	intron (NM_009388, intron 4 of 13)	-10257	NR_037237	100526475		NR_037237	ENSMUSG00000093156	Mir3076	mir-3076|mmu-mir-3076	microRNA 3076	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6677	chr6	115607579	115607779	+	1.26683	NA	intron (NM_023290, intron 1 of 7)	intron (NM_023290, intron 1 of 7)	5741	NM_023290	67027	Mm.101316	NM_023290	ENSMUSG00000000439	Mkrn2	2610002L04Rik|C81377	makorin, ring finger protein, 2	protein-coding	0.010000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-415	chr17	86977303	86977503	+	1.26650	NA	intron (NM_145491, intron 2 of 4)	HAL1ME|LINE|L1	14292	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding	0.015000	0.333333			-14(ATTTTGTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-782	chr10	39350161	39350361	+	1.26608	NA	Intergenic	Intergenic	-19538	NM_001122893	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-208	chr1	75749325	75749525	+	1.26608	NA	Intergenic	Intergenic	202963	NM_001357150	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7957	chrX	46607386	46607586	+	1.26608	NA	Intergenic	RMER6B|LTR|ERVK	278479	NM_028514	73360	Mm.60929	NM_028514	ENSMUSG00000046615	Actrt1	1700061J02Rik|Arp-T1	actin-related protein T1	protein-coding	0.000000	0.378109			43(GTTTTATCATGTACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6239	chr5	143028007	143028207	+	1.26608	NA	intron (NM_207110, intron 13 of 16)	intron (NM_207110, intron 13 of 16)	67752	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding	0.015000	0.442786			82(TCTTTTTCATTAAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7156	chr8	12400932	12401132	+	1.26608	NA	intron (NR_027975, intron 1 of 7)	intron (NR_027975, intron 1 of 7)	5513	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding	0.075000	0.656716			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7927	chrX	13600414	13600614	+	1.26608	NA	intron (NM_009806, intron 9 of 24)	intron (NM_009806, intron 9 of 24)	-32255	NM_011823	23890	Mm.487326	NM_011823	ENSMUSG00000040229	Gpr34	Lypsr1	G protein-coupled receptor 34	protein-coding	0.010000	0.407960			2(TAATTGTTATTCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7538	chr9	15637495	15637695	+	1.26608	NA	intron (NR_040746, intron 4 of 4)	intron (NR_040746, intron 4 of 4)	-9662	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Deup1	4933401K09Rik|Ccdc67	deuterosome assembly protein 1	protein-coding	0.005000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5082	chr3	100304953	100305153	+	1.26608	NA	Intergenic	Intergenic	-121352	NR_040543	73806	Mm.396549	NR_040543	ENSMUSG00000086923	4930406D18Rik	-	RIKEN cDNA 4930406D18 gene	ncRNA	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1417	chr11	94169779	94169979	+	1.26608	NA	Intergenic	Intergenic	-41575	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding	0.010000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4590	chr2	125756593	125756793	+	1.26608	NA	intron (NM_001369056, intron 6 of 12)	intron (NM_001369056, intron 6 of 12)	11293	NM_001369056	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4436	chr2	85136206	85136406	+	1.26608	NA	promoter-TSS (NM_011784)	promoter-TSS (NM_011784)	-54	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding	0.000000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3179	chr16	38651735	38651935	+	1.26608	NA	intron (NM_020260, intron 1 of 11)	intron (NM_020260, intron 1 of 11)	61200	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding	0.030000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2385	chr14	19962229	19962429	+	1.26608	NA	intron (NM_001285908, intron 1 of 3)	Tigger7|DNA|TcMar-Tigger	14364	NM_001285911	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding	0.005000	0.417910	-15(GATGAATAATTCATG,+,0.00),-15(GATGAATAATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7470	chr8	118686022	118686222	+	1.26608	NA	intron (NM_019707, intron 3 of 13)	ORR1D2|LTR|ERVL-MaLR	402511	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding	0.000000	0.457711			-5(CCTTTCTCATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2059	chr13	46645639	46645839	+	1.26608	NA	intron (NM_026056, intron 11 of 12)	intron (NM_026056, intron 11 of 12)	-23783	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7809	chr9	92610999	92611199	+	1.26608	NA	Intergenic	Intergenic	-68230	NR_029474	78575	Mm.407669	NR_029474	ENSMUSG00000103622	B430319G15Rik	D530025C14Rik	RIKEN cDNA B430319G15 gene	ncRNA	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4486	chr2	104459898	104460098	+	1.26608	NA	intron (NM_010434, intron 2 of 15)	intron (NM_010434, intron 2 of 15)	-31058	NR_035432	100316678		NR_035432	ENSMUSG00000084516	Mir1902	Mirn1902|mmu-mir-1902	microRNA 1902	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4146	chr2	3132530	3132730	+	1.26608	NA	intron (NM_001347067, intron 1 of 7)	intron (NM_001347067, intron 1 of 7)	13945	NM_001347067	269233	Mm.23044	NM_001081161	ENSMUSG00000050530	Fam171a1	9630050M13Rik|AA409679	family with sequence similarity 171, member A1	protein-coding	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1875	chr12	107028283	107028483	+	1.26608	NA	Intergenic	Intergenic	-312059	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA	0.035000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5212	chr3	136083668	136083868	+	1.26608	NA	intron (NM_001033350, intron 10 of 16)	intron (NM_001033350, intron 10 of 16)	242298	NM_001310749	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7360	chr8	83770248	83770448	+	1.26608	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-29037	NM_001163030	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-398	chr1	137863596	137863796	+	1.26608	NA	Intergenic	Intergenic	-102759	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7011	chr7	107470313	107470513	+	1.26608	NA	intron (NM_021889, intron 3 of 6)	MTE2b|LTR|ERVL-MaLR	-97020	NM_172907	244198	Mm.77425	NM_172907	ENSMUSG00000051041	Olfml1	6720478C22|AV321997|BC047207|MVAL564|ONT2|mONT2	olfactomedin-like 1	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4233	chr2	29440220	29440420	+	1.26608	NA	intron (NM_001290489, intron 2 of 6)	intron (NM_001290489, intron 2 of 6)	34974	NR_105753	102465170		NR_105753	ENSMUSG00000098539	Mir133c	Gm27865|mmu-mir-133c	microRNA 133c	ncRNA	0.025000	0.477612			-74(TTTTCCATGAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6322	chr6	15635461	15635661	+	1.26608	NA	Intergenic	Intergenic	-85100	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5585	chr4	87065397	87065597	+	1.26608	NA	intron (NM_172426, intron 4 of 10)	intron (NM_172426, intron 4 of 10)	162466	NM_001110240	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2595	chr14	84243963	84244163	+	1.26608	NA	Intergenic	Intergenic	-168773	NR_153783	102635012	Mm.399509	NR_153783	ENSMUSG00000115043	Gm32455	-	predicted gene, 32455	ncRNA	0.000000	0.343284			17(GTTTTGTTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4339	chr2	60832204	60832404	+	1.26608	NA	intron (NM_020296, intron 2 of 13)	intron (NM_020296, intron 2 of 13)	49134	NM_001141931	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1434	chr11	101483926	101484126	+	1.26608	NA	Intergenic	Intergenic	15851	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn|rho7	Rho family GTPase 2	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7092	chr7	131580084	131580284	+	1.26608	NA	Intergenic	Lx8b|LINE|L1	19690	NM_001317350	12237	Mm.927	NM_009774	ENSMUSG00000066979	Bub3	AU019800|AU021329|AU043350|AW146323|C78067	BUB3 mitotic checkpoint protein	protein-coding	0.025000	0.517413		74(CATGCCTATGCATG,+,0.00),74(CATGCCTATGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1539	chr12	12034778	12034978	+	1.26608	NA	Intergenic	Intergenic	-151979	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	tubulin, beta 2a, pseudogene 2	pseudo	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3113	chr16	22661739	22661939	+	1.26608	NA	Intergenic	Intergenic	-4608	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6540	chr6	78139458	78139658	+	1.26608	NA	Intergenic	Intergenic	-159891	NM_001109764	12386	Mm.34637	NM_009819	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	catenin (cadherin associated protein), alpha 2	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3225	chr16	50673483	50673683	+	1.26608	NA	Intergenic	Intergenic	-53549	NR_105782	102466634		NR_105782	ENSMUSG00000098482	Mir6363	Gm28026|mmu-mir-6363	microRNA 6363	ncRNA	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3364	chr16	87177795	87177995	+	1.26608	NA	Intergenic	Intergenic	-49456	NR_153792	102635567	Mm.233725	NR_153792	ENSMUSG00000116979	Gm32865	-	predicted gene, 32865	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4263	chr2	38895706	38895906	+	1.26608	NA	intron (NM_010264, intron 1 of 10)	intron (NM_010264, intron 1 of 10)	30655	NM_010264	14536	Mm.439703	NM_010264	ENSMUSG00000063972	Nr6a1	1700113M01Rik|Gcnf|NCNF|RTR	nuclear receptor subfamily 6, group A, member 1	protein-coding	0.005000	0.363184			-28(TTTAGCATGACATTGA,-,0.00),-9(CTTTACATTACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3298	chr16	68580023	68580223	+	1.26608	NA	Intergenic	Intergenic	-959215	NM_001145977	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.000000	0.358209			-12(GTATTTTTATGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5796	chr4	151824500	151824700	+	1.26608	NA	intron (NM_001195565, intron 3 of 3)	intron (NM_001195565, intron 3 of 3)	37168	NM_001195565	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding	0.005000	0.263682			-61(ATATGCAAAGAAAAAA,-,0.00),-46(ATTAAAAATACAAAAG,-,0.00),76(TTTTTCAAAACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1932	chr13	5492436	5492636	+	1.26608	NA	Intergenic	L1M5|LINE|L1	365556	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7365	chr8	87534975	87535175	+	1.26608	NA	Intergenic	Intergenic	-28832	NM_177901	330820	Mm.212913	NM_177901	ENSMUSG00000069971	4933402J07Rik	-	RIKEN cDNA 4933402J07 gene	protein-coding	0.005000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1019	chr10	108947256	108947456	+	1.26608	NA	intron (NM_001252342, intron 1 of 10)	intron (NM_001252342, intron 1 of 10)	61755	NM_001358506	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7585	chr9	30253018	30253218	+	1.26608	NA	Intergenic	Intergenic	-174211	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding	0.015000	0.477612	24(GATGAATTATTTATC,+,0.00),24(GATGAATTATTTATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5927	chr5	45880908	45881108	+	1.26608	NA	Intergenic	HAL1ME|LINE|L1	-23468	NM_001359873	209707	Mm.71498	NM_172153	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2942	chr15	58367495	58367695	+	1.26592	NA	intron (NM_027211, intron 1 of 8)	intron (NM_027211, intron 1 of 8)	21679	NM_027211	69787	Mm.237985	NM_027211		Anxa13	1810034H17Rik|AV055219	annexin A13	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1311	chr11	61598145	61598345	+	1.26589	NA	Intergenic	RMER10A|LTR|ERVL	-18558	NM_001362586	13855	Mm.139695	NM_010148	ENSMUSG00000001036	Epn2	9530051D10Rik|AA536924|Ibp2	epsin 2	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8161	chrX	166766893	166767093	+	1.26589	NA	Intergenic	Intergenic	104968	NR_046015	382255	Mm.336320	NR_046015	ENSMUSG00000086860	Gm1720	-	predicted gene 1720	ncRNA	0.015000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-302	chr14	78748103	78748303	+	1.26589	NA	Intergenic	Intergenic	-15474	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding	0.035000	0.621891			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-364	chr16	28880535	28880735	+	1.26589	NA	intron (NM_177718, intron 1 of 1)	intron (NM_177718, intron 1 of 1)	49063	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding	0.030000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-585	chr3	133422213	133422413	+	1.26464	NA	Intergenic	L1_Mur3|LINE|L1	112203	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding	0.000000	0.328358			31(CTTTTGTTAAGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7289	chr8	63770052	63770252	+	1.26464	NA	Intergenic	Intergenic	182018	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgo2b	EG244495|Gm4975|Sgol2b	shugoshin 2B	protein-coding	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5202	chr3	133422225	133422425	+	1.26464	NA	Intergenic	L1_Mur3|LINE|L1	112215	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding	0.000000	0.328358			19(CTTTTGTTAAGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4406	chr2	76805543	76805743	+	1.26433	NA	intron (NM_028004, intron 68 of 191)	intron (NM_028004, intron 68 of 191)	130328	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding	0.005000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-104	chr10	99385487	99385687	+	1.26433	NA	Intergenic	Intergenic	122356	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.010000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-582	chr3	131139470	131139670	+	1.26343	NA	intron (NM_010703, intron 3 of 11)	intron (NM_010703, intron 3 of 11)	26779	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-497	chr1	161147867	161148067	+	1.26269	NA	intron (NM_001368766, intron 2 of 7)	intron (NM_001368766, intron 2 of 7)	5255	NM_028664	73844	Mm.38830	NM_028664	ENSMUSG00000044835	Ankrd45	4933409K03Rik	ankyrin repeat domain 45	protein-coding	0.005000	0.353234			-28(ACATTCTCATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5751	chr4	130712318	130712518	+	1.26269	NA	intron (NM_001356566, intron 3 of 17)	intron (NM_001356566, intron 3 of 17)	-37220	NR_028565	100217460		NR_028565	ENSMUSG00000065196	Snord85	MBII-251|Z50	small nucleolar RNA, C/D box 85	snoRNA	0.010000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-858	chr9	13645054	13645254	+	1.26269	NA	intron (NM_001013813, intron 1 of 3)	intron (NM_001013813, intron 1 of 3)	-17306	NM_173776	270118	Mm.116898	NM_173776	ENSMUSG00000031925	Maml2	5930431H10|BC032967	mastermind like transcriptional coactivator 2	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6691	chr6	118785636	118785836	+	1.26269	NA	intron (NM_001256000, intron 3 of 46)	intron (NM_001256000, intron 3 of 46)	-27762	NM_001290335	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-434	chr1	143853241	143853441	+	1.26103	NA	Intergenic	Intergenic	76063	NM_001159866	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding	0.000000	0.378109	-83(TGTAAATAATGCATG,+,0.00),-83(TGTAAATAATGCATG,-,0.00)		30(CTTAGCAAAAGAATGT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-259	chr13	90358339	90358539	+	1.26070	NA	Intergenic	Intergenic	268772	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3148	chr16	29799502	29799702	+	1.25868	NA	Intergenic	Intergenic	179522	NR_037689	328657	Mm.425982	NM_001033403	ENSMUSG00000075286	Gm1968	-	predicted gene 1968	ncRNA	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7071	chr7	126135057	126135257	+	1.25824	NA	intron (NM_028816, intron 9 of 23)	intron (NM_028816, intron 9 of 23)	-52746	NM_001358885	269994	Mm.39599	NM_001101488	ENSMUSG00000046182	Gsg1l	AI852434|C230098I05Rik|G630023A01Rik|Gm637|g1l	GSG1-like	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6844	chr7	49865383	49865583	+	1.25824	NA	Intergenic	Intergenic	-44816	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding	0.005000	0.467662			-72(TTATGCATGATAATCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3887	chr18	59202018	59202218	+	1.25824	NA	intron (NM_001081328, intron 2 of 2)	intron (NM_001081328, intron 2 of 2)	26778	NM_001081328	78923	Mm.84007	NM_001081328	ENSMUSG00000058152	Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1233	chr11	33388734	33388934	+	1.25824	NA	intron (NM_001362875, intron 14 of 28)	Lx7|LINE|L1	124919	NR_110973	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3829	chr18	46016103	46016303	+	1.25824	NA	intron (NR_040342, intron 2 of 3)	intron (NR_040342, intron 2 of 3)	29057	NR_040342	107003	Mm.395148	NR_040342		A330093E20Rik	AU043608	RIKEN cDNA A330093E20 gene	ncRNA	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3178	chr16	38292795	38292995	+	1.25824	NA	intron (NM_001098404, intron 1 of 8)	Lx8b|LINE|L1	1929	NM_001098404	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2865	chr15	37458489	37458689	+	1.25824	NA	promoter-TSS (NM_001359842)	promoter-TSS (NM_001359842)	-78	NM_001359842	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4952	chr3	55360772	55360972	+	1.25824	NA	intron (NM_001357469, intron 3 of 17)	intron (NM_001357469, intron 3 of 17)	-100856	NM_001111051	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-984	chr10	103269125	103269325	+	1.25824	NA	Intergenic	RLTR13C2|LTR|ERVK	-32903	NM_029134	74978	Mm.483817	NM_029134	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4966	chr3	60373678	60373878	+	1.25824	NA	Intergenic	L1M3|LINE|L1	-99052	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind like splicing factor 1	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6423	chr6	43683404	43683604	+	1.25824	NA	Intergenic	RLTR17B_Mm|LTR|ERVK	-17226	NM_001311111	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding	0.005000	0.308458		-23(CATACATATACATG,+,0.00),-23(CATACATATACATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4398	chr2	75511831	75512031	+	1.25824	NA	Intergenic	Intergenic	-67752	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA	0.020000	0.402985			53(CTTTGCTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4568	chr2	122866764	122866964	+	1.25824	NA	Intergenic	Lx2B|LINE|L1	84865	NM_021507	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqor	0610039J17Rik|4930557M22Rik|Sqrdl	sulfide quinone oxidoreductase	protein-coding	0.000000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5804	chr4	154808696	154808896	+	1.25824	NA	Intergenic	Intergenic	-28620	NM_172878	242800	Mm.72944	NM_172878	ENSMUSG00000046637	Ttc34	4932418L02|B230396O12Rik	tetratricopeptide repeat domain 34	protein-coding	0.015000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6547	chr6	81210578	81210778	+	1.25824	NA	Intergenic	Intergenic	684985	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1688	chr12	62707511	62707711	+	1.25824	NA	Intergenic	RLTR13D6|LTR|ERVK	19824	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-631	chr1	189528386	189528586	+	1.25824	NA	Intergenic	Intergenic	-126213	NM_001281848	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2746	chr14	122837009	122837209	+	1.25824	NA	intron (NR_153443, intron 22 of 24)	B1F1|SINE|Alu	-75921	NR_155286	105245866	Mm.390754	NM_001039531	ENSMUSG00000075463	4930594M22Rik	F930011C10Rik|Gm15735	RIKEN cDNA 4930594M22 gene	ncRNA	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3816	chr18	43023131	43023331	+	1.25824	NA	intron (NM_028392, intron 1 of 8)	intron (NM_028392, intron 1 of 8)	36240	NM_028392	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6676	chr6	114952442	114952642	+	1.25824	NA	intron (NM_001356371, intron 2 of 5)	LTR82A|LTR|ERVL	16661	NM_001356371	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2710	chr14	117059007	117059207	+	1.25824	NA	intron (NM_001079844, intron 1 of 9)	intron (NM_001079844, intron 1 of 9)	133810	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding	0.005000	0.308458	70(ACTACATAATGCATC,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6435	chr6	48919290	48919490	+	1.25824	NA	Intergenic	Lx8|LINE|L1	-10506	NM_001081273	69761	Mm.333053	NM_001081273	ENSMUSG00000029813	Doxl1	1600015I10Rik|AI429442	diamine oxidase-like protein 1	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7893	chr9	115564411	115564611	+	1.25824	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	182692	NR_130329	100316675		NR_130329	ENSMUSG00000080409	Mir467h	Mirn467h|mmu-mir-467h	microRNA 467h	ncRNA	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6816	chr7	35679434	35679634	+	1.25824	NA	Intergenic	Intergenic	-32052	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5654	chr4	102919705	102919905	+	1.25824	NA	intron (NM_001285862, intron 11 of 19)	intron (NM_001285862, intron 11 of 19)	-66574	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7976	chrX	60893976	60894176	+	1.25824	NA	promoter-TSS (NM_009237)	promoter-TSS (NM_009237)	423	NR_155290	102631518	Mm.421161	NR_155290		Gm38438	-	predicted gene, 38438	ncRNA	0.060000	0.641791			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6545	chr6	80787332	80787532	+	1.25824	NA	intron (NM_001134743, intron 2 of 2)	intron (NM_001134743, intron 2 of 2)	767789	NM_001347261	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2439	chr14	33913813	33914013	+	1.25824	NA	Intergenic	Intergenic	-9674	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding	0.010000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4992	chr3	68432061	68432261	+	1.25824	NA	intron (NM_001113420, intron 1 of 6)	intron (NM_001113420, intron 1 of 6)	-36022	NM_001282045	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7641	chr9	47747193	47747393	+	1.25824	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	70915	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	-	predicted gene 10677	ncRNA	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1394	chr11	87847754	87847954	+	1.25824	NA	Intergenic	RLTR21|LTR|ERVK	-5361	NM_001039684	380718	Mm.24404	NM_001039684	ENSMUSG00000034121	Mks1	AK190930|B8d3|avc6	Meckel syndrome, type 1	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6599	chr6	96366400	96366600	+	1.25824	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	-200295	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	Npap60|Nup50	nucleoporin 50 pseudogene	pseudo	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1874	chr12	106746992	106747192	+	1.25824	NA	Intergenic	Intergenic	-30768	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA	0.005000	0.442786			-10(CTCTGCATTACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4457	chr2	95020511	95020711	+	1.25824	NA	Intergenic	Intergenic	-582425	NM_001349003	11800	Mm.181824	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452|API-5	apoptosis inhibitor 5	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2666	chr14	103666753	103666953	+	1.25824	NA	intron (NM_198014, intron 2 of 6)	intron (NM_198014, intron 2 of 6)	16625	NM_001361639	105439	Mm.27548	NM_198014	ENSMUSG00000055717	Slain1	9630044O09Rik|AA675320|AW742596	SLAIN motif family, member 1	protein-coding	0.015000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5434	chr4	37166730	37166930	+	1.25824	NA	Intergenic	Intergenic	-82573	NR_151605	102636890	Mm.109154	NR_151605	ENSMUSG00000086026	Gm12374	-	predicted gene 12374	ncRNA	0.005000	0.313433			13(TTTTTGTTATTTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4468	chr2	98005952	98006152	+	1.25824	NA	Intergenic	Lx2B|LINE|L1	538395	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-211	chr1	76112831	76113031	+	1.25824	NA	Intergenic	Intergenic	-376202	NR_038012	620079	Mm.378379	NR_038012	ENSMUSG00000100553	Gm17751	-	predicted gene, 17751	ncRNA	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3029	chr15	92773239	92773439	+	1.25824	NA	Intergenic	Intergenic	176230	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding	0.015000	0.353234			-43(ATTTGAATAATAACGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6036	chr5	75416882	75417082	+	1.25824	NA	Intergenic	URR1B|DNA|hAT-Charlie	-158005	NM_001122733	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3418	chr17	10098512	10098712	+	1.25824	NA	Intergenic	Intergenic	220749	NM_001159517	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding	0.010000	0.417910			-38(ATTTACATCCCAATTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7760	chr9	80173721	80173921	+	1.25824	NA	intron (NM_001039546, intron 1 of 32)	LTR33A_|LTR|ERVL	8787	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Myo6<rsv>|Tlc|rsv|sv	myosin VI	protein-coding	0.005000	0.611940			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3267	chr16	60627548	60627748	+	1.25824	NA	Intergenic	Intergenic	-22117	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7518	chr9	9645833	9646033	+	1.25667	NA	Intergenic	Intergenic	-248498	NR_105745	102466147		NR_105745	ENSMUSG00000098408	Mir6237	Gm27411|mmu-mir-6237	microRNA 6237	ncRNA	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1013	chr10	108409535	108409735	+	1.25636	NA	intron (NM_054056, intron 5 of 6)	intron (NM_054056, intron 5 of 6)	-7616	NR_155870	102640148	Mm.336104	NR_155870	ENSMUSG00000112532	Gm36283	-	predicted gene, 36283	ncRNA	0.015000	0.437811	-23(TATGAATTATGAATT,+,0.00),-23(TATGAATTATGAATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5237	chr3	141098058	141098258	+	1.25636	NA	Intergenic	Intergenic	114197	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.010000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-960	chr10	96658983	96659183	+	1.25636	NA	Intergenic	Intergenic	42082	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding	0.015000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5469	chr4	53507858	53508058	+	1.25636	NA	intron (NM_133891, intron 3 of 15)	intron (NM_133891, intron 3 of 15)	67545	NM_133891	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4608	chr2	130219570	130219770	+	1.25636	NA	intron (NM_138655, intron 5 of 19)	intron (NM_138655, intron 5 of 19)	24476	NM_138655	192140	Mm.219546	NM_138655	ENSMUSG00000060332	Tmc2	CWEA2	transmembrane channel-like gene family 2	protein-coding	0.010000	0.348259			-18(TTGTGCAAGACAATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-452	chr18	83855474	83855674	+	1.25636	NA	Intergenic	Intergenic	230891	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|teashirt1	teashirt zinc finger family member 1	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3256	chr16	57465668	57465868	+	1.25636	NA	intron (NM_001040397, intron 1 of 4)	intron (NM_001040397, intron 1 of 4)	-83474	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding	0.030000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1091	chr10	120720176	120720376	+	1.25636	NA	Intergenic	MIR3|SINE|MIR	-45456	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA	0.010000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1613	chr12	38714366	38714566	+	1.25636	NA	Intergenic	Intergenic	-65616	NM_007960	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding	0.000000	0.333333			-88(ATATTCCCATTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-337	chr1	122327884	122328084	+	1.25636	NA	Intergenic	Intergenic	122839	NR_151524	102638832	Mm.112794	NR_151524	ENSMUSG00000099960	Gm28590	-	predicted gene 28590	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3968	chr18	83855489	83855689	+	1.25636	NA	Intergenic	Intergenic	230876	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|teashirt1	teashirt zinc finger family member 1	protein-coding	0.000000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-221	chr12	119407516	119407716	+	1.25627	NA	Intergenic	Intergenic	-35794	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding	0.000000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-515	chr2	113984112	113984312	+	1.25627	NA	Intergenic	Intergenic	-29353	NR_028423	320846	Mm.441458	NR_028423	ENSMUSG00000087694	A530058N18Rik	-	RIKEN cDNA A530058N18 gene	ncRNA	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4001	chr19	5085572	5085772	+	1.25627	NA	promoter-TSS (NM_001001885)	promoter-TSS (NM_001001885)	-195	NM_001001885	381199	Mm.329663	NM_001001885	ENSMUSG00000061451	Tmem151a	AW125688|Gm961|Tmem151	transmembrane protein 151A	protein-coding	0.105000	0.696517			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1920	chr12	119407512	119407712	+	1.25627	NA	Intergenic	Intergenic	-35798	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding	0.000000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-136	chr11	25855187	25855387	+	1.25627	NA	intron (NR_027973, intron 2 of 5)	intron (NR_027973, intron 2 of 5)	-346953	NR_105791	102466154		NR_105791	ENSMUSG00000099015	Mir6372	Gm27358|mmu-mir-6372	microRNA 6372	ncRNA	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6538	chr6	77018071	77018271	+	1.25627	NA	intron (NM_145732, intron 10 of 18)	intron (NM_145732, intron 10 of 18)	-224306	NR_155299	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4525	chr2	113984111	113984311	+	1.25627	NA	Intergenic	Intergenic	-29354	NR_028423	320846	Mm.441458	NR_028423	ENSMUSG00000087694	A530058N18Rik	-	RIKEN cDNA A530058N18 gene	ncRNA	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5882	chr5	28344281	28344481	+	1.25576	NA	intron (NM_028234, intron 6 of 18)	intron (NM_028234, intron 6 of 18)	27192	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding	0.005000	0.462687			-29(ATTTACATCTCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2112	chr13	65007748	65007948	+	1.25576	NA	Intergenic	Intergenic	-25210	NM_001083890	238683	Mm.295543	NM_001083890	ENSMUSG00000074849	Spata31d1c	4932441B19Rik|Fam75d1c	spermatogenesis associated 31 subfamily D, member 1C	protein-coding	0.000000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-845	chr8	95784819	95785019	+	1.25576	NA	intron (NM_001205226, intron 2 of 48)	B3|SINE|B2	-21911	NR_015574	319960	Mm.386996	NR_015574	ENSMUSG00000074136	4930513N10Rik	-	RIKEN cDNA 4930513N10 gene	ncRNA	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4187	chr2	16534649	16534849	+	1.25576	NA	intron (NM_026162, intron 2 of 13)	intron (NM_026162, intron 2 of 13)	178445	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0.005000	0.363184			-57(CCTTTGGTATGTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-262	chr1	89934761	89934961	+	1.25576	NA	Intergenic	Intergenic	-3685	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2564	chr14	77263879	77264079	+	1.25576	NA	intron (NM_172813, intron 1 of 18)	intron (NM_172813, intron 1 of 18)	107216	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5633	chr4	98811857	98812057	+	1.25576	NA	intron (NM_172872, intron 1 of 9)	intron (NM_172872, intron 1 of 9)	5580	NM_172872	242553	Mm.440211	NM_172872	ENSMUSG00000035407	Kank4	AU021071|Ankrd38|BC060737|C130031J23	KN motif and ankyrin repeat domains 4	protein-coding	0.040000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6397	chr6	36206636	36206836	+	1.25576	NA	Intergenic	Intergenic	-181348	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6328	chr6	17179017	17179217	+	1.25576	NA	Intergenic	Intergenic	-7284	NR_153844	232599	Mm.430719	NM_177689		Gm4876	B930018B01|EG232599	predicted gene 4876	ncRNA	0.000000	0.298507			24(TTATTGTTAGGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3706	chr18	11039537	11039737	+	1.25576	NA	Intergenic	PB1D10|SINE|Alu	-12873	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-41	chr1	14635540	14635740	+	1.25576	NA	Intergenic	Intergenic	120326	NM_010827	17681	Mm.5820	NM_010827	ENSMUSG00000025930	Msc	MyoR|bHLHa22	musculin	protein-coding	0.010000	0.388060			62(TTATTCTCAATGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1056	chr10	115417942	115418142	+	1.25576	NA	intron (NM_001033261, intron 21 of 34)	intron (NM_001033261, intron 21 of 34)	33083	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding	0.005000	0.358209			-49(TTTTCCATGAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3765	chr18	29950151	29950351	+	1.25576	NA	Intergenic	Intergenic	-322614	NR_151699	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.000000	0.427861			8(GTTTCAAAGACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-716	chr10	18999946	19000146	+	1.25576	NA	TTS (NM_009397)	TTS (NM_009397)	11917	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-848	chr10	61382350	61382550	+	1.25576	NA	intron (NM_013753, intron 1 of 19)	intron (NM_013753, intron 1 of 19)	1073	NM_013753	27355	Mm.269699	NM_013753	ENSMUSG00000020092	Pald1	MMPAL|Pald|mKIAA1274	phosphatase domain containing, paladin 1	protein-coding	0.020000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2734	chr14	121126477	121126677	+	1.25576	NA	intron (NM_134082, intron 2 of 26)	intron (NM_134082, intron 2 of 26)	91003	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1872	chr12	105840225	105840425	+	1.25570	NA	Intergenic	Intergenic	55628	NM_001347440	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7025	chr7	112497196	112497396	+	1.25570	NA	intron (NM_020606, intron 1 of 12)	MER63D|DNA|hAT-Blackjack	38387	NR_154466	102636183	Mm.446701	NR_154466		Parvaos	A230071N21Rik	parvin, alpha, opposite strand	ncRNA	0.020000	0.422886			22(ATTAACAAAACAAGAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-232	chr13	23595700	23595900	+	1.25570	NA	intron (NM_001177653, intron 1 of 1)	intron (NM_001177653, intron 1 of 1)	-9830	NM_001290530	319179	Mm.440391	NM_178194	ENSMUSG00000047246	Hist1h2be	Gm11398	histone cluster 1, H2be	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2657	chr14	101788603	101788803	+	1.25570	NA	intron (NM_201529, intron 1 of 30)	intron (NM_201529, intron 1 of 30)	-51920	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2253	chr13	101765162	101765362	+	1.25479	NA	intron (NM_001077495, intron 1 of 15)	intron (NM_001077495, intron 1 of 15)	2955	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.020000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4356	chr2	65156120	65156320	+	1.25479	NA	intron (NM_177025, intron 1 of 13)	intron (NM_177025, intron 1 of 13)	82571	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding	0.005000	0.313433			28(CTTTTGTGATTCTCAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-480	chr2	52133670	52133870	+	1.25479	NA	Intergenic	Intergenic	60933	NM_001355415	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6100	chr5	97427587	97427787	+	1.25467	NA	intron (NR_045981, intron 2 of 7)	intron (NR_045981, intron 2 of 7)	29336	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6278	chr6	3539828	3540028	+	1.25411	NA	intron (NM_001167751, intron 12 of 26)	intron (NM_001167751, intron 12 of 26)	41535	NM_001167751	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3152	chr16	31508204	31508404	+	1.25411	NA	Intergenic	Intergenic	-78528	NR_152205	100047123	Mm.466711	NR_152205		Gm15743	-	predicted gene 15743	ncRNA	0.030000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4819	chr2	181610790	181610990	+	1.25411	NA	intron (NM_133701, intron 2 of 20)	intron (NM_133701, intron 2 of 20)	9571	NM_133701	68879	Mm.292001	NM_133701	ENSMUSG00000002455	Prpf6	1190003A07Rik|2610031L17Rik|ANT-1|U5-102K	pre-mRNA splicing factor 6	protein-coding	0.005000	0.393035			-44(CTATTTTTATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3687	chr18	6066518	6066718	+	1.25411	NA	intron (NM_001039692, intron 4 of 18)	L1MEd|LINE|L1	69480	NM_001039692	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7023	chr7	112390850	112391050	+	1.25411	NA	intron (NM_027587, intron 4 of 9)	intron (NM_027587, intron 4 of 9)	22642	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000038244	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding	0.005000	0.378109		-46(TATGCATTTTCATA,+,0.00),-46(TATGCATTTTCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5205	chr3	134838793	134838993	+	1.25411	NA	intron (NM_021382, intron 1 of 4)	L1_Mur3|LINE|L1	9886	NM_021382	21338	Mm.103810	NM_021382	ENSMUSG00000028172	Tacr3	Nk3r|Nkr|Tac3r	tachykinin receptor 3	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4592	chr2	126044524	126044724	+	1.25411	NA	intron (NM_008008, intron 2 of 3)	intron (NM_008008, intron 2 of 3)	9966	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding	0.015000	0.442786			-5(ATTTGAAAGACTGAGC,-,0.00),25(TCATTCTTTTGTTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3213	chr16	48619691	48619891	+	1.25411	NA	intron (NM_010816, intron 23 of 26)	intron (NM_010816, intron 23 of 26)	152271	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4842	chr3	10819028	10819228	+	1.25411	NA	Intergenic	Intergenic	-378998	NM_029068	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7276	chr8	58844441	58844641	+	1.25411	NA	intron (NM_175032, intron 1 of 11)	intron (NM_175032, intron 1 of 11)	67086	NM_175032	270049	Mm.236368	NM_175032	ENSMUSG00000096914	Galntl6	1700021K10Rik|4930431L04Rik|A830023L05	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6	protein-coding	0.005000	0.407960			7(TCATTCTTATGCTAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4222	chr2	25069285	25069485	+	1.25411	NA	Intergenic	MER21B|LTR|ERVL	9574	NR_106124	102465989		NR_106124	ENSMUSG00000099320	Mir7664	Gm28015|mmu-mir-7664	microRNA 7664	ncRNA	0.010000	0.407960			-69(ATGTATATGACAAAGC,-,0.00),-25(GCTCTTTCATGGAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4832	chr3	8527287	8527487	+	1.25411	NA	intron (NM_025285, intron 1 of 4)	intron (NM_025285, intron 1 of 4)	17860	NM_025285	20257	Mm.29580	NM_025285	ENSMUSG00000027500	Stmn2	AI159727|SCG10|Scgn10|Stmb2	stathmin-like 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6277	chr6	3539622	3539822	+	1.25411	NA	intron (NM_001167751, intron 12 of 26)	intron (NM_001167751, intron 12 of 26)	41329	NM_001167751	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-511	chr1	163682194	163682394	+	1.25411	NA	Intergenic	Intergenic	42938	NM_001143956	240879	Mm.484621	NM_001143956	ENSMUSG00000040113	Mettl11b	Gm207|NTM1B	methyltransferase like 11B	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4788	chr2	169272704	169272904	+	1.25411	NA	Intergenic	Intergenic	294535	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA	0.020000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2308	chr13	112776066	112776266	+	1.25411	NA	Intergenic	Intergenic	-24611	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding	0.010000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3351	chr16	84420372	84420572	+	1.25411	NA	Intergenic	Intergenic	49329	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4469	chr2	98778154	98778354	+	1.25364	NA	Intergenic	Lx2B2|LINE|L1	1310597	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4598	chr2	127774771	127774971	+	1.25364	NA	intron (NM_001355429, intron 4 of 19)	L1MEf|LINE|L1	14020	NM_001369236	53885	Mm.210766	NM_016902	ENSMUSG00000027378	Nphp1	-	nephronophthisis 1 (juvenile) homolog (human)	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6507	chr6	67487077	67487277	+	1.25364	NA	intron (NM_144548, intron 2 of 10)	intron (NM_144548, intron 2 of 10)	4678	NM_144548	209590	Mm.221227	NM_144548	ENSMUSG00000049093	Il23r	IL-23R	interleukin 23 receptor	protein-coding	0.000000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-552	chr3	14391132	14391332	+	1.25364	NA	Intergenic	Intergenic	28115	NR_033591	622229	Mm.486084	NR_033591		Gm6300	EG622229	solute carrier family 7 (cationic amino acid transporter, y+ system), member pseudogene	pseudo	0.000000	0.432836			73(ATTAGCATGAGAGTTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4857	chr3	14391129	14391329	+	1.25364	NA	Intergenic	Intergenic	28112	NR_033591	622229	Mm.486084	NR_033591		Gm6300	EG622229	solute carrier family 7 (cationic amino acid transporter, y+ system), member pseudogene	pseudo	0.000000	0.437811			76(ATTAGCATGAGAGTTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3928	chr18	70598304	70598504	+	1.25364	NA	intron (NM_010773, intron 3 of 6)	intron (NM_010773, intron 3 of 6)	30112	NM_001311071	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5161	chr3	122975959	122976159	+	1.25364	NA	intron (NM_133857, intron 1 of 15)	MER54A|LTR|ERVL	8388	NM_133857	99526	Mm.491248	NM_133857	ENSMUSG00000039701	Usp53	AA939927|Phxr3|Sp6|mKIAA1350|mbo	ubiquitin specific peptidase 53	protein-coding	0.005000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-538	chr2	145636410	145636610	+	1.25234	NA	intron (NM_053195, intron 16 of 16)	intron (NM_053195, intron 16 of 16)	-64685	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000001768	BC039771	-	cDNA sequence BC039771	ncRNA	0.005000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-186	chr12	38891422	38891622	+	1.25234	NA	Intergenic	Intergenic	107811	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1614	chr12	38891484	38891684	+	1.25234	NA	Intergenic	Intergenic	107873	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding	0.000000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-869	chr9	39602661	39602861	+	1.25234	NA	intron (NM_178737, intron 2 of 19)	intron (NM_178737, intron 2 of 19)	891	NM_001199556	244810	Mm.208855	NM_178737	ENSMUSG00000038112	AW551984	3222402N16	expressed sequence AW551984	protein-coding	0.040000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5170	chr3	126764273	126764473	+	1.25086	NA	intron (NM_001025438, intron 4 of 18)	intron (NM_001025438, intron 4 of 18)	167422	NM_001346635	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4422	chr2	79888017	79888217	+	1.25086	NA	intron (NM_001159582, intron 7 of 15)	intron (NM_001159582, intron 7 of 15)	20282	NM_001355144	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding	0.000000	0.308458	-27(TGTGAATAATGGATG,+,0.00),-27(TGTGAATAATGGATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6016	chr5	69673168	69673368	+	1.25086	NA	Intergenic	Intergenic	-80964	NM_001359239	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding	0.000000	0.343284			46(ATTTGAATAACAATGA,-,0.00),52(ATAACAATGACAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3978	chr18	84786667	84786867	+	1.25086	NA	Intergenic	Intergenic	42700	NR_155706	102641800		NR_155706		Gm38576	-	predicted gene, 38576	ncRNA	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-257	chr1	88766390	88766590	+	1.25086	NA	Intergenic	Intergenic	11600	NR_040493	78650	Mm.243767	NR_040493	ENSMUSG00000097398	Platr5	2410088K16Rik	pluripotency associated transcript 5	ncRNA	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8138	chrX	160618647	160618847	+	1.25086	NA	Intergenic	Intergenic	101225	NM_011147	237178	Mm.296779	NM_011147	ENSMUSG00000062168	Ppef1	PPEF-1	protein phosphatase with EF hand calcium-binding domain 1	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6127	chr5	104228729	104228929	+	1.25086	NA	Intergenic	Intergenic	26212	NM_016779	13406	Mm.199008	NM_016779	ENSMUSG00000029307	Dmp1	AG1|AV020965|DMP-1|Dmp|PP	dentin matrix protein 1	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2252	chr13	101758067	101758267	+	1.25086	NA	intron (NM_001077495, intron 1 of 15)	intron (NM_001077495, intron 1 of 15)	10050	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.030000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7753	chr9	79425757	79425957	+	1.25086	NA	Intergenic	Lx9|LINE|L1	93445	NR_045336	100038575	Mm.367838	NR_045336	ENSMUSG00000111765	Gm10635	-	predicted gene 10635	ncRNA	0.000000	0.402985			-67(GTATTGTATTGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4576	chr2	124465073	124465273	+	1.25086	NA	intron (NM_001290997, intron 4 of 20)	intron (NM_001290997, intron 4 of 20)	-145123	NM_199238	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding	0.015000	0.402985			-21(ATGTGCAGAAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3469	chr17	32741164	32741364	+	1.25086	NA	Intergenic	RLTR28|LTR|ERVL	46283	NM_001346705	208292	Mm.38813	NM_172458	ENSMUSG00000024298	Zfp871	4732483N19|9030612M13Rik|AI118577|AI265322|mKIAA3006	zinc finger protein 871	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5737	chr4	126452202	126452402	+	1.25086	NA	intron (NM_001317173, intron 11 of 18)	intron (NM_001317173, intron 11 of 18)	16281	NM_001317174	236511	Mm.30800	NM_153403	ENSMUSG00000041530	Ago1	Eif2c1	argonaute RISC catalytic subunit 1	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3237	chr16	55220438	55220638	+	1.25086	NA	Intergenic	Intergenic	62699	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3470	chr17	32741312	32741512	+	1.25086	NA	Intergenic	RLTR28|LTR|ERVL	46135	NM_001346705	208292	Mm.38813	NM_172458	ENSMUSG00000024298	Zfp871	4732483N19|9030612M13Rik|AI118577|AI265322|mKIAA3006	zinc finger protein 871	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5543	chr4	76608400	76608600	+	1.25086	NA	intron (NR_160919, intron 9 of 39)	intron (NR_160919, intron 9 of 39)	-264257	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.025000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2092	chr13	59489299	59489499	+	1.25086	NA	intron (NM_001284219, intron 16 of 24)	intron (NM_001284219, intron 16 of 24)	55052	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7405	chr8	100289803	100290003	+	1.25086	NA	Intergenic	Intergenic	873229	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3282	chr16	64933497	64933697	+	1.25086	NA	intron (NM_008310, intron 2 of 2)	intron (NM_008310, intron 2 of 2)	81596	NM_001357416	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7084	chr7	129642900	129643100	+	1.25086	NA	Intergenic	Intergenic	51137	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding	0.015000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7553	chr9	22733159	22733359	+	1.25086	NA	intron (NM_001360258, intron 18 of 21)	RLTR16B_MM|LTR|ERVK	257544	NM_001360258	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding	0.015000	0.507463			19(ATGTGCATCACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6039	chr5	76735500	76735700	+	1.25086	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-104999	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Crad|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6088	chr5	91702474	91702674	+	1.25086	NA	Intergenic	MIRb|SINE|MIR	64726	NR_045383	73452	Mm.396233	NR_045383	ENSMUSG00000101978	1700063O14Rik	-	RIKEN cDNA 1700063O14 gene	ncRNA	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5063	chr3	92633851	92634051	+	1.25086	NA	Intergenic	Tigger5|DNA|TcMar-Tigger	-12291	NM_001166172	78382	Mm.235474	NM_001166172	ENSMUSG00000086848	Lce6a	2210420J11Rik	late cornified envelope 6A	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2840	chr15	28337087	28337287	+	1.25086	NA	intron (NM_133365, intron 41 of 78)	intron (NM_133365, intron 41 of 78)	133421	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b3491Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding	0.010000	0.417910		35(CATGCAAATGCATG,+,0.00),35(CATGCAAATGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3791	chr18	35849658	35849858	+	1.25086	NA	intron (NM_001357458, intron 1 of 2)	intron (NM_001357458, intron 1 of 2)	-4929	NM_001357459	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding	0.045000	0.641791			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-40	chr1	14181620	14181820	+	1.25086	NA	intron (NM_010164, intron 16 of 17)	intron (NM_010164, intron 16 of 17)	128479	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.015000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7814	chr9	92846948	92847148	+	1.25086	NA	Intergenic	BGLII_Mus|LTR|ERVK	128332	NR_040770	331003	Mm.50805	NR_040770	ENSMUSG00000101734	4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	ncRNA	0.000000	0.457711			5(CCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4926	chr3	42792850	42793050	+	1.25086	NA	Intergenic	Intergenic	1050332	NM_001099785	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding	0.000000	0.288557			27(ACTCTATCTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4642	chr2	135231132	135231332	+	1.25072	NA	intron (NM_001145830, intron 4 of 31)	L1ME3A|LINE|L1	-15616	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7846	chr9	99111406	99111606	+	1.24994	NA	intron (NM_029094, intron 2 of 23)	intron (NM_029094, intron 2 of 23)	28705	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.010000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-110	chr10	115759619	115759819	+	1.24942	NA	Intergenic	Intergenic	-57565	NM_146010	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4971	chr3	61392844	61393044	+	1.24942	NA	Intergenic	Intergenic	28437	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6393	chr6	35288966	35289166	+	1.24786	NA	intron (NM_172892, intron 3 of 15)	intron (NM_172892, intron 3 of 15)	19060	NM_172892	243755	Mm.23666	NM_172892	ENSMUSG00000029843	Slc13a4	9630060C05Rik|SUT-1|SUT1	solute carrier family 13 (sodium/sulfate symporters), member 4	protein-coding	0.010000	0.507463			44(ATTTGAAAGACTAATG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-195	chr12	73831545	73831745	+	1.24628	NA	Intergenic	Intergenic	-69679	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding	0.020000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2044	chr13	40982731	40982931	+	1.24628	NA	intron (NR_155347, intron 1 of 4)	intron (NR_155347, intron 1 of 4)	-18179	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6084	chr5	90328500	90328700	+	1.24505	NA	intron (NM_030886, intron 1 of 33)	L1M5|LINE|L1	37585	NM_198010	81702	Mm.245522	NM_030886	ENSMUSG00000055204	Ankrd17	4933425K22Rik|A130069E23Rik|A930008M01|AA407558|AA516750|AU040470|Foe|Gtar|Mask|mKIAA0697	ankyrin repeat domain 17	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4806	chr2	178594058	178594258	+	1.24505	NA	Intergenic	Intergenic	163643	NM_001291189	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7278	chr8	60793971	60794171	+	1.24505	NA	Intergenic	Intergenic	-96322	NR_151662	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1228	chr11	31751037	31751237	+	1.24505	NA	Intergenic	MLT2D|LTR|ERVL	73410	NR_102312	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5858	chr5	21721751	21721951	+	1.24505	NA	Intergenic	Intergenic	-15309	NM_028431	73078	Mm.301655	NM_028431	ENSMUSG00000029017	Pmpcb	3110004O18Rik|MPP11|MPPB|MPPP52	peptidase (mitochondrial processing) beta	protein-coding	0.010000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5857	chr5	21657281	21657481	+	1.24505	NA	intron (NM_001363422, intron 4 of 5)	intron (NM_001363422, intron 4 of 5)	11375	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding	0.015000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3563	chr17	66563633	66563833	+	1.24505	NA	intron (NM_028998, intron 2 of 3)	L1M3|LINE|L1	30914	NM_028998	74556	Mm.218634	NM_028998	ENSMUSG00000024105	Themis3	9130404H23Rik	thymocyte selection associated family member 3	protein-coding	0.005000	0.398010	44(AATACATTATGCATT,+,0.00),44(AATACATTATGCATT,-,0.00),51(TATGCATTATTCAGA,+,0.00),51(TATGCATTATTCAGA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2608	chr14	87001478	87001678	+	1.24505	NA	intron (NM_019670, intron 8 of 27)	intron (NM_019670, intron 8 of 27)	139646	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.000000	0.417910			-2(ATTTGCATACTAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1175	chr11	17727099	17727299	+	1.24505	NA	Intergenic	Intergenic	226676	NM_001362970	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing tumor-associated antigen 1	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1017	chr10	108648220	108648420	+	1.24505	NA	intron (NM_001252342, intron 4 of 10)	intron (NM_001252342, intron 4 of 10)	51840	NM_203660	368203	Mm.452758	NM_203660	ENSMUSG00000112039	Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding	0.000000	0.273632			-26(TGATTGTCATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7183	chr8	28403758	28403958	+	1.24505	NA	Intergenic	Intergenic	-319005	NR_033590	666422	Mm.484413	NR_033590	ENSMUSG00000110372	Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-103	chr1	35677605	35677805	+	1.24505	NA	Intergenic	Intergenic	-390695	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4087	chr19	37714409	37714609	+	1.24505	NA	Intergenic	Intergenic	16701	NM_007811	13082	Mm.42230	NM_007811	ENSMUSG00000024987	Cyp26a1	Cyp26|P450RA|P450RAI|RAH	cytochrome P450, family 26, subfamily a, polypeptide 1	protein-coding	0.005000	0.338308			-17(ATTTGAATTGCAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2288	chr13	109759284	109759484	+	1.24505	NA	intron (NM_011056, intron 5 of 16)	intron (NM_011056, intron 5 of 16)	-144425	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5483	chr4	56020436	56020636	+	1.24505	NA	Intergenic	Intergenic	-488061	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding	0.005000	0.293532		35(AATGAATAGACATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-767	chr10	34705383	34705583	+	1.24505	NA	Intergenic	Intergenic	222083	NM_001358769	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0.015000	0.417910			22(GCTTTGTGATTGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6228	chr5	139942644	139942844	+	1.24505	NA	intron (NM_175522, intron 1 of 1)	B4|SINE|B4	34801	NM_175522	243312	Mm.237102	NM_175522	ENSMUSG00000048988	Elfn1	A930017N06Rik|AI197272|Ppp1r28	leucine rich repeat and fibronectin type III, extracellular 1	protein-coding	0.005000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-334	chr15	13441898	13442098	+	1.24505	NA	Intergenic	Lx5c|LINE|L1	-268323	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-333	chr1	121395275	121395475	+	1.24505	NA	Intergenic	Intergenic	-35692	NM_001025156	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3322	chr16	75999368	75999568	+	1.24505	NA	Intergenic	Intergenic	-1316	NR_155447	102632240	Mm.417237	NR_155447	ENSMUSG00000087214	Gm15555	-	predicted gene 15555	ncRNA	0.000000	0.298507			-76(TCATTCTTTTTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5615	chr4	94477096	94477296	+	1.24505	NA	Intergenic	MTEa|LTR|ERVL-MaLR	79600	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.035000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-224	chr1	82274369	82274569	+	1.24505	NA	intron (NM_010570, intron 1 of 1)	intron (NM_010570, intron 1 of 1)	16970	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7839	chr9	98339625	98339825	+	1.24505	NA	intron (NM_001357445, intron 1 of 3)	intron (NM_001357445, intron 1 of 3)	43155	NM_001357446	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1435	chr11	101881690	101881890	+	1.24505	NA	intron (NM_010791, intron 1 of 2)	intron (NM_010791, intron 1 of 2)	12564	NM_010791	17285	Mm.3404	NM_010791	ENSMUSG00000001493	Meox1	AI385561|D330041M02Rik|Mox-1|Mox1	mesenchyme homeobox 1	protein-coding	0.050000	0.671642			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5441	chr4	44130362	44130562	+	1.24505	NA	intron (NM_001355181, intron 10 of 10)	intron (NM_001355181, intron 10 of 10)	-6339	NR_040414	623796	Mm.490409	NR_040414	ENSMUSG00000084274	Gm12504	-	prothymosin alpha pseudogene	pseudo	0.025000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4428	chr2	80590002	80590202	+	1.24505	NA	Intergenic	Intergenic	-8920	NM_001355411	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6269	chr5	150823436	150823636	+	1.24505	NA	Intergenic	Intergenic	-129071	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding	0.005000	0.398010			-89(TTTTTCCCTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6680	chr6	115929060	115929260	+	1.24505	NA	Intergenic	Intergenic	-2748	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding	0.000000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4974	chr3	63351856	63352056	+	1.24505	NA	intron (NM_008604, intron 16 of 22)	intron (NM_008604, intron 16 of 22)	55861	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding	0.005000	0.368159		23(GATGCCTATGCATA,+,0.00),23(GATGCCTATGCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6994	chr7	100430055	100430255	+	1.24505	NA	exon (NM_001017985, exon 21 of 33)	exon (NM_001017985, exon 21 of 33)	-42836	NM_009464	22229	Mm.6254	NM_009464	ENSMUSG00000032942	Ucp3	AI645527|Slc25a9|UCP-3	uncoupling protein 3 (mitochondrial, proton carrier)	protein-coding	0.035000	0.582090			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3646	chr17	86121901	86122101	+	1.24505	NA	intron (NM_030133, intron 7 of 20)	intron (NM_030133, intron 7 of 20)	23174	NM_030133	78586	Mm.146236	NM_030133	ENSMUSG00000024135	Srbd1	AI461933|C85414|D530025C17Rik	S1 RNA binding domain 1	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1042	chr10	113319873	113320073	+	1.24505	NA	Intergenic	Intergenic	-390947	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132	ataxin 7-like 3B	protein-coding	0.000000	0.353234			-62(ATGAACAAGAGAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1429	chr11	97534886	97535086	+	1.24505	NA	exon (NM_018873, exon 8 of 20)	exon (NM_018873, exon 8 of 20)	-34646	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding	0.110000	0.741294			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2931	chr15	54198303	54198503	+	1.24505	NA	Intergenic	MLT2F|LTR|ERVL	80081	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)	protein-coding	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4910	chr3	39212177	39212377	+	1.24505	NA	Intergenic	Intergenic	325337	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4741	chr2	155737828	155738028	+	1.24505	NA	Intergenic	Intergenic	-8453	NM_145537	108687	Mm.273706	NM_145537	ENSMUSG00000038312	Edem2	9530090G24Rik|AI327354	ER degradation enhancer, mannosidase alpha-like 2	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4807	chr2	178594311	178594511	+	1.24505	NA	Intergenic	Intergenic	163896	NM_001291189	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6723	chr6	134522744	134522944	+	1.24467	NA	intron (NM_008514, intron 2 of 22)	intron (NM_008514, intron 2 of 22)	44069	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding	0.010000	0.313433			-21(ATCAACATGATAAAGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-777	chr6	134522752	134522952	+	1.24467	NA	intron (NM_008514, intron 2 of 22)	intron (NM_008514, intron 2 of 22)	44061	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding	0.005000	0.308458			-29(ATCAACATGATAAAGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-429	chr18	28308425	28308625	+	1.24467	NA	Intergenic	Intergenic	-251639	NR_045398	320624	Mm.50107	NR_045398	ENSMUSG00000117473	4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA	0.020000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1924	chr13	3621963	3622163	+	1.24396	NA	Intergenic	LTRIS2|LTR|ERV1	-10955	NM_001360838	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Tasor2	AI645998|Fam208b|Pap20|mKIAA2006	transcription activation suppressor family member 2	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5058	chr3	88231484	88231684	+	1.24396	NA	Intergenic	Intergenic	-15914	NR_162800	114482879		NR_162800		Mir9b-1	mmu-mir-9b-1	microRNA mir-9b-1	ncRNA	0.000000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-223	chr13	3621894	3622094	+	1.24396	NA	Intergenic	LTRIS2|LTR|ERV1	-10886	NM_001360838	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Tasor2	AI645998|Fam208b|Pap20|mKIAA2006	transcription activation suppressor family member 2	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1796	chr12	87010795	87010995	+	1.24396	NA	Intergenic	Intergenic	-10445	NR_155207	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding	0.050000	0.611940			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7404	chr8	100224643	100224843	+	1.24377	NA	Intergenic	Intergenic	808069	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4302	chr2	52133581	52133781	+	1.24377	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	60844	NM_001355415	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding	0.000000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-629	chr4	72441968	72442168	+	1.24377	NA	Intergenic	Intergenic	240824	NR_027923	68285	Mm.37541	NR_027923		C630043F03Rik	AI851307	RIKEN cDNA C630043F03 gene	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1739	chr12	73367704	73367904	+	1.24373	NA	intron (NR_046013, intron 3 of 3)	intron (NR_046013, intron 3 of 3)	41759	NR_046013	380765	Mm.490476	NR_046013	ENSMUSG00000056359	D830013O20Rik	Gm891	RIKEN cDNA D830013O20 gene	ncRNA	0.045000	0.537313			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-709	chr5	131143431	131143631	+	1.24373	NA	intron (NM_145218, intron 2 of 10)	intron (NM_145218, intron 2 of 10)	163991	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Galnt17	AA388321|E330012B09Rik|Galnt19|Gcap8|Wbscr17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.005000	0.358209			51(ATTTCCATAACAGAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4947	chr3	53169529	53169729	+	1.24373	NA	intron (NM_175386, intron 2 of 3)	intron (NM_175386, intron 2 of 3)	128082	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968|Lhfpl6	lipoma HMGIC fusion partner	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1321	chr11	65356578	65356778	+	1.24373	NA	Intergenic	Intergenic	-68845	NR_040280	327946	Mm.383301	NR_040280	ENSMUSG00000085162	Gm12295	A730013G04	predicted gene 12295	ncRNA	0.015000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-194	chr12	73367698	73367898	+	1.24373	NA	intron (NR_046013, intron 3 of 3)	intron (NR_046013, intron 3 of 3)	41765	NR_046013	380765	Mm.490476	NR_046013	ENSMUSG00000056359	D830013O20Rik	Gm891	RIKEN cDNA D830013O20 gene	ncRNA	0.050000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-389	chr1	135031598	135031798	+	1.24373	NA	intron (NM_001033409, intron 4 of 17)	B3A|SINE|B2	69133	NM_001278115	67196	Mm.284587	NM_026024	ENSMUSG00000026429	Ube2t	2700084L22Rik|C80607	ubiquitin-conjugating enzyme E2T	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4449	chr2	91751187	91751387	+	1.24373	NA	intron (NM_001080754, intron 1 of 18)	CT-rich|Low_complexity|Low_complexity	21149	NM_172669	228361	Mm.436667	NM_172669	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6140	chr5	107449037	107449237	+	1.24306	NA	intron (NM_001255991, intron 2 of 8)	intron (NM_001255991, intron 2 of 8)	11140	NM_001255991	100503185	Mm.366650	NM_001255991	ENSMUSG00000111375	Btbd8	EG627196|Gm16115	BTB (POZ) domain containing 8	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5111	chr3	109517594	109517794	+	1.24291	NA	intron (NM_020505, intron 10 of 26)	Lx5c|LINE|L1	-56313	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding	0.005000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4011	chr19	14500033	14500233	+	1.24291	NA	intron (NM_001302947, intron 8 of 19)	intron (NM_001302947, intron 8 of 19)	-61627	NR_003027	19862		NR_003027	ENSMUSG00000095132	Rnu6	-	U6 small nuclear RNA	snRNA	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3557	chr17	65026679	65026879	+	1.24291	NA	Intergenic	Intergenic	-190708	NM_030031	78057	Mm.109380	NM_030031	ENSMUSG00000024088	4930583I09Rik	-	RIKEN cDNA 4930583I09 gene	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1765	chr12	79804886	79805086	+	1.24291	NA	intron (NM_009014, intron 10 of 10)	intron (NM_009014, intron 10 of 10)	119747	NR_131075	77290	Mm.395042	NR_131073	ENSMUSG00000112765	9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA	0.010000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1550	chr12	14765623	14765823	+	1.24291	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	284666	NR_045960	73972	Mm.107680	NR_045960	ENSMUSG00000113644	4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6824	chr7	39848954	39849154	+	1.24291	NA	Intergenic	Intergenic	331288	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5692	chr4	111782329	111782529	+	1.24291	NA	intron (NM_026470, intron 8 of 12)	intron (NM_026470, intron 8 of 12)	4832	NM_001357231	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2110	chr13	64011143	64011343	+	1.24291	NA	Intergenic	Intergenic	77958	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4849	chr3	13370697	13370897	+	1.24291	NA	Intergenic	Intergenic	-100858	NM_001357035	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7321	chr8	77262644	77262844	+	1.24291	NA	intron (NR_156496, intron 20 of 22)	ORR1D1|LTR|ERVL-MaLR	189345	NM_001363420	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2650	chr14	99874072	99874272	+	1.24291	NA	3' UTR (NM_010636, exon 7 of 7)	3' UTR (NM_010636, exon 7 of 7)	275624	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7261	chr8	56478162	56478362	+	1.24252	NA	intron (NR_131020, intron 1 of 2)	intron (NR_131020, intron 1 of 2)	6706	NR_131020	75123	Mm.72666	NR_131020	ENSMUSG00000110310	4930518J21Rik	-	RIKEN cDNA 4930518J21 gene	ncRNA	0.020000	0.378109	44(TTTGCATTATACATA,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-597	chr3	153856212	153856412	+	1.24161	NA	TTS (NM_001282054)	TTS (NM_001282054)	-3888	NR_040373	72317	Mm.440147	NR_040373	ENSMUSG00000086438	Asb17os	2510003D18Rik	ankyrin repeat and SOCS box-containing 17, opposite strand	ncRNA	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5298	chr3	153856220	153856420	+	1.24161	NA	TTS (NM_001282054)	TTS (NM_001282054)	-3896	NR_040373	72317	Mm.440147	NR_040373	ENSMUSG00000086438	Asb17os	2510003D18Rik	ankyrin repeat and SOCS box-containing 17, opposite strand	ncRNA	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5320	chr3	158851029	158851229	+	1.24161	NA	Intergenic	Intergenic	-225235	NR_040750	624759	Mm.491054	NR_040750	ENSMUSG00000106053	Gm20752	-	predicted gene, 20752	ncRNA	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5972	chr5	57723934	57724134	+	1.24126	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	5953	NM_001310606	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1509	chr12	3371193	3371393	+	1.24126	NA	intron (NM_008445, intron 1 of 7)	intron (NM_008445, intron 1 of 7)	6161	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4358	chr2	65441643	65441843	+	1.24126	NA	Intergenic	Intergenic	-77343	NR_105755	102466151		NR_105755	ENSMUSG00000099184	Mir6337	Gm27877|mmu-mir-6337	microRNA 6337	ncRNA	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1776	chr12	82736953	82737153	+	1.24126	NA	intron (NM_015812, intron 2 of 16)	intron (NM_015812, intron 2 of 16)	119554	NM_001282061	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding	0.010000	0.358209			84(GCTTTGTCTTGGAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-634	chr1	189755149	189755349	+	1.24126	NA	intron (NM_008976, intron 1 of 18)	intron (NM_008976, intron 1 of 18)	26981	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding	0.035000	0.587065			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-732	chr6	29064120	29064320	+	1.24126	NA	intron (NM_008493, intron 1 of 2)	L1MA4|LINE|L1	3999	NM_008493	16846	Mm.277072	NM_008493	ENSMUSG00000059201	Lep	ob|obese	leptin	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4742	chr2	155952093	155952293	+	1.24126	NA	Intergenic	B3A|SINE|B2	-4365	NM_177217	16328	Mm.288729	NM_008383	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding	0.000000	0.393035			48(AATAGCAAAAGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2204	chr13	92687306	92687506	+	1.24126	NA	intron (NM_172588, intron 5 of 11)	RLTR13D6|LTR|ERVK	76268	NM_172588	218442	Mm.297970	NM_172588	ENSMUSG00000021703	Serinc5	A130038L21Rik|AIGP3|C86123|TPO1	serine incorporator 5	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3599	chr17	77500079	77500279	+	1.24126	NA	Intergenic	Lx7|LINE|L1	-700069	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4153	chr2	5171650	5171850	+	1.24126	NA	intron (NM_028804, intron 2 of 2)	intron (NM_028804, intron 2 of 2)	33974	NM_028804	74186	Mm.274715	NM_028804	ENSMUSG00000026676	Ccdc3	2310045O21Rik	coiled-coil domain containing 3	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1588	chr12	32976784	32976984	+	1.24126	NA	3' UTR (NM_013635, exon 6 of 6)	3' UTR (NM_013635, exon 6 of 6)	22698	NM_198710	19027	Mm.246304	NM_013635	ENSMUSG00000020570	Sypl	AI314763|AI604763|D12Ertd446e|PanI|Pphn|Sypl1	synaptophysin-like protein	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8024	chrX	93686973	93687173	+	1.24126	NA	intron (NM_211138, intron 1 of 7)	intron (NM_211138, intron 1 of 7)	11961	NM_211138	236899	Mm.166467	NM_177546	ENSMUSG00000035246	Pcyt1b	AW045697|CTTbeta	phosphate cytidylyltransferase 1, choline, beta isoform	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5808	chr5	3588436	3588636	+	1.24126	NA	intron (NM_172991, intron 4 of 4)	L1_Mur3|LINE|L1	-7530	NM_001293806	71382	Mm.379196	NM_027777	ENSMUSG00000005907	Pex1	5430414H02Rik|E330005K07Rik|ZWS1	peroxisomal biogenesis factor 1	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3776	chr18	32992628	32992828	+	1.24126	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	53687	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7592	chr9	31438934	31439134	+	1.24126	NA	intron (NM_144936, intron 1 of 5)	intron (NM_144936, intron 1 of 5)	25204	NM_144936	235135	Mm.390134	NM_144936	ENSMUSG00000041737	Tmem45b	BC018222	transmembrane protein 45b	protein-coding	0.010000	0.537313			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-897	chrX	11907457	11907657	+	1.24126	NA	Intergenic	Intergenic	172996	NM_029510	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding	0.005000	0.482587			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-613	chr4	29411241	29411441	+	1.23944	NA	Intergenic	Intergenic	343262	NR_151693	102634169		NR_151693		Gm11917	-	predicted gene 11917	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4994	chr3	68565545	68565745	+	1.23944	NA	intron (NM_001282044, intron 2 of 7)	intron (NM_001282044, intron 2 of 7)	-6723	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5402	chr4	29411239	29411439	+	1.23944	NA	Intergenic	Intergenic	343260	NR_151693	102634169		NR_151693		Gm11917	-	predicted gene 11917	ncRNA	0.005000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-212	chr12	102064988	102065188	+	1.23944	NA	Intergenic	L1MA4|LINE|L1	-63639	NM_172152	238384	Mm.312448	NM_172152	ENSMUSG00000041771	Slc24a4	A930002M03Rik|AW492432|NCKX4	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	protein-coding	0.005000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-586	chr3	133506680	133506880	+	1.23944	NA	intron (NM_001040400, intron 2 of 10)	MER21B|LTR|ERVL	37610	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding	0.030000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7413	chr8	101698222	101698422	+	1.23842	NA	Intergenic	Intergenic	1086789	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding	0.005000	0.333333			-48(TCATTGTGTGGCTAAT,+,0.00),-34(ATTTAAAAAAGAACAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3920	chr18	69144048	69144248	+	1.23842	NA	Intergenic	Intergenic	-121875	NR_105780	102465187		NR_105780	ENSMUSG00000098366	Mir145b	Gm27644|mmu-mir-145b	microRNA 145b	ncRNA	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3247	chr16	55809626	55809826	+	1.23842	NA	Intergenic	Intergenic	12412	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-918	chr10	87272161	87272361	+	1.23842	NA	Intergenic	Intergenic	214215	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding	0.020000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3707	chr18	11810498	11810698	+	1.23842	NA	Intergenic	Intergenic	-28676	NM_001146287	63955	Mm.40717	NM_022021	ENSMUSG00000040957	Cables1	Cables|ik3-1	CDK5 and Abl enzyme substrate 1	protein-coding	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4750	chr2	158450011	158450211	+	1.23842	NA	intron (NM_001369183, intron 16 of 30)	intron (NM_001369183, intron 16 of 30)	40009	NM_001363006	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding	0.010000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6532	chr6	73180433	73180633	+	1.23842	NA	intron (NM_001164669, intron 12 of 76)	intron (NM_001164669, intron 12 of 76)	41098	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4071	chr19	34119857	34120057	+	1.23842	NA	intron (NM_023903, intron 9 of 9)	intron (NM_023903, intron 9 of 9)	19014	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7780	chr9	83640232	83640432	+	1.23842	NA	Intergenic	Zaphod3|DNA|hAT-Tip100	-51143	NR_046066	100039222	Mm.405596	NR_046066	ENSMUSG00000100155	Gm2109	-	predicted gene 2109	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1767	chr12	79953691	79953891	+	1.23842	NA	Intergenic	L1MEc|LINE|L1	-17527	NR_131074	77290	Mm.395042	NR_131073	ENSMUSG00000112765	9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA	0.000000	0.348259			-42(GTTTTGCTTTGCAAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-142	chr11	39999236	39999436	+	1.23842	NA	Intergenic	Intergenic	-609111	NR_126439	75315	Mm.461295	NR_126439		4930553C11Rik	-	RIKEN cDNA 4930553C11 gene	ncRNA	0.005000	0.298507		-8(AATGAACATGCATA,+,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-910	chrX	152097911	152098111	+	1.23842	NA	Intergenic	MER2|DNA|TcMar-Tigger	-46257	NM_001114664	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2694	chr14	112106911	112107111	+	1.23842	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	431896	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding	0.005000	0.358209			70(CTATTCTTATTTAAAA,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-450	chr18	80770187	80770387	+	1.23842	NA	intron (NM_001201569, intron 15 of 29)	intron (NM_001201569, intron 15 of 29)	-57216	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding	0.005000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-693	chr5	97857088	97857288	+	1.23842	NA	Intergenic	Intergenic	173829	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4458	chr2	95674588	95674788	+	1.23842	NA	Intergenic	Intergenic	-643481	NM_001363048	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7251	chr8	53057725	53057925	+	1.23842	NA	Intergenic	Intergenic	-453877	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0.005000	0.313433			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-275	chr14	11503881	11504081	+	1.23842	NA	Intergenic	Intergenic	-49572	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding	0.005000	0.512438			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-889	chr9	99111431	99111631	+	1.23825	NA	intron (NM_029094, intron 2 of 23)	Charlie25|DNA|hAT-Charlie	28680	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.010000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-672	chr5	50014306	50014506	+	1.23825	NA	intron (NM_133911, intron 3 of 18)	intron (NM_133911, intron 3 of 18)	44590	NM_133911	70693	Mm.272974	NM_133911	ENSMUSG00000029090	Adgra3	3830613O22Rik|AU044632|Gpr125|Tem5-like	adhesion G protein-coupled receptor A3	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5771	chr4	140962912	140963112	+	1.23698	NA	intron (NM_001355515, intron 1 of 7)	intron (NM_001355515, intron 1 of 7)	1741	NM_001355515	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7591	chr9	31294311	31294511	+	1.23494	NA	intron (NM_199315, intron 1 of 6)	B4A|SINE|B4	13862	NM_199315	382066	Mm.335039	NM_199315	ENSMUSG00000042496	Prdm10	Gm1112|tristanin	PR domain containing 10	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6998	chr7	101083267	101083467	+	1.23494	NA	Intergenic	Intergenic	-25408	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|NWK1|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4336	chr2	60230110	60230310	+	1.23494	NA	intron (NM_020575, intron 3 of 9)	B2_Mm1t|SINE|B2	20274	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding	0.005000	0.328358			53(CTTTACATAAGTATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5780	chr4	144793381	144793581	+	1.23494	NA	Intergenic	Intergenic	-6898	NM_001126316	329993	Mm.297407	NM_001126316	ENSMUSG00000078504	Gm438	-	predicted gene 438	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2789	chr15	10921176	10921376	+	1.23494	NA	Intergenic	Intergenic	-31056	NM_030888	81799	Mm.280158	NM_030888	ENSMUSG00000058914	C1qtnf3	2310005P21Rik|Adim|CORS-26|CORS26|CTRP3|Corcs|Cors	C1q and tumor necrosis factor related protein 3	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4692	chr2	142716815	142717015	+	1.23494	NA	intron (NM_001355123, intron 17 of 26)	intron (NM_001355123, intron 17 of 26)	184549	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3331	chr16	78343954	78344154	+	1.23494	NA	intron (NM_009988, intron 7 of 7)	intron (NM_009988, intron 7 of 7)	32703	NR_002700	654432	Mm.458574	NR_002700		Gm7334	EG654432	B-cell translocation gene 3 pseudogene	pseudo	0.020000	0.398010			-57(GTTTACATCAGAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5978	chr5	62072259	62072459	+	1.23494	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	263516	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2910	chr15	50745644	50745844	+	1.23494	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	143305	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	transcriptional repressor GATA binding 1	protein-coding	0.005000	0.313433			-39(ACTTTGTCTTGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5317	chr3	158451715	158451915	+	1.23494	NA	intron (NM_001291452, intron 2 of 26)	intron (NM_001291452, intron 2 of 26)	109946	NM_001370781	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding	0.005000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5665	chr4	104339273	104339473	+	1.23494	NA	intron (NM_001369049, intron 4 of 19)	intron (NM_001369049, intron 4 of 19)	-28165	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.000000	0.353234			-96(CTTTTCAAAACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2210	chr13	93405459	93405659	+	1.23494	NA	TTS (NM_147176)	TTS (NM_147176)	94249	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8045	chrX	102765926	102766126	+	1.23494	NA	Intergenic	RMER13B|LTR|ERVK	-25170	NR_027707	382233	Mm.336195	NR_027707		Gm5166	EG382233	DMRT-like family pseudogene	pseudo	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6748	chr6	140059583	140059783	+	1.23494	NA	Intergenic	Intergenic	18126	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding	0.005000	0.378109			-10(CTTTTCTTATGATAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7973	chrX	59100207	59100407	+	1.23494	NA	intron (NM_001356335, intron 3 of 4)	intron (NM_001356335, intron 3 of 4)	-2571	NR_030574	100124476		NR_030574	ENSMUSG00000070110	Mir504	Mirn504|mir-504|mmu-mir-504	microRNA 504	ncRNA	0.000000	0.407960			-12(TTTTGCATGAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5954	chr5	52142979	52143179	+	1.23494	NA	Intergenic	Intergenic	-7062	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2147	chr13	75303546	75303746	+	1.23494	NA	Intergenic	Intergenic	213789	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.010000	0.308458			30(CTTTTATTTTTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1191	chr11	22334121	22334321	+	1.23494	NA	Intergenic	Intergenic	-47426	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2275	chr13	107995216	107995416	+	1.23494	NA	Intergenic	Intergenic	-49158	NM_001048250	75616	Mm.491164	NM_001048250	ENSMUSG00000071180	Smim15	2810008M24Rik	small integral membrane protein 15	protein-coding	0.030000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6237	chr5	142640141	142640341	+	1.23494	NA	intron (NM_178398, intron 2 of 11)	RMER17B2|LTR|ERVK	10657	NM_178398	74781	Mm.29432	NM_178398	ENSMUSG00000029578	Wipi2	1110018O08Rik|2510001I10Rik	WD repeat domain, phosphoinositide interacting 2	protein-coding	0.010000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1489	chr11	115670588	115670788	+	1.23494	NA	intron (NM_008163, intron 2 of 5)	intron (NM_008163, intron 2 of 5)	28846	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1315	chr11	62472213	62472413	+	1.23494	NA	intron (NM_001039536, intron 1 of 6)	intron (NM_001039536, intron 1 of 6)	13872	NM_001364771	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6308	chr6	13170892	13171092	+	1.23494	NA	intron (NM_001368871, intron 20 of 29)	intron (NM_001368871, intron 20 of 29)	53973	NM_001368871	232585	Mm.389082	NM_001013757	ENSMUSG00000079679	Vwde	Gm467	von Willebrand factor D and EGF domains	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1163	chr11	12867610	12867810	+	1.23494	NA	Intergenic	Intergenic	-402750	NM_001282993	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6679	chr6	115901120	115901320	+	1.23494	NA	intron (NM_031177, intron 15 of 28)	intron (NM_031177, intron 15 of 28)	-30688	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding	0.015000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5035	chr3	81836610	81836810	+	1.23494	NA	Intergenic	B4|SINE|B4	34685	NR_138586	320566	Mm.208417	NR_138586	ENSMUSG00000103695	A830029E22Rik	-	RIKEN cDNA A830029E22 gene	ncRNA	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3962	chr18	82535676	82535876	+	1.23494	NA	intron (NM_001025245, intron 3 of 3)	intron (NM_001025245, intron 3 of 3)	-18687	NM_001025255	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding	0.010000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4252	chr2	34342133	34342333	+	1.23494	NA	intron (NM_001290576, intron 2 of 7)	L1MB5|LINE|L1	29812	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding	0.000000	0.233831			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8	chr1	4819668	4819868	+	1.23494	NA	intron (NM_001355712, intron 2 of 7)	intron (NM_001355712, intron 2 of 7)	11945	NM_008866	18777	Mm.299955	NM_008866	ENSMUSG00000025903	Lypla1	APT-1|Gm39587|LPL-I|Pla1a	lysophospholipase 1	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4746	chr2	157875483	157875683	+	1.23494	NA	intron (NM_025680, intron 13 of 15)	intron (NM_025680, intron 13 of 15)	-39070	NM_198627	277432	Mm.441156	NM_198627	ENSMUSG00000037843	Vstm2l	Gm691	V-set and transmembrane domain containing 2-like	protein-coding	0.005000	0.373134			22(GCTTTATCCTGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-236	chr1	83971359	83971559	+	1.23494	NA	Intergenic	Intergenic	247502	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA	0.005000	0.427861			70(CCATTGTGATACAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4294	chr2	49636926	49637126	+	1.23494	NA	intron (NM_008449, intron 1 of 25)	intron (NM_008449, intron 1 of 25)	17740	NM_008449	16574	Mm.256342	NM_008449	ENSMUSG00000026764	Kif5c	KINN|Khc|NKHC|NKHC2	kinesin family member 5C	protein-coding	0.010000	0.398010			-32(ATGTCCATAATAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6641	chr6	105132845	105133045	+	1.23494	NA	Intergenic	L1_Mur2|LINE|L1	359723	NR_040297	100503536	Mm.366960	NR_040297	ENSMUSG00000108237	Gm19757	-	predicted gene, 19757	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5745	chr4	128503486	128503686	+	1.23494	NA	intron (NM_001281955, intron 44 of 70)	intron (NM_001281955, intron 44 of 70)	106512	NM_177758	269585	Mm.153291	NM_177758	ENSMUSG00000061894	Zscan20	C130001F22|Zfp31|Zkscan20	zinc finger and SCAN domains 20	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-326	chr1	119538455	119538655	+	1.23494	NA	Intergenic	Intergenic	-2390	NR_126486	320069	Mm.406320	NR_126486	ENSMUSG00000101731	3830432H09Rik	-	RIKEN cDNA 3830432H09 gene	ncRNA	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2945	chr15	58782340	58782540	+	1.23494	NA	3' UTR (NM_175212, exon 7 of 7)	3' UTR (NM_175212, exon 7 of 7)	40987	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding	0.010000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3645	chr17	86088137	86088337	+	1.23494	NA	intron (NM_030133, intron 14 of 20)	intron (NM_030133, intron 14 of 20)	56938	NM_030133	78586	Mm.146236	NM_030133	ENSMUSG00000024135	Srbd1	AI461933|C85414|D530025C17Rik	S1 RNA binding domain 1	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-207	chr1	73618615	73618815	+	1.23494	NA	intron (NR_045311, intron 8 of 8)	intron (NR_045311, intron 8 of 8)	-211146	NR_003202	723792	Mm.385493	NR_003202		Pinc	-	pregnancy induced noncoding RNA	ncRNA	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-230	chr1	83387254	83387454	+	1.23494	NA	intron (NM_001356547, intron 1 of 11)	intron (NM_001356547, intron 1 of 11)	20846	NM_172430	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2273	chr13	107484225	107484425	+	1.23494	NA	Intergenic	Intergenic	14503	NR_045084	105120	Mm.417700	NR_045083	ENSMUSG00000114780	AI197445	-	expressed sequence AI197445	ncRNA	0.015000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6574	chr6	87140944	87141144	+	1.23494	NA	intron (NM_054041, intron 17 of 17)	MIRb|SINE|MIR	36298	NM_001167938	52372	Mm.282851	NM_001167937	ENSMUSG00000090891	D6Ertd527e	AU043841	DNA segment, Chr 6, ERATO Doi 527, expressed	protein-coding	0.005000	0.402985			38(ATATGAATGATAAGTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7454	chr8	114685976	114686176	+	1.23494	NA	intron (NM_019573, intron 6 of 8)	intron (NM_019573, intron 6 of 8)	246424	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5787	chr4	148828221	148828421	+	1.23494	NA	intron (NM_027195, intron 1 of 15)	intron (NM_027195, intron 1 of 15)	23929	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding	0.020000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5047	chr3	84328801	84329001	+	1.23494	NA	Intergenic	MER2|DNA|TcMar-Tigger	-24126	NM_001271726	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding	0.010000	0.393035			32(ATATACATGACTGAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5594	chr4	89783868	89784068	+	1.23494	NA	Intergenic	MTD|LTR|ERVL-MaLR	95770	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7936	chrX	21365234	21365434	+	1.23494	NA	TTS (NR_045668)	TTS (NR_045668)	4469	NR_045668	331392	Mm.23126	NM_198633	ENSMUSG00000051537	Gm5124	EG331392	nucleolar and coiled-body phosphoprotein 1 pseudogene	pseudo	0.005000	0.343284			-7(ATAAGCATTACAATGC,-,0.00),51(ATTTGAATAACACAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5707	chr4	117612862	117613062	+	1.23494	NA	intron (NM_001356405, intron 6 of 8)	intron (NM_001356405, intron 6 of 8)	62597	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding	0.010000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6348	chr6	21346344	21346544	+	1.23494	NA	intron (NM_019697, intron 1 of 5)	MER5A|DNA|hAT-Charlie	131098	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121	potassium voltage-gated channel, Shal-related family, member 2	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-996	chr10	106087491	106087691	+	1.23494	NA	Intergenic	RLTR25B|LTR|ERVK	246112	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1360	chr11	75688155	75688355	+	1.23494	NA	intron (NM_001277221, intron 1 of 1)	B3|SINE|B2	8996	NM_001277221	12928	Mm.280125	NM_133656	ENSMUSG00000017776	Crk	Crk-I|Crk-II|Crk-III|Crk3|CrkIII|Crko|c-Crk|p38	v-crk avian sarcoma virus CT10 oncogene homolog	protein-coding	0.005000	0.467662		-44(TATGTATATGCACT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6668	chr6	111792004	111792204	+	1.23494	NA	Intergenic	RLTR13C2|LTR|ERVK	-418604	NR_027865	67336	Mm.378014	NR_027865	ENSMUSG00000100219	1700054K19Rik	-	RIKEN cDNA 1700054K19 gene	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-614	chr1	186433172	186433372	+	1.23437	NA	Intergenic	Intergenic	125409	NR_131124	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA	0.005000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-382	chr16	78953239	78953439	+	1.23382	NA	3' UTR (NM_008941, exon 28 of 28)	3' UTR (NM_008941, exon 28 of 28)	22391	NM_139134	246048	Mm.77895	NM_139134	ENSMUSG00000022860	Chodl	3110074E07Rik|MT75|PRED12	chondrolectin	protein-coding	0.005000	0.308458			-79(TAGTTATGATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5928	chr5	47482388	47482588	+	1.23382	NA	Intergenic	Intergenic	-500667	NM_001291227	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|b2b1200.1Clo|mKIAA4141|slit-2	slit guidance ligand 2	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7727	chr9	73574207	73574407	+	1.23382	NA	intron (NM_001081153, intron 19 of 31)	intron (NM_001081153, intron 19 of 31)	394730	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3091	chr16	13707207	13707407	+	1.23382	NA	Intergenic	BGLII_A|LTR|ERVK	-22529	NR_040574	76684	Mm.491043	NR_040574	ENSMUSG00000086550	Pla2g10os	1810007I06Rik	phospholipase A2, group X, opposite strand	ncRNA	0.030000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6332	chr6	17551367	17551567	+	1.23382	NA	intron (NM_008591, intron 15 of 21)	intron (NM_008591, intron 15 of 21)	-85543	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7147	chr8	10576442	10576642	+	1.23382	NA	intron (NM_001319151, intron 32 of 34)	intron (NM_001319151, intron 32 of 34)	305912	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5285	chr3	149689725	149689925	+	1.23382	NA	Intergenic	Intergenic	415088	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2785	chr15	10516194	10516394	+	1.23382	NA	intron (NM_029430, intron 8 of 10)	intron (NM_029430, intron 8 of 10)	30256	NM_001289447	19355	Mm.38376	NM_011232	ENSMUSG00000022248	Rad1	mRAD1	RAD1 checkpoint DNA exonuclease	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6964	chr7	91091089	91091289	+	1.23382	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	403	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs large MAGUK scaffold protein 2	protein-coding	0.035000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2795	chr15	12675674	12675874	+	1.23382	NA	intron (NM_001081064, intron 2 of 25)	ORR1B2|LTR|ERVL-MaLR	64118	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3	PDZ domain containing 2	protein-coding	0.010000	0.462687			-61(CTTTTCATTACAATGC,-,0.00),-57(TCATTACAATGCTAAT,+,0.00),8(ATTAAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6197	chr5	131474715	131474915	+	1.23382	NA	intron (NM_001363480, intron 9 of 19)	intron (NM_001363480, intron 9 of 19)	-60097	NR_152164	545809	Mm.357553	NR_152164	ENSMUSG00000105387	Gm29681	Gm42590	predicted gene, 29681	ncRNA	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7757	chr9	79894554	79894754	+	1.23382	NA	intron (NM_001357353, intron 2 of 5)	intron (NM_001357353, intron 2 of 5)	-63672	NM_001357354	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7633	chr9	45211485	45211685	+	1.23382	NA	intron (NM_001198971, intron 1 of 4)	intron (NM_001198971, intron 1 of 4)	-7550	NM_001364528	214523	Mm.436756	NM_145403	ENSMUSG00000032091	Tmprss4	CAP2|mCAP2	transmembrane protease, serine 4	protein-coding	0.020000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-378	chr1	130274256	130274456	+	1.23382	NA	Intergenic	Intergenic	-148468	NR_151525	102640368		NR_151525	ENSMUSG00000087691	Gm15674	-	predicted gene 15674	ncRNA	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1334	chr11	70151203	70151403	+	1.23382	NA	Intergenic	B3|SINE|B2	-15320	NM_001204252	17312	Mm.252405	NM_010796	ENSMUSG00000000318	Clec10a	CD301a|M-ASGP-BP-1|Mgl|Mgl1	C-type lectin domain family 10, member A	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3180	chr16	39327264	39327464	+	1.23382	NA	Intergenic	Charlie26a|DNA|hAT-Charlie	-138414	NR_153800	102640746		NR_153800	ENSMUSG00000116965	Gm36742	-	predicted gene, 36742	ncRNA	0.000000	0.308458			8(GTATACTTTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7899	chr9	116865361	116865561	+	1.23382	NA	intron (NM_001172123, intron 4 of 14)	MIR|SINE|MIR	387022	NM_178660	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding	0.000000	0.343284			-15(TATCTATTTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5769	chr4	139677412	139677612	+	1.23382	NA	Intergenic	Intergenic	23974	NM_031873	83770	Mm.190612	NM_031873	ENSMUSG00000028738	Tas1r2	Gpr71|T1r2|TR2	taste receptor, type 1, member 2	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7250	chr8	52900076	52900276	+	1.23382	NA	Intergenic	RLTR13C1|LTR|ERVK	543565	NR_151738	330767	Mm.246790	NR_151738	ENSMUSG00000110013	1190028D05Rik	-	RIKEN cDNA 1190028D05 gene	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2992	chr15	73890654	73890854	+	1.23382	NA	Intergenic	RMER1B|Other|Other	-51083	NM_001368162	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3334	chr16	78953235	78953435	+	1.23382	NA	3' UTR (NM_008941, exon 28 of 28)	3' UTR (NM_008941, exon 28 of 28)	22387	NM_139134	246048	Mm.77895	NM_139134	ENSMUSG00000022860	Chodl	3110074E07Rik|MT75|PRED12	chondrolectin	protein-coding	0.005000	0.308458			-75(TAGTTATGATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6446	chr6	52535297	52535497	+	1.23382	NA	Intergenic	Intergenic	42946	NR_046049	74304	Mm.490579	NR_046049	ENSMUSG00000107895	1700094M24Rik	-	RIKEN cDNA 1700094M24 gene	ncRNA	0.020000	0.502488			-11(CATTTTCCTTGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-336	chr15	28041388	28041588	+	1.23343	NA	Intergenic	Intergenic	-15640	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding	0.015000	0.492537			30(CTTTAAATAACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7002	chr7	102482488	102482688	+	1.23343	NA	Intergenic	MER2|DNA|TcMar-Tigger	-4686	NM_001011782	257947	Mm.376117	NM_001011782	ENSMUSG00000044814	Olfr543	MOR42-2	olfactory receptor 543	protein-coding	0.005000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-66	chr1	191242606	191242806	+	1.23343	NA	Intergenic	Intergenic	18252	NR_151547	100504360	Mm.16927	NM_001033188		D730003I15Rik	AU020850	RIKEN cDNA D730003I15 gene	ncRNA	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-122	chr1	43168299	43168499	+	1.23338	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	-4438	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding	0.020000	0.477612			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-830	chr8	63770156	63770356	+	1.23338	NA	Intergenic	Intergenic	181914	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgo2b	EG244495|Gm4975|Sgol2b	shugoshin 2B	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-62	chr1	21910115	21910315	+	1.23338	NA	intron (NM_001160139, intron 1 of 14)	MTEa|LTR|ERVL-MaLR	51727	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7407	chr8	100295749	100295949	+	1.23320	NA	Intergenic	Intergenic	879175	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-569	chr3	113697534	113697734	+	1.23320	NA	Intergenic	Intergenic	-67485	NM_026043	67225	Mm.316928	NM_026043	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	RNA-binding region (RNP1, RRM) containing 3	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5124	chr3	113697540	113697740	+	1.23320	NA	Intergenic	Intergenic	-67491	NM_026043	67225	Mm.316928	NM_026043	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	RNA-binding region (RNP1, RRM) containing 3	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-912	chr10	86196553	86196753	+	1.23320	NA	intron (NM_013722, intron 6 of 13)	intron (NM_013722, intron 6 of 13)	100799	NR_038024	78170	Mm.444790	NR_038024	ENSMUSG00000112493	4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2567	chr14	77418410	77418610	+	1.23295	NA	intron (NM_172813, intron 4 of 18)	RMER1B|Other|Other	88358	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA	0.015000	0.572139			45(ATCTCCATGACACAAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-598	chr3	154612029	154612229	+	1.23295	NA	intron (NM_001357673, intron 4 of 8)	ORR1C2|LTR|ERVL-MaLR	14932	NM_001357674	12972	Mm.374855	NM_009968	ENSMUSG00000028199	Cryz	Sez9	crystallin, zeta	protein-coding	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3131	chr16	26786969	26787169	+	1.23295	NA	Intergenic	Intergenic	-31567	NR_105063	100504628	Mm.393275	NR_105063	ENSMUSG00000092545	Gm20319	-	predicted gene, 20319	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4514	chr2	109750757	109750957	+	1.23295	NA	Intergenic	Intergenic	27936	NM_001285422	12064	Mm.1442	NM_007540	ENSMUSG00000048482	Bdnf	-	brain derived neurotrophic factor	protein-coding	0.000000	0.353234		-36(CATTCATATGTATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5564	chr4	82311371	82311571	+	1.23212	NA	intron (NM_001286131, intron 8 of 9)	intron (NM_001286131, intron 8 of 9)	194308	NM_001286131	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1631	chr12	44091430	44091630	+	1.23212	NA	Intergenic	Lx8|LINE|L1	118538	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding	0.000000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-618	chr4	50511355	50511555	+	1.23212	NA	Intergenic	Intergenic	-665686	NM_001276355	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding	0.000000	0.303483			-91(CTATTGTTATGCTAAA,+,0.00),71(ATCTGCATAATAATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6284	chr6	4866024	4866224	+	1.23202	NA	Intergenic	L1M2|LINE|L1	-36851	NM_001363809	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|neurabin-I	protein phosphatase 1, regulatory subunit 9A	protein-coding	0.005000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-911	chrX	155281106	155281306	+	1.23202	NA	intron (NM_019736, intron 5 of 14)	MTC|LTR|ERVL-MaLR	18763	NM_019736	56360	Mm.268710	NM_019736	ENSMUSG00000025287	Acot9	0610041P13Rik|Acate2|C76421|MT-ACT48|MTE-2|U8|p48	acyl-CoA thioesterase 9	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1983	chr13	23595646	23595846	+	1.23202	NA	intron (NM_001177653, intron 1 of 1)	intron (NM_001177653, intron 1 of 1)	-9776	NM_001290530	319179	Mm.440391	NM_178194	ENSMUSG00000047246	Hist1h2be	Gm11398	histone cluster 1, H2be	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5190	chr3	131034314	131034514	+	1.23202	NA	Intergenic	Intergenic	-75883	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4433	chr2	84075718	84075918	+	1.23202	NA	Intergenic	Intergenic	-134592	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4196	chr2	18186635	18186835	+	1.23042	NA	intron (NR_045539, intron 16 of 24)	B3A|SINE|B2	122150	NR_045538	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1888	chr12	110551638	110551838	+	1.23042	NA	intron (NM_001364210, intron 6 of 11)	intron (NM_001364210, intron 6 of 11)	-39636	NR_033340	319786	Mm.129691	NR_033340		B930059L03Rik	-	RIKEN cDNA B930059L03 gene	ncRNA	0.015000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4478	chr2	102146481	102146681	+	1.23042	NA	intron (NM_178886, intron 1 of 5)	L1MB8|LINE|L1	39879	NM_001290784	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6337	chr6	18016763	18016963	+	1.23042	NA	intron (NM_023653, intron 3 of 4)	intron (NM_023653, intron 3 of 4)	13582	NM_023653	22413	Mm.33653	NM_023653	ENSMUSG00000010797	Wnt2	2610510E18Rik|Int1l1|Irp|Mirp|Wnt-2|Wnt2a	wingless-type MMTV integration site family, member 2	protein-coding	0.000000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-117	chr10	121056917	121057117	+	1.23042	NA	intron (NM_011915, intron 2 of 9)	intron (NM_011915, intron 2 of 9)	23013	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding	0.010000	0.512438			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-357	chr15	102392540	102392740	+	1.23042	NA	Intergenic	B1_Mus1|SINE|Alu	-13676	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1841	chr12	99819184	99819384	+	1.23042	NA	intron (NM_030172, intron 5 of 5)	L1ME3Cz|LINE|L1	64158	NM_030172	78767	Mm.235920	NM_030172	ENSMUSG00000021176	Efcab11	2610021K21Rik|2610110A13Rik	EF-hand calcium binding domain 11	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4005	chr19	11880531	11880731	+	1.23042	NA	Intergenic	Intergenic	-9326	NM_001011775	257938	Mm.377309	NM_001011775	ENSMUSG00000067545	Olfr1419	MOR266-10	olfactory receptor 1419	protein-coding	0.010000	0.363184			-35(CCATTGTGATGTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4075	chr19	35015247	35015447	+	1.23042	NA	Intergenic	CR1_Mam|LINE|CR1	49951	NR_035473	100316775		NR_035473	ENSMUSG00000089151	Mir1950	mmu-mir-1950	microRNA 1950	ncRNA	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-389	chr17	15247909	15248109	+	1.23042	NA	Intergenic	Intergenic	-7226	NR_046164	328747	Mm.256835	NR_046164	ENSMUSG00000097624	Gm5091	C330048F19	predicted gene 5091	ncRNA	0.030000	0.601990			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6193	chr5	131143581	131143781	+	1.23042	NA	intron (NM_145218, intron 2 of 10)	intron (NM_145218, intron 2 of 10)	163841	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Galnt17	AA388321|E330012B09Rik|Galnt19|Gcap8|Wbscr17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.005000	0.358209			-99(ATTTCCATAACAGAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6240	chr5	143048499	143048699	+	1.23042	NA	intron (NM_207110, intron 13 of 16)	intron (NM_207110, intron 13 of 16)	64421	NM_001359851	108086	Mm.381440	NM_080561	ENSMUSG00000045078	Rnf216	2810055G22Rik|AI647468|AU019462|C86502|F830018F18Rik|TRIAD3|UIP83|Ubce7ip1	ring finger protein 216	protein-coding	0.000000	0.348259		13(ATTAAATATGCATG,+,0.00),13(ATTAAATATGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-862	chr10	67121716	67121916	+	1.22958	NA	Intergenic	L1MA4A|LINE|L1	-5272	NM_207221	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6184	chr5	128103585	128103785	+	1.22958	NA	intron (NM_172885, intron 3 of 8)	intron (NM_172885, intron 3 of 8)	329392	NM_172885	243274	Mm.447698	NM_172885	ENSMUSG00000034310	Tmem132d	C630028F04Rik	transmembrane protein 132D	protein-coding	0.005000	0.388060			3(ATTAGCATATGAAATG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-708	chr5	128103575	128103775	+	1.22958	NA	intron (NM_172885, intron 3 of 8)	intron (NM_172885, intron 3 of 8)	329402	NM_172885	243274	Mm.447698	NM_172885	ENSMUSG00000034310	Tmem132d	C630028F04Rik	transmembrane protein 132D	protein-coding	0.005000	0.398010			13(ATTAGCATATGAAATG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-337	chr15	28110100	28110300	+	1.22907	NA	Intergenic	L1ME1|LINE|L1	-84352	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2837	chr15	28110141	28110341	+	1.22907	NA	Intergenic	L1ME1|LINE|L1	-84393	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding	0.020000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-772	chr6	115607492	115607692	+	1.22859	NA	intron (NM_023290, intron 1 of 7)	intron (NM_023290, intron 1 of 7)	5654	NM_023290	67027	Mm.101316	NM_023290	ENSMUSG00000000439	Mkrn2	2610002L04Rik|C81377	makorin, ring finger protein, 2	protein-coding	0.015000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-404	chr1	138326582	138326782	+	1.22791	NA	Intergenic	Intergenic	52944	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1904	chr12	117029105	117029305	+	1.22791	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	122064	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.020000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3863	chr18	54175134	54175334	+	1.22791	NA	Intergenic	Intergenic	-247061	NR_040338	77433	Mm.159919	NR_040338	ENSMUSG00000096982	Redrum	9430076G02Rik	Redrum, erythroid developmental long intergenic non-protein coding transcript	ncRNA	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7074	chr7	127982614	127982814	+	1.22791	NA	TTS (NM_139149)	TTS (NM_139149)	11153	NM_023258	66824	Mm.24163	NM_023258	ENSMUSG00000030793	Pycard	9130417A21Rik|Asc|CARD5|TMS-1|TNS1|masc	PYD and CARD domain containing	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4454	chr2	92674042	92674242	+	1.22791	NA	Intergenic	Intergenic	73025	NM_001356553	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KS6ST|KSGAL6ST|KSST	carbohydrate sulfotransferase 1	protein-coding	0.015000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4152	chr2	4783296	4783496	+	1.22791	NA	intron (NM_178663, intron 6 of 8)	intron (NM_178663, intron 6 of 8)	65565	NM_001190400	209645	Mm.149539	NM_178663	ENSMUSG00000048186	Bend7	1110017O21Rik|E130319B15Rik	BEN domain containing 7	protein-coding	0.005000	0.393035	-46(TATTCATTATTTATA,+,0.00),-46(TATTCATTATTTATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3480	chr17	37027602	37027802	+	1.22652	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-4304	NM_010814	17441	Mm.210857	NM_010814	ENSMUSG00000076439	Mog	B230317G11Rik	myelin oligodendrocyte glycoprotein	protein-coding	0.005000	0.437811			43(TCATTCTTATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7931	chrX	18185228	18185428	+	1.22652	NA	intron (NM_009483, intron 2 of 28)	RMER6D|LTR|ERVK	22753	NM_001310444	22289	Mm.257498	NM_009483	ENSMUSG00000037369	Kdm6a	Utx	lysine (K)-specific demethylase 6A	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6527	chr6	72740611	72740811	+	1.22652	NA	intron (NM_009332, intron 3 of 11)	intron (NM_009332, intron 3 of 11)	48334	NM_009332	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding	0.035000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2179	chr13	84285258	84285458	+	1.22652	NA	intron (NR_155262, intron 7 of 10)	intron (NR_155262, intron 7 of 10)	63062	NM_001361908	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3667	chr17	90773290	90773490	+	1.22652	NA	intron (NM_001346957, intron 3 of 18)	RLTR25B|LTR|ERVK	20086	NR_136930	102634634		NR_136930		Gm20491	-	enolase 1, alpha non-neuron pseudogene	pseudo	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2101	chr13	62901773	62901973	+	1.22652	NA	Intergenic	Intergenic	-13591	NM_019395	14121	Mm.423078	NM_019395	ENSMUSG00000069805	Fbp1	Fbp-2|Fbp2|Fbp3	fructose bisphosphatase 1	protein-coding	0.005000	0.402985			-38(TGTTTGTCTTGTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5938	chr5	49150420	49150620	+	1.22652	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	135139	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1296	chr11	56247144	56247344	+	1.22652	NA	Intergenic	Intergenic	-206257	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5891	chr5	32070713	32070913	+	1.22652	NA	intron (NM_181279, intron 13 of 13)	intron (NM_181279, intron 13 of 13)	-21910	NR_162804	114483662		NR_162804		Mir12198	mmu-mir-12198	microRNA mir-12198	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2913	chr15	51620718	51620918	+	1.22652	NA	Intergenic	Lx|LINE|L1	-225208	NR_045092	100502643	Mm.131987	NR_045092	ENSMUSG00000115654	Gm19303	-	predicted gene, 19303	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2626	chr14	90876940	90877140	+	1.22652	NA	Intergenic	Intergenic	750149	NR_045712	74967	Mm.390704	NR_045712	ENSMUSG00000115001	4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7193	chr8	32659424	32659624	+	1.22652	NA	Intergenic	Intergenic	290502	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding	0.005000	0.358209			-84(GTTTGCATGACTATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6518	chr6	71114321	71114521	+	1.22652	NA	Intergenic	Intergenic	29959	NM_178413	232078	Mm.37547	NM_178413	ENSMUSG00000054474	Thnsl2	BC051244|TSH2	threonine synthase-like 2 (bacterial)	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1447	chr11	107040616	107040816	+	1.22652	NA	intron (NM_176850, intron 26 of 27)	intron (NM_176850, intron 26 of 27)	12493	NM_001163473	69066	Mm.40679	NM_001163473	ENSMUSG00000078607	1810010H24Rik	-	RIKEN cDNA 1810010H24 gene	protein-coding	0.000000	0.318408	-70(TATCCATTATTCAAC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6064	chr5	83220114	83220314	+	1.22652	NA	Intergenic	L1_Mur1|LINE|L1	134981	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding	0.020000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-907	chr10	83569728	83569928	+	1.22652	NA	intron (NM_001033375, intron 14 of 32)	B3|SINE|B2	25887	NM_001033375	319277	Mm.491194	NM_001033375	ENSMUSG00000034560	Washc4	A230046K03Rik|AA589518|Kiaa1033|mKIAA1033	WASH complex subunit 4	protein-coding	0.005000	0.417910			57(CTATTGGCATGCTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7721	chr9	72459820	72460020	+	1.22652	NA	3' UTR (NM_009359, exon 12 of 12)	3' UTR (NM_009359, exon 12 of 12)	21391	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7102	chr7	134714388	134714588	+	1.22652	NA	intron (NM_001033420, intron 1 of 51)	intron (NM_001033420, intron 1 of 51)	43801	NM_001033420	330662	Mm.436572	NM_001033420	ENSMUSG00000058325	Dock1	9130006G06Rik|AI854900|D630004B07Rik|b2b3190Clo	dedicator of cytokinesis 1	protein-coding	0.015000	0.363184			-20(ATTTAAAAGGCAGAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2876	chr15	40586174	40586374	+	1.22652	NA	Intergenic	Intergenic	-58997	NR_046185	432945	Mm.321981	NR_046185	ENSMUSG00000056332	Gm16294	EG432945	predicted gene 16294	ncRNA	0.005000	0.308458	66(AATGCATAAGTAATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-901	chr10	79652324	79652524	+	1.22652	NA	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-6686	NM_001033473	382384	Mm.244510	NM_001033473	ENSMUSG00000035963	Odf3l2	Gm1157	outer dense fiber of sperm tails 3-like 2	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4404	chr2	76557377	76557577	+	1.22652	NA	intron (NM_145525, intron 11 of 26)	intron (NM_145525, intron 11 of 26)	58471	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4105	chr19	48649408	48649608	+	1.22652	NA	intron (NM_025696, intron 6 of 26)	intron (NM_025696, intron 6 of 26)	443483	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0.015000	0.363184			-41(ATATTGTTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4854	chr3	14158785	14158985	+	1.22652	NA	intron (NM_001357033, intron 8 of 8)	Lx6|LINE|L1	-204232	NR_033591	622229	Mm.486084	NR_033591		Gm6300	EG622229	solute carrier family 7 (cationic amino acid transporter, y+ system), member pseudogene	pseudo	0.010000	0.338308			33(TCTTTGTAATGAAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4942	chr3	51518730	51518930	+	1.22652	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	34864	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding	0.020000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3576	chr17	69721071	69721271	+	1.22652	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-247902	NM_001360665	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	DLG associated protein 1	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7708	chr9	68233306	68233506	+	1.22652	NA	Intergenic	Intergenic	-207692	NR_045745	434412	Mm.490707	NR_045745	ENSMUSG00000111841	Gm20745	-	predicted gene, 20745	ncRNA	0.005000	0.343284			-3(ATTTACAAAACAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4231	chr2	28630522	28630722	+	1.22652	NA	Intergenic	Intergenic	-8640	NM_008114	14582	Mm.373385	NM_008114	ENSMUSG00000026815	Gfi1b	Gfi-1B	growth factor independent 1B	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4945	chr3	52580946	52581146	+	1.22652	NA	Intergenic	Lx8|LINE|L1	64082	NR_153344	102631981	Mm.394225	NR_153344		Gm30173	-	predicted gene, 30173	ncRNA	0.040000	0.527363			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-301	chr14	78747608	78747808	+	1.22647	NA	Intergenic	Intergenic	-14979	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding	0.010000	0.363184		-4(AATGAATGTGCATA,+,0.00)	1(ATGTGCATACCAAATG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-599	chr3	156304406	156304606	+	1.22433	NA	Intergenic	Intergenic	257181	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	ncRNA	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5902	chr5	34188860	34189060	+	1.22433	NA	Intergenic	Intergenic	-1250	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding	0.000000	0.482587			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-757	chr6	83428736	83428936	+	1.22429	NA	intron (NM_183138, intron 2 of 10)	intron (NM_183138, intron 2 of 10)	12842	NM_183138	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4707	chr2	145636526	145636726	+	1.22411	NA	intron (NM_053195, intron 16 of 16)	intron (NM_053195, intron 16 of 16)	-64569	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000001768	BC039771	-	cDNA sequence BC039771	ncRNA	0.010000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-208	chr12	94051101	94051301	+	1.22411	NA	Intergenic	Intergenic	123863	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA	0.000000	0.278607		79(CATGAATATGGAGA,+,0.00)	22(ATCAACAAAAGAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6069	chr5	86047632	86047832	+	1.22411	NA	intron (NM_007683, intron 4 of 18)	intron (NM_007683, intron 4 of 18)	17851	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1576	chr12	28068332	28068532	+	1.22411	NA	Intergenic	Intergenic	479905	NM_001177964	68511	Mm.310284	NM_001177964	ENSMUSG00000020633	Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1025	chr10	110949631	110949831	+	1.22411	NA	intron (NM_001359622, intron 11 of 16)	intron (NM_001359622, intron 11 of 16)	29555	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding	0.015000	0.412935			-41(ATTTAAAAACCAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1822	chr12	94050955	94051155	+	1.22411	NA	Intergenic	Intergenic	123717	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA	0.000000	0.223881			29(ATTTAAATGAAAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2191	chr13	90358328	90358528	+	1.22411	NA	Intergenic	Intergenic	268761	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2887	chr15	42509846	42510046	+	1.22410	NA	intron (NM_001286062, intron 3 of 8)	intron (NM_001286062, intron 3 of 8)	167031	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.010000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-48	chr1	163104622	163104822	+	1.22410	NA	Intergenic	Intergenic	-19052	NM_030071	78258	Mm.78368	NM_030071	ENSMUSG00000071890	Mroh9	4921528O07Rik|Armc11	maestro heat-like repeat family member 9	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3386	chr16	92860666	92860866	+	1.22410	NA	Intergenic	Lx5|LINE|L1	-34692	NM_001111022	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4753	chr2	159119450	159119650	+	1.22410	NA	Intergenic	Intergenic	324743	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding	0.020000	0.432836			73(ATTTAAATCAGAGTGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-441	chr18	62708240	62708440	+	1.22410	NA	intron (NM_001168423, intron 1 of 4)	intron (NM_001168423, intron 1 of 4)	33047	NM_001168423	100038417	Mm.387557	NM_001168423	ENSMUSG00000073551	Spink13	Gm10534|Spink5l3	serine peptidase inhibitor, Kazal type 13	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5501	chr4	62319464	62319664	+	1.22410	NA	intron (NM_001355385, intron 19 of 27)	ORR1D1|LTR|ERVL-MaLR	28017	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding	0.005000	0.417910			16(CTATTTTCATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1942	chr13	9583840	9584040	+	1.22410	NA	intron (NM_001081426, intron 17 of 36)	intron (NM_001081426, intron 17 of 36)	179870	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding	0.005000	0.398010	-74(AATGAAATATTCATT,+,0.00),-74(AATGAAATATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-339	chr1	122626777	122626977	+	1.22410	NA	Intergenic	L1_Mur3|LINE|L1	421732	NR_151524	102638832	Mm.112794	NR_151524	ENSMUSG00000099960	Gm28590	-	predicted gene 28590	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3355	chr16	85155591	85155791	+	1.22410	NA	intron (NM_007471, intron 1 of 15)	intron (NM_007471, intron 1 of 15)	18016	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2527	chr14	66973087	66973287	+	1.22410	NA	Intergenic	Intergenic	35690	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding	0.005000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4969	chr3	60565889	60566089	+	1.22410	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	64810	NM_001253710	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind like splicing factor 1	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2875	chr15	39823643	39823843	+	1.22410	NA	intron (NM_001164466, intron 7 of 9)	intron (NM_001164466, intron 7 of 9)	26698	NR_045788	100503072	Mm.446661	NR_045788	ENSMUSG00000087695	Gm16291	-	predicted gene 16291	ncRNA	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6768	chr6	146413465	146413665	+	1.22356	NA	intron (NM_019923, intron 9 of 56)	intron (NM_019923, intron 9 of 56)	88658	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-974	chr10	99046650	99046850	+	1.22356	NA	Intergenic	Intergenic	-60332	NR_153333	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding	0.015000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7559	chr9	24315871	24316071	+	1.22356	NA	3' UTR (NM_175678, exon 10 of 10)	3' UTR (NM_175678, exon 10 of 10)	187169	NM_001359948	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding	0.005000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-546	chr2	174924505	174924705	+	1.22356	NA	Intergenic	Intergenic	143164	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	-	predicted gene 14393	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2188	chr13	87928752	87928952	+	1.22356	NA	Intergenic	Intergenic	-892620	NM_010103	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1|Sox2-cre|Sox2Cre|Tg(Sox2-cre)1Amc	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5307	chr3	156304123	156304323	+	1.22356	NA	Intergenic	Intergenic	257464	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	ncRNA	0.010000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-434	chr18	34093354	34093554	+	1.22356	NA	Intergenic	B3|SINE|B2	-86248	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding	0.020000	0.537313			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-678	chr5	62552032	62552232	+	1.22258	NA	Intergenic	Intergenic	214045	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2135	chr13	71750424	71750624	+	1.22258	NA	Intergenic	RLTR25A|LTR|ERVK	213199	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois homeobox 1	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3548	chr17	62495206	62495406	+	1.22258	NA	Intergenic	Intergenic	386011	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5982	chr5	62552028	62552228	+	1.22258	NA	Intergenic	Intergenic	214049	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding	0.000000	0.328358			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-159	chr11	86624381	86624581	+	1.22258	NA	intron (NM_029478, intron 7 of 11)	intron (NM_029478, intron 7 of 11)	-40323	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1214	chr11	28048540	28048740	+	1.22246	NA	Intergenic	Intergenic	535684	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding	0.005000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-500	chr2	84075640	84075840	+	1.22106	NA	Intergenic	Intergenic	-134514	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding	0.010000	0.383085			-45(ATCTGAATAAGAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5424	chr4	35554666	35554866	+	1.22106	NA	Intergenic	MLT1E3|LTR|ERVL-MaLR	290438	NM_175516	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2799	chr15	12922161	12922361	+	1.22106	NA	intron (NM_026799, intron 29 of 34)	intron (NM_026799, intron 29 of 34)	97446	NM_026799	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1696	chr12	64954915	64955115	+	1.22106	NA	intron (NM_025707, intron 2 of 4)	intron (NM_025707, intron 2 of 4)	10521	NM_025707	66689	Mm.248678	NM_025707	ENSMUSG00000020948	Klhl28	2810440N09Rik|4122402F11Rik|4931401E10Rik|Btbd5	kelch-like 28	protein-coding	0.005000	0.393035			-3(GATCTGACATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7643	chr9	48483252	48483452	+	1.22106	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-2741	NM_001357501	104444	Mm.21911	NM_024233	ENSMUSG00000032026	Rexo2	1810038D15Rik|AW107347|Rex2|Sfn|Smfn	RNA exonuclease 2	protein-coding	0.010000	0.457711			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-563	chr3	75711199	75711399	+	1.22106	NA	Intergenic	Intergenic	-55568	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA	0.005000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-866	chr9	31203278	31203478	+	1.22106	NA	intron (NM_001102456, intron 1 of 16)	L1ME3B|LINE|L1	8470	NM_001102455	11804	Mm.19133	NM_009691	ENSMUSG00000031996	Aplp2	AI790698|APLP-2|CDEBP	amyloid beta (A4) precursor-like protein 2	protein-coding	0.025000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1187	chr11	20927989	20928189	+	1.22106	NA	Intergenic	RMER15|LTR|ERVL	-96981	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3146	chr16	29470917	29471117	+	1.21880	NA	intron (NM_172613, intron 7 of 29)	intron (NM_172613, intron 7 of 29)	70466	NM_172613	224079	Mm.54954	NM_172613	ENSMUSG00000038094	Atp13a4	4631413J11Rik|4832416L12|9330174J19Rik	ATPase type 13A4	protein-coding	0.010000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-501	chr2	91751233	91751433	+	1.21880	NA	intron (NM_001080754, intron 1 of 18)	CT-rich|Low_complexity|Low_complexity	21195	NM_172669	228361	Mm.436667	NM_172669	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding	0.000000	0.487562			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-636	chr4	94472308	94472508	+	1.21880	NA	Intergenic	Intergenic	84388	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1695	chr12	64894908	64895108	+	1.21880	NA	Intergenic	Lx7|LINE|L1	-22903	NM_001025605	217648	Mm.341586	NM_001025605	ENSMUSG00000047227	Gm527	-	predicted gene 527	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1494	chr11	118202550	118202750	+	1.21880	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	10092	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding	0.055000	0.661692			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5313	chr3	157348731	157348931	+	1.21880	NA	Intergenic	Intergenic	185259	NR_152231	381498	Mm.402095	NR_152231	ENSMUSG00000105834	4930592C13Rik	Gm1657|Gm43159	RIKEN cDNA 4930592C13 gene	ncRNA	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4361	chr2	65792682	65792882	+	1.21844	NA	Intergenic	RLTR20A3_MM|LTR|ERVK	-52985	NM_001290666	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2236	chr13	97966137	97966337	+	1.21844	NA	intron (NM_012026, intron 20 of 35)	intron (NM_012026, intron 20 of 35)	215125	NR_152263	111365222	Mm.440079	NR_152263		Eyelinc18	-	uncharacterized EyeLinc18	ncRNA	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-450	chr1	150844800	150845000	+	1.21844	NA	intron (NM_001024720, intron 4 of 106)	intron (NM_001024720, intron 4 of 106)	148535	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding	0.000000	0.328358			78(ATTAGCATCAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-476	chr1	155423264	155423464	+	1.21844	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-5920	NM_011273	19775	Mm.266215	NM_011273	ENSMUSG00000026469	Xpr1	Rmc-1|Rmc1|Sxv|Syg1|XR	xenotropic and polytropic retrovirus receptor 1	protein-coding	0.005000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-832	chr10	56911046	56911246	+	1.21844	NA	Intergenic	Intergenic	479165	NR_152768	102640560	Mm.417249	NR_152768		Gm36595	-	predicted gene, 36595	ncRNA	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2255	chr13	102349631	102349831	+	1.21844	NA	Intergenic	Intergenic	-343816	NM_001360519	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly-78|Ly78|RP105	CD180 antigen	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1251	chr11	39999311	39999511	+	1.21844	NA	Intergenic	Intergenic	-609186	NR_126439	75315	Mm.461295	NR_126439		4930553C11Rik	-	RIKEN cDNA 4930553C11 gene	ncRNA	0.010000	0.298507		-83(AATGAACATGCATA,+,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-294	chr14	73349865	73350065	+	1.21844	NA	Intergenic	Intergenic	-24143	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb|pp105	RB transcriptional corepressor 1	protein-coding	0.000000	0.273632			-78(TTTAGAATAACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1820	chr12	93305580	93305780	+	1.21844	NA	Intergenic	Intergenic	139143	NR_126436	75295	Mm.243878	NR_126436	ENSMUSG00000113164	4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2127	chr13	70057992	70058192	+	1.21844	NA	intron (NR_131156, intron 2 of 2)	intron (NR_131156, intron 2 of 2)	-29744	NR_045965	74280	Mm.273343	NR_045965	ENSMUSG00000099639	1700084F23Rik	1700003E18Rik|4930589D02Rik	RIKEN cDNA 1700084F23 gene	ncRNA	0.030000	0.452736	12(AATGCATAATAGATG,-,0.00)		26(GTATGCATGACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4414	chr2	77588833	77589033	+	1.21697	NA	intron (NM_178723, intron 3 of 9)	intron (NM_178723, intron 3 of 9)	32481	NM_001363039	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding	0.000000	0.368159			25(ATTTGCTTACCAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5518	chr4	65093978	65094178	+	1.21697	NA	Intergenic	Intergenic	-30096	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding	0.000000	0.293532			9(ATTAGAAAGATAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1439	chr11	103879508	103879708	+	1.21697	NA	intron (NM_008740, intron 9 of 20)	intron (NM_008740, intron 9 of 20)	74448	NM_008740	18195	Mm.260117	NM_008740	ENSMUSG00000034187	Nsf	AI316878|AU020090|AU067812|SKD2	N-ethylmaleimide sensitive fusion protein	protein-coding	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3996	chr18	89601292	89601492	+	1.21697	NA	intron (NM_001039173, intron 1 of 7)	intron (NM_001039173, intron 1 of 7)	168148	NM_001039173	623279	Mm.447164	NM_001039173	ENSMUSG00000073514	Dok6	Dok-6	docking protein 6	protein-coding	0.000000	0.268657			-71(ATATAAATTACAAATA,-,0.00),-10(AAATTGAGATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5677	chr4	107717759	107717959	+	1.21697	NA	Intergenic	Intergenic	-33629	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding	0.010000	0.502488			25(GTTTTGGTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7924	chrX	11928054	11928254	+	1.21697	NA	Intergenic	Intergenic	152399	NM_029510	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding	0.030000	0.402985			-86(ATTTACAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1181	chr11	19728602	19728802	+	1.21697	NA	Intergenic	LTR104_Mam|LTR|Gypsy	-195740	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related EVH1 domain containing 2	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6114	chr5	101737280	101737480	+	1.21697	NA	Intergenic	Lx7|LINE|L1	-27750	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding	0.020000	0.417910			32(ATCAGAAAGAAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4859	chr3	15920552	15920752	+	1.21697	NA	Intergenic	Intergenic	-72165	NM_001173459	100038947	Mm.330924	NM_001173459	ENSMUSG00000074677	Sirpb1c	-	signal-regulatory protein beta 1C	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7165	chr8	17421651	17421851	+	1.21697	NA	intron (NM_053171, intron 1 of 69)	intron (NM_053171, intron 1 of 69)	113634	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding	0.025000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3448	chr17	26608968	26609168	+	1.21697	NA	intron (NM_026170, intron 2 of 9)	intron (NM_026170, intron 2 of 9)	47556	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4780	chr2	166758110	166758310	+	1.21697	NA	Intergenic	Intergenic	-35557	NM_023815	76367	Mm.330796	NM_023815	ENSMUSG00000042854	Trp53rkb	2810408M09Rik|4933401B08Rik|5630401H01Rik|Nori-2|PRPK|Tp53rk|Trp53rk|Trp53tk|mNori-2p	transformation related protein 53 regulating kinase B	protein-coding	0.015000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5328	chr4	6561757	6561957	+	1.21697	NA	Intergenic	Intergenic	-107586	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding	0.020000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1219	chr11	29364343	29364543	+	1.21697	NA	Intergenic	Intergenic	-9215	NM_001363368	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7669	chr9	57810855	57811055	+	1.21697	NA	intron (NM_019689, intron 1 of 7)	intron (NM_019689, intron 1 of 7)	23279	NM_019689	56380	Mm.425588	NM_019689	ENSMUSG00000004661	Arid3b	Bdp|Dri2	AT rich interactive domain 3B (BRIGHT-like)	protein-coding	0.015000	0.497512			76(ATTAAAAAAACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2726	chr14	120395750	120395950	+	1.21697	NA	intron (NM_001360380, intron 6 of 7)	intron (NM_001360380, intron 6 of 7)	-82611	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1020	chr10	109858753	109858953	+	1.21697	NA	intron (NM_001368815, intron 7 of 37)	intron (NM_001368815, intron 7 of 37)	141537	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding	0.005000	0.437811			77(GTATTCTCTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1099	chr10	122006762	122006962	+	1.21697	NA	intron (NM_001081037, intron 1 of 21)	intron (NM_001081037, intron 1 of 21)	40453	NM_001081037	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.015000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5925	chr5	45702126	45702326	+	1.21697	NA	intron (NM_001359874, intron 4 of 4)	intron (NM_001359874, intron 4 of 4)	25352	NR_027993	100041576	Mm.451765	NR_027993	ENSMUSG00000015882	Gm3414	-	predicted gene 3414	ncRNA	0.010000	0.378109			14(GTTTACATCAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1856	chr12	102146464	102146664	+	1.21697	NA	intron (NM_172152, intron 2 of 16)	L1MB3|LINE|L1	17837	NM_001362345	238384	Mm.312448	NM_172152	ENSMUSG00000041771	Slc24a4	A930002M03Rik|AW492432|NCKX4	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5708	chr4	117652864	117653064	+	1.21697	NA	intron (NM_001356405, intron 8 of 8)	intron (NM_001356405, intron 8 of 8)	29261	NM_023178	66233	Mm.29142	NM_023178	ENSMUSG00000009640	Dmap1	1500016M21Rik|DNMAP1|DNMTAP1|Dmtap1|mKIAA1425	DNA methyltransferase 1-associated protein 1	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8004	chrX	84983536	84983736	+	1.21697	NA	intron (NM_007868, intron 62 of 78)	intron (NM_007868, intron 62 of 78)	-64659	NM_001314037	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3384	chr16	92243087	92243287	+	1.21697	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-49202	NM_134110	246133	Mm.156736	NM_134110	ENSMUSG00000039672	Kcne2	2200002I16Rik|AW048273|MiRP1	potassium voltage-gated channel, Isk-related subfamily, gene 2	protein-coding	0.025000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2797	chr15	12733047	12733247	+	1.21697	NA	intron (NM_001081064, intron 1 of 25)	intron (NM_001081064, intron 1 of 25)	6745	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3	PDZ domain containing 2	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7986	chrX	71480530	71480730	+	1.21697	NA	intron (NM_138309, intron 1 of 8)	intron (NM_138309, intron 1 of 8)	12219	NM_001199349	171486	Mm.283879	NM_138309	ENSMUSG00000035776	Cd99l2	AW548191|Mic2l1|Xap89	CD99 antigen-like 2	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5859	chr5	22471345	22471545	+	1.21697	NA	Intergenic	Intergenic	57585	NR_004442	100042049	Mm.21724	NR_004442		Gm15421	-	ribosomal protein L22 like 1 pseudogene	pseudo	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5522	chr4	67190594	67190794	+	1.21697	NA	Intergenic	Intergenic	363143	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-214	chr1	77696545	77696745	+	1.21697	NA	Intergenic	Intergenic	-181557	NM_007936	13838	Mm.400747	NM_007936	ENSMUSG00000026235	Epha4	2900005C20Rik|AI385584|Cek8|Hek8|Sek|Sek1|Tyro1|rb	Eph receptor A4	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6134	chr5	106617309	106617509	+	1.21697	NA	non-coding (NR_156476, exon 3 of 3)	non-coding (NR_156476, exon 3 of 3)	78610	NM_001363321	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding	0.015000	0.328358			31(CTATTATGATACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7982	chrX	68840845	68841045	+	1.21697	NA	Intergenic	MLT2B2|LTR|ERVL	52108	NM_001098842	627927	Mm.391264	NM_001098842	ENSMUSG00000056815	Gm6812	EG627927	predicted gene 6812	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7953	chrX	42708791	42708991	+	1.21697	NA	intron (NM_011855, intron 16 of 32)	intron (NM_011855, intron 16 of 32)	203569	NM_001313691	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3401	chr16	97554071	97554271	+	1.21697	NA	intron (NR_003508, intron 10 of 13)	L1M3|LINE|L1	18088	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding	0.005000	0.407960	-38(CAGGAATAATTCATG,+,0.00),-38(CAGGAATAATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5854	chr5	21005698	21005898	+	1.21697	NA	intron (NM_001356590, intron 9 of 18)	intron (NM_001356590, intron 9 of 18)	29449	NM_001356592	19248	Mm.319117	NM_011203	ENSMUSG00000028771	Ptpn12	P19-PTP|PTP-P19|PTP-PEST|PTPG1	protein tyrosine phosphatase, non-receptor type 12	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2986	chr15	70344095	70344295	+	1.21697	NA	Intergenic	L1ME3|LINE|L1	419962	NR_045071	100503580	Mm.404646	NR_045071	ENSMUSG00000116483	Gm19782	-	predicted gene, 19782	ncRNA	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-998	chr10	106526916	106527116	+	1.21697	NA	intron (NM_177373, intron 2 of 31)	intron (NM_177373, intron 2 of 31)	56706	NM_001359673	327814	Mm.391424	NM_177373	ENSMUSG00000053825	Ppfia2	5330438O12|B230207K17Rik|E130120L08Rik|mKIAA4112	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	protein-coding	0.000000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3103	chr16	18011163	18011363	+	1.21697	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	30698	NM_016983	22363	Mm.377118	NM_016983	ENSMUSG00000059280	Vpreb2	CD179b|VpreB1|Vpreb-2	pre-B lymphocyte gene 2	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6161	chr5	115705991	115706191	+	1.21697	NA	intron (NR_151598, intron 2 of 11)	MER103C|DNA|hAT-Charlie	25530	NR_151599	75665	Mm.233914	NM_001080808	ENSMUSG00000041609	Bicdl1	2210403N09Rik|BICDR-1|Ccdc64	BICD family like cargo adaptor 1	protein-coding	0.015000	0.338308			-46(ATCTCCAAGAGAGAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3948	chr18	79176628	79176828	+	1.21697	NA	Intergenic	Intergenic	-67337	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6222	chr5	138819791	138819991	+	1.21697	NA	promoter-TSS (NM_001195128)	promoter-TSS (NM_001195128)	-189	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding	0.035000	0.641791			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-288	chr1	97630366	97630566	+	1.21697	NA	Intergenic	Intergenic	31210	NM_001355073	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-642	chr1	192380799	192380999	+	1.21697	NA	intron (NM_001038607, intron 7 of 10)	intron (NM_001038607, intron 7 of 10)	190122	NM_010600	16510	Mm.4489	NM_010600	ENSMUSG00000058248	Kcnh1	EAG1|Kv10.1|M-eag	potassium voltage-gated channel, subfamily H (eag-related), member 1	protein-coding	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6054	chr5	81610069	81610269	+	1.21697	NA	intron (NM_001359829, intron 7 of 23)	intron (NM_001359829, intron 7 of 23)	514544	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7219	chr8	41017339	41017539	+	1.21697	NA	promoter-TSS (NR_015457)	promoter-TSS (NR_015457)	-299	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA	0.030000	0.497512			-23(TTAATTTTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7978	chrX	66903923	66904123	+	1.21697	NA	Intergenic	Intergenic	-64898	NR_030149	723888		NR_030149	ENSMUSG00000070071	Mir465	Mirn465|mir-465a|mmu-mir-465	microRNA 465	ncRNA	0.000000	0.368159			-11(CCACTCTTATGTTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7947	chrX	37203323	37203523	+	1.21697	NA	Intergenic	B3|SINE|B2	7618	NM_001033234	194854	Mm.296429	NM_001033234	ENSMUSG00000073243	Gm9	-	predicted gene 9	protein-coding	0.015000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-708	chr10	14690320	14690520	+	1.21697	NA	intron (NM_025418, intron 1 of 7)	MLT1J|LTR|ERVL-MaLR	15069	NM_025418	66201	Mm.227983	NM_025418	ENSMUSG00000019868	Vta1	1110001D18Rik|1110059P08Rik|AU040813|C85340|LIP5|SBP1	vesicle (multivesicular body) trafficking 1	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2304	chr13	112257074	112257274	+	1.21697	NA	Intergenic	L1MA4|LINE|L1	-31277	NM_001168403	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding	0.005000	0.383085			27(ATTTGCAAGAAAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3924	chr18	69813166	69813366	+	1.21697	NA	Intergenic	Intergenic	-112293	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding	0.010000	0.422886			23(CTTTGAATAACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-692	chr10	9603749	9603949	+	1.21631	NA	Intergenic	Intergenic	71359	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding	0.005000	0.412935			76(CTTAGCATCACAAATA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-168	chr11	108263541	108263741	+	1.21622	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	80247	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5459	chr4	50511406	50511606	+	1.21621	NA	Intergenic	Intergenic	-665737	NM_001276355	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding	0.005000	0.333333			20(ATCTGCATAATAATTG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-748	chr6	61492572	61492772	+	1.21621	NA	intron (NM_183310, intron 5 of 10)	intron (NM_183310, intron 5 of 10)	-311862	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA	0.010000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-273	chr14	8592537	8592737	+	1.21597	NA	intron (NM_028934, intron 4 of 15)	intron (NM_028934, intron 4 of 15)	73653	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding	0.010000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-530	chr2	137153141	137153341	+	1.21556	NA	Intergenic	Intergenic	-36721	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0.030000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4657	chr2	137153126	137153326	+	1.21556	NA	Intergenic	Intergenic	-36706	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0.030000	0.477612			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-100	chr10	85272173	85272373	+	1.21556	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-87219	NM_007771	12952	Mm.26237	NM_007771	ENSMUSG00000020038	Cry1	AU020726|AU021000|Phll1	cryptochrome 1 (photolyase-like)	protein-coding	0.020000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7144	chr8	9962320	9962520	+	1.21556	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	13903	NM_176953	319583	Mm.80584	NM_176953	ENSMUSG00000049717	Lig4	5830471N16Rik|tiny	ligase IV, DNA, ATP-dependent	protein-coding	0.000000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-158	chr11	86473522	86473722	+	1.21556	NA	Intergenic	Intergenic	-11035	NM_029788	76892	Mm.262707	NM_029788	ENSMUSG00000020521	Rnft1	0610013E23Rik|AV007605	ring finger protein, transmembrane 1	protein-coding	0.005000	0.333333		11(TATGAATATTTAAA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-909	chr10	85272179	85272379	+	1.21556	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-87225	NM_007771	12952	Mm.26237	NM_007771	ENSMUSG00000020038	Cry1	AU020726|AU021000|Phll1	cryptochrome 1 (photolyase-like)	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7316	chr8	75391202	75391402	+	1.21556	NA	Intergenic	L1_Mus3|LINE|L1	-57392	NM_027944	71831	Mm.443238	NM_027944	ENSMUSG00000031620	Iqcm	1700007B14Rik	IQ motif containing M	protein-coding	0.005000	0.358209			-62(ATCAACATAGGAATGG,-,0.00),20(AAATTCTTAGGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-203	chr12	89273070	89273270	+	1.21556	NA	intron (NM_172544, intron 6 of 19)	intron (NM_172544, intron 6 of 19)	319780	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0.000000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-58	chr1	184906192	184906392	+	1.21513	NA	intron (NM_145515, intron 15 of 17)	intron (NM_145515, intron 15 of 17)	-23256	NM_178692	226777	Mm.169542	NM_178692	ENSMUSG00000039349	C130074G19Rik	-	RIKEN cDNA C130074G19 gene	protein-coding	0.005000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-296	chr14	75367554	75367754	+	1.21513	NA	intron (NR_030568, intron 2 of 3)	intron (NR_030568, intron 2 of 3)	20492	NR_030568	100124475		NR_030568	ENSMUSG00000077981	Mir466f-3	Mirn466f-3	microRNA 466f-3	ncRNA	0.000000	0.407960			-33(CCTTTGTGAAGGAAAT,+,0.00),20(TTTTGCATGAAAACAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-601	chr1	184906186	184906386	+	1.21513	NA	intron (NM_145515, intron 15 of 17)	intron (NM_145515, intron 15 of 17)	-23250	NM_178692	226777	Mm.169542	NM_178692	ENSMUSG00000039349	C130074G19Rik	-	RIKEN cDNA C130074G19 gene	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2546	chr14	75367526	75367726	+	1.21513	NA	intron (NR_030568, intron 2 of 3)	intron (NR_030568, intron 2 of 3)	20520	NR_030568	100124475		NR_030568	ENSMUSG00000077981	Mir466f-3	Mirn466f-3	microRNA 466f-3	ncRNA	0.000000	0.407960			-5(CCTTTGTGAAGGAAAT,+,0.00),48(TTTTGCATGAAAACAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2994	chr15	75671941	75672141	+	1.21485	NA	intron (NM_001355589, intron 3 of 13)	intron (NM_001355589, intron 3 of 13)	6759	NM_001355589	72960	Mm.182401	NM_028404	ENSMUSG00000000934	Top1mt	2900052H09Rik	DNA topoisomerase 1, mitochondrial	protein-coding	0.015000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1350	chr11	74428947	74429147	+	1.21485	NA	intron (NM_001015046, intron 8 of 24)	L1MEi|LINE|L1	64376	NM_001011851	258153	Mm.376124	NM_001011851	ENSMUSG00000058275	Olfr412	MOR127-5P	olfactory receptor 412	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7263	chr8	56495433	56495633	+	1.21485	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-10565	NR_131020	75123	Mm.72666	NR_131020	ENSMUSG00000110310	4930518J21Rik	-	RIKEN cDNA 4930518J21 gene	ncRNA	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3372	chr16	88331779	88331979	+	1.21485	NA	Intergenic	Intergenic	-41614	NM_001346964	14805	Mm.5134	NM_010348	ENSMUSG00000022935	Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	glutamate receptor, ionotropic, kainate 1	protein-coding	0.000000	0.338308			-46(GTTTGCAAGACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6467	chr6	57796173	57796373	+	1.21485	NA	intron (NM_146168, intron 1 of 4)	intron (NM_146168, intron 1 of 4)	28852	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	vesicular, overexpressed in cancer, prosurvival protein 1	protein-coding	0.000000	0.412935			-17(ATTTAAATTACCATGA,-,0.00),-11(ATTACCATGAAAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5221	chr3	137523030	137523230	+	1.21485	NA	Intergenic	Intergenic	29532	NM_177665	229862	Mm.246591	NM_177665		Gm4861	9230109N16|EG229862	predicted gene 4861	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2827	chr15	25057495	25057695	+	1.21485	NA	Intergenic	Lx5c|LINE|L1	356169	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4898	chr3	31499444	31499644	+	1.21485	NA	Intergenic	Intergenic	-189225	NM_172861	241919	Mm.285366	NM_172861	ENSMUSG00000069072	Slc7a14	A930013N06|BC061928	solute carrier family 7 (cationic amino acid transporter, y+ system), member 14	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5976	chr5	60901550	60901750	+	1.21485	NA	Intergenic	Intergenic	-907193	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5486	chr4	56953439	56953639	+	1.21485	NA	Intergenic	Intergenic	-6110	NM_175518	242474	Mm.296632	NM_175518	ENSMUSG00000055296	Tmem245	A630051L19Rik|AI957324|D730040F13Rik	transmembrane protein 245	protein-coding	0.020000	0.497512			-27(TTTTTGTTTTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8050	chrX	103567127	103567327	+	1.21485	NA	intron (NR_028381, intron 9 of 10)	intron (NR_028381, intron 9 of 10)	5769	NR_030558	100124494		NR_030558	ENSMUSG00000065509	Mir421	Mirn421|mmu-mir-421	microRNA 421	ncRNA	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1671	chr12	55307751	55307951	+	1.21485	NA	intron (NM_025373, intron 2 of 6)	(CA)n|Simple_repeat|Simple_repeat	-4851	NM_021529	59032	Mm.427307	NM_021529	ENSMUSG00000021022	Ppp2r3c	4930511A21Rik|5730412A08Rik|G4-1|G5pr	protein phosphatase 2, regulatory subunit B'', gamma	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6842	chr7	49716404	49716604	+	1.21485	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-42602	NM_001146053	53415	Mm.20801	NM_016865	ENSMUSG00000039745	Htatip2	AW111545|Cc3|Tip30	HIV-1 Tat interactive protein 2	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5332	chr4	8706623	8706823	+	1.21485	NA	intron (NM_001277149, intron 1 of 37)	intron (NM_001277149, intron 1 of 37)	16317	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-861	chr10	67026869	67027069	+	1.21485	NA	intron (NR_110511, intron 2 of 6)	intron (NR_110511, intron 2 of 6)	21894	NR_110511	102634101	Mm.445258	NR_110511	ENSMUSG00000112925	Gm31763	-	predicted gene, 31763	ncRNA	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7132	chr8	3848830	3849030	+	1.21485	NA	3' UTR (NM_130905, exon 6 of 6)	3' UTR (NM_130905, exon 6 of 6)	5356	NM_130905	170780	Mm.52281	NM_130905	ENSMUSG00000040197	Cd209e	SIGNR4|mSIGNR4	CD209e antigen	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4351	chr2	64066358	64066558	+	1.21485	NA	intron (NM_001267847, intron 1 of 3)	intron (NM_001267847, intron 1 of 3)	31580	NM_001267847	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	Fgn|fi|fidget	fidgetin	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1840	chr12	99709023	99709223	+	1.21485	NA	Intergenic	Lx8|LINE|L1	-81149	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5255	chr3	146633102	146633302	+	1.21485	NA	Intergenic	Intergenic	-8730	NR_045949	100286843	Mm.475299	NR_045949	ENSMUSG00000085810	Gm16325	-	predicted gene 16325	ncRNA	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-244	chr1	86082941	86083141	+	1.21485	NA	intron (NM_027357, intron 8 of 24)	(TG)n|Simple_repeat|Simple_repeat	18422	NM_027357	70247	Mm.280013	NM_027357	ENSMUSG00000026229	Psmd1	2410026J11Rik|P112|S1	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4448	chr2	90823085	90823285	+	1.21485	NA	intron (NR_151502, intron 18 of 21)	intron (NR_151502, intron 18 of 21)	-23970	NM_019758	56428	Mm.28023	NM_019758	ENSMUSG00000027282	Mtch2	2310034D24Rik|4930539J07Rik|HSPC032	mitochondrial carrier 2	protein-coding	0.010000	0.422886			-36(TCATTCTCATTCAAAC,+,0.00),27(ATTTGCTTGAAAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5880	chr5	28298683	28298883	+	1.21485	NA	Intergenic	Intergenic	-18406	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2316	chr13	115819915	115820115	+	1.21485	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	489673	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	ISL1 transcription factor, LIM/homeodomain	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-763	chr10	31709963	31710163	+	1.21485	NA	intron (NM_001013411, intron 5 of 6)	intron (NM_001013411, intron 5 of 6)	-100338	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3133	chr16	27111313	27111513	+	1.21485	NA	Intergenic	Intergenic	-119761	NM_001013761	239789	Mm.326909	NM_001013761	ENSMUSG00000068428	Gmnc	Gemc1|Gm1778|Gm606	geminin coiled-coil domain containing	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-432	chr1	143830759	143830959	+	1.21485	NA	Intergenic	Intergenic	53581	NM_001159866	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding	0.010000	0.467662			-60(ATAAGAAAGACAGTGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7729	chr9	74110238	74110438	+	1.21485	NA	promoter-TSS (NM_001033500)	promoter-TSS (NM_001033500)	4	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding	0.060000	0.706468			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7122	chr7	141379685	141379885	+	1.21485	NA	Intergenic	Intergenic	-12375	NM_011528	21351	Mm.29182	NM_011528	ENSMUSG00000025503	Taldo1	-	transaldolase 1	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1024	chr10	110945402	110945602	+	1.21485	NA	exon (NM_172554, exon 16 of 17)	exon (NM_172554, exon 16 of 17)	25326	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-898	chr10	78159037	78159237	+	1.21485	NA	Intergenic	L1MC|LINE|L1	10618	NM_138601	28295	Mm.268691	NM_138601	ENSMUSG00000053329	Gatd3a	C21orf33|D10Jhu81e|ES1	glutamine amidotransferase like class 1 domain containing 3A	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3699	chr18	9726635	9726835	+	1.21485	NA	intron (NM_130449, intron 2 of 9)	intron (NM_130449, intron 2 of 9)	19087	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1162	chr11	12520664	12520864	+	1.21485	NA	Intergenic	MER2|DNA|TcMar-Tigger	-55804	NM_001282993	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3623	chr17	80891905	80892105	+	1.21485	NA	Intergenic	Intergenic	-4788	NR_131127	320784	Mm.474182	NR_131127	ENSMUSG00000112121	C230072F16Rik	-	RIKEN cDNA C230072F16 gene	ncRNA	0.005000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5852	chr5	20038419	20038619	+	1.21485	NA	intron (NM_015823, intron 1 of 21)	L1MD2|LINE|L1	131001	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding	0.005000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6850	chr7	51898816	51899016	+	1.21485	NA	intron (NM_001330607, intron 3 of 7)	intron (NM_001330607, intron 3 of 7)	19949	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2587	chr14	79883740	79883940	+	1.21485	NA	Intergenic	Intergenic	-14664	NR_033535	100038734	Mm.387484	NR_033535	ENSMUSG00000095959	Gm10845	-	predicted gene 10845	ncRNA	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2984	chr15	69202351	69202551	+	1.21458	NA	Intergenic	Intergenic	-68082	NR_130983	75076		NR_130983	ENSMUSG00000116167	4930504C09Rik	-	RIKEN cDNA 4930504C09 gene	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3780	chr18	34093213	34093413	+	1.21426	NA	Intergenic	Intergenic	-86107	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5535	chr4	72441604	72441804	+	1.21426	NA	Intergenic	A-rich|Low_complexity|Low_complexity	240460	NR_027923	68285	Mm.37541	NR_027923		C630043F03Rik	AI851307	RIKEN cDNA C630043F03 gene	ncRNA	0.000000	0.278607			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-523	chr2	127774889	127775089	+	1.21281	NA	intron (NM_001355429, intron 4 of 19)	L1MEf|LINE|L1	13902	NM_001369236	53885	Mm.210766	NM_016902	ENSMUSG00000027378	Nphp1	-	nephronophthisis 1 (juvenile) homolog (human)	protein-coding	0.000000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1325	chr11	66606804	66607004	+	1.21097	NA	Intergenic	Intergenic	-80778	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6692	chr6	118833467	118833667	+	1.21097	NA	intron (NM_001256000, intron 3 of 46)	intron (NM_001256000, intron 3 of 46)	-46591	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA	0.010000	0.422886			31(ATTTGCATCACCATCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3700	chr18	10242480	10242680	+	1.21097	NA	Intergenic	Intergenic	-60788	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding	0.000000	0.462687		20(AATGCATATGCTTG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7391	chr8	97326040	97326240	+	1.21097	NA	Intergenic	Intergenic	-1437739	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6988	chr7	97652806	97653006	+	1.21097	NA	intron (NR_154552, intron 2 of 2)	intron (NR_154552, intron 2 of 2)	-7794	NR_126461	75448	Mm.439818	NR_126461	ENSMUSG00000086433	Rsf1os1	1700006D18Rik	remodeling and spacing factor 1, opposite strand 1	ncRNA	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3910	chr18	65749092	65749292	+	1.21097	NA	intron (NM_177028, intron 13 of 14)	intron (NM_177028, intron 13 of 14)	50924	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3274	chr16	63934206	63934406	+	1.21097	NA	Intergenic	Intergenic	-70131	NM_010140	13837	Mm.1977	NM_010140	ENSMUSG00000052504	Epha3	AW492086|Cek4|EK4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6594	chr6	94327076	94327276	+	1.21097	NA	Intergenic	Intergenic	-43259	NM_001286784	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.000000	0.323383			-16(GTTTGAAAGAAAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3787	chr18	35207148	35207348	+	1.21097	NA	intron (NM_009818, intron 7 of 17)	intron (NM_009818, intron 7 of 17)	7776	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2340	chr14	9057560	9057760	+	1.21097	NA	Intergenic	Intergenic	391270	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA	0.005000	0.348259			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-798	chr7	87319296	87319496	+	1.21097	NA	intron (NM_001285833, intron 8 of 19)	intron (NM_001285833, intron 8 of 19)	72747	NM_001285835	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding	0.000000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3539	chr17	56580074	56580274	+	1.21097	NA	intron (NM_001029979, intron 2 of 20)	B4A|SINE|B4	4411	NM_001029979	224902	Mm.214973	NM_001029979	ENSMUSG00000042625	Safb2	AA389433|AI255170|mKIAA0138	scaffold attachment factor B2	protein-coding	0.005000	0.477612			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-476	chr2	39459905	39460105	+	1.21097	NA	Intergenic	Intergenic	-233656	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik|Pp6C	protein phosphatase 6, catalytic subunit	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1681	chr12	59073865	59074065	+	1.21097	NA	TTS (NM_008891)	TTS (NM_008891)	7046	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding	0.000000	0.268657			-59(ATTTAAATGACAGTGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1782	chr12	83633849	83634049	+	1.21097	NA	intron (NM_027349, intron 1 of 18)	intron (NM_027349, intron 1 of 18)	1706	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5883	chr5	28344591	28344791	+	1.21097	NA	intron (NM_028234, intron 6 of 18)	intron (NM_028234, intron 6 of 18)	27502	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding	0.000000	0.383085			12(ATTTAAATGAGATTAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7137	chr8	4629268	4629468	+	1.21097	NA	exon (NM_145591, exon 4 of 4)	exon (NM_145591, exon 4 of 4)	16028	NM_001368404	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2037	chr13	40575382	40575582	+	1.21076	NA	Intergenic	Intergenic	-152326	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA	0.020000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1892	chr12	116056040	116056240	+	1.21076	NA	intron (NM_001004066, intron 2 of 2)	MTD|LTR|ERVL-MaLR	8416	NM_019565	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding	0.005000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-213	chr12	116056097	116056297	+	1.21076	NA	intron (NM_001004066, intron 2 of 2)	MTD|LTR|ERVL-MaLR	8473	NM_019565	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2487	chr14	50995590	50995790	+	1.21076	NA	Intergenic	Intergenic	-12061	NM_001162863	75019	Mm.318775	NM_029145	ENSMUSG00000021872	Rnase10	4930474F22Rik|Rah1	ribonuclease, RNase A family, 10 (non-active)	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3201	chr16	44786918	44787118	+	1.21076	NA	intron (NM_021325, intron 1 of 6)	intron (NM_021325, intron 1 of 6)	21282	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3668	chr17	91339202	91339402	+	1.21076	NA	Intergenic	BGLII|LTR|ERVK	-246500	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.005000	0.427861			-1(ATTTGTAAAATAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5168	chr3	126681041	126681241	+	1.21076	NA	intron (NM_001025438, intron 2 of 18)	intron (NM_001025438, intron 2 of 18)	84190	NM_001346635	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding	0.015000	0.338308			27(TTTTTTTTTTTGAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-238	chr13	40575383	40575583	+	1.21076	NA	Intergenic	Intergenic	-152325	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA	0.020000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4769	chr2	162911801	162912001	+	1.21002	NA	Intergenic	Intergenic	-19607	NM_026499	67996	Mm.24042	NM_026499	ENSMUSG00000016921	Srsf6	1210001E11Rik|AI314910|AW146126|Sfrs6	serine/arginine-rich splicing factor 6	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4766	chr2	161166814	161167014	+	1.21002	NA	Intergenic	Intergenic	-57828	NM_173368	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding	0.000000	0.502488			46(CTATACATGACAGTGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4202	chr2	20622852	20623052	+	1.21002	NA	intron (NM_001081006, intron 3 of 21)	intron (NM_001081006, intron 3 of 21)	103439	NM_001369134	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.000000	0.412935			-27(ATTTACCTAAGAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2894	chr15	43940366	43940566	+	1.21002	NA	Intergenic	Intergenic	-70437	NM_175502	239408	Mm.41219	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1111	chr10	123478841	123479041	+	1.21002	NA	intron (NR_153334, intron 2 of 6)	intron (NR_153334, intron 2 of 6)	214865	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Tafa2	6330575M02|FAM19A2 TAFA-2|Fam19a2|Sam2|Tafa-2	TAFA chemokine like family member 2	protein-coding	0.015000	0.402985	38(CATGAATAATTTAAG,+,0.00),38(CATGAATAATTTAAG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3848	chr18	51131297	51131497	+	1.21002	NA	intron (NM_001081224, intron 1 of 1)	intron (NM_001081224, intron 1 of 1)	13499	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1038	chr10	112060059	112060259	+	1.21002	NA	promoter-TSS (NM_027018)	promoter-TSS (NM_027018)	-30	NM_027018	69286	Mm.47058	NM_027018	ENSMUSG00000020213	Glipr1l1	1700011E04Rik	GLI pathogenesis-related 1 like 1	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4944	chr3	52580444	52580644	+	1.21002	NA	Intergenic	Intergenic	63580	NR_153344	102631981	Mm.394225	NR_153344		Gm30173	-	predicted gene, 30173	ncRNA	0.010000	0.353234			82(ATTTACAATATAATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1756	chr12	79449801	79450001	+	1.21002	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	152550	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding	0.025000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-467	chr1	153204275	153204475	+	1.21002	NA	Intergenic	Intergenic	-17928	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3476	chr17	36879372	36879572	+	1.21002	NA	Intergenic	Intergenic	9898	NM_011280	19824	Mm.299155	NM_011280	ENSMUSG00000073400	Trim10	AI324236|BB139825|Herf1|Rnf9	tripartite motif-containing 10	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2046	chr13	41635238	41635438	+	1.21002	NA	3' UTR (NM_001163572, exon 3 of 3)	3' UTR (NM_001163572, exon 3 of 3)	29456	NM_001368686	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding	0.000000	0.293532			20(CATTTTTCTTATAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2644	chr14	98643130	98643330	+	1.21002	NA	Intergenic	Intergenic	402906	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2699	chr14	115019152	115019352	+	1.21002	NA	Intergenic	Intergenic	-24419	NR_029785	723905		NR_029785	ENSMUSG00000065508	Mir17	Mirn17|mir-17|mmu-mir-17	microRNA 17	ncRNA	0.000000	0.293532			33(ATTTGCATATGAACAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5726	chr4	124621516	124621716	+	1.21002	NA	Intergenic	Intergenic	-36030	NM_011141	18991	Mm.297371	NM_011141	ENSMUSG00000090125	Pou3f1	Oct-6|Oct6|Otf-6|Otf6|Scip|Test1|Tst-1|Tst1	POU domain, class 3, transcription factor 1	protein-coding	0.015000	0.472637			15(ATTTAAAAGAAAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1143	chr11	5220719	5220919	+	1.21002	NA	intron (NM_032396, intron 3 of 8)	MLT1F2|LTR|ERVL-MaLR	40791	NM_032396	84035	Mm.209989	NM_032396	ENSMUSG00000020393	Kremen1	AV002070|Kremen|Krm1	kringle containing transmembrane protein 1	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1916	chr12	118909172	118909372	+	1.21002	NA	intron (NM_029961, intron 16 of 27)	intron (NM_029961, intron 16 of 27)	57149	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-930	chr10	89437658	89437858	+	1.21002	NA	intron (NM_001033331, intron 1 of 10)	L2b|LINE|L2	6209	NM_001079876	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3205	chr16	45582498	45582698	+	1.21002	NA	intron (NM_198106, intron 18 of 27)	intron (NM_198106, intron 18 of 27)	-27842	NM_008099	14525	Mm.4799	NM_008099	ENSMUSG00000022659	Gcsam	Gcet|Gcet2|M17|M17-L	germinal center associated, signaling and motility	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1886	chr12	109935921	109936121	+	1.21002	NA	Intergenic	L1MB5|LINE|L1	188143	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7164	chr8	17084763	17084963	+	1.21002	NA	intron (NM_053171, intron 2 of 69)	intron (NM_053171, intron 2 of 69)	450522	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6521	chr6	71569630	71569830	+	1.21002	NA	intron (NM_025783, intron 3 of 5)	L1M3|LINE|L1	23607	NM_001355674	66700	Mm.181278	NM_025783	ENSMUSG00000053119	Chmp3	25.1|4921505F14Rik|9130011K15Rik|CGI-49|D6Ertd286e|NEDF|Vps24	charged multivesicular body protein 3	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7925	chrX	13413286	13413486	+	1.21002	NA	Intergenic	MERVL_2A-int|LTR|ERVL	-47704	NM_173415	236690	Mm.90233	NM_173415	ENSMUSG00000051228	Nyx	CLNP|CSNB1|CSNB4|nob	nyctalopin	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-585	chr1	179756472	179756672	+	1.21002	NA	intron (NM_026375, intron 31 of 35)	intron (NM_026375, intron 31 of 35)	-11372	NM_001370897	383592		NM_001370897	ENSMUSG00000087236	Kif28	Gm1305|Kif28p	kinesin family member 28	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7431	chr8	106985492	106985692	+	1.21002	NA	intron (NM_001368316, intron 2 of 5)	intron (NM_001368316, intron 2 of 5)	-45677	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding	0.005000	0.447761		-55(CATGCATTTTTATG,-,0.00)	-31(ATTAAAATGAAAAGGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6417	chr6	42390019	42390219	+	1.21002	NA	Intergenic	Intergenic	-10119	NM_001001452	387514	Mm.377921	NM_001001452	ENSMUSG00000046652	Tas2r143	Gm1404|Tas2r43|mt2r36	taste receptor, type 2, member 143	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2293	chr13	110072774	110072974	+	1.21002	NA	intron (NM_001360099, intron 4 of 4)	intron (NM_001360099, intron 4 of 4)	169065	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6963	chr7	91090933	91091133	+	1.21002	NA	exon (NM_011807, exon 1 of 23)	exon (NM_011807, exon 1 of 23)	247	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs large MAGUK scaffold protein 2	protein-coding	0.040000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6810	chr7	31018951	31019151	+	1.21002	NA	Intergenic	Intergenic	21266	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA	0.015000	0.442786			85(GTATTCTAATGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1109	chr10	123385142	123385342	+	1.21002	NA	intron (NM_001252387, intron 1 of 4)	MTE2a|LTR|ERVL-MaLR	121166	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Tafa2	6330575M02|FAM19A2 TAFA-2|Fam19a2|Sam2|Tafa-2	TAFA chemokine like family member 2	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-119	chr1	42169570	42169770	+	1.21002	NA	Intergenic	Intergenic	525155	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1846	chr12	100221971	100222171	+	1.21002	NA	Intergenic	C-rich|Low_complexity|Low_complexity	21927	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm|Cam1	calmodulin 1	protein-coding	0.010000	0.522388			-65(ATTTAAAAGACTAGGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-517	chr1	164783262	164783462	+	1.21002	NA	Intergenic	Intergenic	-13301	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3695	chr18	7705573	7705773	+	1.21002	NA	Intergenic	Intergenic	-78810	NM_001161620	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding	0.015000	0.422886			-35(TTTTGCAAGCCAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3395	chr16	95559781	95559981	+	1.21002	NA	intron (NM_001302152, intron 1 of 10)	(CTATT)n|Simple_repeat|Simple_repeat	26712	NM_001302152	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	ETS transcription factor	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1541	chr12	12329052	12329252	+	1.21002	NA	intron (NM_029758, intron 3 of 12)	B4|SINE|B4	63323	NR_045829	70858	Mm.410838	NR_045829	ENSMUSG00000114136	4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA	0.015000	0.477612			67(CCATTATTATTCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8121	chrX	152084495	152084695	+	1.21002	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-59673	NM_001114664	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2870	chr15	39043347	39043547	+	1.21002	NA	Intergenic	Intergenic	-33485	NM_001364813	68588	Mm.41556	NM_026778	ENSMUSG00000054196	Cthrc1	1110014B07Rik	collagen triple helix repeat containing 1	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-906	chr10	83187995	83188195	+	1.21002	NA	intron (NM_021439, intron 2 of 2)	ORR1A2|LTR|ERVL-MaLR	149722	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5323	chr4	5515395	5515595	+	1.21002	NA	Intergenic	RLTR13D6|LTR|ERVK	-116833	NR_038183	73872	Mm.427301	NR_038183	ENSMUSG00000086066	4930423M02Rik	-	RIKEN cDNA 4930423M02 gene	ncRNA	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7752	chr9	79425586	79425786	+	1.21002	NA	Intergenic	Lx9|LINE|L1	93616	NR_045336	100038575	Mm.367838	NR_045336	ENSMUSG00000111765	Gm10635	-	predicted gene 10635	ncRNA	0.000000	0.373134		-46(CATAAATAGTCATG,+,0.00),-46(CATAAATAGTCATG,-,0.00)	-43(AAATAGTCATGTAGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-702	chr5	107449119	107449319	+	1.20911	NA	intron (NM_001255991, intron 2 of 8)	intron (NM_001255991, intron 2 of 8)	11222	NM_001255991	100503185	Mm.366650	NM_001255991	ENSMUSG00000111375	Btbd8	EG627196|Gm16115	BTB (POZ) domain containing 8	protein-coding	0.015000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7239	chr8	47985256	47985456	+	1.20848	NA	intron (NM_133791, intron 1 of 22)	intron (NM_133791, intron 1 of 22)	5188	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding	0.000000	0.527363			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-727	chr6	15756216	15756416	+	1.20848	NA	intron (NM_175088, intron 3 of 4)	intron (NM_175088, intron 3 of 4)	35655	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5391	chr4	25798637	25798837	+	1.20800	NA	intron (NM_010243, intron 1 of 2)	intron (NM_010243, intron 1 of 2)	1266	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.030000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7442	chr8	109135397	109135597	+	1.20794	NA	intron (NR_126329, intron 2 of 9)	intron (NR_126329, intron 2 of 9)	60275	NR_126329	628686	Mm.203332	NR_126329	ENSMUSG00000097393	D030068K23Rik	-	RIKEN cDNA D030068K23 gene	ncRNA	0.000000	0.373134			20(TTCTTCTCTTGTTAAT,+,0.00),55(ATTAGAAAGGCAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7241	chr8	48213800	48214000	+	1.20794	NA	Intergenic	LTR72_RN|LTR|ERV1	103887	NM_001161515	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding	0.015000	0.482587			84(ATTTTCAAAGCAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7149	chr8	10982129	10982329	+	1.20794	NA	Intergenic	Intergenic	-25621	NR_046017	619321	Mm.403007	NR_046017	ENSMUSG00000096938	9530052E02Rik	-	RIKEN cDNA 9530052E02 gene	ncRNA	0.000000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-743	chr6	48071588	48071788	+	1.20794	NA	intron (NM_001362062, intron 4 of 5)	L1M5|LINE|L1	14905	NM_001362062	69228	Mm.207555	NM_001163475	ENSMUSG00000057691	Zfp746	2810407L07Rik|AI317225|Znf746	zinc finger protein 746	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7744	chr9	77719827	77720027	+	1.20794	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-34608	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding	0.005000	0.412935			-86(GATTGCATAAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5826	chr5	9993637	9993837	+	1.20794	NA	Intergenic	Intergenic	-268385	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding	0.005000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-825	chr8	48213846	48214046	+	1.20794	NA	Intergenic	LTR72_RN|LTR|ERV1	103933	NM_001161515	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding	0.015000	0.482587			38(ATTTTCAAAGCAATGC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-371	chr16	44977263	44977463	+	1.20794	NA	intron (NM_029018, intron 5 of 5)	intron (NM_029018, intron 5 of 5)	33685	NM_001128133	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding	0.010000	0.432836			21(CATTTGTCAAGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6433	chr6	48071618	48071818	+	1.20794	NA	intron (NM_001362062, intron 4 of 5)	L1M5|LINE|L1	14875	NM_001362062	69228	Mm.207555	NM_001163475	ENSMUSG00000057691	Zfp746	2810407L07Rik|AI317225|Znf746	zinc finger protein 746	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4955	chr3	56159305	56159505	+	1.20794	NA	intron (NM_030595, intron 1 of 57)	Charlie10a|DNA|hAT-Charlie	24296	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2150	chr13	76069048	76069248	+	1.20794	NA	intron (NM_029847, intron 5 of 7)	intron (NM_029847, intron 5 of 7)	-12152	NM_175495	238725	Mm.167172	NM_175495	ENSMUSG00000045509	Gpr150	C030001A19Rik|PGR11	G protein-coupled receptor 150	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5621	chr4	96089824	96090024	+	1.20794	NA	Intergenic	RLTR13G|LTR|ERVK	-12377	NM_001346540	230459	Mm.268175	NM_145548	ENSMUSG00000028571	Cyp2j13	-	cytochrome P450, family 2, subfamily j, polypeptide 13	protein-coding	0.010000	0.432836	-90(ATTGCATTATTCATG,+,0.00),-90(ATTGCATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-900	chr10	78787182	78787382	+	1.20794	NA	intron (NM_009200, intron 1 of 9)	intron (NM_009200, intron 1 of 9)	6786	NM_009200	20513	Mm.6257	NM_009200	ENSMUSG00000005357	Slc1a6	EAAT4	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7385	chr8	95363893	95364093	+	1.20794	NA	intron (NM_008609, intron 1 of 9)	Lx8|LINE|L1	11697	NM_008609	17388	Mm.217116	NM_008609	ENSMUSG00000031790	Mmp15	AI503551|MT-MMP 2|MT2-MMP	matrix metallopeptidase 15	protein-coding	0.000000	0.427861			-76(GTATTTTTATTTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1812	chr12	91225287	91225487	+	1.20794	NA	intron (NM_181815, intron 19 of 25)	intron (NM_181815, intron 19 of 25)	115158	NR_030473	735273		NR_030473	ENSMUSG00000076118	Mir669c	Mirn669c|Mirn669c-1	microRNA 669c	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7474	chr8	120532793	120532993	+	1.20751	NA	intron (NM_198671, intron 1 of 15)	intron (NM_198671, intron 1 of 15)	-2964	NM_001145897	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding	0.055000	0.621891			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-257	chr13	84373270	84373470	+	1.20683	NA	Intergenic	Intergenic	151074	NM_001361908	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0.020000	0.477612			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-465	chr2	3890999	3891199	+	1.20545	NA	Intergenic	Intergenic	-126584	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|mKIAA1294	FERM domain containing 4A	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6315	chr6	14504832	14505032	+	1.20545	NA	Intergenic	Intergenic	250342	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory subunit 3A	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3838	chr18	48935226	48935426	+	1.20448	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-587963	NR_033785	67321	Mm.245802	NR_033785	ENSMUSG00000100297	1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6526	chr6	72686787	72686987	+	1.20448	NA	intron (NM_009332, intron 3 of 11)	intron (NM_009332, intron 3 of 11)	57056	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	-	predicted gene 15401	ncRNA	0.020000	0.407960			55(ATTTTAATAACAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3485	chr17	41150613	41150813	+	1.20448	NA	Intergenic	L1MA4A|LINE|L1	216028	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mmut	D230010K02Rik|Mcm|Mut	methylmalonyl-Coenzyme A mutase	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1563	chr12	24928315	24928515	+	1.20448	NA	intron (NM_026037, intron 4 of 12)	intron (NM_026037, intron 4 of 12)	-46517	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2067	chr13	49552421	49552621	+	1.20448	NA	intron (NM_001172481, intron 2 of 7)	intron (NM_001172481, intron 2 of 7)	8078	NM_025711	66695	Mm.383216	NM_025711	ENSMUSG00000021388	Aspn	4631401G09Rik|AA986886|Plap1|Slrr1c	asporin	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1876	chr12	107285598	107285798	+	1.20448	NA	Intergenic	Intergenic	449790	NR_045973	74968	Mm.359821	NR_045973	ENSMUSG00000085641	4930465M20Rik	4930431H15Rik	RIKEN cDNA 4930465M20 gene	ncRNA	0.025000	0.417910			-8(TCTTTCTTTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7162	chr8	15395895	15396095	+	1.20448	NA	Intergenic	Intergenic	338342	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1298	chr11	56890685	56890885	+	1.20448	NA	Intergenic	Intergenic	-120833	NM_001113325	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding	0.005000	0.393035			73(ATTTACATAATTAGGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1097	chr10	121958758	121958958	+	1.20448	NA	intron (NM_001081037, intron 1 of 21)	intron (NM_001081037, intron 1 of 21)	88457	NM_001081037	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.020000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5798	chr4	152194865	152195065	+	1.20448	NA	intron (NM_001146057, intron 1 of 8)	ORR1C1|LTR|ERVL-MaLR	-4879	NM_001146058	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2003	chr13	29641995	29642195	+	1.20409	NA	intron (NR_131896, intron 8 of 16)	intron (NR_131896, intron 8 of 16)	213578	NM_144536	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7827	chr9	94737267	94737467	+	1.20409	NA	intron (NM_177909, intron 4 of 15)	MIR3|SINE|MIR	-14462	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA	0.010000	0.447761			19(ATTTACAAGTCAATCA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-888	chr9	94737275	94737475	+	1.20409	NA	intron (NM_177909, intron 4 of 15)	intron (NM_177909, intron 4 of 15)	-14454	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA	0.010000	0.457711			11(ATTTACAAGTCAATCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6818	chr7	35991235	35991435	+	1.20409	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-188346	NM_177739	668501	Mm.286296	NM_177739	ENSMUSG00000044452	Zfp507	1810022O10Rik|A230056M16Rik|AL024009|AU021817|BB105092|Gm480|Znf507|mKIAA1084	zinc finger protein 507	protein-coding	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-855	chr10	65541002	65541202	+	1.20409	NA	Intergenic	Intergenic	367137	NR_155764	102632897	Mm.183448	NR_155764	ENSMUSG00000112913	Gm30853	-	predicted gene, 30853	ncRNA	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7870	chr9	106359078	106359278	+	1.20358	NA	Intergenic	Intergenic	-9454	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding	0.000000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1258	chr11	41439416	41439616	+	1.20358	NA	Intergenic	Intergenic	561341	NM_008073	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding	0.015000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-143	chr11	41439367	41439567	+	1.20358	NA	Intergenic	Intergenic	561390	NM_008073	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding	0.015000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-504	chr2	98777955	98778155	+	1.20358	NA	Intergenic	Lx2B2|LINE|L1	1310398	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3136	chr16	27391740	27391940	+	1.20358	NA	intron (NM_001025615, intron 1 of 9)	intron (NM_001025615, intron 1 of 9)	2884	NM_026202	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding	0.020000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-355	chr15	99763665	99763865	+	1.20108	NA	intron (NM_028015, intron 1 of 9)	ORR1A4-int|LTR|ERVL-MaLR	8750	NM_028015	71949	Mm.390821	NM_028015	ENSMUSG00000023021	Cers5	2310081H14Rik|AU045339|AW544927|Lass5|Trh4	ceramide synthase 5	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6424	chr6	43857601	43857801	+	1.20108	NA	Intergenic	Intergenic	-191423	NM_001311111	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4675	chr2	140275088	140275288	+	1.20108	NA	intron (NM_001033296, intron 5 of 19)	intron (NM_001033296, intron 5 of 19)	104542	NM_027093	69487	Mm.287921	NM_027093	ENSMUSG00000027384	Ndufaf5	2310003L22Rik	NADH:ubiquinone oxidoreductase complex assembly factor 5	protein-coding	0.005000	0.363184			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-675	chr5	52256899	52257099	+	1.20108	NA	Intergenic	Intergenic	-40566	NR_040717	414111	Mm.417638	NR_040717	ENSMUSG00000106464	C130083M11Rik	-	RIKEN cDNA C130083M11 gene	ncRNA	0.010000	0.487562			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-780	chr6	142770451	142770651	+	1.20108	NA	exon (NM_009908, exon 5 of 8)	exon (NM_009908, exon 5 of 8)	13865	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding	0.035000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3057	chr15	99763626	99763826	+	1.20108	NA	intron (NM_028015, intron 1 of 9)	ORR1A4-int|LTR|ERVL-MaLR	8789	NM_028015	71949	Mm.390821	NM_028015	ENSMUSG00000023021	Cers5	2310081H14Rik|AU045339|AW544927|Lass5|Trh4	ceramide synthase 5	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5955	chr5	52256817	52257017	+	1.20108	NA	Intergenic	Intergenic	-40484	NR_040717	414111	Mm.417638	NR_040717	ENSMUSG00000106464	C130083M11Rik	-	RIKEN cDNA C130083M11 gene	ncRNA	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2098	chr13	60605207	60605407	+	1.20108	NA	intron (NM_134062, intron 2 of 26)	intron (NM_134062, intron 2 of 26)	3096	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding	0.015000	0.402985			-36(CTATTGTTATTTAACT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6661	chr6	109747832	109748032	+	1.20108	NA	Intergenic	B4|SINE|B4	-897580	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding	0.005000	0.402985			77(ATATACATGAATATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6629	chr6	102192818	102193018	+	1.20062	NA	intron (NM_008779, intron 18 of 21)	intron (NM_008779, intron 18 of 21)	-73182	NR_131018	75893	Mm.2968	NR_131017	ENSMUSG00000107563	4930587E11Rik	4930523E13Rik|Gm44188	RIKEN cDNA 4930587E11 gene	ncRNA	0.000000	0.298507			-88(ATTTGCATTATACAAA,-,0.00),-40(ATTTTCCTATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4861	chr3	16086321	16086521	+	1.20011	NA	Intergenic	RLTR13D3A|LTR|ERVK	-80089	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2320	chr13	116694664	116694864	+	1.19886	NA	Intergenic	Intergenic	143414	NR_153406	74680	Mm.488118	NR_153406	ENSMUSG00000114290	4930435F18Rik	-	RIKEN cDNA 4930435F18 gene	ncRNA	0.010000	0.348259	-15(TATACATTATTCATT,+,0.00),-15(TATACATTATTCATT,-,0.00)		-3(ATTTCCTAAACAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7362	chr8	85477966	85478166	+	1.19886	NA	Intergenic	Intergenic	-14510	NM_173866	108682	Mm.127905	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1683	chr12	59661140	59661340	+	1.19886	NA	Intergenic	Intergenic	-441757	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0.005000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-874	chr9	54051534	54051734	+	1.19886	NA	intron (NM_001033535, intron 1 of 1)	HAL1|LINE|L1	16777	NM_001033535	244882	Mm.325589	NM_001033535	ENSMUSG00000074345	Tnfaip8l3	9930029P06Rik|Gm517	tumor necrosis factor, alpha-induced protein 8-like 3	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6774	chr6	147254894	147255094	+	1.19886	NA	intron (NM_008970, intron 3 of 3)	intron (NM_008970, intron 3 of 3)	9019	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4607	chr2	130219320	130219520	+	1.19886	NA	intron (NM_138655, intron 5 of 19)	intron (NM_138655, intron 5 of 19)	24226	NM_138655	192140	Mm.219546	NM_138655	ENSMUSG00000060332	Tmc2	CWEA2	transmembrane channel-like gene family 2	protein-coding	0.010000	0.343284			45(TATTTGTGAAGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6511	chr6	70103483	70103683	+	1.19886	NA	Intergenic	LTRIS2|LTR|ERV1	688592	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-51	chr1	19419360	19419560	+	1.19886	NA	Intergenic	Intergenic	207406	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding	0.000000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-575	chr3	119320757	119320957	+	1.19886	NA	intron (NM_170778, intron 20 of 22)	intron (NM_170778, intron 20 of 22)	462531	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.303483			7(CCTTATTCATTCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-109	chr1	38038974	38039174	+	1.19886	NA	intron (NM_198303, intron 12 of 23)	B3|SINE|B2	41064	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding	0.000000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-843	chr8	85478117	85478317	+	1.19886	NA	Intergenic	Intergenic	-14359	NM_173866	108682	Mm.127905	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding	0.020000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-913	chr10	86200359	86200559	+	1.19886	NA	intron (NM_013722, intron 6 of 13)	intron (NM_013722, intron 6 of 13)	-99953	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding	0.010000	0.412935			-35(CCCTTTTCATGAAAAT,+,0.00),-33(CTTTTCATGAAAATGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-239	chr13	42276717	42276917	+	1.19886	NA	Intergenic	Intergenic	-24659	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6371	chr6	28724508	28724708	+	1.19886	NA	intron (NM_019776, intron 13 of 23)	intron (NM_019776, intron 13 of 23)	107139	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6473	chr6	59358823	59359023	+	1.19880	NA	intron (NM_183183, intron 1 of 1)	intron (NM_183183, intron 1 of 1)	67383	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1066	chr10	116561775	116561975	+	1.19880	NA	intron (NM_001037846, intron 1 of 15)	intron (NM_001037846, intron 1 of 15)	18661	NM_001359248	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding	0.000000	0.358209			-35(ATTTAATTGACTAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2816	chr15	21008522	21008722	+	1.19777	NA	Intergenic	Intergenic	-102830	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4879	chr3	26796120	26796320	+	1.19777	NA	intron (NM_027583, intron 4 of 9)	intron (NM_027583, intron 4 of 9)	158589	NM_029150	70862	Mm.330943	NM_027583	ENSMUSG00000039335	Spata16	4921511F01Rik|4930503K02Rik|Nyd-sp12	spermatogenesis associated 16	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8126	chrX	155281082	155281282	+	1.19777	NA	intron (NM_019736, intron 5 of 14)	MTC|LTR|ERVL-MaLR	18739	NM_019736	56360	Mm.268710	NM_019736	ENSMUSG00000025287	Acot9	0610041P13Rik|Acate2|C76421|MT-ACT48|MTE-2|U8|p48	acyl-CoA thioesterase 9	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3008	chr15	86287626	86287826	+	1.19777	NA	intron (NM_001358062, intron 1 of 9)	intron (NM_001358062, intron 1 of 9)	10051	NM_001358062	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5776	chr4	142969069	142969269	+	1.19730	NA	Intergenic	Intergenic	166993	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA	0.010000	0.358209	-58(TCTGAATAAGGCATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-941	chr10	92573708	92573908	+	1.19730	NA	Intergenic	Intergenic	148610	NM_008682	17997	Mm.2998	NM_008682	ENSMUSG00000019988	Nedd1	-	neural precursor cell expressed, developmentally down-regulated gene 1	protein-coding	0.010000	0.378109			-7(AATTGAATTACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3285	chr16	66129197	66129397	+	1.19730	NA	Intergenic	RLTR13D2|LTR|ERVK	314108	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding	0.000000	0.393035	40(CATGAATAATACAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3097	chr16	15541947	15542147	+	1.19730	NA	Intergenic	RLTR17|LTR|ERVK	52471	NM_023585	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7297	chr8	66345127	66345327	+	1.19730	NA	intron (NM_175188, intron 4 of 7)	RLTR13B1|LTR|ERVK	-41074	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-344	chr1	124517687	124517887	+	1.19730	NA	Intergenic	Intergenic	-472228	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7679	chr9	61241446	61241646	+	1.19730	NA	Intergenic	Intergenic	52263	NR_045334	622037	Mm.126243	NR_045334	ENSMUSG00000111658	B930092H01Rik	-	RIKEN cDNA B930092H01 gene	ncRNA	0.015000	0.467662	24(ACTGAATTATTTATG,+,0.00),24(ACTGAATTATTTATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1953	chr13	13446933	13447133	+	1.19730	NA	intron (NM_010917, intron 1 of 19)	intron (NM_010917, intron 1 of 19)	9431	NM_010917	18073	Mm.4691	NM_010917	ENSMUSG00000005397	Nid1	A630025O17|Nid|entactin|entactin-1|nidogen-1	nidogen 1	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1517	chr12	4196183	4196383	+	1.19730	NA	intron (NM_001159537, intron 6 of 21)	RMER10A|LTR|ERVL	37682	NM_134046	52504	Mm.70546	NM_134046	ENSMUSG00000020652	Cenpo	2810429O05Rik|8430427C03Rik|D12Ertd482e	centromere protein O	protein-coding	0.010000	0.527363			54(CCTTTGGTATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-939	chr10	91521338	91521538	+	1.19730	NA	Intergenic	Intergenic	-300819	NR_151510	102633753	Mm.416936	NR_151510		4930534H03Rik	-	RIKEN cDNA 4930534H03 gene	ncRNA	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5963	chr5	54771326	54771526	+	1.19730	NA	Intergenic	Intergenic	421434	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13	predicted gene 10440	ncRNA	0.005000	0.417910			-96(ATTTACATCATAGAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5603	chr4	92152905	92153105	+	1.19730	NA	Intergenic	Intergenic	-5784	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6441	chr6	49930187	49930387	+	1.19730	NA	Intergenic	Intergenic	107577	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding	0.010000	0.442786	-25(AGTGCATAATGTATG,+,0.00),-25(AGTGCATAATGTATG,-,0.00)		80(CCTTTGTCATCCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1055	chr10	115400317	115400517	+	1.19730	NA	intron (NM_001033261, intron 3 of 34)	intron (NM_001033261, intron 3 of 34)	15458	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding	0.020000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3200	chr16	44510072	44510272	+	1.19730	NA	intron (NM_172506, intron 3 of 18)	intron (NM_172506, intron 3 of 18)	47957	NR_037242	100526478		NR_037242	ENSMUSG00000093046	Mir3081	mir-3081|mmu-mir-3081	microRNA 3081	ncRNA	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5971	chr5	56701242	56701442	+	1.19730	NA	Intergenic	Intergenic	1016577	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1585	chr12	31804996	31805196	+	1.19730	NA	intron (NM_001163126, intron 10 of 22)	intron (NM_001163126, intron 10 of 22)	-91213	NM_175191	73010	Mm.441517	NM_175191	ENSMUSG00000044067	Gpr22	2900068K05Rik|AW061316	G protein-coupled receptor 22	protein-coding	0.000000	0.308458			-21(TAATTCATATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2833	chr15	27247070	27247270	+	1.19730	NA	Intergenic	Intergenic	-219507	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3414	chr17	8910254	8910454	+	1.19730	NA	intron (NM_001290707, intron 3 of 22)	intron (NM_001290707, intron 3 of 22)	60369	NM_001347321	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1659	chr12	52232041	52232241	+	1.19730	NA	intron (NM_029760, intron 6 of 10)	RLTR13B1|LTR|ERVK	134395	NM_029760	76826	Mm.244781	NM_029760	ENSMUSG00000035142	Nubpl	2410170E07Rik	nucleotide binding protein-like	protein-coding	0.000000	0.388060	34(CATGAATAATGCAAT,+,0.00),34(CATGAATAATGCAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5824	chr5	9755874	9756074	+	1.19730	NA	Intergenic	RLTR13D6|LTR|ERVK	-30622	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3035	chr15	94334873	94335073	+	1.19730	NA	intron (NM_177431, intron 18 of 38)	intron (NM_177431, intron 18 of 38)	69377	NM_177431	223838	Mm.214132	NM_177431	ENSMUSG00000022449	Adamts20	Adamst20|bt	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 20	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3383	chr16	92040821	92041021	+	1.19730	NA	Intergenic	Intergenic	-17401	NM_017391	53881	Mm.217354	NM_017391	ENSMUSG00000089774	Slc5a3	AA623876|BF642829|Smit1	solute carrier family 5 (inositol transporters), member 3	protein-coding	0.000000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6852	chr7	51967728	51967928	+	1.19730	NA	intron (NM_001330607, intron 7 of 7)	intron (NM_001330607, intron 7 of 7)	37886	NR_027704	75744	Mm.386823	NM_001160345	ENSMUSG00000074093	Svip	1700006C13Rik|6620401M08Rik	small VCP/p97-interacting protein	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5324	chr4	6057110	6057310	+	1.19730	NA	Intergenic	Intergenic	-133895	NM_026534	68053	Mm.404043	NM_026534	ENSMUSG00000028243	Ubxn2b	3110003A22Rik|6430407D20Rik|AI451665|p37	UBX domain protein 2B	protein-coding	0.000000	0.318408			31(TTTGTGTCATACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7100	chr7	134156193	134156393	+	1.19730	NA	intron (NM_007400, intron 2 of 22)	L1MA5A|LINE|L1	68804	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5440	chr4	44130143	44130343	+	1.19730	NA	intron (NM_001355181, intron 10 of 10)	B1_Mus2|SINE|Alu	-6120	NR_040414	623796	Mm.490409	NR_040414	ENSMUSG00000084274	Gm12504	-	prothymosin alpha pseudogene	pseudo	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-144	chr1	51028236	51028436	+	1.19730	NA	intron (NM_019790, intron 4 of 9)	intron (NM_019790, intron 4 of 9)	100813	NM_019790	56363	Mm.245154	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik|TR-2	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0.000000	0.308458			19(ATATTATTATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6288	chr6	6058643	6058843	+	1.19730	NA	intron (NM_015829, intron 14 of 17)	intron (NM_015829, intron 14 of 17)	-81350	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	ncRNA	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-105	chr1	36212440	36212640	+	1.19730	NA	intron (NM_198899, intron 6 of 40)	intron (NM_198899, intron 6 of 40)	31762	NM_198899	320011	Mm.261022	NM_198899	ENSMUSG00000037470	Uggt1	0910001L17Rik|A930007H10Rik|AA589501|AI414429|AI448372|C820010P03Rik|GT|UGT1|Ugcgl1	UDP-glucose glycoprotein glucosyltransferase 1	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4995	chr3	68587725	68587925	+	1.19708	NA	intron (NM_013928, intron 1 of 6)	intron (NM_013928, intron 1 of 6)	15457	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1605	chr12	36612752	36612952	+	1.19708	NA	intron (NM_178629, intron 9 of 9)	MIR|SINE|MIR	197236	NR_037309	100499526		NR_037309	ENSMUSG00000092917	Mir3472	mmu-mir-3472	microRNA 3472	ncRNA	0.005000	0.278607			3(GCATTGTTATGAAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-182	chr12	28068516	28068716	+	1.19708	NA	Intergenic	Intergenic	479721	NM_001177964	68511	Mm.310284	NM_001177964	ENSMUSG00000020633	Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding	0.000000	0.373134			-92(ATTTTGATATGCTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-695	chr5	101538037	101538237	+	1.19708	NA	Intergenic	Intergenic	126574	NM_144955	18096	Mm.193072	NM_144955	ENSMUSG00000035187	Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding	0.020000	0.412935			60(ATTAGAATGATAATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-318	chr14	105389965	105390165	+	1.19613	NA	Intergenic	Intergenic	-37494	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3190	chr16	42747462	42747662	+	1.19563	NA	intron (NR_040521, intron 1 of 3)	intron (NR_040521, intron 1 of 3)	128025	NR_040521	75722	Mm.243747	NR_040521	ENSMUSG00000075070	4932412D23Rik	Gm10809	RIKEN cDNA 4932412D23 gene	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7367	chr8	90313307	90313507	+	1.19563	NA	intron (NM_172913, intron 1 of 6)	intron (NM_172913, intron 1 of 6)	34845	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding	0.015000	0.467662			-69(ATTTGCAAGGCAAACC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1850	chr12	100791210	100791410	+	1.19563	NA	intron (NM_001361020, intron 2 of 13)	L1MB3|LINE|L1	12253	NM_001361020	217830	Mm.218590	NM_145448	ENSMUSG00000021185	Dglucy	9030617O03Rik	D-glutamate cyclase	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-694	chr10	11725399	11725599	+	1.19563	NA	Intergenic	L1M5|LINE|L1	116275	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4640	chr2	135152979	135153179	+	1.19563	NA	intron (NM_001145830, intron 3 of 31)	intron (NM_001145830, intron 3 of 31)	62537	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3005	chr15	84086483	84086683	+	1.19563	NA	intron (NM_001356515, intron 5 of 7)	intron (NM_001356515, intron 5 of 7)	19171	NM_001356515	29859	Mm.248796	NM_013873	ENSMUSG00000018865	Sult4a1	2400007A17Rik|AI853543|BR-STL|BR-STL-1|NST|ST4A1|Sultx3|mBR-STL	sulfotransferase family 4A, member 1	protein-coding	0.040000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7244	chr8	48755252	48755452	+	1.19563	NA	Intergenic	Intergenic	-80662	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0.005000	0.363184	57(AATGCATATTACATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7225	chr8	41520322	41520522	+	1.19563	NA	Intergenic	RLTR25A|LTR|ERVK	-103304	NM_013522	14300	Mm.217312	NM_013522	ENSMUSG00000031590	Frg1	-	FSHD region gene 1	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2727	chr14	120452395	120452595	+	1.19563	NA	Intergenic	Intergenic	-25966	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6349	chr6	21411857	21412057	+	1.19563	NA	intron (NM_019697, intron 1 of 5)	intron (NM_019697, intron 1 of 5)	196611	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121	potassium voltage-gated channel, Shal-related family, member 2	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4617	chr2	132339712	132339912	+	1.19563	NA	Intergenic	RMER17C|LTR|ERVK	45635	NM_144944	246313	Mm.283777	NM_144944	ENSMUSG00000050558	Prokr2	B830005M06Rik|EG-VEGRF2|Gpcr73l1|Gpr73l1|PKR2	prokineticin receptor 2	protein-coding	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2151	chr13	76112172	76112372	+	1.19563	NA	intron (NM_001081352, intron 7 of 43)	intron (NM_001081352, intron 7 of 43)	13538	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	-	tetratricopeptide repeat domain 37	protein-coding	0.010000	0.393035			31(GTTTGAATTAGAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4550	chr2	118416908	118417108	+	1.19563	NA	intron (NM_001355383, intron 3 of 35)	intron (NM_001355383, intron 3 of 35)	27896	NM_001177806	27103	Mm.217616	NM_013719	ENSMUSG00000005102	Eif2ak4	2610011M03|GCN2|MGCN2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6234	chr5	141734047	141734247	+	1.19563	NA	intron (NM_177879, intron 4 of 44)	Charlie1a|DNA|hAT-Charlie	492613	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding	0.000000	0.223881		-79(AATGAATATGTATT,+,0.00),-79(AATGAATATGTATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-787	chr10	40053446	40053646	+	1.19563	NA	intron (NM_001114332, intron 4 of 5)	intron (NM_001114332, intron 4 of 5)	-28278	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7788	chr9	85424008	85424208	+	1.19563	NA	Intergenic	MTE2a-int|LTR|ERVL-MaLR	-96958	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Tent5a	BAP014|D930050G01Rik|Fam46a	terminal nucleotidyltransferase 5A	protein-coding	0.000000	0.447761			-56(ATTAGCATCATAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5117	chr3	110075814	110076014	+	1.19563	NA	intron (NM_030699, intron 2 of 7)	MTEb-int|LTR|ERVL-MaLR	67558	NM_001163348	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5243	chr3	142876244	142876444	+	1.19563	NA	intron (NM_178654, intron 1 of 21)	intron (NM_178654, intron 1 of 21)	5660	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5970	chr5	56313928	56314128	+	1.19563	NA	Intergenic	Lx6|LINE|L1	1403891	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA	0.000000	0.398010			-88(CTTTTCTCTTTCTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-376	chr1	129935808	129936008	+	1.19563	NA	intron (NM_172485, intron 14 of 27)	RLTR12A|LTR|ERVK	-486916	NR_151525	102640368		NR_151525	ENSMUSG00000087691	Gm15674	-	predicted gene 15674	ncRNA	0.010000	0.393035			-1(ATTTGAATAACAGAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-955	chr10	95846955	95847155	+	1.19563	NA	Intergenic	L1MB3|LINE|L1	-93608	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding	0.015000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-137	chr11	28048484	28048684	+	1.19563	NA	Intergenic	Intergenic	535740	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3275	chr16	64072629	64072829	+	1.19563	NA	Intergenic	Intergenic	-208554	NM_010140	13837	Mm.1977	NM_010140	ENSMUSG00000052504	Epha3	AW492086|Cek4|EK4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5570	chr4	82985128	82985328	+	1.19563	NA	intron (NM_177863, intron 14 of 35)	intron (NM_177863, intron 14 of 35)	35874	NR_154662	329872	Mm.242337	NM_177863	ENSMUSG00000059049	Frem1	BC037594|D430009N09|D630008K06|crf11|eye<m02Jus>|eyes2|heb|qbrick	Fras1 related extracellular matrix protein 1	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-587	chr1	180072315	180072515	+	1.19563	NA	exon (NM_001359547, exon 11 of 39)	exon (NM_001359547, exon 11 of 39)	111326	NM_001033285	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3453	chr17	28503990	28504190	+	1.19563	NA	Intergenic	Intergenic	-17941	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4931	chr3	47429655	47429855	+	1.19563	NA	Intergenic	Intergenic	-528973	NR_105800	102465199		NR_105800	ENSMUSG00000098417	Mir6379	Gm27730|mmu-mir-6379	microRNA 6379	ncRNA	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3834	chr18	47475366	47475566	+	1.19563	NA	Intergenic	Intergenic	22798	NR_033453	77668	Mm.98433	NR_033453	ENSMUSG00000117602	9130209A04Rik	-	RIKEN cDNA 9130209A04 gene	ncRNA	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-731	chr10	23226936	23227136	+	1.19563	NA	intron (NM_001347372, intron 2 of 18)	intron (NM_001347372, intron 2 of 18)	122854	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4545	chr2	116938964	116939164	+	1.19563	NA	Intergenic	MER77B|LTR|ERVL	38912	NR_040336	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4384	chr2	70816722	70816922	+	1.19563	NA	intron (NR_156421, intron 1 of 6)	MIR|SINE|MIR	7982	NM_001362963	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7467	chr8	118433602	118433802	+	1.19563	NA	intron (NM_019707, intron 1 of 13)	MLT1J1|LTR|ERVL-MaLR	150091	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding	0.005000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3089	chr16	13049294	13049494	+	1.19563	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-60342	NM_015769	50505	Mm.287837	NM_015769	ENSMUSG00000022545	Ercc4	AI606920|Xpf	excision repair cross-complementing rodent repair deficiency, complementation group 4	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4958	chr3	57037611	57037811	+	1.19563	NA	Intergenic	Intergenic	264277	NM_001355130	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5415	chr4	33486021	33486221	+	1.19563	NA	intron (NM_001305273, intron 14 of 15)	Lx6|LINE|L1	48040	NR_106198	102465904		NR_106198	ENSMUSG00000098310	Mir8118	Gm27954|mmu-mir-8118	microRNA 8118	ncRNA	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6579	chr6	89469755	89469955	+	1.19563	NA	intron (NM_025351, intron 4 of 7)	intron (NM_025351, intron 4 of 7)	-107242	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding	0.000000	0.407960			-49(ATCTGCATAAGTAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4949	chr3	53218995	53219195	+	1.19563	NA	intron (NM_175386, intron 2 of 3)	intron (NM_175386, intron 2 of 3)	177548	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968|Lhfpl6	lipoma HMGIC fusion partner	protein-coding	0.010000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7369	chr8	91509971	91510171	+	1.19563	NA	intron (NM_011936, intron 7 of 8)	intron (NM_011936, intron 7 of 8)	196546	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5831	chr5	13177254	13177454	+	1.19563	NA	Intergenic	Lx|LINE|L1	-219430	NM_001243072	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1718	chr12	70252580	70252780	+	1.19563	NA	intron (NM_001110202, intron 7 of 11)	intron (NM_001110202, intron 7 of 11)	24839	NR_045174	414124	Mm.416164	NR_045174	ENSMUSG00000085298	F730035M05Rik	-	RIKEN cDNA F730035M05 gene	ncRNA	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7206	chr8	36828812	36829012	+	1.19563	NA	intron (NM_001194940, intron 4 of 17)	intron (NM_001194940, intron 4 of 17)	-95858	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-689	chr10	8752240	8752440	+	1.19563	NA	intron (NM_175155, intron 9 of 19)	intron (NM_175155, intron 9 of 19)	133730	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4214	chr2	23077337	23077537	+	1.19563	NA	intron (NM_001355639, intron 3 of 13)	B2_Mm2|SINE|B2	8365	NM_001355642	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5339	chr4	9910338	9910538	+	1.19563	NA	Intergenic	Intergenic	6959	NR_004448	74662	Mm.483401	NR_004448	ENSMUSG00000082843	4930448K20Rik	1700009K09Rik	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6318	chr6	15201931	15202131	+	1.19563	NA	intron (NM_212435, intron 2 of 16)	intron (NM_212435, intron 2 of 16)	16525	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5354	chr4	14082127	14082327	+	1.19563	NA	Intergenic	Intergenic	209082	NR_131155	100040030	Mm.366499	NR_131155		Gm2560	-	predicted gene 2560	ncRNA	0.005000	0.333333			-99(CCATTTTCATGCAATT,+,0.00),21(CTTTTGTTATTCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-881	chr10	71448410	71448610	+	1.19563	NA	Intergenic	Intergenic	100747	NM_001347191	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding	0.010000	0.487562			34(ATTTGCATACGAAGGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4566	chr2	122011490	122011690	+	1.19563	NA	3' UTR (NM_001290992, exon 13 of 13)	3' UTR (NM_001290992, exon 13 of 13)	-16990	NM_144545	78655	Mm.458184	NM_144545	ENSMUSG00000027236	Eif3j1	1810016I04Rik|2700079K05Rik|AA409117|AA409446|C78575|Eif3j|Eif3j-1|Eif3j-2|Eif3j2|Eif3s1|eIF-3-alpha-A|eIF-3-alpha-B|eIF3-alpha|eIF3-p35|eIF3j-A|eIF3j-B	eukaryotic translation initiation factor 3, subunit J1	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5122	chr3	110950348	110950548	+	1.19563	NA	Intergenic	Intergenic	-699449	NM_178891	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0.010000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6421	chr6	43594309	43594509	+	1.19563	NA	intron (NM_001311111, intron 3 of 7)	L1_Mur2|LINE|L1	71869	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2227	chr13	96431861	96432061	+	1.19523	NA	intron (NM_001369169, intron 10 of 14)	intron (NM_001369169, intron 10 of 14)	39199	NM_001042714	271144	Mm.470057	NM_001042714	ENSMUSG00000047117	Ankdd1b	9330128J19Rik	ankyrin repeat and death domain containing 1B	protein-coding	0.010000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-891	chr9	104361661	104361861	+	1.19523	NA	Intergenic	Intergenic	-24039	NM_019807	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding	0.020000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1807	chr12	89414757	89414957	+	1.19523	NA	intron (NM_172544, intron 8 of 19)	intron (NM_172544, intron 8 of 19)	-397626	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2126	chr13	70044351	70044551	+	1.19523	NA	intron (NR_131156, intron 2 of 2)	intron (NR_131156, intron 2 of 2)	-16103	NR_045965	74280	Mm.273343	NR_045965	ENSMUSG00000099639	1700084F23Rik	1700003E18Rik|4930589D02Rik	RIKEN cDNA 1700084F23 gene	ncRNA	0.000000	0.467662			-21(CTTCTCTCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3654	chr17	88498370	88498570	+	1.19523	NA	Intergenic	Intergenic	-31654	NM_028658	73825	Mm.271817	NM_028658	ENSMUSG00000034709	Ppp1r21	1110018J12Rik|AI426045|AW550781|Ccdc128|Klraq1	protein phosphatase 1, regulatory subunit 21	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3228	chr16	51385478	51385678	+	1.19523	NA	Intergenic	Intergenic	601709	NR_153657	629091	Mm.364775	NR_153657		Gm29686	-	predicted gene, 29686	ncRNA	0.000000	0.388060	50(AATGCAAAATTTATG,+,0.00),50(AATGCAAAATTTATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7861	chr9	104361692	104361892	+	1.19523	NA	Intergenic	Intergenic	-24070	NM_019807	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding	0.020000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4713	chr2	147065694	147065894	+	1.19523	NA	intron (NM_011917, intron 27 of 29)	intron (NM_011917, intron 27 of 29)	19551	NM_023504	228731	Mm.315498	NM_023504	ENSMUSG00000054160	Nkx2-4	1700001P03Rik|Nkx-2.4|tinman	NK2 homeobox 4	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7860	chr9	104255741	104255941	+	1.19523	NA	intron (NM_001163026, intron 1 of 55)	intron (NM_001163026, intron 1 of 55)	7089	NM_001163026	235567	Mm.217256	NM_001163026	ENSMUSG00000032560	Dnajc13	D030002L11Rik|Gm1124|RME-8|Rme8|mKIAA0678	DnaJ heat shock protein family (Hsp40) member C13	protein-coding	0.010000	0.402985			51(TTTTAATCATGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6825	chr7	39867656	39867856	+	1.19523	NA	Intergenic	PB1D7|SINE|Alu	349990	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3873	chr18	56753642	56753842	+	1.19523	NA	TTS (NM_010721)	TTS (NM_010721)	45929	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3865	chr18	54667730	54667930	+	1.19523	NA	Intergenic	Intergenic	56086	NR_045400	328957	Mm.402781	NR_045400	ENSMUSG00000118154	9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4855	chr3	14181284	14181484	+	1.19523	NA	3' UTR (NM_001163328, exon 9 of 9)	3' UTR (NM_001163328, exon 9 of 9)	-181733	NR_033591	622229	Mm.486084	NR_033591		Gm6300	EG622229	solute carrier family 7 (cationic amino acid transporter, y+ system), member pseudogene	pseudo	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4442	chr2	87536576	87536776	+	1.19523	NA	Intergenic	Intergenic	4641	NM_206823	110511	Mm.424751	NM_206823	ENSMUSG00000061520	Olfr153	GA_x6K02T2Q125-49033418-49034341|MOR177-5|Olfr4-2|V5	olfactory receptor 153	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-615	chr1	186562025	186562225	+	1.19523	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-3444	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7694	chr9	65178834	65179034	+	1.19523	NA	intron (NM_008988, intron 5 of 13)	intron (NM_008988, intron 5 of 13)	-35756	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding	0.025000	0.611940			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2426	chr14	31743463	31743663	+	1.19523	NA	intron (NM_001024604, intron 7 of 27)	intron (NM_001024604, intron 7 of 27)	86852	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1897	chr12	116479217	116479417	+	1.19523	NA	Intergenic	RLTR25B|LTR|ERVK	-6403	NM_011215	19276	Mm.206054	NM_011215	ENSMUSG00000056553	Ptprn2	4930425H11Rik|IA2beta|PTP-NP|Phol|mKIAA0387|phogrin	protein tyrosine phosphatase, receptor type, N polypeptide 2	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3048	chr15	96364198	96364398	+	1.19523	NA	intron (NM_175251, intron 11 of 20)	intron (NM_175251, intron 11 of 20)	76776	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|BAF200|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding	0.025000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3583	chr17	71489885	71490085	+	1.19523	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-14642	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding	0.010000	0.507463			60(CCATACCTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7584	chr9	30013249	30013449	+	1.19523	NA	Intergenic	Intergenic	-50080	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-639	chr1	191242549	191242749	+	1.19484	NA	Intergenic	Intergenic	18195	NR_151547	100504360	Mm.16927	NM_001033188		D730003I15Rik	AU020850	RIKEN cDNA D730003I15 gene	ncRNA	0.020000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-549	chr3	6575427	6575627	+	1.19484	NA	Intergenic	L1_Mus4|LINE|L1	44916	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding	0.010000	0.348259			-61(ATTAGCATAAAACAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4826	chr3	6575601	6575801	+	1.19484	NA	Intergenic	L1_Mus4|LINE|L1	44742	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6738	chr6	137541385	137541585	+	1.19484	NA	intron (NM_001271588, intron 1 of 20)	intron (NM_001271588, intron 1 of 20)	-21590	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0.015000	0.527363			85(ATAAGCAACAGAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1855	chr12	102065076	102065276	+	1.19398	NA	Intergenic	L1MA4|LINE|L1	-63551	NM_172152	238384	Mm.312448	NM_172152	ENSMUSG00000041771	Slc24a4	A930002M03Rik|AW492432|NCKX4	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7403	chr8	100145057	100145257	+	1.19398	NA	Intergenic	Intergenic	728483	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5191	chr3	131139223	131139423	+	1.19398	NA	intron (NM_010703, intron 3 of 11)	intron (NM_010703, intron 3 of 11)	26532	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding	0.010000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4410	chr2	77048797	77048997	+	1.19342	NA	intron (NM_001025576, intron 12 of 23)	intron (NM_001025576, intron 12 of 23)	-66350	NM_011652	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6725	chr6	135076518	135076718	+	1.19342	NA	intron (NM_181444, intron 1 of 3)	RMER13B|LTR|ERVK	10956	NM_181444	232431	Mm.23575	NM_181444	ENSMUSG00000046733	Gprc5a	Rai3|Raig1	G protein-coupled receptor, family C, group 5, member A	protein-coding	0.000000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-118	chr10	121701370	121701570	+	1.19342	NA	Intergenic	Intergenic	-38460	NM_001359720	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6259	chr5	149277712	149277912	+	1.19342	NA	intron (NM_001308462, intron 2 of 3)	intron (NM_001308462, intron 2 of 3)	12808	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6056	chr5	81960681	81960881	+	1.19342	NA	Intergenic	Intergenic	163932	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7245	chr8	50425520	50425720	+	1.19342	NA	Intergenic	Intergenic	57508	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA	0.015000	0.402985		-59(AATGCAAATGGATG,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-495	chr2	77048783	77048983	+	1.19342	NA	intron (NM_001025576, intron 12 of 23)	intron (NM_001025576, intron 12 of 23)	-66336	NM_011652	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6512	chr6	70103951	70104151	+	1.19342	NA	Intergenic	RLTR13G|LTR|ERVK	688124	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1495	chr11	118202669	118202869	+	1.19342	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	9973	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding	0.040000	0.601990			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4484	chr2	103405306	103405506	+	1.19342	NA	Intergenic	L2a|LINE|L2	-6692	NM_001145813	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4129	chr19	57606348	57606548	+	1.19342	NA	Intergenic	Intergenic	-4586	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding	0.030000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-172	chr11	114345999	114346199	+	1.19274	NA	Intergenic	Intergenic	102761	NR_027643	319819	Mm.50754	NM_177008	ENSMUSG00000062391	4932435O22Rik	-	RIKEN cDNA 4932435O22 gene	ncRNA	0.010000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-333	chr15	13061992	13062192	+	1.19194	NA	intron (NM_007666, intron 3 of 11)	intron (NM_007666, intron 3 of 11)	111583	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.010000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-682	chr5	71923414	71923614	+	1.19194	NA	intron (NM_001370968, intron 5 of 9)	intron (NM_001370968, intron 5 of 9)	223582	NM_008069	14400	Mm.38567	NM_008069	ENSMUSG00000029212	Gabrb1	AW061132|B230208N19Rik|Gabrb-1	gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	protein-coding	0.015000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-403	chr17	62495164	62495364	+	1.19194	NA	Intergenic	Intergenic	386053	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0.010000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-417	chr17	91339255	91339455	+	1.19194	NA	Intergenic	BGLII|LTR|ERVK	-246553	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.005000	0.462687			-54(ATTTGTAAAATAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6020	chr5	71923335	71923535	+	1.19194	NA	intron (NM_001370968, intron 5 of 9)	intron (NM_001370968, intron 5 of 9)	223503	NM_008069	14400	Mm.38567	NM_008069	ENSMUSG00000029212	Gabrb1	AW061132|B230208N19Rik|Gabrb-1	gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	protein-coding	0.010000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2802	chr15	13061976	13062176	+	1.19194	NA	intron (NM_007666, intron 3 of 11)	intron (NM_007666, intron 3 of 11)	111599	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-344	chr15	67438170	67438370	+	1.19172	NA	Intergenic	Intergenic	211501	NR_045140	69334	Mm.63770	NR_045140	ENSMUSG00000102069	1700012I11Rik	-	RIKEN cDNA 1700012I11 gene	ncRNA	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3407	chr17	5065998	5066198	+	1.19172	NA	intron (NM_001085355, intron 2 of 19)	intron (NM_001085355, intron 2 of 19)	71024	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|BAF250B|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding	0.015000	0.447761			22(ATCTACAAGAGAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1977	chr13	20601114	20601314	+	1.19172	NA	intron (NM_080288, intron 21 of 21)	intron (NM_080288, intron 21 of 21)	128224	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.010000	0.348259			-61(TTTTTCGCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3860	chr18	54037269	54037469	+	1.19172	NA	Intergenic	Intergenic	175256	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1018	chr10	108799489	108799689	+	1.19172	NA	intron (NM_001252342, intron 3 of 10)	intron (NM_001252342, intron 3 of 10)	-99429	NM_203660	368203	Mm.452758	NM_203660	ENSMUSG00000112039	Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3894	chr18	62708037	62708237	+	1.19172	NA	intron (NM_001168423, intron 1 of 4)	intron (NM_001168423, intron 1 of 4)	33250	NM_001168423	100038417	Mm.387557	NM_001168423	ENSMUSG00000073551	Spink13	Gm10534|Spink5l3	serine peptidase inhibitor, Kazal type 13	protein-coding	0.010000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3463	chr17	30420449	30420649	+	1.19172	NA	intron (NM_172618, intron 6 of 11)	intron (NM_172618, intron 6 of 11)	-24369	NR_030688	623169	Mm.440508	NR_030688		Gm6402	EG623169	ribosomal protein S17 pseudogene	pseudo	0.015000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6082	chr5	89919847	89920047	+	1.19172	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-36613	NM_177872	330119	Mm.133062	NM_177872	ENSMUSG00000043635	Adamts3	1100001H14Rik|6330442E02Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 3	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7094	chr7	132117707	132117907	+	1.19172	NA	intron (NM_018867, intron 3 of 13)	intron (NM_018867, intron 3 of 13)	36934	NM_018867	55987	Mm.471654	NM_018867	ENSMUSG00000030862	Cpxm2	4632435C11Rik|CPX-2|Cpx2	carboxypeptidase X 2 (M14 family)	protein-coding	0.010000	0.393035			-35(ATTTCTAAGATAATAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-31	chr1	113533636	113533836	+	1.19172	NA	Intergenic	RLTR17|LTR|ERVK	-1116818	NR_157044	102635484		NR_157044		Gm32810	Gm18406	predicted gene, 32810	ncRNA	0.005000	0.407960			25(ATTACCATCAAAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3053	chr15	97498865	97499065	+	1.19172	NA	Intergenic	PB1D10|SINE|Alu	206857	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8127	chrX	156097998	156098198	+	1.19172	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-441385	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo	0.010000	0.427861			-66(ATTTGAATACGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2959	chr15	62366958	62367158	+	1.19172	NA	Intergenic	Intergenic	-147607	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo	0.010000	0.343284			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-491	chr2	68411281	68411481	+	1.19114	NA	intron (NM_016866, intron 1 of 17)	MIRb|SINE|MIR	60600	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding	0.025000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7736	chr9	75673321	75673521	+	1.19114	NA	intron (NM_009130, intron 6 of 11)	ORR1C1|LTR|ERVL-MaLR	10635	NM_009130	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding	0.000000	0.437811			-22(GTTTGAATCAGAATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-806	chr7	112883804	112884004	+	1.18998	NA	intron (NM_001166584, intron 11 of 13)	intron (NM_001166584, intron 11 of 13)	-70058	NM_175279	78748	Mm.349943	NM_175279	ENSMUSG00000098132	Rassf10	4632411J06Rik	Ras association (RalGDS/AF-6) domain family (N-terminal) member 10	protein-coding	0.015000	0.646766			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7308	chr8	71913841	71914041	+	1.18998	NA	exon (NM_001166645, exon 3 of 3)	exon (NM_001166645, exon 3 of 3)	5335	NM_001166645	382019	Mm.251482	NM_001166645	ENSMUSG00000089857	Zfp882	Gm15468	zinc finger protein 882	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3317	chr16	73341867	73342067	+	1.18835	NA	Intergenic	Intergenic	678818	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.000000	0.318408			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-741	chr6	44900368	44900568	+	1.18835	NA	Intergenic	Intergenic	-159593	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.000000	0.393035			-28(CCATTTCAATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5388	chr4	25779121	25779321	+	1.18823	NA	intron (NM_010243, intron 1 of 2)	intron (NM_010243, intron 1 of 2)	20782	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-611	chr4	25779138	25779338	+	1.18823	NA	intron (NM_010243, intron 1 of 2)	intron (NM_010243, intron 1 of 2)	20765	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.005000	0.393035			73(ACATGGTCATGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2719	chr14	119122374	119122574	+	1.18823	NA	Intergenic	Intergenic	-15791	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding	0.005000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-370	chr16	44787007	44787207	+	1.18823	NA	intron (NM_021325, intron 1 of 6)	intron (NM_021325, intron 1 of 6)	21371	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7420	chr8	103122431	103122631	+	1.18823	NA	Intergenic	Intergenic	225003	NR_036588	69794	Mm.396139	NR_036588	ENSMUSG00000110340	1600027J07Rik	-	RIKEN cDNA 1600027J07 gene	ncRNA	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8119	chrX	152019292	152019492	+	1.18823	NA	intron (NM_019710, intron 1 of 24)	B4A|SINE|B4	2964	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2621	chr14	89651395	89651595	+	1.18766	NA	Intergenic	Intergenic	-244729	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	poly(A)-binding protein, cytoplasmic pseudogene	pseudo	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-472	chr1	153860937	153861137	+	1.18766	NA	Intergenic	Intergenic	-9842	NM_178243	240817	Mm.439405	NM_178243	ENSMUSG00000045968	Teddm2	5830403L16Rik|AJ554213|Me9|e92	transmembrane epididymal family member 2	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4884	chr3	27607444	27607644	+	1.18766	NA	intron (NM_001356953, intron 4 of 26)	intron (NM_001356953, intron 4 of 26)	-22549	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA	0.015000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2807	chr15	13455939	13456139	+	1.18766	NA	Intergenic	Intergenic	-282364	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6372	chr6	29064193	29064393	+	1.18766	NA	intron (NM_008493, intron 1 of 2)	L1MA4|LINE|L1	4072	NM_008493	16846	Mm.277072	NM_008493	ENSMUSG00000059201	Lep	ob|obese	leptin	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4520	chr2	110785222	110785422	+	1.18766	NA	intron (NM_001355244, intron 2 of 23)	intron (NM_001355244, intron 2 of 23)	54737	NM_001355244	228432	Mm.483325	NM_001081556	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding	0.000000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1157	chr11	11025533	11025733	+	1.18766	NA	Intergenic	Intergenic	-88383	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4940	chr3	51314927	51315127	+	1.18766	NA	intron (NM_001356358, intron 3 of 10)	intron (NM_001356358, intron 3 of 10)	25617	NM_001291059	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3284	chr16	65391315	65391515	+	1.18766	NA	Intergenic	Intergenic	-129097	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7618	chr9	39602614	39602814	+	1.18654	NA	intron (NM_178737, intron 2 of 19)	intron (NM_178737, intron 2 of 19)	938	NM_001199556	244810	Mm.208855	NM_178737	ENSMUSG00000038112	AW551984	3222402N16	expressed sequence AW551984	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1482	chr11	114346316	114346516	+	1.18654	NA	Intergenic	Intergenic	102444	NR_027643	319819	Mm.50754	NM_177008	ENSMUSG00000062391	4932435O22Rik	-	RIKEN cDNA 4932435O22 gene	ncRNA	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6297	chr6	8413271	8413471	+	1.18654	NA	intron (NM_001302353, intron 4 of 4)	intron (NM_001302353, intron 4 of 4)	95790	NR_040452	320312	Mm.374890	NR_040452	ENSMUSG00000087305	A430035B10Rik	2810488G03Rik	RIKEN cDNA A430035B10 gene	ncRNA	0.010000	0.358209	-61(AATACATTATTCAGG,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-835	chr8	71913928	71914128	+	1.18404	NA	exon (NM_001166645, exon 3 of 3)	exon (NM_001166645, exon 3 of 3)	5422	NM_001166645	382019	Mm.251482	NM_001166645	ENSMUSG00000089857	Zfp882	Gm15468	zinc finger protein 882	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-899	chrX	57663805	57664005	+	1.18344	NA	Intergenic	Intergenic	-160148	NM_001033360	245424	Mm.336070	NM_001033360	ENSMUSG00000036357	Gpr101	GPCR6|Gm365	G protein-coupled receptor 101	protein-coding	0.010000	0.358209			-78(GTCTGCATAAAAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4496	chr2	106762227	106762427	+	1.18344	NA	intron (NM_001356554, intron 3 of 6)	intron (NM_001356554, intron 3 of 6)	66726	NM_029837	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1950	chr13	12423034	12423234	+	1.18331	NA	intron (NM_144835, intron 28 of 44)	RMER1B|Other|Other	27759	NM_144835	217995	Mm.171186	NM_144835	ENSMUSG00000050244	Heatr1	AA517551|B130016L12Rik|BC019693	HEAT repeat containing 1	protein-coding	0.015000	0.477612			67(TCTGTGTCATGGAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3509	chr17	50545479	50545679	+	1.18331	NA	intron (NM_013880, intron 1 of 5)	Lx7|LINE|L1	36032	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7290	chr8	63770190	63770390	+	1.18331	NA	Intergenic	Intergenic	181880	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgo2b	EG244495|Gm4975|Sgol2b	shugoshin 2B	protein-coding	0.005000	0.318408		87(CATACATATTCAGG,+,0.00),87(CATACATATTCAGG,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-398	chr17	50545485	50545685	+	1.18331	NA	intron (NM_013880, intron 1 of 5)	Lx7|LINE|L1	36038	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding	0.005000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-717	chr5	146878204	146878404	+	1.18331	NA	Intergenic	Intergenic	33233	NM_026864	68895	Mm.266978	NM_026864	ENSMUSG00000029641	Rasl11a	1110065D03Rik|AI852031	RAS-like, family 11, member A	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3293	chr16	67210545	67210745	+	1.18331	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	410263	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1926	chr13	4667227	4667427	+	1.18186	NA	Intergenic	Intergenic	-58163	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding	0.005000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-386	chr16	87747914	87748114	+	1.18186	NA	Intergenic	Intergenic	49060	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding	0.020000	0.402985			24(ATCTATATGACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4412	chr2	77263434	77263634	+	1.18186	NA	intron (NM_175465, intron 1 of 17)	MTE2b|LTR|ERVL-MaLR	17058	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4619	chr2	132474915	132475115	+	1.18186	NA	Intergenic	Intergenic	-15713	NR_028286	70371	Mm.394667	NR_028286	ENSMUSG00000086379	1700026D11Rik	-	RIKEN cDNA 1700026D11 gene	ncRNA	0.015000	0.402985		8(TATAAATATTGATT,+,0.00),8(TATAAATATTGATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6531	chr6	73180178	73180378	+	1.18186	NA	intron (NM_001164669, intron 12 of 76)	Lx5c|LINE|L1	41353	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding	0.015000	0.373134			79(ATTTGCAAGAAAACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2177	chr13	83633897	83634097	+	1.18186	NA	intron (NM_001347567, intron 5 of 10)	intron (NM_001347567, intron 5 of 10)	60390	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1368	chr11	78007343	78007543	+	1.18186	NA	intron (NM_174852, intron 3 of 14)	intron (NM_174852, intron 3 of 14)	24627	NM_174852	268448	Mm.274329	NM_174852	ENSMUSG00000037791	Phf12	2410142K10Rik|F630045O13|PF1|mKIAA1523	PHD finger protein 12	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3589	chr17	74920189	74920389	+	1.18186	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-85240	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding	0.010000	0.462687			9(GCATTCTAATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1601	chr12	35747583	35747783	+	1.18186	NA	Intergenic	Intergenic	-52565	NR_045050	71581	Mm.100110	NR_045050	ENSMUSG00000113985	9130015A21Rik	100043575|Gm4527	RIKEN cDNA 9130015A21 gene	ncRNA	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5662	chr4	104018736	104018936	+	1.18186	NA	intron (NM_001369049, intron 2 of 19)	intron (NM_001369049, intron 2 of 19)	-348702	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.005000	0.427861	26(CATGAATTATCTATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3193	chr16	43121415	43121615	+	1.18186	NA	intron (NM_001285805, intron 2 of 10)	intron (NM_001285805, intron 2 of 10)	-125769	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|J20|ODA-8S|Oda8|Tg(PDGFB-APPSwInd)20Lms|Zfp288	zinc finger and BTB domain containing 20	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-358	chr1	127568888	127569088	+	1.18186	NA	intron (NM_028135, intron 2 of 7)	RMER17B|LTR|ERVK	109033	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|A-cre|Act-Cre|SV31|Tg(ACTB-cre)2Mrt|actin-cre|cre<actin>	transmembrane protein 163	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6367	chr6	27774767	27774967	+	1.18186	NA	intron (NM_008174, intron 3 of 10)	intron (NM_008174, intron 3 of 10)	161883	NR_030420	735266		NR_030420	ENSMUSG00000076067	Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	ncRNA	0.000000	0.273632			-17(ATTTAAACAAGAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1301	chr11	58145555	58145755	+	1.18186	NA	intron (NM_172558, intron 14 of 27)	intron (NM_172558, intron 14 of 27)	22884	NM_001166669	216766	Mm.275349	NM_172558	ENSMUSG00000037275	Gemin5	AA407055|AA407208|AI451603|BB194447|C330013N08	gem nuclear organelle associated protein 5	protein-coding	0.005000	0.457711			12(GCATTCCTATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-490	chr1	159299823	159300023	+	1.18186	NA	intron (NM_011931, intron 11 of 19)	B3A|SINE|B2	6150	NR_144489	100846986		NR_144489		Pou5f1-rs1	Gm21053|Oct4P2|Otf-3rs|Otf3-rs1|Otf3a	POU domain, class 5, transcription factor 1, related sequence 1	pseudo	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-801	chr10	44685325	44685525	+	1.18186	NA	Intergenic	Intergenic	-226677	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding	0.005000	0.502488			-15(ACTTAGGCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-484	chr1	157307690	157307890	+	1.18186	NA	intron (NM_177644, intron 1 of 17)	intron (NM_177644, intron 1 of 17)	-104562	NR_027984	69953	Mm.286863	NM_027274	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	ncRNA	0.005000	0.313433			-80(GTTTGAATCACAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3073	chr16	8935862	8936062	+	1.18186	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	105862	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1620	chr12	40614681	40614881	+	1.18186	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	168728	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding	0.005000	0.303483			45(GTTAAAATGATAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-373	chr1	128566916	128567116	+	1.18186	NA	Intergenic	B3A|SINE|B2	25283	NM_001356509	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|CXC-R4|CXCR-4|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3714	chr18	14029481	14029681	+	1.18186	NA	Intergenic	Intergenic	-56848	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5149	chr3	119415182	119415382	+	1.18186	NA	intron (NM_170778, intron 21 of 22)	intron (NM_170778, intron 21 of 22)	368106	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4837	chr3	10005980	10006180	+	1.18186	NA	Intergenic	B1F1|SINE|Alu	-6505	NM_001272098	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding	0.030000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7267	chr8	57427672	57427872	+	1.18180	NA	Intergenic	L1MB2|LINE|L1	-28151	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5998	chr5	65683929	65684129	+	1.18180	NA	intron (NM_001081321, intron 2 of 32)	intron (NM_001081321, intron 2 of 32)	14207	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|B230308N11Rik|E230024D05Rik	PDS5 cohesin associated factor A	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5523	chr4	67783849	67784049	+	1.18180	NA	Intergenic	Intergenic	538012	NR_151548	102633975		NR_151548		Gm12911	-	predicted gene 12911	ncRNA	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7897	chr9	116000268	116000468	+	1.18180	NA	intron (NM_028638, intron 11 of 14)	intron (NM_028638, intron 11 of 14)	90913	NM_028638	73748	Mm.485018	NM_028638	ENSMUSG00000056880	Gadl1	1110027M19Rik|ADC|CSADC	glutamate decarboxylase-like 1	protein-coding	0.045000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7714	chr9	70328433	70328633	+	1.18180	NA	intron (NM_181072, intron 9 of 27)	intron (NM_181072, intron 9 of 27)	77220	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8026	chrX	93863361	93863561	+	1.18180	NA	Intergenic	Intergenic	-31311	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	pyruvate dehydrogenase kinase, isoenzyme 3	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6380	chr6	31830805	31831005	+	1.18180	NA	Intergenic	Intergenic	-164774	NR_152155	434003	Mm.332979	NR_152155	ENSMUSG00000084973	Gm13848	-	predicted gene 13848	ncRNA	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1003	chr10	106975818	106976018	+	1.18180	NA	intron (NM_198636, intron 9 of 10)	intron (NM_198636, intron 9 of 10)	147719	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding	0.005000	0.393035			-76(TCATGTGCATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1829	chr12	96124528	96124728	+	1.18180	NA	Intergenic	Intergenic	-77406	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo	0.005000	0.353234	14(TATAAATAATGCATG,+,0.00),14(TATAAATAATGCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1153	chr11	8618530	8618730	+	1.18180	NA	intron (NM_001083587, intron 1 of 30)	L1MEc|LINE|L1	45905	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding	0.025000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5805	chr4	156005664	156005864	+	1.18180	NA	intron (NM_001302467, intron 5 of 7)	ORR1D2-int|LTR|ERVL-MaLR	-7931	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding	0.020000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6501	chr6	65796700	65796900	+	1.18180	NA	intron (NM_029549, intron 2 of 10)	RLTR23|LTR|ERV1	17838	NM_027547	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding	0.010000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7435	chr8	107952982	107953182	+	1.18180	NA	Intergenic	Intergenic	-364600	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding	0.005000	0.308458			-71(TTTTAAATGATAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4307	chr2	53359511	53359711	+	1.18180	NA	Intergenic	Intergenic	167527	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1555	chr12	15900476	15900676	+	1.18180	NA	Intergenic	Intergenic	-83791	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4279	chr2	44573820	44574020	+	1.18180	NA	intron (NM_001362986, intron 8 of 10)	intron (NM_001362986, intron 8 of 10)	287702	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding	0.000000	0.333333			64(CTTTTGCTTTGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7052	chr7	122079105	122079305	+	1.18180	NA	3' UTR (NM_138589, exon 7 of 7)	3' UTR (NM_138589, exon 7 of 7)	12007	NM_138589	28018	Mm.282122	NM_138589	ENSMUSG00000030870	Ubfd1	AI467302|D7Wsu105e|D7Wsu128e|Ubph	ubiquitin family domain containing 1	protein-coding	0.005000	0.353234			-95(TCTTTGGTATTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7222	chr8	41177091	41177291	+	1.18180	NA	Intergenic	Intergenic	37965	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding	0.000000	0.328358	65(TGTGAATAATTCATT,+,0.00),65(TGTGAATAATTCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3877	chr18	57384917	57385117	+	1.18180	NA	intron (NM_028447, intron 8 of 8)	B1_Mur1|SINE|Alu	-20398	NR_152223	100503007	Mm.238087	NR_152223		Gm19500	-	predicted gene, 19500	ncRNA	0.010000	0.442786			19(ATCAAAATAACAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3203	chr16	45057851	45058051	+	1.18180	NA	Intergenic	Intergenic	-36060	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding	0.010000	0.402985			36(ATTTGAATGACATAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2637	chr14	97053653	97053853	+	1.18180	NA	Intergenic	Intergenic	-534719	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2142	chr13	73488329	73488529	+	1.18180	NA	intron (NM_145376, intron 2 of 13)	T-rich|Low_complexity|Low_complexity	21198	NM_001368681	210992	Mm.284649	NM_145376	ENSMUSG00000021608	Lpcat1	2900035H07Rik|Aytl2|BB137372|BC005662|C87117|LPCAT|LPCAT-1|lysoPAFAT|mLPCAT1|rd11	lysophosphatidylcholine acyltransferase 1	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-319	chr1	113282097	113282297	+	1.18180	NA	Intergenic	RMER15|LTR|ERVL	-865279	NR_157044	102635484		NR_157044		Gm32810	Gm18406	predicted gene, 32810	ncRNA	0.010000	0.442786			-11(TCATAGTTCTGTAAAT,+,0.00),23(CATTTGTTTTTCAATT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5674	chr4	105670347	105670547	+	1.18180	NA	Intergenic	Intergenic	513100	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|PRG-2|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding	0.010000	0.338308	-65(TATAAATAAGGCATG,+,0.00),-65(TATAAATAAGGCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3552	chr17	63075037	63075237	+	1.18180	NA	intron (NM_015794, intron 8 of 8)	intron (NM_015794, intron 8 of 8)	-193820	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7647	chr9	49130632	49130832	+	1.18180	NA	Intergenic	Intergenic	27953	NM_030709	80893	Mm.72799	NM_030709	ENSMUSG00000032268	Tmprss5	spinesin	transmembrane protease, serine 5 (spinesin)	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-966	chr10	97118474	97118674	+	1.18180	NA	Intergenic	Intergenic	82806	NR_045358	75301	Mm.108650	NR_045358	ENSMUSG00000111924	4930556N09Rik	-	RIKEN cDNA 4930556N09 gene	ncRNA	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5449	chr4	49016694	49016894	+	1.18180	NA	Intergenic	Lx7|LINE|L1	-42668	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	Plppr1	E130309F12Rik|Lppr1|PRG-3|mKIAA4247	phospholipid phosphatase related 1	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5399	chr4	28904719	28904919	+	1.18180	NA	intron (NM_001290434, intron 5 of 16)	intron (NM_001290434, intron 5 of 16)	91674	NM_001122889	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1944	chr13	9921145	9921345	+	1.18180	NA	intron (NM_033269, intron 4 of 4)	Lx8|LINE|L1	-155924	NM_144516	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-114	chr1	39512024	39512224	+	1.18180	NA	Intergenic	Intergenic	-23577	NM_028043	52846	Mm.259421	NM_028043	ENSMUSG00000003135	Cnot11	2410015L18Rik|C40|D1Bwg0212e	CCR4-NOT transcription complex, subunit 11	protein-coding	0.025000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5706	chr4	116881588	116881788	+	1.18180	NA	intron (NM_001029912, intron 1 of 13)	intron (NM_001029912, intron 1 of 13)	4286	NM_001029912	74464	Mm.218946	NM_001029912	ENSMUSG00000033948	Zswim5	4933426E21Rik|AI503093|mKIAA1511	zinc finger SWIM-type containing 5	protein-coding	0.010000	0.333333			47(TTTTACATAACAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3315	chr16	73280662	73280862	+	1.18180	NA	Intergenic	Intergenic	617613	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding	0.005000	0.393035			-45(ATTTGCAATAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2985	chr15	69641729	69641929	+	1.18180	NA	Intergenic	RLTR23|LTR|ERV1	-282404	NR_045071	100503580	Mm.404646	NR_045071	ENSMUSG00000116483	Gm19782	-	predicted gene, 19782	ncRNA	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-65	chr1	21919601	21919801	+	1.18180	NA	intron (NM_001160139, intron 1 of 14)	intron (NM_001160139, intron 1 of 14)	42241	NM_023872	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2908	chr15	49539393	49539593	+	1.18180	NA	Intergenic	Intergenic	-747504	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3079	chr16	11145990	11146190	+	1.18180	NA	intron (NM_145931, intron 17 of 22)	intron (NM_145931, intron 17 of 22)	-11558	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4117	chr19	49984629	49984829	+	1.18180	NA	Intergenic	RLTR41|LTR|ERV1	693917	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-112	chr1	38767868	38768068	+	1.18180	NA	Intergenic	Intergenic	68719	NM_001029878	381338	Mm.487137	NM_028403	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding	0.035000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-68	chr1	23394174	23394374	+	1.18180	NA	Intergenic	Intergenic	-11099	NM_001081079	70155	Mm.28013	NM_001081079	ENSMUSG00000026158	Ogfrl1	2210417C17Rik	opioid growth factor receptor-like 1	protein-coding	0.000000	0.323383			13(GTTTTGTTTTGCATTT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1270	chr11	44953463	44953663	+	1.18180	NA	intron (NM_001362579, intron 11 of 16)	intron (NM_001362579, intron 11 of 16)	163365	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-619	chr1	187482551	187482751	+	1.18180	NA	Intergenic	Intergenic	-126355	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6155	chr5	112835005	112835205	+	1.18180	NA	intron (NM_028901, intron 17 of 43)	intron (NM_028901, intron 17 of 43)	41813	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4472	chr2	101616012	101616212	+	1.18180	NA	intron (NM_001362688, intron 1 of 7)	intron (NM_001362688, intron 1 of 7)	4934	NM_001362687	68170	Mm.31263	NM_026592	ENSMUSG00000027165	B230118H07Rik	NWC	RIKEN cDNA B230118H07 gene	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6894	chr7	70239562	70239762	+	1.18180	NA	intron (NR_131145, intron 1 of 3)	RLTR13B1|LTR|ERVK	98160	NR_131145	624549	Mm.116344	NR_131144	ENSMUSG00000109097	Gm29683	Gm44536	predicted gene, 29683	ncRNA	0.015000	0.432836	-4(CATGAATAATGCAAT,+,0.00),-4(CATGAATAATGCAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6722	chr6	134515406	134515606	+	1.18180	NA	intron (NM_008514, intron 3 of 22)	RLTR12B|LTR|ERVK	51407	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8173	chrX	168775872	168776072	+	1.18180	NA	Intergenic	Intergenic	-19127	NM_009707	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding	0.020000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3743	chr18	22863627	22863827	+	1.18152	NA	intron (NM_001361223, intron 6 of 11)	intron (NM_001361223, intron 6 of 11)	174936	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding	0.000000	0.353234			-75(ATTTGCATGAGTCTGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-601	chr3	156305473	156305673	+	1.18152	NA	Intergenic	Intergenic	256114	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	ncRNA	0.005000	0.412935			-8(ATTTACAGGACAAGAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6792	chr7	12967316	12967516	+	1.18146	NA	intron (NM_001362140, intron 1 of 2)	intron (NM_001362140, intron 1 of 2)	1578	NM_001362140	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1455	chr11	108263443	108263643	+	1.18063	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	80345	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding	0.010000	0.532338			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-854	chr8	128237206	128237406	+	1.18063	NA	Intergenic	Intergenic	40919	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA	0.000000	0.378109			-85(TCTTGGTCATGCTAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4186	chr2	16534563	16534763	+	1.18001	NA	intron (NM_026162, intron 2 of 13)	intron (NM_026162, intron 2 of 13)	178359	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0.005000	0.353234			29(CCTTTGGTATGTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2712	chr14	117172656	117172856	+	1.18001	NA	intron (NM_001079844, intron 1 of 9)	intron (NM_001079844, intron 1 of 9)	247459	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding	0.005000	0.378109			-14(ATTATCATAAGAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5869	chr5	25296902	25297102	+	1.18001	NA	intron (NM_001081383, intron 43 of 58)	MER5A1|DNA|hAT-Charlie	50629	NM_001359890	231050	Mm.246718	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	polypeptide N-acetylgalactosaminyltransferase 11	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7408	chr8	100499677	100499877	+	1.18001	NA	Intergenic	Intergenic	1083103	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.388060		12(CATTAATAAGCATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7609	chr9	35291352	35291552	+	1.18001	NA	Intergenic	Intergenic	10347	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2430	chr14	32351251	32351451	+	1.18001	NA	Intergenic	MLTR11A|LTR|ERVK	29332	NM_001081130	239017	Mm.318302	NM_001081130	ENSMUSG00000021913	Ogdhl	-	oxoglutarate dehydrogenase-like	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5231	chr3	138841462	138841662	+	1.18001	NA	intron (NR_121195, intron 1 of 7)	intron (NR_121195, intron 1 of 7)	99354	NR_121195	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7883	chr9	112160964	112161164	+	1.18001	NA	3' UTR (NM_001177623, exon 10 of 10)	3' UTR (NM_001177623, exon 10 of 10)	24885	NM_001362009	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7692	chr9	64825874	64826074	+	1.18001	NA	intron (NM_001162917, intron 2 of 34)	L1ME2z|LINE|L1	14963	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding	0.000000	0.348259			-13(AAATTGTCATTAAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-519	chr1	165563343	165563543	+	1.18001	NA	intron (NM_173029, intron 26 of 33)	intron (NM_173029, intron 26 of 33)	71098	NM_001347128	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding	0.000000	0.333333			-10(CAATTATGTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4905	chr3	33142247	33142447	+	1.18001	NA	intron (NM_001163516, intron 1 of 12)	intron (NM_001163516, intron 1 of 12)	844	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding	0.035000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5049	chr3	85618133	85618333	+	1.18001	NA	intron (NM_144896, intron 8 of 12)	L1MC2|LINE|L1	44104	NM_144896	229487	Mm.52275	NM_144896	ENSMUSG00000028085	Gatb	9430026F02Rik|Pet112|Pet112l	glutamyl-tRNA(Gln) amidotransferase, subunit B	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6097	chr5	95997264	95997464	+	1.18001	NA	Intergenic	Intergenic	40425	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6202	chr5	132199142	132199342	+	1.18001	NA	intron (NM_001363480, intron 2 of 19)	MIR3|SINE|MIR	318973	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA	0.010000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1769	chr12	80865680	80865880	+	1.18001	NA	intron (NM_001242419, intron 3 of 6)	intron (NM_001242419, intron 3 of 6)	58667	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA	0.000000	0.328358			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-470	chr2	16534590	16534790	+	1.18001	NA	intron (NM_026162, intron 2 of 13)	intron (NM_026162, intron 2 of 13)	178386	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0.005000	0.348259			2(CCTTTGGTATGTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3078	chr16	11085955	11086155	+	1.18001	NA	intron (NM_134105, intron 1 of 4)	intron (NM_134105, intron 1 of 4)	1875	NM_134105	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding	0.000000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-540	chr2	159119347	159119547	+	1.18001	NA	Intergenic	Intergenic	324640	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4264	chr2	39459865	39460065	+	1.18001	NA	Intergenic	Intergenic	-233616	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik|Pp6C	protein phosphatase 6, catalytic subunit	protein-coding	0.000000	0.308458			-69(ATTTACAAAAAAGAAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-432	chr18	32992726	32992926	+	1.18001	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	53785	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1992	chr13	26124972	26125172	+	1.18001	NA	Intergenic	RLTR16B_MM|LTR|ERVK	-158756	NR_045062	100503530	Mm.86763	NR_045062	ENSMUSG00000086531	Gm11351	-	predicted gene 11351	ncRNA	0.010000	0.482587			-59(ATATGCACCACAAAGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-612	chr4	25798503	25798703	+	1.17987	NA	intron (NM_010243, intron 1 of 2)	intron (NM_010243, intron 1 of 2)	1400	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5943	chr5	50014431	50014631	+	1.17917	NA	intron (NM_133911, intron 3 of 18)	intron (NM_133911, intron 3 of 18)	44465	NM_133911	70693	Mm.272974	NM_133911	ENSMUSG00000029090	Adgra3	3830613O22Rik|AU044632|Gpr125|Tem5-like	adhesion G protein-coupled receptor A3	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6374	chr6	30196111	30196311	+	1.17892	NA	Intergenic	Intergenic	19588	NR_038124	100463519	Mm.361139	NR_038124		BB283400	BF465573|Rncr4	expressed sequence BB283400	ncRNA	0.020000	0.592040			-40(CATTTCCCTTGCAAAA,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-108	chr10	110949707	110949907	+	1.17866	NA	intron (NM_001359622, intron 11 of 16)	intron (NM_001359622, intron 11 of 16)	29631	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding	0.025000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2866	chr15	37580265	37580465	+	1.17744	NA	intron (NM_001359841, intron 2 of 7)	intron (NM_001359841, intron 2 of 7)	100209	NM_001359839	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-108	chr1	37711693	37711893	+	1.17744	NA	intron (NM_028096, intron 1 of 9)	MER2|DNA|TcMar-Tigger	8018	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding	0.010000	0.417910			-76(CAAATGTTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1616	chr12	39645739	39645939	+	1.17744	NA	Intergenic	Intergenic	391537	NM_007487	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding	0.020000	0.457711			9(CATTTCTTATACTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3183	chr16	40342502	40342702	+	1.17744	NA	intron (NM_001361281, intron 1 of 8)	intron (NM_001361281, intron 1 of 8)	358238	NM_001361281	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Gm29907|Lam|Lamp	limbic system-associated membrane protein	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-350	chr1	125420242	125420442	+	1.17744	NA	intron (NM_001205385, intron 2 of 12)	intron (NM_001205385, intron 2 of 12)	15385	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7571	chr9	27650090	27650290	+	1.17744	NA	Intergenic	Intergenic	252978	NM_001305058	75469	Mm.45824	NM_029299	ENSMUSG00000031991	Spata19	1700001L23Rik|AV047838|spergen-1	spermatogenesis associated 19	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1845	chr12	99941771	99941971	+	1.17744	NA	intron (NM_028354, intron 14 of 15)	intron (NM_028354, intron 14 of 15)	-22628	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5632	chr4	98681910	98682110	+	1.17744	NA	intron (NM_001005787, intron 13 of 15)	intron (NM_001005787, intron 13 of 15)	18745	NR_151609	102638531		NR_151609		Gm35073	-	predicted gene, 35073	ncRNA	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2920	chr15	52020288	52020488	+	1.17744	NA	Intergenic	Intergenic	-19719	NM_175503	239435	Mm.24204	NM_175503	ENSMUSG00000068522	Aard	A5D3|AV328152	alanine and arginine rich domain containing protein	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6888	chr7	67860781	67860981	+	1.17744	NA	Intergenic	Intergenic	-57385	NR_045954	73904	Mm.70992	NR_045954	ENSMUSG00000097697	4833412C05Rik	Bigheart	RIKEN cDNA 4833412C05 gene	ncRNA	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4744	chr2	157186648	157186848	+	1.17744	NA	intron (NM_011249, intron 11 of 21)	intron (NM_011249, intron 11 of 21)	17786	NM_011249	19650	Mm.244671	NM_011249	ENSMUSG00000027641	Rbl1	AW547426|PRB1|p107	RB transcriptional corepressor like 1	protein-coding	0.005000	0.457711			-42(GCTTTGTATTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1236	chr11	35859165	35859365	+	1.17744	NA	intron (NM_170779, intron 17 of 22)	intron (NM_170779, intron 17 of 22)	-24737	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6585	chr6	92028580	92028780	+	1.17744	NA	intron (NM_172731, intron 3 of 20)	intron (NM_172731, intron 3 of 20)	49715	NM_172731	232237	Mm.295740	NM_172731	ENSMUSG00000034037	Fgd5	C330025N11Rik|ZFYVE23|mFLJ00274	FYVE, RhoGEF and PH domain containing 5	protein-coding	0.040000	0.587065			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1510	chr12	3518849	3519049	+	1.17744	NA	Intergenic	Intergenic	-53442	NM_001355528	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding	0.005000	0.437811			-79(ATTAGAAGAACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-760	chr10	31379027	31379227	+	1.17744	NA	intron (NM_009413, intron 2 of 6)	intron (NM_009413, intron 2 of 6)	35308	NM_011509	100041294	Mm.7821	NM_011509		Supt4b	Gm3258|Supt4h1b|Supt4h2	suppressor of Ty 4B	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2317	chr13	115896880	115897080	+	1.17744	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	412708	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	ISL1 transcription factor, LIM/homeodomain	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1103	chr10	122999411	122999611	+	1.17744	NA	intron (NM_001163025, intron 33 of 33)	intron (NM_001163025, intron 33 of 33)	-13787	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA	0.015000	0.452736			-13(TTTTTGTCATGGAGAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3118	chr16	23046432	23046632	+	1.17744	NA	Intergenic	Intergenic	-11768	NM_001102411	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3641	chr17	85619360	85619560	+	1.17744	NA	Intergenic	Intergenic	-1064	NR_038086	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA	0.045000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6010	chr5	68128560	68128760	+	1.17744	NA	intron (NM_001018019, intron 2 of 3)	intron (NM_001018019, intron 2 of 3)	96825	NM_001018019	433899	Mm.332422	NM_001018019	ENSMUSG00000068082	Grxcr1	Tg(Eno2-Gabrb3)0370Brll|pi|tde	glutaredoxin, cysteine rich 1	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7851	chr9	101041810	101042010	+	1.17744	NA	Intergenic	RSINE1|SINE|B4	-7026	NM_001311149	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1461	chr11	110177698	110177898	+	1.17744	NA	intron (NM_147218, intron 37 of 38)	L2a|LINE|L2	-9645	NM_147220	217262	Mm.291459	NM_147220	ENSMUSG00000041797	Abca9	D630040K07Rik	ATP-binding cassette, sub-family A (ABC1), member 9	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5126	chr3	113831526	113831726	+	1.17744	NA	Intergenic	Intergenic	-198914	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5846	chr5	18424132	18424332	+	1.17744	NA	Intergenic	Intergenic	-63819	NM_010305	14677	Mm.254629	NM_010305	ENSMUSG00000057614	Gnai1	AU046200|Gialpha1|Gnai-1	guanine nucleotide binding protein (G protein), alpha inhibiting 1	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1129	chr10	126056530	126056730	+	1.17744	NA	Intergenic	Intergenic	90411	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2053	chr13	43351120	43351320	+	1.17744	NA	Intergenic	Intergenic	-19496	NM_178848	68346	Mm.35325	NM_178848	ENSMUSG00000054021	Sirt5	0610012J09Rik|1500032M05Rik|AV001953	sirtuin 5	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5863	chr5	23496130	23496330	+	1.17744	NA	exon (NM_026984, exon 17 of 26)	exon (NM_026984, exon 17 of 26)	61766	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding	0.010000	0.363184			-65(ATTTACATCACCATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5492	chr4	58847272	58847472	+	1.17744	NA	intron (NM_001355696, intron 14 of 48)	intron (NM_001355696, intron 14 of 48)	-61652	NM_146920	258922	Mm.223327	NM_146920	ENSMUSG00000043385	Olfr267	MOR262-1	olfactory receptor 267	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5229	chr3	138500068	138500268	+	1.17744	NA	Intergenic	Intergenic	-10786	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2379	chr14	17927557	17927757	+	1.17744	NA	intron (NM_001113417, intron 3 of 9)	intron (NM_001113417, intron 3 of 9)	-53987	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0.000000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8132	chrX	158023034	158023234	+	1.17744	NA	intron (NM_177751, intron 1 of 21)	intron (NM_177751, intron 1 of 21)	20063	NM_001310719	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	Cnk2|Ksr2	connector enhancer of kinase suppressor of Ras 2	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1217	chr11	28946743	28946943	+	1.17744	NA	Intergenic	B3|SINE|B2	93638	NM_146015	216616	Mm.44176	NM_146015	ENSMUSG00000020467	Efemp1	-	epidermal growth factor-containing fibulin-like extracellular matrix protein 1	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6434	chr6	48699680	48699880	+	1.17744	NA	Intergenic	Intergenic	8464	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5981	chr5	62483575	62483775	+	1.17744	NA	Intergenic	Intergenic	282502	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8036	chrX	100425394	100425594	+	1.17744	NA	intron (NM_001290395, intron 1 of 7)	L1M3|LINE|L1	-3414	NM_001163191	408193	Mm.469910	NM_001163191	ENSMUSG00000051582	Otud6a	EG408193|Hshin6	OTU domain containing 6A	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3630	chr17	82273998	82274198	+	1.17744	NA	Intergenic	RMER10B|LTR|ERVL	-535711	NM_011406	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding	0.000000	0.378109			36(TTTTACATAACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3711	chr18	13693860	13694060	+	1.17744	NA	intron (NM_145492, intron 7 of 7)	intron (NM_145492, intron 7 of 7)	278773	NM_001360804	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1720	chr12	70719326	70719526	+	1.17744	NA	Intergenic	Intergenic	-106088	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2747	chr14	123169663	123169863	+	1.17744	NA	non-coding (NR_045143, exon 2 of 5)	non-coding (NR_045143, exon 2 of 5)	577	NR_045143	380934	Mm.393838	NR_045143	ENSMUSG00000115016	AA536875	Gm1591	expressed sequence AA536875	ncRNA	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4298	chr2	50824823	50825023	+	1.17744	NA	Intergenic	Intergenic	-84761	NR_033595	227885	Mm.301654	NR_033595	ENSMUSG00000083270	Gm13498	-	heat shock protein 90 alpha (cytosolic), class B member 1 pseudogene	pseudo	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5526	chr4	69148179	69148379	+	1.17744	NA	Intergenic	L1_Mus2|LINE|L1	-193882	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2051	chr13	43117379	43117579	+	1.17744	NA	intron (NM_001005740, intron 8 of 12)	RCHARR1|DNA|hAT-Charlie	-5360	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-485	chr1	157633696	157633896	+	1.17744	NA	Intergenic	Intergenic	107626	NM_001159986	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-452	chr1	150942245	150942445	+	1.17744	NA	intron (NM_001024720, intron 1 of 106)	intron (NM_001024720, intron 1 of 106)	51090	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding	0.000000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1753	chr12	78248085	78248285	+	1.17744	NA	intron (NM_145965, intron 1 of 22)	intron (NM_145965, intron 1 of 22)	21530	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding	0.010000	0.303483			29(CTATTGACATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3112	chr16	22625276	22625476	+	1.17744	NA	intron (NM_001346673, intron 1 of 23)	intron (NM_001346673, intron 1 of 23)	20050	NR_105781	102465962		NR_105781	ENSMUSG00000098448	Mir6362	Gm27812|mmu-mir-6362	microRNA 6362	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1884	chr12	109425121	109425321	+	1.17744	NA	Intergenic	Intergenic	-27602	NR_033813	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta like non-canonical Notch ligand 1	protein-coding	0.025000	0.592040			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-667	chr10	3417609	3417809	+	1.17744	NA	intron (NM_133485, intron 1 of 3)	intron (NM_133485, intron 1 of 3)	51559	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory inhibitor subunit 14C	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1502	chr11	120515660	120515860	+	1.17744	NA	Intergenic	Intergenic	-14967	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding	0.060000	0.616915			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5013	chr3	75232825	75233025	+	1.17744	NA	Intergenic	Intergenic	37153	NM_026460	67931	Mm.259446	NM_026460	ENSMUSG00000034139	Serpini2	Spi14	serine (or cysteine) peptidase inhibitor, clade I, member 2	protein-coding	0.000000	0.427861			17(ATTTAACTAAGAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4368	chr2	67711733	67711933	+	1.17744	NA	Intergenic	Intergenic	36376	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA	0.005000	0.363184	11(TATGCTTTATGCAAA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7668	chr9	57722617	57722817	+	1.17744	NA	intron (NM_153799, intron 3 of 6)	intron (NM_153799, intron 3 of 6)	14148	NM_153799	353190	Mm.268104	NM_153799	ENSMUSG00000038957	Edc3	AA517853|Lsm16|Yjdc	enhancer of mRNA decapping 3	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6354	chr6	23432656	23432856	+	1.17744	NA	intron (NM_153163, intron 9 of 29)	intron (NM_153163, intron 9 of 29)	-184492	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8023	chrX	93559809	93560009	+	1.17744	NA	intron (NM_008892, intron 26 of 36)	MER3|DNA|hAT-Charlie	72246	NM_008892	18968	Mm.1923	NM_008892	ENSMUSG00000006678	Pola1	AW321876|Pola	polymerase (DNA directed), alpha 1	protein-coding	0.015000	0.303483			-67(CGTTACCCATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2485	chr14	49668922	49669122	+	1.17744	NA	Intergenic	Intergenic	114361	NM_001358244	67419	Mm.318710	NM_026142	ENSMUSG00000036242	Armh4	3632451O06Rik|AU067705	armadillo-like helical domain containing 4	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7904	chr9	119192319	119192519	+	1.17744	NA	TTS (NM_133980)	TTS (NM_133980)	-2024	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding	0.020000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5491	chr4	58749046	58749246	+	1.17744	NA	Intergenic	Intergenic	36574	NM_146920	258922	Mm.223327	NM_146920	ENSMUSG00000043385	Olfr267	MOR262-1	olfactory receptor 267	protein-coding	0.030000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7177	chr8	25749168	25749368	+	1.17744	NA	intron (NM_028102, intron 5 of 17)	RLTR13D3A|LTR|ERVK	5012	NM_028102	72108	Mm.246875	NM_028102	ENSMUSG00000061313	Ddhd2	2010305K11Rik|SAMWD1|mKIAA0725	DDHD domain containing 2	protein-coding	0.000000	0.393035	51(ACTGTATTATTCATG,+,0.00),51(ACTGTATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1057	chr10	115471193	115471393	+	1.17744	NA	intron (NM_010195, intron 7 of 17)	intron (NM_010195, intron 7 of 17)	86334	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding	0.020000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1281	chr11	48459353	48459553	+	1.17744	NA	Intergenic	Intergenic	-340907	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding	0.000000	0.383085			-21(ATATGCAAAAAAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3559	chr17	65931049	65931249	+	1.17744	NA	intron (NM_023053, intron 3 of 4)	intron (NM_023053, intron 3 of 4)	20038	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding	0.020000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-790	chr7	48153080	48153280	+	1.17726	NA	Intergenic	Intergenic	15805	NM_207538	404239	Mm.377927	NM_207538	ENSMUSG00000070551	Mrgprb5	Mgrg11|MrgB5	MAS-related GPR, member B5	protein-coding	0.000000	0.298507			73(ATTAACAAAAAAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6862	chr7	56011180	56011380	+	1.17726	NA	intron (NM_153578, intron 1 of 4)	MTD-int|LTR|ERVL-MaLR	8320	NM_153578	233280	Mm.389901	NM_153578	ENSMUSG00000047037	Nipa1	1110027G09Rik|A830014A18Rik|FSP3|Spg6	non imprinted in Prader-Willi/Angelman syndrome 1 homolog (human)	protein-coding	0.000000	0.402985			-24(ATTTACATTGCTAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2013	chr13	32465835	32466035	+	1.17726	NA	Intergenic	Intergenic	-127391	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	GDP-mannose 4, 6-dehydratase	protein-coding	0.020000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7812	chr9	92717276	92717476	+	1.17726	NA	Intergenic	Intergenic	-1340	NR_040770	331003	Mm.50805	NR_040770	ENSMUSG00000101734	4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	ncRNA	0.015000	0.457711			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-766	chr6	103810645	103810845	+	1.17726	NA	Intergenic	Intergenic	153939	NR_144494	100846987		NR_144494		Pou5f1-rs5	Gm21054|Oct4P5|Otf3-rs5|Otf3e	POU domain, class 5, transcription factor 1, related sequence 5	pseudo	0.010000	0.407960			-59(CCTTTCTTATTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6820	chr7	36774197	36774397	+	1.17726	NA	TTS (NM_172298)	TTS (NM_172298)	76179	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding	0.020000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-497	chr2	79047851	79048051	+	1.17726	NA	Intergenic	Intergenic	178273	NM_001356395	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding	0.010000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-481	chr2	52661875	52662075	+	1.17726	NA	intron (NM_001037099, intron 2 of 13)	intron (NM_001037099, intron 2 of 13)	13884	NM_001285428	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding	0.010000	0.288557			35(TTTTACATAAAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7548	chr9	18745786	18745986	+	1.17726	NA	Intergenic	Intergenic	9747	NM_146606	18322	Mm.246530	NM_146606	ENSMUSG00000054141	Olfr24	MOR132-1|MTPCR51	olfactory receptor 24	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5661	chr4	104012743	104012943	+	1.17726	NA	intron (NM_001369049, intron 2 of 19)	intron (NM_001369049, intron 2 of 19)	-354695	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.010000	0.507463		-91(GATGGATATGCATC,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5697	chr4	114579077	114579277	+	1.17726	NA	intron (NM_001085549, intron 2 of 6)	intron (NM_001085549, intron 2 of 6)	172453	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat	TraB domain containing 2B	protein-coding	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5565	chr4	82311535	82311735	+	1.17682	NA	intron (NM_001286131, intron 8 of 9)	intron (NM_001286131, intron 8 of 9)	194144	NM_001286131	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding	0.015000	0.432836			-7(ACTTTGCTATTTAAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-96	chr10	67121662	67121862	+	1.17592	NA	Intergenic	L1MA4A|LINE|L1	-5326	NM_207221	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2338	chr14	8592571	8592771	+	1.17592	NA	intron (NM_028934, intron 4 of 15)	intron (NM_028934, intron 4 of 15)	73619	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4732	chr2	153139975	153140175	+	1.17592	NA	intron (NM_001172117, intron 10 of 12)	intron (NM_001172117, intron 10 of 12)	-21226	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding	0.015000	0.552239			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-834	chr8	71913727	71913927	+	1.17592	NA	exon (NM_001166645, exon 3 of 3)	exon (NM_001166645, exon 3 of 3)	5221	NM_001166645	382019	Mm.251482	NM_001166645	ENSMUSG00000089857	Zfp882	Gm15468	zinc finger protein 882	protein-coding	0.005000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-378	chr16	67210727	67210927	+	1.17513	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	410081	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3294	chr16	67210728	67210928	+	1.17513	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	410080	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2838	chr15	28166421	28166621	+	1.17427	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-37245	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b3491Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7787	chr9	85302766	85302966	+	1.17427	NA	Intergenic	Intergenic	24258	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Tent5a	BAP014|D930050G01Rik|Fam46a	terminal nucleotidyltransferase 5A	protein-coding	0.005000	0.313433			-59(ATTTGAATTATAATAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-338	chr15	28166379	28166579	+	1.17427	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-37287	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b3491Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding	0.000000	0.293532			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-883	chr9	85302730	85302930	+	1.17427	NA	Intergenic	Intergenic	24294	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Tent5a	BAP014|D930050G01Rik|Fam46a	terminal nucleotidyltransferase 5A	protein-coding	0.010000	0.353234			-23(ATTTGAATTATAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4374	chr2	68411315	68411515	+	1.17427	NA	intron (NM_016866, intron 1 of 17)	intron (NM_016866, intron 1 of 17)	60566	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2977	chr15	68015175	68015375	+	1.17410	NA	Intergenic	Intergenic	243581	NM_198644	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7563	chr9	24840037	24840237	+	1.17410	NA	Intergenic	Intergenic	-65834	NM_020496	57246	Mm.31452	NM_020496	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding	0.005000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-345	chr15	68015192	68015392	+	1.17410	NA	Intergenic	Intergenic	243564	NM_198644	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding	0.000000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-77	chr10	5381538	5381738	+	1.17410	NA	intron (NM_153399, intron 13 of 31)	intron (NM_153399, intron 13 of 31)	106676	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|KASH1|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7743	chr9	77719670	77719870	+	1.17410	NA	Intergenic	L1MEf|LINE|L1	-34765	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding	0.000000	0.353234			71(GATTGCATAAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2555	chr14	76238263	76238463	+	1.17410	NA	Intergenic	Intergenic	-13099	NR_152108	72893	Mm.233565	NR_152108		2900040C04Rik	-	RIKEN cDNA 2900040C04 gene	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3202	chr16	44977288	44977488	+	1.17410	NA	intron (NM_029018, intron 5 of 5)	intron (NM_029018, intron 5 of 5)	33710	NM_001128133	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding	0.010000	0.402985			-4(CATTTGTCAAGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3735	chr18	20962702	20962902	+	1.17410	NA	intron (NM_001364973, intron 1 of 5)	intron (NM_001364973, intron 1 of 5)	1438	NM_001364973	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik|C730049O14Rik	ring finger protein 125	protein-coding	0.060000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3215	chr16	49291221	49291421	+	1.17410	NA	Intergenic	ORR1F-int|LTR|ERVL-MaLR	233921	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7845	chr9	99111198	99111398	+	1.17275	NA	intron (NM_029094, intron 2 of 23)	intron (NM_029094, intron 2 of 23)	28913	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7060	chr7	123345157	123345357	+	1.17117	NA	intron (NM_001122642, intron 1 of 19)	intron (NM_001122642, intron 1 of 19)	24658	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5199	chr3	132982290	132982490	+	1.17117	NA	3' UTR (NM_026231, exon 12 of 12)	3' UTR (NM_026231, exon 12 of 12)	-32099	NM_033525	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3779	chr18	34092977	34093177	+	1.17076	NA	Intergenic	RMER10A|LTR|ERVL	-85871	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding	0.005000	0.507463			36(GCTTTGATATGTTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-154	chr11	68107418	68107618	+	1.17076	NA	intron (NM_001361351, intron 5 of 6)	intron (NM_001361351, intron 5 of 6)	-113374	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1329	chr11	68107338	68107538	+	1.17076	NA	intron (NM_001361351, intron 5 of 6)	intron (NM_001361351, intron 5 of 6)	-113454	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA	0.010000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-562	chr3	68565423	68565623	+	1.17012	NA	intron (NM_001282044, intron 2 of 7)	intron (NM_001282044, intron 2 of 7)	-6845	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7498	chr8	128237082	128237282	+	1.17012	NA	Intergenic	Intergenic	41043	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA	0.000000	0.338308	-19(AATGAATTATACATT,+,0.00),-19(AATGAATTATACATT,-,0.00)		-36(ATTTACAAAAATAAGG,-,0.00),39(TCTTGGTCATGCTAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2680	chr14	105389953	105390153	+	1.17004	NA	Intergenic	Intergenic	-37506	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.010000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-520	chr2	120770586	120770786	+	1.16969	NA	intron (NM_001024857, intron 9 of 14)	B3|SINE|B2	-39169	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1575	chr12	27826287	27826487	+	1.16969	NA	Intergenic	Intergenic	-483669	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7472	chr8	119318578	119318778	+	1.16969	NA	intron (NM_019707, intron 13 of 13)	intron (NM_019707, intron 13 of 13)	-25860	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding	0.015000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6979	chr7	95396705	95396905	+	1.16969	NA	Intergenic	Intergenic	-774439	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2928	chr15	54089965	54090165	+	1.16969	NA	Intergenic	Intergenic	-187629	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4528	chr2	114622162	114622362	+	1.16969	NA	intron (NM_025675, intron 3 of 8)	intron (NM_025675, intron 3 of 8)	32702	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Dph6	5730421E18Rik|Atpbd4	diphthamine biosynthesis 6	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-457	chr1	152369088	152369288	+	1.16969	NA	Intergenic	Intergenic	17494	NM_025677	66637	Mm.379120	NM_025677	ENSMUSG00000014980	Tsen15	5730449L18Rik|AL023077|Sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.005000	0.398010		-98(AATGCATATGGATT,+,0.00),-98(AATGCATATGGATT,-,0.00)	-40(GCTTTTGCTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2219	chr13	95332708	95332908	+	1.16969	NA	intron (NM_001302539, intron 1 of 1)	L1M2|LINE|L1	2197	NR_034043	100217450	Mm.442313	NR_034043	ENSMUSG00000088108	Snora47	MBI-115	small nucleolar RNA, H/ACA box 47	snoRNA	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6379	chr6	31736350	31736550	+	1.16969	NA	Intergenic	Intergenic	-70319	NR_152155	434003	Mm.332979	NR_152155	ENSMUSG00000084973	Gm13848	-	predicted gene 13848	ncRNA	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7779	chr9	83639969	83640169	+	1.16969	NA	Intergenic	RLTR41A2|LTR|ERV1	-51406	NR_046066	100039222	Mm.405596	NR_046066	ENSMUSG00000100155	Gm2109	-	predicted gene 2109	ncRNA	0.020000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-713	chr10	17563632	17563832	+	1.16969	NA	Intergenic	Intergenic	-159496	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1257	chr11	40675045	40675245	+	1.16969	NA	Intergenic	B3A|SINE|B2	17537	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding	0.000000	0.402985			-41(TTTTTTTCATTCACAT,+,0.00),13(TATTGCTCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6203	chr5	132212585	132212785	+	1.16969	NA	intron (NM_001363480, intron 2 of 19)	RMER15-int|LTR|ERVL	330535	NM_001363480	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5642	chr4	100160379	100160579	+	1.16969	NA	intron (NM_001312690, intron 1 of 3)	intron (NM_001312690, intron 1 of 3)	64688	NM_013845	26563	Mm.57252	NM_013845	ENSMUSG00000035305	Ror1	2810404D04Rik|Ntrkr1	receptor tyrosine kinase-like orphan receptor 1	protein-coding	0.000000	0.378109	-77(AATCCATAATTCATG,+,0.00),-77(AATCCATAATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1538	chr12	11906618	11906818	+	1.16969	NA	Intergenic	Intergenic	-23819	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	tubulin, beta 2a, pseudogene 2	pseudo	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1372	chr11	79857323	79857523	+	1.16969	NA	Intergenic	Intergenic	104964	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	UTP6 small subunit processome component	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3937	chr18	73650431	73650631	+	1.16969	NA	intron (NM_001364968, intron 5 of 8)	intron (NM_001364968, intron 5 of 8)	53260	NM_001364968	17128	Mm.100399	NM_008540	ENSMUSG00000024515	Smad4	AW743858|D18Wsu70e|DPC4|Madh4	SMAD family member 4	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7119	chr7	139477638	139477838	+	1.16921	NA	intron (NM_001355162, intron 2 of 15)	intron (NM_001355162, intron 2 of 15)	77244	NM_001355162	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding	0.005000	0.378109			57(CTTTGCAAAGGAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2941	chr15	58047122	58047322	+	1.16921	NA	3' UTR (NM_001042438, exon 5 of 5)	3' UTR (NM_001042438, exon 5 of 5)	-12928	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2667	chr14	103948434	103948634	+	1.16921	NA	Intergenic	Intergenic	78608	NR_045953	73877	Mm.399172	NR_045953	ENSMUSG00000115727	4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	ncRNA	0.005000	0.388060	-81(TATAAATTATGTATG,+,0.00),-81(TATAAATTATGTATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5112	chr3	109517912	109518112	+	1.16921	NA	intron (NM_020505, intron 10 of 26)	(TG)n|Simple_repeat|Simple_repeat	-55995	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6861	chr7	55827713	55827913	+	1.16921	NA	intron (NM_001360873, intron 20 of 21)	intron (NM_001360873, intron 20 of 21)	-14258	NM_001164661	20430	Mm.37249	NM_011370	ENSMUSG00000030447	Cyfip1	E030028J09Rik|P140SRA-1|P140sra1|Shyc|Sra-1|Sra1|l(7)1Rl|l71Rl|l7Rl1|mKIAA0068|pl-1	cytoplasmic FMR1 interacting protein 1	protein-coding	0.025000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5896	chr5	32842067	32842267	+	1.16921	NA	intron (NM_194340, intron 3 of 10)	intron (NM_194340, intron 3 of 10)	12063	NM_194340	215476	Mm.248721	NM_194340	ENSMUSG00000054280	Prr14l	6030436E02Rik|C330019G07Rik|Prl14l	proline rich 14-like	protein-coding	0.005000	0.388060			44(GTTTGAATGAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5390	chr4	25798438	25798638	+	1.16855	NA	intron (NM_010243, intron 1 of 2)	intron (NM_010243, intron 1 of 2)	1465	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5335	chr4	9002611	9002811	+	1.16797	NA	Intergenic	Intergenic	251387	NM_001355382	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4168	chr2	9934894	9935094	+	1.16797	NA	intron (NM_027748, intron 4 of 6)	intron (NM_027748, intron 4 of 6)	28845	NR_152218	100126244	Mm.86343	NR_152218		Gm13262	-	predicted gene 13262	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-699	chr10	12785322	12785522	+	1.16797	NA	intron (NM_011682, intron 1 of 73)	intron (NM_011682, intron 1 of 73)	76313	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7166	chr8	18522690	18522890	+	1.16797	NA	Intergenic	Intergenic	-72341	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT|Tg(HLA-A2.1)1Enge	microcephaly, primary autosomal recessive 1	protein-coding	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-131	chr1	44556692	44556892	+	1.16797	NA	intron (NM_028450, intron 1 of 10)	intron (NM_028450, intron 1 of 10)	5121	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding	0.010000	0.343284			22(TTTTTGACTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5517	chr4	65003698	65003898	+	1.16797	NA	Intergenic	Intergenic	-120376	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding	0.000000	0.343284			9(TCATTCTCTTGTAAAT,+,0.00),33(GTTTTCTCATGTTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4712	chr2	147033141	147033341	+	1.16797	NA	intron (NM_011917, intron 13 of 29)	L2a|LINE|L2	20242	NM_001356402	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding	0.005000	0.437811			2(ATTTCCATGGGAAGAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6706	chr6	121143211	121143411	+	1.16797	NA	Intergenic	Intergenic	-12289	NM_001270475	194401	Mm.122399	NM_153396	ENSMUSG00000051586	Mical3	C130040D16Rik|Mical-3|mKIAA1364	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2943	chr15	58383637	58383837	+	1.16797	NA	intron (NM_027211, intron 1 of 8)	intron (NM_027211, intron 1 of 8)	5537	NM_027211	69787	Mm.237985	NM_027211		Anxa13	1810034H17Rik|AV055219	annexin A13	protein-coding	0.025000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6709	chr6	125882126	125882326	+	1.16797	NA	intron (NM_001364563, intron 13 of 23)	B3A|SINE|B2	171038	NM_001364563	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2672	chr14	105164727	105164927	+	1.16797	NA	intron (NM_001368684, intron 1 of 21)	MTEa-int|LTR|ERVL-MaLR	12487	NM_134077	74213	Mm.124957	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding	0.025000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8047	chrX	103464566	103464766	+	1.16797	NA	non-coding (NR_001463, exon 7 of 7)	non-coding (NR_001463, exon 7 of 7)	18567	NR_001463	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA	0.005000	0.318408	-33(CATGAATATTTCATG,+,0.00),-33(CATGAATATTTCATG,-,0.00)		75(GCATTCTTTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6976	chr7	94138459	94138659	+	1.16797	NA	Intergenic	Intergenic	-954383	NM_001358087	100040298	Mm.260904	NM_001358087		Gm15501	EyeLinc5	predicted pseudogene 15501	protein-coding	0.000000	0.308458			-33(CCTTTATCATTAAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2446	chr14	36908683	36908883	+	1.16797	NA	intron (NM_001347503, intron 3 of 7)	intron (NM_001347503, intron 3 of 7)	10752	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5675	chr4	105945997	105946197	+	1.16797	NA	Intergenic	L1MB7|LINE|L1	-295116	NR_151521	105244641	Mm.404914	NR_151521		Gm12724	-	predicted gene 12724	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1854	chr12	102031399	102031599	+	1.16797	NA	Intergenic	L2a|LINE|L2	55525	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2919	chr15	51842557	51842757	+	1.16797	NA	intron (NM_080635, intron 1 of 7)	intron (NM_080635, intron 1 of 7)	22804	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding	0.005000	0.328358			77(TACTTGTCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3059	chr15	100636992	100637192	+	1.16797	NA	promoter-TSS (NR_104337)	promoter-TSS (NR_104337)	-152	NM_174992	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding	0.090000	0.676617			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-384	chr1	133228207	133228407	+	1.16797	NA	Intergenic	Intergenic	-17790	NM_182930	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding	0.005000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4167	chr2	9057664	9057864	+	1.16797	NA	Intergenic	Intergenic	-131751	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA	0.015000	0.373134	-28(TATGCATAATTCATG,+,0.00),-28(TATGCATAATTCATG,-,0.00)		16(ATTTCCAATAAAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5395	chr4	26586504	26586704	+	1.16797	NA	Intergenic	L2a|LINE|L2	118845	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7054	chr7	122289556	122289756	+	1.16797	NA	intron (NM_001316672, intron 1 of 16)	CpG	531	NM_001316672	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding	0.065000	0.691542			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2505	chr14	60924474	60924674	+	1.16797	NA	Intergenic	RMER12C|LTR|ERVK	113413	NM_001164155	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding	0.000000	0.412935			-6(CCTTTCTCTGGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5897	chr5	33386523	33386723	+	1.16797	NA	intron (NR_153108, intron 2 of 12)	intron (NR_153108, intron 2 of 12)	7927	NM_027674	71101	Mm.132178	NM_027674	ENSMUSG00000037355	Uvssa	4933407H18Rik|D330017J19Rik|Kiaa1530|mKIAA1530	UV stimulated scaffold protein A	protein-coding	0.000000	0.422886			40(TTTTTCATATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5651	chr4	101955012	101955212	+	1.16797	NA	Intergenic	Intergenic	14705	NM_001085516	332923	Mm.473672	NM_001085516	ENSMUSG00000070890	Gm12794	-	predicted gene 12794	protein-coding	0.010000	0.412935			19(ATTTCCAAAAGAAGCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1399	chr11	88465693	88465893	+	1.16797	NA	intron (NM_054043, intron 7 of 13)	intron (NM_054043, intron 7 of 13)	113020	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3588	chr17	73153883	73154083	+	1.16797	NA	intron (NM_001081071, intron 1 of 5)	intron (NM_001081071, intron 1 of 5)	45998	NM_001081071	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7103	chr7	134821308	134821508	+	1.16797	NA	intron (NM_001033420, intron 23 of 51)	MamRep434|DNA|TcMar-Tigger	117022	NM_001143802	627214	Mm.323610	NM_001143802	ENSMUSG00000073805	Insyn2a	B830028B13Rik|Fam196a|InSyn2	inhibitory synaptic factor 2A	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1862	chr12	103380017	103380217	+	1.16797	NA	intron (NR_033587, intron 1 of 5)	L1ME4a|LINE|L1	3223	NR_033587	68149	Mm.127378	NM_026580	ENSMUSG00000021203	Otub2	2010015L18Rik|4930586I02Rik|AI413508|AW557219|OTB2|OTU2	OTU domain, ubiquitin aldehyde binding 2	protein-coding	0.005000	0.333333			4(CTTTTGTTATGTATAC,+,0.00),70(ATCAGAAAAAGAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2506	chr14	60924668	60924868	+	1.16797	NA	Intergenic	RMER12C|LTR|ERVK	113219	NM_001164155	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6256	chr5	148853214	148853414	+	1.16797	NA	Intergenic	Intergenic	75333	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6226	chr5	139350134	139350334	+	1.16757	NA	Intergenic	B4|SINE|B4	-2382	NM_001160265	545817	Mm.482474	NM_001160265	ENSMUSG00000029541	Cyp2w1	Gm455	cytochrome P450, family 2, subfamily w, polypeptide 1	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3022	chr15	91252977	91253177	+	1.16757	NA	Intergenic	Intergenic	-61070	NM_001358967	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding	0.010000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2336	chr14	7928643	7928843	+	1.16757	NA	intron (NM_001081427, intron 34 of 45)	intron (NM_001081427, intron 34 of 45)	-28557	NM_001371278									0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2597	chr14	85366932	85367132	+	1.16757	NA	Intergenic	Intergenic	-878938	NR_040457	75155	Mm.399239	NR_040457	ENSMUSG00000115271	4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA	0.000000	0.343284			-59(ATCTGAATAAAAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-753	chr10	29459328	29459528	+	1.16757	NA	intron (NM_028351, intron 4 of 4)	intron (NM_028351, intron 4 of 4)	76439	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding	0.005000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7082	chr7	129084890	129085090	+	1.16757	NA	Intergenic	Intergenic	-172104	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3490	chr17	43111502	43111702	+	1.16757	NA	Intergenic	MLTR14|LTR|ERV1	46689	NR_045154	545207	Mm.329050	NR_045153	ENSMUSG00000117011	E130008D07Rik	-	RIKEN cDNA E130008D07 gene	ncRNA	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-854	chr10	65540764	65540964	+	1.16757	NA	Intergenic	Intergenic	367375	NR_155764	102632897	Mm.183448	NR_155764	ENSMUSG00000112913	Gm30853	-	predicted gene, 30853	ncRNA	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-79	chr1	25886851	25887051	+	1.16757	NA	Intergenic	Intergenic	-57244	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4954	chr3	56158900	56159100	+	1.16757	NA	intron (NM_030595, intron 1 of 57)	RMER1A|Other|Other	24701	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2561	chr14	77239534	77239734	+	1.16757	NA	intron (NM_172813, intron 1 of 18)	intron (NM_172813, intron 1 of 18)	82871	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-115	chr1	39888592	39888792	+	1.16738	NA	Intergenic	Intergenic	-12221	NM_001252200	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0.000000	0.388060			79(ACATTCTCATTAAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2321	chr13	117023620	117023820	+	1.16738	NA	intron (NM_001081009, intron 3 of 26)	intron (NM_001081009, intron 3 of 26)	1811	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding	0.030000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-15	chr1	39888578	39888778	+	1.16738	NA	Intergenic	Intergenic	-12235	NM_001252200	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2180	chr13	84373092	84373292	+	1.16735	NA	Intergenic	Intergenic	150896	NM_001361908	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5278	chr3	148899450	148899650	+	1.16735	NA	intron (NM_001081298, intron 1 of 23)	intron (NM_001081298, intron 1 of 23)	55085	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.020000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-256	chr13	84373095	84373295	+	1.16735	NA	Intergenic	Intergenic	150899	NM_001361908	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2290	chr13	109926248	109926448	+	1.16618	NA	intron (NM_011056, intron 8 of 16)	intron (NM_011056, intron 8 of 16)	22539	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA	0.020000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6552	chr6	81772121	81772321	+	1.16532	NA	Intergenic	Intergenic	123442	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7200	chr8	34815560	34815760	+	1.16532	NA	intron (NM_176933, intron 1 of 3)	intron (NM_176933, intron 1 of 3)	8050	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding	0.025000	0.502488			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-245	chr13	59592809	59593009	+	1.16532	NA	intron (NM_030153, intron 2 of 22)	MTD|LTR|ERVL-MaLR	7576	NM_030153	78689	Mm.253902	NM_030153	ENSMUSG00000021555	Naa35	A330021G12Rik|A330027C19Rik|AI158944|C030004C14Rik|Mak10	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2094	chr13	59592806	59593006	+	1.16532	NA	intron (NM_030153, intron 2 of 22)	MTD|LTR|ERVL-MaLR	7573	NM_030153	78689	Mm.253902	NM_030153	ENSMUSG00000021555	Naa35	A330021G12Rik|A330027C19Rik|AI158944|C030004C14Rik|Mak10	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	protein-coding	0.005000	0.482587			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-285	chr14	34062291	34062491	+	1.16532	NA	intron (NM_172808, intron 9 of 16)	MTEa-int|LTR|ERVL-MaLR	8921	NM_172808	239029	Mm.477093	NM_172808	ENSMUSG00000047441	Antxrl	1700112N15Rik|4933430J11	anthrax toxin receptor-like	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2552	chr14	75967271	75967471	+	1.16532	NA	intron (NM_026816, intron 4 of 7)	intron (NM_026816, intron 4 of 7)	12368	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding	0.005000	0.308458			-81(ATTTACAACAAAAGAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2440	chr14	34062032	34062232	+	1.16532	NA	intron (NM_172808, intron 9 of 16)	MTEa-int|LTR|ERVL-MaLR	8662	NM_172808	239029	Mm.477093	NM_172808	ENSMUSG00000047441	Antxrl	1700112N15Rik|4933430J11	anthrax toxin receptor-like	protein-coding	0.010000	0.323383			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-324	chr14	119795883	119796083	+	1.16532	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	46756	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA	0.010000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-647	chr4	105323404	105323604	+	1.16532	NA	Intergenic	Intergenic	166157	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|PRG-2|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding	0.010000	0.447761			
merged_common-2	chr7	112883650	112883850	+	1.16437	NA	intron (NM_001166584, intron 11 of 13)	intron (NM_001166584, intron 11 of 13)	-70212	NM_175279	78748	Mm.349943	NM_175279	ENSMUSG00000098132	Rassf10	4632411J06Rik	Ras association (RalGDS/AF-6) domain family (N-terminal) member 10	protein-coding	0.005000	0.477612			-19(TTATTCTTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6287	chr6	5892734	5892934	+	1.16402	NA	intron (NM_001191023, intron 5 of 15)	intron (NM_001191023, intron 5 of 15)	84559	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	ncRNA	0.015000	0.407960			-52(CGTTTCTTTTGCATAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-525	chr2	133314936	133315136	+	1.16402	NA	Intergenic	Intergenic	-237123	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1630	chr12	44091239	44091439	+	1.16402	NA	Intergenic	Lx8|LINE|L1	118729	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6112	chr5	101537936	101538136	+	1.16402	NA	Intergenic	Intergenic	126675	NM_144955	18096	Mm.193072	NM_144955	ENSMUSG00000035187	Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6559	chr6	83428890	83429090	+	1.16402	NA	intron (NM_183138, intron 2 of 10)	intron (NM_183138, intron 2 of 10)	12688	NM_183138	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4628	chr2	133314971	133315171	+	1.16402	NA	Intergenic	Intergenic	-237088	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6392	chr6	35288568	35288768	+	1.16369	NA	intron (NM_172892, intron 3 of 15)	intron (NM_172892, intron 3 of 15)	19458	NM_172892	243755	Mm.23666	NM_172892	ENSMUSG00000029843	Slc13a4	9630060C05Rik|SUT-1|SUT1	solute carrier family 13 (sodium/sulfate symporters), member 4	protein-coding	0.020000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4039	chr19	20915816	20916016	+	1.16275	NA	intron (NM_028953, intron 2 of 20)	intron (NM_028953, intron 2 of 20)	38286	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding	0.010000	0.393035			-55(GTCTGAAAAACAAAAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-809	chr7	119988463	119988663	+	1.16275	NA	intron (NM_001370806, intron 40 of 60)	intron (NM_001370806, intron 40 of 60)	88452	NR_126475	73919	Mm.46381	NM_029610	ENSMUSG00000030922	Lyrm1	1110065L10Rik|2310004B22Rik|4930404J24Rik	LYR motif containing 1	protein-coding	0.000000	0.398010			-10(GTTTTGACATACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4512	chr2	108936439	108936639	+	1.16275	NA	Intergenic	Intergenic	341751	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0.010000	0.412935	-83(TATAAATTATTCATT,+,0.00),-83(TATAAATTATTCATT,-,0.00)		-6(GTTATCATGACAATGT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-723	chr6	8413430	8413630	+	1.16275	NA	intron (NM_001302353, intron 4 of 4)	intron (NM_001302353, intron 4 of 4)	95631	NR_040452	320312	Mm.374890	NR_040452	ENSMUSG00000087305	A430035B10Rik	2810488G03Rik	RIKEN cDNA A430035B10 gene	ncRNA	0.010000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-514	chr2	108936449	108936649	+	1.16275	NA	Intergenic	Intergenic	341741	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0.010000	0.402985	-93(TATAAATTATTCATT,+,0.00),-93(TATAAATTATTCATT,-,0.00)		-16(GTTATCATGACAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7823	chr9	94558884	94559084	+	1.16252	NA	Intergenic	RMER15-int|LTR|ERVL	-20903	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	Dipk2a	1190002N15Rik|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6831	chr7	40468209	40468409	+	1.16169	NA	Intergenic	Intergenic	-206428	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA	0.000000	0.407960			-96(CTTTGTTCTTGTTAAT,+,0.00),30(CCAGTGCCATGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4309	chr2	53613158	53613358	+	1.16169	NA	Intergenic	L1M2|LINE|L1	421174	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7167	chr8	18634472	18634672	+	1.16169	NA	intron (NM_173189, intron 8 of 13)	intron (NM_173189, intron 8 of 13)	39441	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT|Tg(HLA-A2.1)1Enge	microcephaly, primary autosomal recessive 1	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1016	chr10	108644113	108644313	+	1.16169	NA	intron (NM_001252342, intron 4 of 10)	intron (NM_001252342, intron 4 of 10)	55947	NM_203660	368203	Mm.452758	NM_203660	ENSMUSG00000112039	Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1467	chr11	110989751	110989951	+	1.16169	NA	intron (NM_001252207, intron 2 of 2)	intron (NM_001252207, intron 2 of 2)	-7636	NM_001252209	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-503	chr1	162088642	162088842	+	1.16169	NA	intron (NM_001038619, intron 15 of 20)	intron (NM_001038619, intron 15 of 20)	83773	NR_040562	72753	Mm.452125	NR_040562	ENSMUSG00000090260	2810442N19Rik	-	RIKEN cDNA 2810442N19 gene	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4511	chr2	108877219	108877419	+	1.16169	NA	Intergenic	Intergenic	400971	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-169	chr1	57768989	57769189	+	1.16169	NA	Intergenic	L1ME3Cz|LINE|L1	-5772	NM_144882	67198	Mm.159989	NM_144882	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	spermatogenesis associated, serine-rich 2-like	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4266	chr2	41517712	41517912	+	1.16169	NA	intron (NM_053011, intron 7 of 90)	intron (NM_053011, intron 7 of 90)	929756	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1105	chr10	123061613	123061813	+	1.16169	NA	intron (NM_001163025, intron 1 of 33)	intron (NM_001163025, intron 1 of 33)	14792	NM_001163024	67074	Mm.169924	NM_153395	ENSMUSG00000034602	Mon2	2610528O22Rik|AW495628|Sf21|mKIAA1040	MON2 homolog, regulator of endosome to Golgi trafficking	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1377	chr11	82116946	82117146	+	1.16169	NA	TTS (NM_021443)	TTS (NM_021443)	1861	NM_021443	20307	Mm.42029	NM_021443	ENSMUSG00000009185	Ccl8	1810063B20Rik|AB023418|HC14|MCP-2|Mcp2|Scya8	chemokine (C-C motif) ligand 8	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1156	chr11	10920456	10920656	+	1.16169	NA	Intergenic	Intergenic	-193460	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3300	chr16	69756982	69757182	+	1.16169	NA	Intergenic	ORR1A1-int|LTR|ERVL-MaLR	43299	NR_130991	78110	Mm.211406	NR_130991	ENSMUSG00000107073	4930428D20Rik	Gm43265	RIKEN cDNA 4930428D20 gene	ncRNA	0.015000	0.452736	72(AATGCAAAATGCATT,+,0.00),72(AATGCAAAATGCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6683	chr6	116748861	116749061	+	1.16169	NA	Intergenic	Intergenic	-32203	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding	0.000000	0.393035			-26(TTTAGCACAACAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1362	chr11	75956586	75956786	+	1.16169	NA	Intergenic	Intergenic	-30795	NM_001291159	380714	Mm.425697	NM_029548	ENSMUSG00000020847	Rph3al	Gm1753|Noc2	rabphilin 3A-like (without C2 domains)	protein-coding	0.020000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2896	chr15	43983004	43983204	+	1.16169	NA	Intergenic	Intergenic	-113075	NM_175502	239408	Mm.41219	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-202	chr1	71241578	71241778	+	1.16169	NA	Intergenic	RLTR25A|LTR|ERVK	-138706	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	-	BRCA1 associated RING domain 1	protein-coding	0.005000	0.383085			-23(GAATTCTTTTGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6170	chr5	122392431	122392631	+	1.16169	NA	intron (NM_019824, intron 1 of 6)	intron (NM_019824, intron 1 of 6)	653	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding	0.045000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8114	chrX	145499038	145499238	+	1.16169	NA	Intergenic	Intergenic	-11499	NM_001290274	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2874	chr15	39778677	39778877	+	1.16169	NA	intron (NM_022722, intron 9 of 9)	intron (NM_022722, intron 9 of 9)	-18268	NR_045788	100503072	Mm.446661	NR_045788	ENSMUSG00000087695	Gm16291	-	predicted gene 16291	ncRNA	0.015000	0.427861			33(ATTTGCATCACAACAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4588	chr2	125559111	125559311	+	1.16169	NA	Intergenic	Intergenic	-52773	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-751	chr10	28817596	28817796	+	1.16169	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	149336	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1200	chr11	25357403	25357603	+	1.16169	NA	non-coding (NR_045853, exon 4 of 8)	non-coding (NR_045853, exon 4 of 8)	31396	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	ncRNA	0.040000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5446	chr4	48144418	48144618	+	1.16169	NA	intron (NM_026343, intron 3 of 7)	Lx7|LINE|L1	19599	NM_026343	67727	Mm.171334	NM_026343	ENSMUSG00000061455	Stx17	4833418L03Rik|6330411F21Rik|9030425C21Rik|AW048351	syntaxin 17	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3530	chr17	53678886	53679086	+	1.16169	NA	exon (NM_028232, exon 7 of 9)	exon (NM_028232, exon 7 of 9)	10329	NM_028232	72415	Mm.153202	NM_028232	ENSMUSG00000023940	Sgo1	3300001M08Rik|C81037|Sgol1	shugoshin 1	protein-coding	0.020000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4913	chr3	40061969	40062169	+	1.16169	NA	Intergenic	Intergenic	460843	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA	0.000000	0.308458			44(ATTTTGTGATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2090	chr13	58335757	58335957	+	1.16169	NA	intron (NM_175214, intron 4 of 16)	L1M2|LINE|L1	19090	NM_175214	75050	Mm.385742	NM_175214	ENSMUSG00000060176	Kif27	4930517I18Rik	kinesin family member 27	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2251	chr13	101605812	101606012	+	1.16169	NA	Intergenic	Intergenic	86718	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8136	chrX	159459047	159459247	+	1.16169	NA	promoter-TSS (NM_001313752)	promoter-TSS (NM_001313752)	22	NM_001359321	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding	0.000000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4357	chr2	65260979	65261179	+	1.16169	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-22288	NM_001363076	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4024	chr19	16650830	16651030	+	1.16169	NA	intron (NM_173028, intron 59 of 71)	L1MB7|LINE|L1	130003	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding	0.005000	0.278607			-8(GTTTACATAAAAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1741	chr12	74536186	74536386	+	1.16169	NA	Intergenic	Intergenic	238812	NM_198866	386753	Mm.341686	NM_198866		Dbpht2	Spot2	DNA binding protein with his-thr domain	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5090	chr3	101936261	101936461	+	1.16169	NA	Intergenic	Intergenic	-11908	NM_001039371	242126	Mm.90204	NM_001039371	ENSMUSG00000033147	Slc22a15	2610034P21Rik|4930477M19|A530052I06Rik|BB219042	solute carrier family 22 (organic anion/cation transporter), member 15	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7785	chr9	85178334	85178534	+	1.16169	NA	Intergenic	L2c|LINE|L2	148690	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Tent5a	BAP014|D930050G01Rik|Fam46a	terminal nucleotidyltransferase 5A	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2738	chr14	121925274	121925474	+	1.16169	NA	intron (NM_026861, intron 4 of 8)	L1MB3|LINE|L1	-9486	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6780	chr6	149067259	149067459	+	1.16169	NA	intron (NM_177192, intron 3 of 20)	intron (NM_177192, intron 3 of 20)	34321	NM_177192	320560	Mm.426874	NM_177192	ENSMUSG00000030313	Dennd5b	9330160C06Rik|AI852444|D030011O10Rik|Gm17524	DENN/MADD domain containing 5B	protein-coding	0.005000	0.343284			23(TATTTTTTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2538	chr14	71562072	71562272	+	1.16169	NA	Intergenic	Intergenic	-294537	NR_046274	74667	Mm.159286	NR_046274	ENSMUSG00000115304	4930434J06Rik	-	RIKEN cDNA 4930434J06 gene	ncRNA	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6394	chr6	35506971	35507171	+	1.16169	NA	Intergenic	Intergenic	32817	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2352	chr14	11358180	11358380	+	1.16169	NA	Intergenic	Intergenic	75803	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1941	chr13	9508228	9508428	+	1.16169	NA	intron (NM_001081426, intron 3 of 36)	intron (NM_001081426, intron 3 of 36)	231803	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding	0.005000	0.373134			69(GCTTTGCTTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3227	chr16	51013850	51014050	+	1.16169	NA	Intergenic	Lx2|LINE|L1	230541	NR_131006	78639	Mm.160109	NR_131005	ENSMUSG00000092276	1700116B05Rik	-	RIKEN cDNA 1700116B05 gene	ncRNA	0.010000	0.388060		34(CATGCAAATGGATG,+,0.00)	27(AAATTCACATGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-556	chr3	39318570	39318770	+	1.16073	NA	Intergenic	Intergenic	431730	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1076	chr10	117824391	117824591	+	1.16073	NA	intron (NM_024457, intron 2 of 7)	ID_B1|SINE|B4	21483	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding	0.010000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-63	chr1	187787266	187787466	+	1.16018	NA	intron (NM_001357535, intron 1 of 7)	intron (NM_001357535, intron 1 of 7)	135125	NM_001357535	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1880	chr12	107947708	107947908	+	1.16001	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	55606	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding	0.005000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-103	chr10	99046866	99047066	+	1.16001	NA	Intergenic	Intergenic	-60116	NR_153333	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding	0.000000	0.422886		-54(CATTCATTTGCATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2877	chr15	40652529	40652729	+	1.16001	NA	Intergenic	Intergenic	-2413	NM_001356998	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding	0.025000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7342	chr8	79676450	79676650	+	1.15921	NA	3' UTR (NM_001256033, exon 21 of 21)	3' UTR (NM_001256033, exon 21 of 21)	35190	NR_152614	24015	Mm.5831	NM_015751	ENSMUSG00000058355	Abce1	C79080|Oabp|RLI|RNS41|RNS4I|Rnaseli	ATP-binding cassette, sub-family E (OABP), member 1	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1760	chr12	79524690	79524890	+	1.15921	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	227439	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding	0.025000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-868	chr9	33343766	33343966	+	1.15921	NA	Intergenic	Intergenic	-414900	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6572	chr6	86053083	86053283	+	1.15921	NA	intron (NM_001271858, intron 1 of 15)	intron (NM_001271858, intron 1 of 15)	24502	NM_001271858	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding	0.015000	0.383085			-44(GTTTGCACCACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5494	chr4	59154118	59154318	+	1.15921	NA	Intergenic	Intergenic	-15235	NM_001370843	100155	Mm.331636	NM_001033200	ENSMUSG00000038598	Shoc1	AI481877|Gm426|Mzip2	shortage in chiasmata 1	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4915	chr3	40453710	40453910	+	1.15921	NA	Intergenic	Intergenic	69102	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA	0.010000	0.547264			-85(ATTTCAAAGAAAAGAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2793	chr15	12274206	12274406	+	1.15921	NA	Intergenic	Intergenic	-47190	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-403	chr1	138326381	138326581	+	1.15921	NA	Intergenic	Intergenic	52743	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding	0.010000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-132	chr11	11025575	11025775	+	1.15921	NA	Intergenic	Intergenic	-88341	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4194	chr2	18148741	18148941	+	1.15857	NA	intron (NR_045539, intron 11 of 24)	ID4|SINE|ID	84256	NR_045538	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7055	chr7	122345880	122346080	+	1.15857	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	56855	NM_001316672	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2972	chr15	67438153	67438353	+	1.15857	NA	Intergenic	Intergenic	211484	NR_045140	69334	Mm.63770	NR_045140	ENSMUSG00000102069	1700012I11Rik	-	RIKEN cDNA 1700012I11 gene	ncRNA	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6260	chr5	149649201	149649401	+	1.15857	NA	Intergenic	Intergenic	-12965	NM_001347534	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7459	chr8	115255488	115255688	+	1.15857	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	451306	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding	0.025000	0.437811			-4(GCTTTATCTTTGAAAG,+,0.00),3(CTTTGAAAGAGAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4652	chr2	136813365	136813565	+	1.15857	NA	Intergenic	Intergenic	-77753	NM_028201	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding	0.010000	0.378109			-18(ATTTAAAAGAAAGAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-835	chr10	57492191	57492391	+	1.15857	NA	intron (NM_008297, intron 1 of 11)	RLTR20D|LTR|ERVK	5906	NM_008297	15500	Mm.261395	NM_008297	ENSMUSG00000019878	Hsf2	AI661205	heat shock factor 2	protein-coding	0.000000	0.487562		73(CATTCATATGCAGA,+,0.00),79(TATGCAGATTCATG,-,0.00)	66(TCTTTAGCATTCATAT,+,0.00),72(GCATTCATATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5855	chr5	21163753	21163953	+	1.15857	NA	Intergenic	ORR1C1-int|LTR|ERVL-MaLR	-12426	NR_153366	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding	0.005000	0.393035			6(ATCTGCATAAGTGTGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5123	chr3	112574719	112574919	+	1.15857	NA	Intergenic	Intergenic	581908	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2|Amy2-2|Amy2a|PA|mAmy2-1	amylase 2b	protein-coding	0.005000	0.353234		-71(CATGCATATGTAGC,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1110	chr10	123402913	123403113	+	1.15857	NA	intron (NM_001252387, intron 1 of 4)	intron (NM_001252387, intron 1 of 4)	138937	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Tafa2	6330575M02|FAM19A2 TAFA-2|Fam19a2|Sam2|Tafa-2	TAFA chemokine like family member 2	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7460	chr8	115255654	115255854	+	1.15857	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	451140	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding	0.055000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1230	chr11	32387299	32387499	+	1.15857	NA	intron (NM_177364, intron 3 of 12)	ORR1A2|LTR|ERVL-MaLR	39559	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3638	chr17	85072626	85072826	+	1.15857	NA	intron (NM_001163623, intron 7 of 13)	intron (NM_001163623, intron 7 of 13)	17541	NM_001163623	213760	Mm.259035	NM_145984	ENSMUSG00000024127	Prepl	2810457N15Rik|9530014L06Rik|D030028O16Rik|mKIAA0436	prolyl endopeptidase-like	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4035	chr19	18585070	18585270	+	1.15851	NA	intron (NM_017375, intron 8 of 9)	intron (NM_017375, intron 8 of 9)	46643	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding	0.010000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-844	chr8	95363800	95364000	+	1.15851	NA	intron (NM_008609, intron 1 of 9)	Lx8|LINE|L1	11604	NM_008609	17388	Mm.217116	NM_008609	ENSMUSG00000031790	Mmp15	AI503551|MT-MMP 2|MT2-MMP	matrix metallopeptidase 15	protein-coding	0.005000	0.373134			17(GTATTTTTATTTAAAC,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-151	chr11	64531903	64532103	+	1.15851	NA	Intergenic	Intergenic	-95329	NR_028445	654805	Mm.436132	NR_028445		F930015N05Rik	-	RIKEN cDNA F930015N05 gene	ncRNA	0.005000	0.437811			34(ATGATCATGAGAAAAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-765	chr6	102536488	102536688	+	1.15851	NA	Intergenic	Intergenic	-71921	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0.005000	0.373134			74(TTATTACTATGTAGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-826	chr8	50425608	50425808	+	1.15851	NA	Intergenic	Intergenic	57596	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6633	chr6	102536482	102536682	+	1.15851	NA	Intergenic	Intergenic	-71915	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0.005000	0.353234			80(TTATTACTATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7972	chrX	57663743	57663943	+	1.15851	NA	Intergenic	Intergenic	-160086	NM_001033360	245424	Mm.336070	NM_001033360	ENSMUSG00000036357	Gpr101	GPCR6|Gm365	G protein-coupled receptor 101	protein-coding	0.010000	0.343284			-16(GTCTGCATAAAAAAGT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-456	chr19	18585126	18585326	+	1.15851	NA	intron (NM_017375, intron 8 of 9)	intron (NM_017375, intron 8 of 9)	46587	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7384	chr8	95363772	95363972	+	1.15851	NA	intron (NM_008609, intron 1 of 9)	Lx8|LINE|L1	11576	NM_008609	17388	Mm.217116	NM_008609	ENSMUSG00000031790	Mmp15	AI503551|MT-MMP 2|MT2-MMP	matrix metallopeptidase 15	protein-coding	0.005000	0.348259			45(GTATTTTTATTTAAAC,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-411	chr17	75603951	75604151	+	1.15851	NA	Intergenic	Intergenic	-52105	NM_001357860	72722	Mm.24641	NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	family with sequence similarity 98, member A	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3246	chr16	55631178	55631378	+	1.15752	NA	Intergenic	Intergenic	136547	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2643	chr14	98414438	98414638	+	1.15720	NA	Intergenic	Intergenic	-244773	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund family transcription factor 1	protein-coding	0.035000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-70	chr1	192870395	192870595	+	1.15720	NA	Intergenic	Intergenic	-14743	NM_198247	214791	Mm.22806	NM_198247	ENSMUSG00000016262	Sertad4	4833404A09|C130018M11Rik	SERTA domain containing 4	protein-coding	0.005000	0.323383			-42(TTTTAAATAATAATAG,-,0.00),49(TTAGTGTTATGCAAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-369	chr16	42466600	42466800	+	1.15706	NA	Intergenic	Intergenic	-126049	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding	0.010000	0.412935			-85(CTTTTGACTTGAAAAT,+,0.00),61(ATTTTCATACCAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6183	chr5	128041648	128041848	+	1.15706	NA	intron (NM_172885, intron 3 of 8)	intron (NM_172885, intron 3 of 8)	391329	NM_172885	243274	Mm.447698	NM_172885	ENSMUSG00000034310	Tmem132d	C630028F04Rik	transmembrane protein 132D	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2739	chr14	122113329	122113529	+	1.15706	NA	intron (NM_080556, intron 1 of 16)	intron (NM_080556, intron 1 of 16)	6347	NM_080556	68059	Mm.275191	NM_080556	ENSMUSG00000025544	Tm9sf2	1500001N15Rik|AA536814|D14Ertd64e|P76	transmembrane 9 superfamily member 2	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5179	chr3	127544693	127544893	+	1.15706	NA	promoter-TSS (NR_146435)	promoter-TSS (NR_146435)	-296	NR_146435	110008574		NR_146435		LOC110008574	-	miR-302 host gene	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3189	chr16	42466606	42466806	+	1.15706	NA	Intergenic	Intergenic	-126055	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding	0.010000	0.422886			-91(CTTTTGACTTGAAAAT,+,0.00),55(ATTTTCATACCAATGT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-487	chr2	65156207	65156407	+	1.15706	NA	intron (NM_177025, intron 1 of 13)	intron (NM_177025, intron 1 of 13)	82484	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding	0.005000	0.338308			-59(CTTTTGTGATTCTCAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6811	chr7	34246935	34247135	+	1.15682	NA	intron (NM_172741, intron 8 of 12)	intron (NM_172741, intron 8 of 12)	-16699	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding	0.000000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-205	chr12	90916252	90916452	+	1.15611	NA	Intergenic	Intergenic	-129496	NR_045858	71349	Mm.442093	NR_045858	ENSMUSG00000085004	5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1809	chr12	90916244	90916444	+	1.15611	NA	Intergenic	Intergenic	-129504	NR_045858	71349	Mm.442093	NR_045858	ENSMUSG00000085004	5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1427	chr11	97218186	97218386	+	1.15555	NA	intron (NM_008942, intron 18 of 22)	intron (NM_008942, intron 18 of 22)	-30394	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5683	chr4	109150287	109150487	+	1.15555	NA	intron (NM_001368727, intron 3 of 23)	MER5A|DNA|hAT-Charlie	-12474	NM_001355190	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4349	chr2	62981554	62981754	+	1.15555	NA	intron (NM_133207, intron 2 of 15)	intron (NM_133207, intron 2 of 15)	202633	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding	0.010000	0.313433		-10(ACTGCATATTTATG,-,0.00)	-7(GCATATTTATGTAAAT,+,0.00),83(ATTAACAAAACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1426	chr11	96997317	96997517	+	1.15555	NA	Intergenic	CpG	-14458	NM_001363225	78912	Mm.491183	NM_030220	ENSMUSG00000018678	Sp2	4930480I16Rik|mKIAA0048	Sp2 transcription factor	protein-coding	0.060000	0.666667			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6025	chr5	72956323	72956523	+	1.15555	NA	intron (NM_153567, intron 4 of 8)	intron (NM_153567, intron 4 of 8)	42061	NM_153567	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-878	chr10	70873116	70873316	+	1.15555	NA	Intergenic	Intergenic	-217253	NR_045292	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA	0.010000	0.542289			55(CTCTGATCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4691	chr2	142689099	142689299	+	1.15555	NA	intron (NM_001355123, intron 24 of 26)	intron (NM_001355123, intron 24 of 26)	212265	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7784	chr9	85133445	85133645	+	1.15555	NA	Intergenic	Intergenic	193579	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Tent5a	BAP014|D930050G01Rik|Fam46a	terminal nucleotidyltransferase 5A	protein-coding	0.020000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-79	chr10	9575485	9575685	+	1.15555	NA	Intergenic	Intergenic	99623	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-80	chr1	26507987	26508187	+	1.15555	NA	Intergenic	Intergenic	179373	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4224	chr2	26230233	26230433	+	1.15555	NA	intron (NM_153559, intron 1 of 12)	intron (NM_153559, intron 1 of 12)	7066	NM_001302956	227638	Mm.116769	NM_153559	ENSMUSG00000036327	Qsox2	BC030934|Qscn6l1|Soxn	quiescin Q6 sulfhydryl oxidase 2	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5681	chr4	107954785	107954985	+	1.15555	NA	intron (NR_131071, intron 1 of 2)	MYSERV6-int|LTR|ERVK	953	NR_131071	77223	Mm.401926	NR_131071	ENSMUSG00000086713	4930407G08Rik	-	RIKEN cDNA 4930407G08 gene	ncRNA	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-691	chr10	9575693	9575893	+	1.15555	NA	Intergenic	Intergenic	99415	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding	0.010000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1857	chr12	102618103	102618303	+	1.15555	NA	intron (NM_172584, intron 3 of 9)	intron (NM_172584, intron 3 of 9)	63262	NM_007693	12652	Mm.4137	NM_007693	ENSMUSG00000021194	Chga	ChrA|cgA	chromogranin A	protein-coding	0.020000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1582	chr12	30893760	30893960	+	1.15555	NA	TTS (NM_001159743)	TTS (NM_001159743)	9536	NM_001159743	100294583	Mm.399726	NM_001159743	ENSMUSG00000054204	Alkal2	6230419C23Rik|Fam150b	ALK and LTK ligand 2	protein-coding	0.010000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6588	chr6	92636071	92636271	+	1.15555	NA	intron (NM_001081146, intron 2 of 8)	L1MB7|LINE|L1	-68805	NM_001134461	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding	0.010000	0.343284			38(AATTTCATGACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2868	chr15	38418725	38418925	+	1.15555	NA	Intergenic	B3|SINE|B2	71722	NR_105916	102465574		NR_105916	ENSMUSG00000099110	Mir6951	Gm27765|mmu-mir-6951	microRNA 6951	ncRNA	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4360	chr2	65565739	65565939	+	1.15555	NA	intron (NM_001355168, intron 1 of 26)	intron (NM_001355168, intron 1 of 26)	1653	NM_001355171	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	sodium channel, voltage-gated, type III, alpha	protein-coding	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1132	chr10	127023750	127023950	+	1.15555	NA	intron (NM_025537, intron 5 of 5)	intron (NM_025537, intron 5 of 5)	6964	NM_025537	66399	Mm.29900	NM_025537	ENSMUSG00000040521	Tsfm	2310050B20Rik|9430024O13Rik|EF-TS|EF-Tsmt	Ts translation elongation factor, mitochondrial	protein-coding	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-161	chr1	55430075	55430275	+	1.15555	NA	intron (NM_001114663, intron 1 of 5)	intron (NM_001114663, intron 1 of 5)	24229	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding	0.000000	0.343284			-62(ACATTGTGATGTTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6477	chr6	60961294	60961494	+	1.15555	NA	intron (NM_001163507, intron 3 of 7)	intron (NM_001163507, intron 3 of 7)	17077	NM_027613	70945	Mm.389770	NM_027613	ENSMUSG00000054641	Mmrn1	4921530G03Rik|Emilin4|Mmrn	multimerin 1	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2481	chr14	48524275	48524475	+	1.15555	NA	Intergenic	Intergenic	78023	NR_132324	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding	0.025000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3642	chr17	85823667	85823867	+	1.15555	NA	Intergenic	Intergenic	-135513	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-879	chr10	70910347	70910547	+	1.15555	NA	Intergenic	L1M2|LINE|L1	249243	NM_001347189	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding	0.000000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-323	chr14	119122837	119123037	+	1.15515	NA	Intergenic	Intergenic	-15328	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding	0.005000	0.298507			83(ATTTGAAAGACATAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-653	chr1	194236813	194237013	+	1.15515	NA	Intergenic	Intergenic	-14154	NR_040477	74942	Mm.60689	NR_040477	ENSMUSG00000103692	4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7240	chr8	47985471	47985671	+	1.15438	NA	intron (NM_133791, intron 1 of 22)	intron (NM_133791, intron 1 of 22)	4973	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding	0.000000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-133	chr11	22008353	22008553	+	1.15438	NA	intron (NM_153078, intron 23 of 24)	intron (NM_153078, intron 23 of 24)	-6802	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding	0.015000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-863	chr9	27071167	27071367	+	1.15438	NA	intron (NM_178113, intron 23 of 35)	intron (NM_178113, intron 23 of 35)	41092	NM_178113	78658	Mm.251777	NM_178113	ENSMUSG00000035024	Ncapd3	2810487N22Rik|4632407J06Rik|AI195468|AU018739|B130055D15Rik|mKIAA0056	non-SMC condensin II complex, subunit D3	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5308	chr3	156304550	156304750	+	1.15299	NA	Intergenic	Intergenic	257037	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	ncRNA	0.000000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-522	chr2	125219454	125219654	+	1.15299	NA	intron (NM_183354, intron 23 of 26)	intron (NM_183354, intron 23 of 26)	-27694	NM_001159646	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding	0.010000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-839	chr8	78719540	78719740	+	1.15299	NA	intron (NM_029736, intron 10 of 11)	intron (NM_029736, intron 10 of 11)	101512	NM_030145	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.030000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-469	chr2	11340700	11340900	+	1.15299	NA	intron (NR_040369, intron 1 of 3)	RLTR13D3A|LTR|ERVK	1311	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	-	predicted gene 13293	ncRNA	0.015000	0.497512			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-887	chr9	94558864	94559064	+	1.15297	NA	Intergenic	RMER15-int|LTR|ERVL	-20883	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	Dipk2a	1190002N15Rik|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.000000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-204	chr12	90916070	90916270	+	1.15152	NA	Intergenic	Intergenic	-129678	NR_045858	71349	Mm.442093	NR_045858	ENSMUSG00000085004	5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3935	chr18	72484594	72484794	+	1.15068	NA	Intergenic	Intergenic	-133625	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0.005000	0.308458		31(AATGCATATGTAAA,-,0.00),50(TGTGCATATTCATT,+,0.00),50(TGTGCATATTCATT,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-594	chr3	148899755	148899955	+	1.15068	NA	intron (NM_001081298, intron 1 of 23)	intron (NM_001081298, intron 1 of 23)	54780	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2085	chr13	58011545	58011745	+	1.15050	NA	intron (NM_001362415, intron 12 of 14)	intron (NM_001362415, intron 12 of 14)	11555	NR_030544	100124491		NR_030544	ENSMUSG00000077962	Mir874	Mirn874|mir-874|mmu-mir-874	microRNA 874	ncRNA	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1069	chr10	117106523	117106723	+	1.15002	NA	intron (NM_177798, intron 1 of 9)	intron (NM_177798, intron 1 of 9)	41851	NM_177798	327826	Mm.135965	NM_177798	ENSMUSG00000020170	Frs2	4732458E18|C330018A15Rik|Frs2alpha|SNT1	fibroblast growth factor receptor substrate 2	protein-coding	0.000000	0.378109			-38(CCATTTTCATTTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3482	chr17	38011361	38011561	+	1.15002	NA	Intergenic	MMSAT4|Satellite|Satellite	48323	NM_146327	258324	Mm.329044	NM_146327	ENSMUSG00000081724	Olfr129	MOR263-9	olfactory receptor 129	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4290	chr2	47961310	47961510	+	1.15002	NA	Intergenic	Lx10|LINE|L1	-852699	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0.000000	0.412935			63(GAATTGTGATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2859	chr15	35028810	35029010	+	1.15002	NA	intron (NM_019635, intron 6 of 10)	intron (NM_019635, intron 6 of 10)	126896	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding	0.000000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-113	chr10	117106575	117106775	+	1.15002	NA	intron (NM_177798, intron 1 of 9)	intron (NM_177798, intron 1 of 9)	41799	NM_177798	327826	Mm.135965	NM_177798	ENSMUSG00000020170	Frs2	4732458E18|C330018A15Rik|Frs2alpha|SNT1	fibroblast growth factor receptor substrate 2	protein-coding	0.005000	0.368159			-90(CCATTTTCATTTAAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-850	chr8	109135460	109135660	+	1.15002	NA	intron (NR_126329, intron 2 of 9)	intron (NR_126329, intron 2 of 9)	60338	NR_126329	628686	Mm.203332	NR_126329	ENSMUSG00000097393	D030068K23Rik	-	RIKEN cDNA D030068K23 gene	ncRNA	0.005000	0.328358			-43(TTCTTCTCTTGTTAAT,+,0.00),-8(ATTAGAAAGGCAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1265	chr11	43703675	43703875	+	1.15002	NA	intron (NM_001363141, intron 1 of 2)	intron (NM_001363141, intron 1 of 2)	21777	NM_001363141	70802	Mm.397449	NM_027557	ENSMUSG00000044950	Pwwp2a	4631424J17Rik|AI891583|AU024105|D930040F23Rik	PWWP domain containing 2A	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1114	chr10	124068007	124068207	+	1.14991	NA	Intergenic	Intergenic	-400967	NR_028310	75030	Mm.159403	NR_028310	ENSMUSG00000112364	4930503E24Rik	-	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7432	chr8	107407815	107408015	+	1.14991	NA	intron (NR_039557, intron 2 of 3).3	intron (NR_039557, intron 2 of 3).3	-4710	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2486	chr14	50914634	50914834	+	1.14991	NA	TTS (NM_133676)	TTS (NM_133676)	10159	NM_133676	66246	Mm.274791	NM_133676	ENSMUSG00000006289	Osgep	1500019L24Rik|GCPL-1|PRSMG1	O-sialoglycoprotein endopeptidase	protein-coding	0.010000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2544	chr14	74822821	74823021	+	1.14991	NA	intron (NM_001033439, intron 4 of 19)	intron (NM_001033439, intron 4 of 19)	90624	NM_001285423	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding	0.010000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-139	chr11	30912744	30912944	+	1.14991	NA	Intergenic	ORR1C1-int|LTR|ERVL-MaLR	27486	NM_175490	237716	Mm.338361	NM_175490	ENSMUSG00000043999	Gpr75	-	G protein-coupled receptor 75	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7095	chr7	132345716	132345916	+	1.14991	NA	Intergenic	Intergenic	-28588	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAc4S-6ST|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate sulfotransferase 15	protein-coding	0.015000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5444	chr4	46643476	46643676	+	1.14991	NA	intron (NM_198664, intron 2 of 12)	intron (NM_198664, intron 2 of 12)	6623	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding	0.005000	0.587065			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-542	chr1	172197304	172197504	+	1.14991	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	9400	NM_001329869	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4334	chr2	59645842	59646042	+	1.14991	NA	promoter-TSS (NM_001290659)	promoter-TSS (NM_001290659)	-827	NM_001290659	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.000000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-999	chr10	106728171	106728371	+	1.14991	NA	intron (NM_001359678, intron 1 of 30)	intron (NM_001359678, intron 1 of 30)	95743	NM_001359678	327814	Mm.391424	NM_177373	ENSMUSG00000053825	Ppfia2	5330438O12|B230207K17Rik|E130120L08Rik|mKIAA4112	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2897	chr15	44806534	44806734	+	1.14991	NA	TTS (NR_040309)	TTS (NR_040309)	-18571	NM_001032727	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-299	chr14	77239498	77239698	+	1.14991	NA	intron (NM_172813, intron 1 of 18)	intron (NM_172813, intron 1 of 18)	82835	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3901	chr18	63040808	63041008	+	1.14991	NA	intron (NM_001039485, intron 40 of 53)	intron (NM_001039485, intron 40 of 53)	62992	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding	0.025000	0.482587			8(ATCTTCATCACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2170	chr13	81477047	81477247	+	1.14991	NA	intron (NM_054053, intron 53 of 89)	intron (NM_054053, intron 53 of 89)	155997	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Adgrv1	Frings|Gpr98|Mass1|Mgr1|VLGR1	adhesion G protein-coupled receptor V1	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-623	chr1	187939777	187939977	+	1.14926	NA	intron (NM_001357534, intron 2 of 7)	intron (NM_001357534, intron 2 of 7)	-57950	NM_001357536	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding	0.010000	0.363184	19(CATGAATAATTCAGC,+,0.00),19(CATGAATAATTCAGC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6221	chr5	138703180	138703380	+	1.14926	NA	Intergenic	Intergenic	-51801	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding	0.000000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-289	chr14	50995522	50995722	+	1.14926	NA	Intergenic	MurSatRep1|Unknown|Unknown	-12129	NM_001162863	75019	Mm.318775	NM_029145	ENSMUSG00000021872	Rnase10	4930474F22Rik|Rah1	ribonuclease, RNase A family, 10 (non-active)	protein-coding	0.005000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-383	chr16	79610828	79611028	+	1.14926	NA	Intergenic	Intergenic	-388448	NM_030146	78654		NM_030146		1700066C05Rik	-	RIKEN cDNA 1700066C05 gene	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5098	chr3	104182766	104182966	+	1.14926	NA	intron (NM_001159354, intron 1 of 20)	Lx8|LINE|L1	37540	NM_133853	99470	Mm.264849	NM_133853	ENSMUSG00000052539	Magi3	4732496O19Rik|6530407C02Rik|AA407180|AI120132|mKIAA1634	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.000000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-676	chr5	56313979	56314179	+	1.14883	NA	Intergenic	Lx6|LINE|L1	1403840	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1589	chr12	33038804	33039004	+	1.14835	NA	exon (NM_001024478, exon 17 of 20)	exon (NM_001024478, exon 17 of 20)	53971	NM_001024478	68764	Mm.60083	NM_001024478	ENSMUSG00000035860	Cdhr3	1110049B09Rik|BB172694|Cdh28	cadherin-related family member 3	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7561	chr9	24497182	24497382	+	1.14835	NA	intron (NM_001359948, intron 1 of 22)	intron (NM_001359948, intron 1 of 22)	5858	NM_001359948	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5607	chr4	94295421	94295621	+	1.14835	NA	Intergenic	RLTR13D2|LTR|ERVK	261275	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.000000	0.388060	45(CATGAATAATACAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4025	chr19	16754241	16754441	+	1.14835	NA	exon (NM_173028, exon 6 of 72)	exon (NM_173028, exon 6 of 72)	26592	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding	0.020000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-494	chr1	160299298	160299498	+	1.14835	NA	intron (NM_001038621, intron 2 of 8)	RLTR11C_MM|LTR|ERVK	-3426	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7231	chr8	44899313	44899513	+	1.14835	NA	Intergenic	Intergenic	-50795	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3447	chr17	26334908	26335108	+	1.14835	NA	Intergenic	Intergenic	-79851	NM_001081656	240055	Mm.133211	NM_001081656	ENSMUSG00000034413	Neurl1b	C230078M08Rik|EG240055	neuralized E3 ubiquitin protein ligase 1B	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5906	chr5	36563952	36564152	+	1.14835	NA	intron (NM_001113362, intron 3 of 14)	intron (NM_001113362, intron 3 of 14)	18345	NM_133910	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding	0.005000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6933	chr7	83376841	83377041	+	1.14835	NA	Intergenic	MLT2D|LTR|ERVL	-207990	NM_177695	233424	Mm.486619	NM_177695	ENSMUSG00000038540	Tmc3	9030203A06	transmembrane channel-like gene family 3	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2309	chr13	112942988	112943188	+	1.14835	NA	intron (NM_172594, intron 8 of 26)	intron (NM_172594, intron 8 of 26)	15408	NM_172594	218629	Mm.35094	NM_172594	ENSMUSG00000042426	Dhx29	3732415M03|AU043276|Ddxx|E130202M19Rik	DEAH (Asp-Glu-Ala-His) box polypeptide 29	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7532	chr9	14568728	14568928	+	1.14835	NA	intron (NM_001081395, intron 6 of 12)	ORR1D2|LTR|ERVL-MaLR	46172	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-735	chr10	24397207	24397407	+	1.14835	NA	intron (NR_163910, intron 3 of 4)	intron (NR_163910, intron 3 of 4)	173790	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	monooxygenase, DBH-like 1	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1282	chr11	48459814	48460014	+	1.14835	NA	Intergenic	Intergenic	-340446	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3571	chr17	68630002	68630202	+	1.14835	NA	intron (NM_177278, intron 14 of 20)	intron (NM_177278, intron 14 of 20)	-207034	NM_001206661	622645	Mm.86422	NM_001206661	ENSMUSG00000095407	Tmem200c	EG622645|Gm6338	transmembrane protein 200C	protein-coding	0.010000	0.388060			33(GATTTGTCATGGTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1193	chr11	22837629	22837829	+	1.14835	NA	intron (NM_001169114, intron 1 of 1)	intron (NM_001169114, intron 1 of 1)	22006	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding	0.010000	0.318408			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-406	chr17	68629952	68630152	+	1.14835	NA	intron (NM_177278, intron 14 of 20)	intron (NM_177278, intron 14 of 20)	-207084	NM_001206661	622645	Mm.86422	NM_001206661	ENSMUSG00000095407	Tmem200c	EG622645|Gm6338	transmembrane protein 200C	protein-coding	0.010000	0.358209			83(GATTTGTCATGGTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-726	chr10	21087835	21088035	+	1.14835	NA	Intergenic	Intergenic	47115	NM_001177776	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding	0.000000	0.393035			-52(ATTTACATAAAAATAT,-,0.00),39(ATTTGCATGGCACTTT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-824	chr8	47985443	47985643	+	1.14829	NA	intron (NM_133791, intron 1 of 22)	intron (NM_133791, intron 1 of 22)	5001	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-844	chr10	58949984	58950184	+	1.14795	NA	intron (NM_172788, intron 1 of 9)	intron (NM_172788, intron 1 of 9)	136725	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5832	chr5	13659889	13660089	+	1.14795	NA	Intergenic	Intergenic	-131630	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1881	chr12	107947884	107948084	+	1.14795	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	55430	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7182	chr8	27889427	27889627	+	1.14787	NA	Intergenic	Intergenic	195326	NR_033590	666422	Mm.484413	NR_033590	ENSMUSG00000110372	Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo	0.025000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1833	chr12	97435204	97435404	+	1.14787	NA	Intergenic	Intergenic	824155	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3892	chr18	62141976	62142176	+	1.14787	NA	Intergenic	Intergenic	37905	NM_007420	11555	Mm.5598	NM_007420	ENSMUSG00000045730	Adrb2	Adrb-2|Badm|Gpcr7	adrenergic receptor, beta 2	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1658	chr12	52146130	52146330	+	1.14787	NA	intron (NM_029760, intron 4 of 10)	intron (NM_029760, intron 4 of 10)	48484	NM_029760	76826	Mm.244781	NM_029760	ENSMUSG00000035142	Nubpl	2410170E07Rik	nucleotide binding protein-like	protein-coding	0.000000	0.393035			-68(ACTTTGCCATGTTAAT,+,0.00),-8(ATCTAAATAACAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-25	chr1	9256497	9256697	+	1.14787	NA	intron (NM_001290393, intron 1 of 19)	intron (NM_001290393, intron 1 of 19)	43280	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3286	chr16	66375152	66375352	+	1.14787	NA	Intergenic	RMER5|LTR|ERV1	-281866	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2933	chr15	54788570	54788770	+	1.14787	NA	Intergenic	L1_Rod|LINE|L1	42760	NM_010930	18133	Mm.5167	NM_010930	ENSMUSG00000037362	Ccn3	C130088N23Rik|Nov	cellular communication network factor 3	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7350	chr8	80873082	80873282	+	1.14787	NA	intron (NM_021356, intron 1 of 9)	intron (NM_021356, intron 1 of 9)	7297	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3622	chr17	80891768	80891968	+	1.14787	NA	Intergenic	Intergenic	-4925	NR_131127	320784	Mm.474182	NR_131127	ENSMUSG00000112121	C230072F16Rik	-	RIKEN cDNA C230072F16 gene	ncRNA	0.015000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2496	chr14	58018976	58019176	+	1.14787	NA	Intergenic	Intergenic	-19814	NM_028643	68514	Mm.26834	NM_028643	ENSMUSG00000021973	Micu2	1110008L20Rik|4833427E09Rik|AU041871|Efha1|Smhs2	mitochondrial calcium uptake 2	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2099	chr13	62206516	62206716	+	1.14787	NA	Intergenic	MMSAT4|Satellite|Satellite	76726	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3684	chr18	6012901	6013101	+	1.14787	NA	Intergenic	Intergenic	123097	NM_001039692	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-617	chr1	187200155	187200355	+	1.14787	NA	intron (NM_029067, intron 1 of 6)	intron (NM_029067, intron 1 of 6)	15191	NM_029067	74717	Mm.250430	NM_028848	ENSMUSG00000026611	Spata17	1700065F16Rik|4930504I07Rik|4930513F16Rik|MSRG-11	spermatogenesis associated 17	protein-coding	0.005000	0.278607			-20(ATTTTAAAAAGAATCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5160	chr3	122520311	122520511	+	1.14787	NA	intron (NM_001355264, intron 6 of 9)	intron (NM_001355264, intron 6 of 9)	21270	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6995	chr7	100550506	100550706	+	1.14787	NA	exon (NM_198831, exon 7 of 8)	exon (NM_198831, exon 7 of 8)	13506	NM_183270	68185	Mm.228995	NM_183270	ENSMUSG00000044881	Coa4	5330414O08Rik|AI115477|AW047259|Chchd8|E2ig2	cytochrome c oxidase assembly factor 4	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4411	chr2	77260096	77260296	+	1.14787	NA	intron (NM_175465, intron 1 of 17)	intron (NM_175465, intron 1 of 17)	20396	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding	0.010000	0.517413			13(ATCTGCAAAATAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7195	chr8	33357363	33357563	+	1.14787	NA	intron (NM_001122822, intron 1 of 33)	RLTR11B|LTR|ERVK	28064	NM_001122822	22427	Mm.228805	NM_011721	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome RecQ like helicase	protein-coding	0.005000	0.417910			-39(CCTTTGTTGTGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6707	chr6	122289366	122289566	+	1.14787	NA	Intergenic	Intergenic	-4725	NR_163697	625931	Mm.391496	NR_163697		Gm6637	EG625931	predicted gene 6637	pseudo	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2381	chr14	18358488	18358688	+	1.14787	NA	Intergenic	T-rich|Low_complexity|Low_complexity	-26744	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding	0.000000	0.417910			64(ATGTGCATGTGAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5256	chr3	146928277	146928477	+	1.14787	NA	intron (NM_001302957, intron 10 of 21)	intron (NM_001302957, intron 10 of 21)	76010	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7490	chr8	127173178	127173378	+	1.14787	NA	intron (NM_001363431, intron 2 of 24)	intron (NM_001363431, intron 2 of 24)	109222	NM_033620	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding	0.020000	0.437811			-61(TCTTGCTCTTGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6773	chr6	147204178	147204378	+	1.14787	NA	intron (NR_033640, intron 2 of 2)	intron (NR_033640, intron 2 of 2)	24037	NR_033640	100039641	Mm.170402	NR_033640	ENSMUSG00000085600	E330012B07Rik	Gm15768	RIKEN cDNA E330012B07 gene	ncRNA	0.000000	0.318408			85(ATTTGCATAACTACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5401	chr4	29272235	29272435	+	1.14787	NA	Intergenic	RLTR35B_MM|LTR|ERVL	204256	NR_151693	102634169		NR_151693		Gm11917	-	predicted gene 11917	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-193	chr1	66386773	66386973	+	1.14787	NA	intron (NM_008632, intron 6 of 13)	intron (NM_008632, intron 6 of 13)	65149	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1293	chr11	53212481	53212681	+	1.14787	NA	Intergenic	Intergenic	87898	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6241	chr5	143334004	143334204	+	1.14787	NA	Intergenic	Intergenic	4796	NR_027874	67672	Mm.30983	NR_027874	ENSMUSG00000089889	0610040B10Rik	-	RIKEN cDNA 0610040B10 gene	ncRNA	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4914	chr3	40366779	40366979	+	1.14787	NA	Intergenic	Intergenic	156033	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7429	chr8	106292557	106292757	+	1.14787	NA	intron (NM_021491, intron 1 of 8)	intron (NM_021491, intron 1 of 8)	10428	NR_126091	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-559	chr1	175762869	175763069	+	1.14787	NA	intron (NM_029453, intron 10 of 27)	intron (NM_029453, intron 10 of 27)	64376	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1413	chr11	93026341	93026541	+	1.14787	NA	Intergenic	Intergenic	-71925	NM_001361707	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3744	chr18	23775638	23775838	+	1.14787	NA	promoter-TSS (NR_105778)	promoter-TSS (NR_105778)	-749	NR_105778	102465185		NR_105778	ENSMUSG00000098607	Mir6360	Gm27296|mmu-mir-6360	microRNA 6360	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6157	chr5	114273902	114274102	+	1.14787	NA	promoter-TSS (NM_148935)	promoter-TSS (NM_148935)	-241	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding	0.055000	0.671642			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5258	chr3	147019543	147019743	+	1.14787	NA	Intergenic	Intergenic	167276	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5485	chr4	56874176	56874376	+	1.14787	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-9065	NM_018761	54366	Mm.218891	NM_018761	ENSMUSG00000038816	Ctnnal1	ACRP|AI616177|AW545119|C86009|Catnal1	catenin (cadherin associated protein), alpha-like 1	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4447	chr2	90739264	90739464	+	1.14787	NA	Intergenic	Intergenic	-6194	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding	0.005000	0.278607		-65(AATGAATATGGATG,+,0.00),-65(AATGAATATGGATG,-,0.00)	-43(ATTTAAATAGCAAAAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-426	chr18	22863534	22863734	+	1.14630	NA	intron (NM_001361223, intron 6 of 11)	intron (NM_001361223, intron 6 of 11)	175029	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding	0.000000	0.348259			-73(ATAAGCAATAGAAAGG,-,0.00),18(ATTTGCATGAGTCTGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-722	chr6	5892771	5892971	+	1.14630	NA	intron (NM_001191023, intron 5 of 15)	intron (NM_001191023, intron 5 of 15)	84522	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	ncRNA	0.015000	0.407960			-89(CGTTTCTTTTGCATAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-119	chr10	122410816	122411016	+	1.14630	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-37583	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding	0.000000	0.447761			-46(GTTTGAATAAGAATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-718	chr5	150723555	150723755	+	1.14630	NA	intron (NM_175310, intron 6 of 34)	RMER10A|LTR|ERVL	49828	NM_175310	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6265	chr5	150723547	150723747	+	1.14630	NA	intron (NM_175310, intron 6 of 34)	intron (NM_175310, intron 6 of 34)	49820	NM_175310	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding	0.000000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-738	chr6	35288848	35289048	+	1.14588	NA	intron (NM_172892, intron 3 of 15)	intron (NM_172892, intron 3 of 15)	19178	NM_172892	243755	Mm.23666	NM_172892	ENSMUSG00000029843	Slc13a4	9630060C05Rik|SUT-1|SUT1	solute carrier family 13 (sodium/sulfate symporters), member 4	protein-coding	0.010000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1909	chr12	117751574	117751774	+	1.14444	NA	intron (NM_175930, intron 26 of 27)	intron (NM_175930, intron 26 of 27)	-92187	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding	0.030000	0.497512			80(CATTTCCTTTGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-220	chr12	117751585	117751785	+	1.14444	NA	intron (NM_175930, intron 26 of 27)	intron (NM_175930, intron 26 of 27)	-92176	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding	0.025000	0.497512			69(CATTTCCTTTGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-72	chr1	194593556	194593756	+	1.14444	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-26173	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding	0.005000	0.462687			-90(ATTTGAATAGGAATGC,-,0.00),63(ATTTCAAAAGCAAAAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-187	chr12	44091500	44091700	+	1.14444	NA	Intergenic	Lx8|LINE|L1	118468	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7734	chr9	75672912	75673112	+	1.14444	NA	intron (NM_009130, intron 6 of 11)	L2b|LINE|L2	11044	NM_009130	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-611	chr1	185725644	185725844	+	1.14429	NA	intron (NR_030555, intron 4 of 6)	L1ME1|LINE|L1	188408	NR_030555	100124483		NR_030555	ENSMUSG00000076976	Mir297c	Mirn297c	microRNA 297c	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1788	chr12	85991258	85991458	+	1.14429	NA	intron (NM_001364627, intron 29 of 31)	intron (NM_001364627, intron 29 of 31)	87683	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7626	chr9	43044319	43044519	+	1.14429	NA	intron (NM_001359232, intron 1 of 40)	intron (NM_001359232, intron 1 of 40)	61299	NM_001359232	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-253	chr1	88437697	88437897	+	1.14429	NA	Intergenic	Intergenic	30787	NM_029269	75396	Mm.173058	NM_029269	ENSMUSG00000026295	Spp2	0610038O04Rik|pp-24|spp24	secreted phosphoprotein 2	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4094	chr19	43476032	43476232	+	1.14429	NA	intron (NM_031396, intron 6 of 10)	intron (NM_031396, intron 6 of 10)	35696	NM_031396	83674	Mm.329864	NM_031396	ENSMUSG00000025189	Cnnm1	AI846314|Acdp1|CLP-1	cyclin M1	protein-coding	0.020000	0.477612			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-687	chr5	82933931	82934131	+	1.14429	NA	Intergenic	Intergenic	-134966	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mir-1187|mmu-mir-1187	microRNA 1187	ncRNA	0.020000	0.313433			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-36	chr1	131365914	131366114	+	1.14429	NA	intron (NM_001081011, intron 4 of 22)	ORR1E|LTR|ERVL-MaLR	-86451	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-E|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1028	chr10	111081920	111082120	+	1.14429	NA	Intergenic	Intergenic	-71954	NM_001359624	320150	Mm.339281	NM_172554	ENSMUSG00000035798	Zdhhc17	A230053P19Rik|BB187739|D130071N24Rik|DHHC-17|Hip14	zinc finger, DHHC domain containing 17	protein-coding	0.005000	0.328358			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-176	chr12	5068857	5069057	+	1.14429	NA	Intergenic	L1MEf|LINE|L1	151604	NM_001362349	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding	0.010000	0.378109			-67(TCTATGTGATTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5157	chr3	121532346	121532546	+	1.14429	NA	promoter-TSS (NM_145394)	promoter-TSS (NM_145394)	-102	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding	0.040000	0.641791			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2182	chr13	85855734	85855934	+	1.14429	NA	Intergenic	Lx6|LINE|L1	190961	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit 7C	protein-coding	0.005000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-148	chr11	51526802	51527002	+	1.14429	NA	intron (NM_153393, intron 4 of 28)	intron (NM_153393, intron 4 of 28)	-57855	NM_028398	72947	Mm.256875	NM_028398	ENSMUSG00000020359	Phykpl	2900006B13Rik|Agxt2l2	5-phosphohydroxy-L-lysine phospholyase	protein-coding	0.030000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3976	chr18	84393739	84393939	+	1.14429	NA	intron (NM_001033341, intron 4 of 8)	intron (NM_001033341, intron 4 of 8)	195665	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4385	chr2	71594795	71594995	+	1.14429	NA	intron (NR_039557, intron 2 of 3)	intron (NR_039557, intron 2 of 3)	-48141	NM_010054	13392	Mm.3896	NM_010054	ENSMUSG00000023391	Dlx2	AW121999|Dlx-2|Tes-1	distal-less homeobox 2	protein-coding	0.030000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1289	chr11	51526827	51527027	+	1.14429	NA	intron (NM_153393, intron 4 of 28)	intron (NM_153393, intron 4 of 28)	-57830	NM_028398	72947	Mm.256875	NM_028398	ENSMUSG00000020359	Phykpl	2900006B13Rik|Agxt2l2	5-phosphohydroxy-L-lysine phospholyase	protein-coding	0.030000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1520	chr12	5068855	5069055	+	1.14429	NA	Intergenic	L1MEf|LINE|L1	151602	NM_001362349	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding	0.010000	0.373134			-65(TCTATGTGATTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3081	chr16	11558846	11559046	+	1.14429	NA	intron (NM_028964, intron 14 of 20)	Lx2|LINE|L1	153298	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5498	chr4	59860071	59860271	+	1.14429	NA	intron (NM_172468, intron 2 of 8)	intron (NM_172468, intron 2 of 8)	54521	NM_172468	209131	Mm.259705	NM_172468	ENSMUSG00000028385	Snx30	4732481H14Rik|C030041J06Rik	sorting nexin family member 30	protein-coding	0.010000	0.532338			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-374	chr16	55631208	55631408	+	1.14245	NA	Intergenic	Intergenic	136577	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4487	chr2	104723109	104723309	+	1.14204	NA	intron (NM_144804, intron 6 of 8)	intron (NM_144804, intron 6 of 8)	-6919	NM_001033768	241593	Mm.423301	NM_001033768	ENSMUSG00000074997	Pin1rt1	Pin1-ps1|Pin1l	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1, retrogene 1	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1337	chr11	70916323	70916523	+	1.14204	NA	intron (NM_019400, intron 8 of 17)	intron (NM_019400, intron 8 of 17)	53550	NM_001083331	19069	Mm.288962	NM_172394	ENSMUSG00000040667	Nup88	Nup84|Prei2	nucleoporin 88	protein-coding	0.000000	0.407960			-57(TATTTCTTATTCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-678	chr10	5381635	5381835	+	1.14204	NA	intron (NM_153399, intron 13 of 31)	intron (NM_153399, intron 13 of 31)	106579	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|KASH1|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding	0.000000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-61	chr1	185183897	185184097	+	1.14204	NA	Intergenic	Intergenic	-20171	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding	0.030000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-291	chr1	98025504	98025704	+	1.14204	NA	intron (NM_001357127, intron 1 of 25)	intron (NM_001357127, intron 1 of 25)	22189	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA	0.010000	0.293532			-15(CATTTGTAATGCTAAC,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-581	chr3	131034242	131034442	+	1.14204	NA	Intergenic	Intergenic	-75955	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding	0.000000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-155	chr11	70916318	70916518	+	1.14204	NA	intron (NM_019400, intron 8 of 17)	intron (NM_019400, intron 8 of 17)	53555	NM_001083331	19069	Mm.288962	NM_172394	ENSMUSG00000040667	Nup88	Nup84|Prei2	nucleoporin 88	protein-coding	0.000000	0.402985			-52(TATTTCTTATTCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7878	chr9	110404958	110405158	+	1.14204	NA	intron (NM_001081043, intron 1 of 24)	B3A|SINE|B2	3152	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1903	chr12	117028573	117028773	+	1.14188	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	122596	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	-	predicted gene 10421	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-919	chr10	87812826	87813026	+	1.14188	NA	Intergenic	Intergenic	-45339	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding	0.015000	0.467662			-95(ATTTGCAAGGCAGAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2278	chr13	108288738	108288938	+	1.14188	NA	Intergenic	Intergenic	-27499	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding	0.010000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-628	chr4	72441497	72441697	+	1.14188	NA	Intergenic	Intergenic	240353	NR_027923	68285	Mm.37541	NR_027923		C630043F03Rik	AI851307	RIKEN cDNA C630043F03 gene	ncRNA	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1188	chr11	22008110	22008310	+	1.14188	NA	intron (NM_153078, intron 23 of 24)	intron (NM_153078, intron 23 of 24)	-6559	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding	0.020000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-536	chr1	170492673	170492873	+	1.14188	NA	intron (NR_154593, intron 2 of 9)	Tigger18a|DNA|TcMar-Tigger	64337	NR_154593	70729	Mm.409310	NM_027528	ENSMUSG00000038473	Nos1ap	6330408P19Rik|Capon	nitric oxide synthase 1 (neuronal) adaptor protein	protein-coding	0.000000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-644	chr4	104012586	104012786	+	1.14124	NA	intron (NM_001369049, intron 2 of 19)	intron (NM_001369049, intron 2 of 19)	-354852	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.020000	0.402985		66(GATGGATATGCATC,+,0.00)	21(TACTTGTTTTGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4158	chr2	6738016	6738216	+	1.14124	NA	intron (NM_001110230, intron 2 of 14)	intron (NM_001110230, intron 2 of 14)	-16454	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-911	chr10	86089810	86090010	+	1.14124	NA	intron (NM_013722, intron 7 of 13)	intron (NM_013722, intron 7 of 13)	-5944	NR_038024	78170	Mm.444790	NR_038024	ENSMUSG00000112493	4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA	0.010000	0.358209			-26(TTTAAAATGACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5169	chr3	126723191	126723391	+	1.14124	NA	intron (NM_001025438, intron 3 of 18)	intron (NM_001025438, intron 3 of 18)	126340	NM_001346635	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding	0.015000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-468	chr2	6737993	6738193	+	1.14124	NA	intron (NM_001110230, intron 2 of 14)	intron (NM_001110230, intron 2 of 14)	-16431	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7298	chr8	66448697	66448897	+	1.14124	NA	intron (NM_175188, intron 6 of 7)	intron (NM_175188, intron 6 of 7)	37733	NM_001357208	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding	0.010000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-579	chr3	126723164	126723364	+	1.14124	NA	intron (NM_001025438, intron 3 of 18)	intron (NM_001025438, intron 3 of 18)	126313	NM_001346635	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding	0.020000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5066	chr3	93506337	93506537	+	1.14124	NA	Intergenic	Intergenic	-14059	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding	0.040000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4761	chr2	160396260	160396460	+	1.14124	NA	Intergenic	Intergenic	-29295	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding	0.020000	0.398010			33(ATTTAAAAGTGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1172	chr11	16257083	16257283	+	1.14124	NA	promoter-TSS (NM_145967)	promoter-TSS (NM_145967)	-559	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3382	chr16	91869721	91869921	+	1.14124	NA	intron (NM_010587, intron 28 of 38)	intron (NM_010587, intron 28 of 38)	61809	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|Atp5po|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding	0.020000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7857	chr9	103623594	103623794	+	1.14124	NA	intron (NM_178638, intron 2 of 5)	intron (NM_178638, intron 2 of 5)	66604	NR_040764	319215	Mm.425597	NR_040764	ENSMUSG00000099616	4932413F04Rik	-	RIKEN cDNA 4932413F04 gene	ncRNA	0.020000	0.502488			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-690	chr5	89578760	89578960	+	1.14124	NA	intron (NM_133192, intron 3 of 3)	intron (NM_133192, intron 3 of 3)	-37576	NR_037571	631105	Mm.7732	NR_037571		Gm7056	Gm149	predicted gene 7056	ncRNA	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5660	chr4	104012572	104012772	+	1.14124	NA	intron (NM_001369049, intron 2 of 19)	intron (NM_001369049, intron 2 of 19)	-354866	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.020000	0.407960		80(GATGGATATGCATC,+,0.00)	35(TACTTGTTTTGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6316	chr6	14505104	14505304	+	1.14110	NA	Intergenic	Intergenic	250070	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory subunit 3A	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6529	chr6	72749026	72749226	+	1.14110	NA	intron (NM_009332, intron 3 of 11)	intron (NM_009332, intron 3 of 11)	39919	NM_009332	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2353	chr14	11376579	11376779	+	1.14110	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	94202	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA	0.005000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-797	chr7	84681062	84681262	+	1.14110	NA	intron (NM_001360577, intron 1 of 7)	intron (NM_001360577, intron 1 of 7)	-1766	NM_001360580	65098	Mm.209349	NM_022985	ENSMUSG00000030629	Zfand6	3110005P07Rik|Awp1|Za20d3	zinc finger, AN1-type domain 6	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-975	chr10	99046820	99047020	+	1.14110	NA	Intergenic	Intergenic	-60162	NR_153333	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding	0.000000	0.398010		-8(CATTCATTTGCATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-132	chr1	44645475	44645675	+	1.14110	NA	intron (NM_028450, intron 1 of 10)	L1M4|LINE|L1	93904	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding	0.000000	0.248756			-48(TCTTTATTATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2263	chr13	104039934	104040134	+	1.14110	NA	intron (NM_029447, intron 9 of 12)	intron (NM_029447, intron 9 of 12)	69580	NM_029447	75805	Mm.127692	NM_029447	ENSMUSG00000021710	Nln	4930472G13Rik|C79345	neurolysin (metallopeptidase M3 family)	protein-coding	0.010000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-62	chr1	186433285	186433485	+	1.14107	NA	Intergenic	Intergenic	125296	NR_131124	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA	0.015000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-976	chr10	99385415	99385615	+	1.14038	NA	Intergenic	Intergenic	122284	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3806	chr18	40059707	40059907	+	1.14038	NA	Intergenic	Intergenic	159592	NM_023311	67180	Mm.270382	NM_023311	ENSMUSG00000024487	Yipf5	2610311I19Rik|AA408236|Yip1a	Yip1 domain family, member 5	protein-coding	0.005000	0.348259			66(GCTTTTTCAATCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2339	chr14	8592862	8593062	+	1.14038	NA	intron (NM_028934, intron 4 of 15)	L1M4|LINE|L1	73328	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding	0.025000	0.313433			-10(ATTTGTATAATAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5051	chr3	85618870	85619070	+	1.13992	NA	exon (NM_144896, exon 9 of 13)	exon (NM_144896, exon 9 of 13)	44841	NM_144896	229487	Mm.52275	NM_144896	ENSMUSG00000028085	Gatb	9430026F02Rik|Pet112|Pet112l	glutamyl-tRNA(Gln) amidotransferase, subunit B	protein-coding	0.025000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3230	chr16	52251726	52251926	+	1.13992	NA	intron (NM_009655, intron 15 of 15)	intron (NM_009655, intron 15 of 15)	201255	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7882	chr9	111869644	111869844	+	1.13891	NA	Intergenic	Intergenic	-179396	NM_016853	20840	Mm.1414	NM_016853	ENSMUSG00000032502	Stac	-	src homology three (SH3) and cysteine rich domain	protein-coding	0.010000	0.333333			29(GTTTCCATGACAACAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4265	chr2	39460057	39460257	+	1.13891	NA	Intergenic	Intergenic	-233808	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik|Pp6C	protein phosphatase 6, catalytic subunit	protein-coding	0.005000	0.333333			-66(GTTTACTCATGTAATT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1271	chr11	45008175	45008375	+	1.13891	NA	TTS (NM_001290709)	TTS (NM_001290709)	108653	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA	0.025000	0.542289			-9(AATTTGGAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2216	chr13	94449997	94450197	+	1.13891	NA	intron (NM_009680, intron 12 of 26)	intron (NM_009680, intron 12 of 26)	91137	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding	0.010000	0.328358			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-146	chr11	45008127	45008327	+	1.13891	NA	TTS (NM_001290709)	TTS (NM_001290709)	108701	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA	0.025000	0.522388			39(AATTTGGAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-754	chr10	29459693	29459893	+	1.13891	NA	intron (NM_028351, intron 4 of 4)	intron (NM_028351, intron 4 of 4)	76074	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1642	chr12	46036680	46036880	+	1.13891	NA	Intergenic	MIRb|SINE|MIR	781987	NM_001364637	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5322	chr4	4138238	4138438	+	1.13891	NA	5' UTR (NM_001002927, exon 1 of 2)	5' UTR (NM_001002927, exon 1 of 2)	107	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding	0.025000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1123	chr10	125220306	125220506	+	1.13891	NA	3' UTR (NM_001358915, exon 6 of 6)	3' UTR (NM_001358915, exon 6 of 6)	88410	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.000000	0.323383			-50(ATTACCAAAACAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5448	chr4	48584562	48584762	+	1.13891	NA	promoter-TSS (NM_001356272)	promoter-TSS (NM_001356272)	-512	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|TR-1|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding	0.040000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2891	chr15	42720856	42721056	+	1.13891	NA	Intergenic	Intergenic	-43979	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5290	chr3	152166714	152166914	+	1.13891	NA	promoter-TSS (NM_016867)	promoter-TSS (NM_016867)	-914	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding	0.025000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7731	chr9	74893045	74893245	+	1.13891	NA	Intergenic	Intergenic	31224	NM_008262	15379	Mm.303355	NM_008262	ENSMUSG00000043013	Onecut1	D9Ertd423e|HNF-6|Hfh12|Hnf6|Hnf6b|OC-1|Oc1	one cut domain, family member 1	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4510	chr2	108794999	108795199	+	1.13891	NA	Intergenic	Intergenic	483191	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0.015000	0.363184			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-623	chr4	62653645	62653845	+	1.13891	NA	intron (NM_134257, intron 10 of 15)	intron (NM_134257, intron 10 of 15)	-20229	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding	0.010000	0.532338			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-342	chr15	42720888	42721088	+	1.13891	NA	Intergenic	Intergenic	-44011	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.000000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-271	chr13	116694748	116694948	+	1.13891	NA	Intergenic	Intergenic	143330	NR_153406	74680	Mm.488118	NR_153406	ENSMUSG00000114290	4930435F18Rik	-	RIKEN cDNA 4930435F18 gene	ncRNA	0.005000	0.363184	-99(TATACATTATTCATT,+,0.00),-99(TATACATTATTCATT,-,0.00)		-87(ATTTCCTAAACAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-431	chr1	143819803	143820003	+	1.13891	NA	Intergenic	Intergenic	42625	NM_001159866	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5046	chr3	84116163	84116363	+	1.13891	NA	intron (NM_029797, intron 5 of 7)	MIR|SINE|MIR	39523	NM_029797	76915	Mm.274829	NM_029797	ENSMUSG00000033752	Mnd1	2610034E18Rik|AI591601|Gaj	meiotic nuclear divisions 1	protein-coding	0.005000	0.328358			35(ATTAACAACAGAATTT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-668	chr5	44627928	44628128	+	1.13891	NA	intron (NM_001077398, intron 2 of 8)	MIR|SINE|MIR	171718	NM_001359070	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding	0.010000	0.457711			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-188	chr12	46036692	46036892	+	1.13891	NA	Intergenic	MIRb|SINE|MIR	781975	NM_001364637	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1859	chr12	102745050	102745250	+	1.13846	NA	3' UTR (NM_001324515, exon 2 of 2)	3' UTR (NM_001324515, exon 2 of 2)	1390	NM_177140	320351	Mm.86546	NM_177140	ENSMUSG00000046675	Tmem251	D230037D09Rik	transmembrane protein 251	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1990	chr13	25869579	25869779	+	1.13828	NA	Intergenic	Intergenic	96637	NR_045062	100503530	Mm.86763	NR_045062	ENSMUSG00000086531	Gm11351	-	predicted gene 11351	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6791	chr7	12967096	12967296	+	1.13753	NA	intron (NM_001362140, intron 1 of 2)	B1_Mur2|SINE|Alu	1358	NM_001362140	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding	0.005000	0.487562			-68(TTTTGAAAGACAATCT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-10	chr1	29341600	29341800	+	1.13683	NA	Intergenic	Intergenic	-79788	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-742	chr10	25287058	25287258	+	1.13561	NA	intron (NM_018747, intron 2 of 7)	intron (NM_018747, intron 2 of 7)	12005	NM_018747	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding	0.020000	0.447761			-84(ACTCTCCCATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7379	chr8	94273962	94274162	+	1.13561	NA	intron (NM_001357268, intron 1 of 20)	intron (NM_001357268, intron 1 of 20)	5456	NM_001357268	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3701	chr18	10316609	10316809	+	1.13561	NA	Intergenic	Intergenic	-8470	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding	0.005000	0.417910		-46(CATGAAAATGTATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6848	chr7	50269456	50269656	+	1.13561	NA	intron (NM_001037906, intron 11 of 19)	L1MA9|LINE|L1	294206	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7327	chr8	77452636	77452836	+	1.13561	NA	promoter-TSS (NM_001363421)	promoter-TSS (NM_001363421)	-647	NM_001363421	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7412	chr8	101637835	101638035	+	1.13561	NA	Intergenic	L2a|LINE|L2	1147176	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2057	chr13	45190192	45190392	+	1.13561	NA	Intergenic	Intergenic	-188196	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5698	chr4	114637263	114637463	+	1.13561	NA	Intergenic	Intergenic	-184357	NR_033617	433746	Mm.388908	NR_033617	ENSMUSG00000055198	Gm12830	-	predicted gene 12830	ncRNA	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-215	chr1	78093073	78093273	+	1.13561	NA	Intergenic	RMER1B|Other|Other	103963	NM_001159520	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding	0.015000	0.412935		-25(CTTGCAAATTCATT,+,0.00)	85(TCTGTGTCATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4530	chr2	115136136	115136336	+	1.13561	NA	Intergenic	Intergenic	208044	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	ncRNA	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1415	chr11	93873805	93874005	+	1.13561	NA	intron (NM_001013375, intron 7 of 13)	B2_Mm2|SINE|B2	11861	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-717	chr10	19450284	19450484	+	1.13561	NA	Intergenic	Intergenic	-36331	NR_152784	102635880	Mm.331974	NR_152784	ENSMUSG00000110902	Gm33104	-	predicted gene, 33104	ncRNA	0.000000	0.303483			-40(ATTTGAATAATAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1939	chr13	8845465	8845665	+	1.13561	NA	intron (NM_001039388, intron 7 of 13)	intron (NM_001039388, intron 7 of 13)	25479	NM_172445	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6377	chr6	31204657	31204857	+	1.13561	NA	intron (NR_110469, intron 1 of 3)	intron (NR_110469, intron 1 of 3)	13717	NR_110469	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2779	chr15	9898270	9898470	+	1.13561	NA	Intergenic	Intergenic	-149502	NM_001305044	320277	Mm.127822	NM_177123	ENSMUSG00000072663	Spef2	C230086A09Rik	sperm flagellar 2	protein-coding	0.005000	0.412935			-2(CTAGTGTTATTCAGAT,+,0.00),43(TTTTGCAAGTCAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7130	chr7	145198483	145198683	+	1.13561	NA	intron (NR_132643, intron 19 of 22)	intron (NR_132643, intron 19 of 22)	9536	NM_001369202	100040049	Mm.102235	NM_001369202	ENSMUSG00000109305	Smim38	1810010D01Rik|Gm2572	small integral membrane protein 38	protein-coding	0.000000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3445	chr17	25547156	25547356	+	1.13561	NA	Intergenic	MLTR11B|LTR|ERVK	23430	NM_011447	20681	Mm.258220	NM_011447	ENSMUSG00000024176	Sox8	-	SRY (sex determining region Y)-box 8	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6103	chr5	97954754	97954954	+	1.13561	NA	intron (NM_133738, intron 12 of 16)	intron (NM_133738, intron 12 of 16)	76163	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1738	chr12	73085996	73086196	+	1.13561	NA	Intergenic	Intergenic	27149	NM_011382	20474	Mm.249575	NM_011382	ENSMUSG00000034460	Six4	AI047561|AREC3|TrexBF	sine oculis-related homeobox 4	protein-coding	0.010000	0.477612			-24(TCATAGTCATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6148	chr5	110241912	110242112	+	1.13561	NA	exon (NM_027922, exon 6 of 13)	exon (NM_027922, exon 6 of 13)	11008	NM_027922	71782	Mm.288442	NM_027922	ENSMUSG00000029501	Ankle2	1110001J12Rik|AI661024|D5Ertd585e	ankyrin repeat and LEM domain containing 2	protein-coding	0.005000	0.348259			-65(CATTTTGCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-583	chr1	178876431	178876631	+	1.13561	NA	intron (NM_001161665, intron 9 of 14)	intron (NM_001161665, intron 9 of 14)	347406	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding	0.015000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7476	chr8	122876679	122876879	+	1.13561	NA	Intergenic	Intergenic	28405	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7483	chr8	124339633	124339833	+	1.13561	NA	intron (NM_139272, intron 14 of 15)	intron (NM_139272, intron 14 of 15)	94203	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding	0.010000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1183	chr11	20038789	20038989	+	1.13561	NA	Intergenic	Intergenic	74062	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding	0.025000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4437	chr2	85162350	85162550	+	1.13561	NA	Intergenic	MIRc|SINE|MIR	26090	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding	0.010000	0.353234			-35(ATTTGAAACAAAATAT,-,0.00),81(ATAAACATCATAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1707	chr12	68493155	68493355	+	1.13561	NA	Intergenic	Intergenic	665931	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1358	chr11	75116385	75116585	+	1.13561	NA	intron (NM_001002764, intron 13 of 18)	intron (NM_001002764, intron 13 of 18)	-50494	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-946	chr10	93289005	93289205	+	1.13561	NA	intron (NM_013508, intron 1 of 4)	intron (NM_013508, intron 1 of 4)	22054	NM_001322265	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7169	chr8	18944614	18944814	+	1.13561	NA	intron (NM_001113350, intron 2 of 6)	BGLII_Mus|LTR|ERVK	6157	NM_001286469	319581	Mm.111354	NM_176951	ENSMUSG00000039814	Xkr5	5430438H03Rik|XRG5	X-linked Kx blood group related 5	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6152	chr5	111319021	111319221	+	1.13561	NA	Intergenic	Intergenic	-11576	NM_019640	56305	Mm.200516	NM_019640	ENSMUSG00000050017	Pitpnb	PI-TP-beta	phosphatidylinositol transfer protein, beta	protein-coding	0.005000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7010	chr7	106645233	106645433	+	1.13561	NA	promoter-TSS (NM_001277179)	promoter-TSS (NM_001277179)	-688	NM_001277180	434223	Mm.276443	NM_001277179		Gm1966	-	predicted gene 1966	protein-coding	0.000000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-436	chr18	40059802	40060002	+	1.13509	NA	Intergenic	Intergenic	159497	NM_023311	67180	Mm.270382	NM_023311	ENSMUSG00000024487	Yipf5	2610311I19Rik|AA408236|Yip1a	Yip1 domain family, member 5	protein-coding	0.010000	0.427861			-29(GCTTTTTCAATCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-43	chr1	152953862	152954062	+	1.13509	NA	Intergenic	Intergenic	-1139	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2028	chr13	36400826	36401026	+	1.13489	NA	intron (NM_001039189, intron 4 of 5)	intron (NM_001039189, intron 4 of 5)	283283	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3295	chr16	67210895	67211095	+	1.13489	NA	intron (NM_178721, intron 1 of 9)	L1MA7|LINE|L1	409913	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3452	chr17	28431229	28431429	+	1.13489	NA	intron (NM_010220, intron 3 of 10)	intron (NM_010220, intron 3 of 10)	54820	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding	0.025000	0.402985			-46(GTTTACATTATAAAAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-235	chr13	36400932	36401132	+	1.13489	NA	intron (NM_001039189, intron 4 of 5)	intron (NM_001039189, intron 4 of 5)	283389	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4175	chr2	11340930	11341130	+	1.13458	NA	intron (NR_040369, intron 1 of 3)	RLTR13D3A|LTR|ERVK	1541	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	-	predicted gene 13293	ncRNA	0.000000	0.388060	30(ATTGTATTATTCATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1026	chr10	110949845	110950045	+	1.13458	NA	intron (NM_001359622, intron 11 of 16)	intron (NM_001359622, intron 11 of 16)	29769	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding	0.015000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-812	chr7	125878350	125878550	+	1.13458	NA	TTS (NM_001101488)	TTS (NM_001101488)	170580	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding	0.025000	0.457711		-24(CATGACTATTTATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4495	chr2	106761829	106762029	+	1.13452	NA	intron (NM_001356554, intron 3 of 6)	intron (NM_001356554, intron 3 of 6)	66328	NM_029837	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2441	chr14	34062273	34062473	+	1.13452	NA	intron (NM_172808, intron 9 of 16)	MTEa-int|LTR|ERVL-MaLR	8903	NM_172808	239029	Mm.477093	NM_172808	ENSMUSG00000047441	Antxrl	1700112N15Rik|4933430J11	anthrax toxin receptor-like	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1140	chr11	5009698	5009898	+	1.13452	NA	intron (NM_001355659, intron 2 of 22)	intron (NM_001355659, intron 2 of 22)	22974	NM_001243044	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-370	chr1	128459535	128459735	+	1.13452	NA	Intergenic	Intergenic	-42219	NM_145507	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6659	chr6	108965943	108966143	+	1.13452	NA	Intergenic	Intergenic	137402	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding	0.005000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-510	chr2	106761808	106762008	+	1.13452	NA	intron (NM_001356554, intron 3 of 6)	intron (NM_001356554, intron 3 of 6)	66307	NM_029837	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding	0.000000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-180	chr12	24928279	24928479	+	1.13403	NA	intron (NM_026037, intron 4 of 12)	intron (NM_026037, intron 4 of 12)	-46553	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding	0.020000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6793	chr7	16343889	16344089	+	1.13403	NA	intron (NM_019748, intron 6 of 8)	intron (NM_019748, intron 6 of 8)	34406	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding	0.015000	0.383085			-94(TTTTAAAAAAGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3721	chr18	16649475	16649675	+	1.13403	NA	intron (NM_007664, intron 3 of 15)	intron (NM_007664, intron 3 of 15)	159671	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding	0.005000	0.338308		-91(TTTGAATATGTATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2592	chr14	80302114	80302314	+	1.13403	NA	Intergenic	Intergenic	301912	NM_001351947	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4724	chr2	150173096	150173296	+	1.13403	NA	Intergenic	RLTR22_Mur|LTR|ERVK	-8559	NM_001145863	100271882		NM_001145863	ENSMUSG00000079009	Gm14139	-	predicted gene 14139	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7013	chr7	109071954	109072154	+	1.13403	NA	intron (NM_178780, intron 1 of 4)	intron (NM_178780, intron 1 of 4)	11270	NM_001038624	320360	Mm.71007	NM_178780	ENSMUSG00000048330	Ric3	E130307J04Rik	RIC3 acetylcholine receptor chaperone	protein-coding	0.005000	0.427861			67(CCAGTGTGATGTTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-106	chr10	108799603	108799803	+	1.13403	NA	intron (NM_001252342, intron 3 of 10)	intron (NM_001252342, intron 3 of 10)	-99543	NM_203660	368203	Mm.452758	NM_203660	ENSMUSG00000112039	Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2027	chr13	36345268	36345468	+	1.13403	NA	intron (NM_001039189, intron 4 of 5)	intron (NM_001039189, intron 4 of 5)	227725	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.020000	0.442786			23(CTTTGCATGAGAGCGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8078	chrX	130468989	130469189	+	1.13403	NA	Intergenic	Intergenic	719347	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5209	chr3	135720514	135720714	+	1.13403	NA	Intergenic	L1MA4A|LINE|L1	-29067	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7854	chr9	102465714	102465914	+	1.13403	NA	Intergenic	Intergenic	-40324	NM_024291	16716	Mm.101692	NM_024291	ENSMUSG00000035606	Ky	CD1|D9Mgc44e|ky	kyphoscoliosis peptidase	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4575	chr2	124428106	124428306	+	1.13403	NA	intron (NM_001290997, intron 4 of 20)	intron (NM_001290997, intron 4 of 20)	-182090	NM_199238	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding	0.000000	0.368159		5(TTTGAATATGGATG,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2322	chr13	117072160	117072360	+	1.13403	NA	Intergenic	Intergenic	-46729	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding	0.020000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5506	chr4	62824666	62824866	+	1.13403	NA	Intergenic	Intergenic	-140801	NM_001369118	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding	0.030000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3126	chr16	25504849	25505049	+	1.13403	NA	Intergenic	Intergenic	-178816	NM_001127260	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7309	chr8	72578862	72579062	+	1.13403	NA	intron (NR_151663, intron 1 of 2)	intron (NR_151663, intron 1 of 2)	7139	NM_001357284	74166	Mm.212927	NM_144534	ENSMUSG00000031791	Tmem38a	1110001E17Rik|AI413399|SPR-27|TRIC-A|mg33a	transmembrane protein 38A	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-648	chr1	193215962	193216162	+	1.13403	NA	Intergenic	Lx8|LINE|L1	-14516	NM_153137	215243	Mm.261259	NM_153137	ENSMUSG00000037318	Traf3ip3	6030423D04Rik|AI115021|T3jam	TRAF3 interacting protein 3	protein-coding	0.000000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-698	chr5	103367158	103367358	+	1.13403	NA	Intergenic	Intergenic	20660	NR_152117	75519	Mm.416851	NR_152117	ENSMUSG00000105426	1700021F02Rik	Gm42618	RIKEN cDNA 1700021F02 gene	ncRNA	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2540	chr14	73349858	73350058	+	1.13403	NA	Intergenic	Intergenic	-24136	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb|pp105	RB transcriptional corepressor 1	protein-coding	0.000000	0.273632			-71(TTTAGAATAACAAAGC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-566	chr3	85618796	85618996	+	1.13381	NA	exon (NM_144896, exon 9 of 13)	exon (NM_144896, exon 9 of 13)	44767	NM_144896	229487	Mm.52275	NM_144896	ENSMUSG00000028085	Gatb	9430026F02Rik|Pet112|Pet112l	glutamyl-tRNA(Gln) amidotransferase, subunit B	protein-coding	0.025000	0.542289			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-202	chr12	88544455	88544655	+	1.13313	NA	Intergenic	L1MD2|LINE|L1	-167232	NR_045888	71818	Mm.490789	NR_045888	ENSMUSG00000113434	3200001D21Rik	-	RIKEN cDNA 3200001D21 gene	ncRNA	0.000000	0.393035	79(TATGCTAAATGCATG,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-33	chr1	123972240	123972440	+	1.13313	NA	intron (NM_199021, intron 1 of 25)	intron (NM_199021, intron 1 of 25)	73219	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.000000	0.273632			-71(CAATTCTTATTCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4506	chr2	107601541	107601741	+	1.13313	NA	Intergenic	Intergenic	311052	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2375	chr14	16971054	16971254	+	1.13313	NA	intron (NM_001289760, intron 1 of 9)	intron (NM_001289760, intron 1 of 9)	111177	NM_001289761	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5741	chr4	127329314	127329514	+	1.13313	NA	promoter-TSS (NM_008126)	promoter-TSS (NM_008126)	-289	NM_008126	14620	Mm.90003	NM_008126	ENSMUSG00000042367	Gjb3	Cnx31|Cx31|D4Wsu144e|Gjb-3	gap junction protein, beta 3	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-343	chr1	123972222	123972422	+	1.13313	NA	intron (NM_199021, intron 1 of 25)	intron (NM_199021, intron 1 of 25)	73237	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.000000	0.308458			-53(CAATTCTTATTCAAAA,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-512	chr2	107601558	107601758	+	1.13313	NA	Intergenic	MER63C|DNA|hAT-Blackjack	311069	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding	0.000000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-385	chr16	84987835	84988035	+	1.13313	NA	intron (NM_007471, intron 11 of 15)	intron (NM_007471, intron 11 of 15)	15724	NR_045889	100038614	Mm.441351	NR_045889	ENSMUSG00000115518	Gm10791	-	predicted gene 10791	ncRNA	0.015000	0.422886			-36(ATTTAAATGCTAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3353	chr16	84987802	84988002	+	1.13313	NA	intron (NM_007471, intron 11 of 15)	intron (NM_007471, intron 11 of 15)	15691	NR_045889	100038614	Mm.441351	NR_045889	ENSMUSG00000115518	Gm10791	-	predicted gene 10791	ncRNA	0.010000	0.402985			-3(ATTTAAATGCTAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6621	chr6	101550938	101551138	+	1.13313	NA	Intergenic	Intergenic	-173141	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1803	chr12	88544458	88544658	+	1.13313	NA	Intergenic	L1MD2|LINE|L1	-167235	NR_045888	71818	Mm.490789	NR_045888	ENSMUSG00000113434	3200001D21Rik	-	RIKEN cDNA 3200001D21 gene	ncRNA	0.000000	0.393035	76(TATGCTAAATGCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2742	chr14	122257037	122257237	+	1.13313	NA	intron (NM_029556, intron 1 of 7)	intron (NM_029556, intron 1 of 7)	-23499	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA	0.015000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1802	chr12	88544307	88544507	+	1.13313	NA	Intergenic	L1MD2|LINE|L1	-167084	NR_045888	71818	Mm.490789	NR_045888	ENSMUSG00000113434	3200001D21Rik	-	RIKEN cDNA 3200001D21 gene	ncRNA	0.000000	0.383085			21(TTTTTCTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-325	chr1	119497622	119497822	+	1.13313	NA	intron (NM_022327, intron 1 of 4)	MTD|LTR|ERVL-MaLR	7060	NM_022327	64143	Mm.27832	NM_022327	ENSMUSG00000004451	Ralb	5730472O18Rik	v-ral simian leukemia viral oncogene B	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1037	chr10	111995890	111996090	+	1.13273	NA	intron (NM_028608, intron 1 of 5)	L1MA7|LINE|L1	1274	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2429	chr14	31934821	31935021	+	1.13016	NA	Intergenic	Intergenic	-94182	NM_030166	78754	Mm.40681	NM_030166	ENSMUSG00000021903	Galnt15	4631401E18Rik|Galntl2|mpp-GalNAc-T15	polypeptide N-acetylgalactosaminyltransferase 15	protein-coding	0.015000	0.407960			-79(ATTTGAAACACAGTAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-426	chr1	143065732	143065932	+	1.13016	NA	Intergenic	Intergenic	-574865	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding	0.000000	0.298507			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-41	chr1	143065802	143066002	+	1.13016	NA	Intergenic	Intergenic	-574795	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding	0.000000	0.303483			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-872	chr9	50570300	50570500	+	1.13016	NA	intron (NM_001357222, intron 2 of 5)	intron (NM_001357222, intron 2 of 5)	-9132	NM_025687	66654	Mm.442255	NM_025687	ENSMUSG00000032065	Tex12	5730518K06Rik	testis expressed 12	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6819	chr7	36728070	36728270	+	1.13016	NA	intron (NM_172298, intron 1 of 1)	intron (NM_172298, intron 1 of 1)	30052	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4848	chr3	13370488	13370688	+	1.13016	NA	Intergenic	Intergenic	-101067	NM_001357035	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0.010000	0.373134			-43(CTTTGAATGAGAAGAC,-,0.00),48(ATTTGAATAAGCAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3900	chr18	63040619	63040819	+	1.13016	NA	intron (NM_001039485, intron 40 of 53)	intron (NM_001039485, intron 40 of 53)	62803	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding	0.015000	0.378109		-13(AATGATTATTCATG,+,0.00),-13(AATGATTATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-312	chr1	107527187	107527387	+	1.13016	NA	Intergenic	Intergenic	-1716	NM_198028	241197	Mm.123919	NM_198028	ENSMUSG00000092572	Serpinb10	9830131G07|BB233602|Serpinb10-ps	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 10	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6494	chr6	64309533	64309733	+	1.13016	NA	intron (NM_001370966, intron 9 of 15)	intron (NM_001370966, intron 9 of 15)	-419492	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-139	chr1	47307146	47307346	+	1.13016	NA	Intergenic	Intergenic	159879	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA	0.000000	0.333333			-14(CTATCCATAACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6887	chr7	67730857	67731057	+	1.13016	NA	3' UTR (NM_207663, exon 5 of 5)	3' UTR (NM_207663, exon 5 of 5)	28785	NM_207663	233335	Mm.60526	NM_183312	ENSMUSG00000030554	Synm	4930412K21Rik|AI852401|Dmn|E130104F11|Syn|Synemin	synemin, intermediate filament protein	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6648	chr6	106837773	106837973	+	1.13016	NA	Intergenic	Intergenic	-37786	NM_175357	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding	0.010000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-768	chr6	106837788	106837988	+	1.13016	NA	Intergenic	Intergenic	-37801	NM_175357	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5676	chr4	106193720	106193920	+	1.13016	NA	Intergenic	Intergenic	-47393	NR_151521	105244641	Mm.404914	NR_151521		Gm12724	-	predicted gene 12724	ncRNA	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5918	chr5	42881059	42881259	+	1.13016	NA	Intergenic	MIR|SINE|MIR	-352094	NM_001368805	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.000000	0.333333			9(CTTTGCAATACAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6977	chr7	94618393	94618593	+	1.13016	NA	Intergenic	Intergenic	-1434317	NM_001358087	100040298	Mm.260904	NM_001358087		Gm15501	EyeLinc5	predicted pseudogene 15501	protein-coding	0.000000	0.328358			-98(ATTTGAATGTCAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3774	chr18	32555307	32555507	+	1.13016	NA	intron (NM_001048207, intron 1 of 2)	intron (NM_001048207, intron 1 of 2)	4627	NM_001048207	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6080	chr5	89355418	89355618	+	1.13016	NA	Intergenic	Intergenic	102380	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	vitamin D binding protein	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2940	chr15	58047017	58047217	+	1.13016	NA	3' UTR (NM_001042438, exon 5 of 5)	3' UTR (NM_001042438, exon 5 of 5)	-12823	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3233	chr16	53227343	53227543	+	1.13016	NA	Intergenic	Intergenic	-411699	NR_040495	73820	Mm.60493	NR_040495	ENSMUSG00000116611	4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA	0.015000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-689	chr5	89355391	89355591	+	1.13016	NA	Intergenic	Intergenic	102407	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	vitamin D binding protein	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7649	chr9	50570276	50570476	+	1.13016	NA	intron (NM_001357222, intron 2 of 5)	intron (NM_001357222, intron 2 of 5)	-9108	NM_025687	66654	Mm.442255	NM_025687	ENSMUSG00000032065	Tex12	5730518K06Rik	testis expressed 12	protein-coding	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2048	chr13	42276906	42277106	+	1.13016	NA	Intergenic	HAL1|LINE|L1	-24470	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6775	chr6	147255229	147255429	+	1.13016	NA	intron (NM_008970, intron 3 of 3)	intron (NM_008970, intron 3 of 3)	8684	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6808	chr7	29481387	29481587	+	1.13016	NA	intron (NM_001081028, intron 2 of 22)	L2b|LINE|L2	23973	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding	0.030000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1312	chr11	61598368	61598568	+	1.13016	NA	Intergenic	RMER10A|LTR|ERVL	-18781	NM_001362586	13855	Mm.139695	NM_010148	ENSMUSG00000001036	Epn2	9530051D10Rik|AA536924|Ibp2	epsin 2	protein-coding	0.005000	0.522388			-8(ACTTTGGTATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5781	chr4	144980539	144980739	+	1.13016	NA	intron (NM_001276465, intron 68 of 69)	intron (NM_001276465, intron 68 of 69)	87502	NM_001357274	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding	0.020000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-30	chr1	107527153	107527353	+	1.13016	NA	Intergenic	Intergenic	-1750	NM_198028	241197	Mm.123919	NM_198028	ENSMUSG00000092572	Serpinb10	9830131G07|BB233602|Serpinb10-ps	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 10	protein-coding	0.000000	0.308458			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-749	chr6	66207816	66208016	+	1.13016	NA	Intergenic	Intergenic	-64589	NR_136927	102633773	Mm.272086	NR_136927	ENSMUSG00000107653	Gm31520	-	sterol-C5-desaturase pseudogene	pseudo	0.005000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-359	chr16	12078364	12078564	+	1.12998	NA	intron (NM_028277, intron 2 of 4)	intron (NM_028277, intron 2 of 4)	94351	NM_001174086	72555	Mm.310139	NM_028277	ENSMUSG00000022494	Shisa9	2700045P11Rik|Ckamp44	shisa family member 9	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2055	chr13	44751786	44751986	+	1.12998	NA	intron (NM_021878, intron 2 of 18)	intron (NM_021878, intron 2 of 18)	20615	NM_001360281	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding	0.000000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-712	chr5	136403671	136403871	+	1.12836	NA	intron (NM_001291233, intron 3 of 23)	intron (NM_001291233, intron 3 of 23)	-27968	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA	0.040000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-313	chr1	107978505	107978705	+	1.12836	NA	Intergenic	MER126|DNA|DNA	61346	NR_102307	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA	0.015000	0.462687			12(CCATTTATATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4583	chr2	125219636	125219836	+	1.12836	NA	intron (NM_183354, intron 23 of 26)	intron (NM_183354, intron 23 of 26)	-27512	NM_001159646	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding	0.000000	0.323383			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-425	chr18	21128905	21129105	+	1.12836	NA	3' UTR (NM_001033445, exon 6 of 6)	3' UTR (NM_001033445, exon 6 of 6)	56661	NM_008586	17288	Mm.2682	NM_008586	ENSMUSG00000024313	Mep1b	Mep-1b	meprin 1 beta	protein-coding	0.020000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1101	chr10	122410860	122411060	+	1.12836	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-37539	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding	0.005000	0.462687			-90(GTTTGAATAAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2476	chr14	47830110	47830310	+	1.12825	NA	Intergenic	Intergenic	-68654	NR_045959	73961	Mm.390702	NR_045959	ENSMUSG00000115609	4930447J18Rik	4930425M13Rik	RIKEN cDNA 4930447J18 gene	ncRNA	0.005000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-673	chr5	50215076	50215276	+	1.12825	NA	Intergenic	Lx8b|LINE|L1	-37586	NR_106197	102465903		NR_106197	ENSMUSG00000099124	Mir8117	Gm27323|mmu-mir-8117	microRNA 8117	ncRNA	0.000000	0.288557			-46(AACTGCAAGAAAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5946	chr5	50215122	50215322	+	1.12825	NA	Intergenic	Lx8b|LINE|L1	-37540	NR_106197	102465903		NR_106197	ENSMUSG00000099124	Mir8117	Gm27323|mmu-mir-8117	microRNA 8117	ncRNA	0.000000	0.333333			-92(AACTGCAAGAAAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7874	chr9	110053980	110054180	+	1.12825	NA	intron (NM_001311164, intron 1 of 9)	intron (NM_001311164, intron 1 of 9)	2059	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2017	chr13	34248375	34248575	+	1.12825	NA	intron (NM_001033167, intron 3 of 10)	intron (NM_001033167, intron 3 of 10)	85511	NM_001101430	69666	Mm.24788	NM_001101430	ENSMUSG00000071451	Psmg4	PAC-4|mPAC4	proteasome (prosome, macropain) assembly chaperone 4	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3930	chr18	70628935	70629135	+	1.12797	NA	Intergenic	Intergenic	60743	NM_001311071	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding	0.000000	0.238806			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2846	chr15	30401025	30401225	+	1.12797	NA	intron (NM_008729, intron 2 of 22)	AT_rich|Low_complexity|Low_complexity	228591	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding	0.010000	0.412935		20(CATCTATATGCATA,+,0.00)	25(ATATGCATAACTATAT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-662	chr5	14543059	14543259	+	1.12797	NA	intron (NM_011995, intron 3 of 24)	RLTR17B_Mm|LTR|ERVK	28241	NM_011995	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding	0.005000	0.273632		-72(TATACATATGTATA,+,0.00),-72(TATACATATGTATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5797	chr4	152120796	152120996	+	1.12797	NA	TTS (NM_033042)	TTS (NM_033042)	4553	NM_033042	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding	0.025000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6578	chr6	88962904	88963104	+	1.12742	NA	Intergenic	Lx|LINE|L1	60753	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding	0.005000	0.507463			-45(TTTTTCTTTTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2190	chr13	90358210	90358410	+	1.12742	NA	Intergenic	Intergenic	268643	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3150	chr16	30916865	30917065	+	1.12742	NA	Intergenic	Intergenic	164467	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-567	chr3	104182772	104182972	+	1.12742	NA	intron (NM_001159354, intron 1 of 20)	Lx8|LINE|L1	37534	NM_133853	99470	Mm.264849	NM_133853	ENSMUSG00000052539	Magi3	4732496O19Rik|6530407C02Rik|AA407180|AI120132|mKIAA1634	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1889	chr12	110552274	110552474	+	1.12742	NA	intron (NM_001364210, intron 6 of 11)	intron (NM_001364210, intron 6 of 11)	-39000	NR_033340	319786	Mm.129691	NR_033340		B930059L03Rik	-	RIKEN cDNA B930059L03 gene	ncRNA	0.030000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-860	chr10	66905104	66905304	+	1.12552	NA	Intergenic	Intergenic	15180	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5018	chr3	75710995	75711195	+	1.12552	NA	Intergenic	Intergenic	-55364	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3241	chr16	55513337	55513537	+	1.12552	NA	Intergenic	Intergenic	18706	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7627	chr9	43047384	43047584	+	1.12552	NA	intron (NM_001359232, intron 1 of 40)	intron (NM_001359232, intron 1 of 40)	58234	NM_001359232	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding	0.000000	0.388060			-12(ATTAGCATCATAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1264	chr11	43703543	43703743	+	1.12552	NA	intron (NM_001363141, intron 1 of 2)	PB1D10|SINE|Alu	21645	NM_001363141	70802	Mm.397449	NM_027557	ENSMUSG00000044950	Pwwp2a	4631424J17Rik|AI891583|AU024105|D930040F23Rik	PWWP domain containing 2A	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2773	chr15	7684029	7684229	+	1.12552	NA	Intergenic	Intergenic	-125919	NM_001301332	14573	Mm.4679	NM_010275	ENSMUSG00000022144	Gdnf	AI385739|ATF	glial cell line derived neurotrophic factor	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2682	chr14	105712934	105713134	+	1.12552	NA	Intergenic	Intergenic	-89264	NR_105814	102465207		NR_105814	ENSMUSG00000098780	Mir6390	Gm27562|mmu-mir-6390	microRNA 6390	ncRNA	0.010000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-145	chr11	43703599	43703799	+	1.12552	NA	intron (NM_001363141, intron 1 of 2)	PB1D10|SINE|Alu	21701	NM_001363141	70802	Mm.397449	NM_027557	ENSMUSG00000044950	Pwwp2a	4631424J17Rik|AI891583|AU024105|D930040F23Rik	PWWP domain containing 2A	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-233	chr13	25869531	25869731	+	1.12506	NA	Intergenic	Intergenic	96685	NR_045062	100503530	Mm.86763	NR_045062	ENSMUSG00000086531	Gm11351	-	predicted gene 11351	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7294	chr8	64826595	64826795	+	1.12463	NA	intron (NM_178633, intron 2 of 14)	B4|SINE|B4	23229	NM_178633	77113	Mm.350347	NM_178633	ENSMUSG00000031605	Klhl2	6030411N21Rik|8530402H02Rik|ABP-KELCH|AU020744|Mav	kelch-like 2, Mayven	protein-coding	0.020000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4032	chr19	18082355	18082555	+	1.12463	NA	Intergenic	Intergenic	-244823	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding	0.020000	0.462687			-86(TCATTGTCATTTACAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2065	chr13	48758444	48758644	+	1.12463	NA	Intergenic	Intergenic	95508	NM_007526	12022	Mm.42241	NM_007526	ENSMUSG00000021381	Barx1	-	BarH-like homeobox 1	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6883	chr7	66375778	66375978	+	1.12463	NA	intron (NM_146191, intron 2 of 33)	intron (NM_146191, intron 2 of 33)	5846	NR_106024	102465640		NR_106024	ENSMUSG00000098353	Mir7057	Gm27550|mmu-mir-7057	microRNA 7057	ncRNA	0.015000	0.472637			-85(CTTTTTTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7409	chr8	100784416	100784616	+	1.12463	NA	Intergenic	Intergenic	1367842	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4833	chr3	9159181	9159381	+	1.12463	NA	Intergenic	Intergenic	-91286	NM_177660	229055	Mm.103262	NM_177660	ENSMUSG00000069114	Zbtb10	4832414A18|AU021107|RINZF	zinc finger and BTB domain containing 10	protein-coding	0.035000	0.587065			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-53	chr1	19525295	19525495	+	1.12463	NA	Intergenic	Intergenic	313341	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding	0.000000	0.333333	-20(GATGAATGATTTATA,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2425	chr14	31111014	31111214	+	1.12463	NA	intron (NM_001359854, intron 30 of 32)	intron (NM_001359854, intron 30 of 32)	17816	NM_001308466	66487	Mm.379116	NM_001308091	ENSMUSG00000058351	Smim4	2010107H07Rik|Gm41122	small integral membrane protein 4	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1766	chr12	79919145	79919345	+	1.12463	NA	intron (NR_131074, intron 2 of 3)	B3A|SINE|B2	5488	NR_131075	77290	Mm.395042	NR_131073	ENSMUSG00000112765	9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA	0.020000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4234	chr2	29440620	29440820	+	1.12463	NA	intron (NM_001290489, intron 2 of 6)	intron (NM_001290489, intron 2 of 6)	34574	NR_105753	102465170		NR_105753	ENSMUSG00000098539	Mir133c	Gm27865|mmu-mir-133c	microRNA 133c	ncRNA	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-534	chr1	169432897	169433097	+	1.12463	NA	Intergenic	L1MEc|LINE|L1	98467	NM_001355159	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	NUF2, NDC80 kinetochore complex component	protein-coding	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3732	chr18	20152483	20152683	+	1.12463	NA	Intergenic	Intergenic	-37810	NM_013504	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3405	chr17	3505854	3506054	+	1.12463	NA	intron (NM_011878, intron 17 of 26)	B1_Mur1|SINE|Alu	22464	NM_001286757	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3868	chr18	55546222	55546422	+	1.12463	NA	Intergenic	Intergenic	-553731	NM_001360787	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3324	chr16	76358043	76358243	+	1.12463	NA	intron (NM_173440, intron 1 of 3)	intron (NM_173440, intron 1 of 3)	14906	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding	0.045000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-957	chr10	96093738	96093938	+	1.12463	NA	Intergenic	Intergenic	-132369	NR_110448	74881	Mm.410819	NR_110448	ENSMUSG00000112762	4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA	0.005000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-229	chr13	14321189	14321389	+	1.12463	NA	intron (NM_001081348, intron 8 of 28)	intron (NM_001081348, intron 8 of 28)	201937	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6655	chr6	108494327	108494527	+	1.12463	NA	intron (NM_010585, intron 52 of 61)	intron (NM_010585, intron 52 of 61)	4684	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2225	chr13	96060187	96060387	+	1.12463	NA	intron (NM_029210, intron 2 of 12)	intron (NM_029210, intron 2 of 12)	72290	NM_029210	75209	Mm.40436	NM_029210	ENSMUSG00000051111	Sv2c	4930527L09Rik|AI841971	synaptic vesicle glycoprotein 2c	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1412	chr11	92886750	92886950	+	1.12463	NA	Intergenic	MIRb|SINE|MIR	-211516	NM_001361707	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0.000000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-40	chr1	140451432	140451632	+	1.12463	NA	intron (NM_001081027, intron 13 of 27)	intron (NM_001081027, intron 13 of 27)	204870	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA	0.015000	0.333333			-63(ATTTGAATGGAAAACA,-,0.00),6(CATTTCTCTTGAAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5060	chr3	90340107	90340307	+	1.12463	NA	Intergenic	Lx9|LINE|L1	-1447	NM_139304	229542	Mm.270999	NM_139304	ENSMUSG00000042390	Gatad2b	AL118180|C430014D17Rik|P66beta|mKIAA1150	GATA zinc finger domain containing 2B	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3343	chr16	82729422	82729622	+	1.12463	NA	Intergenic	Intergenic	1528825	NM_001113208	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0.000000	0.308458			32(ATTTGAAAGGAAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5987	chr5	63431655	63431855	+	1.12463	NA	Intergenic	Intergenic	-217348	NM_177006	319807	Mm.319487	NM_028470	ENSMUSG00000090061	Nwd2	3110047P20Rik|B830017A01Rik|Hn1-ps2|mKIAA1239	NACHT and WD repeat domain containing 2	protein-coding	0.005000	0.338308			-61(GTTATCTCATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-576	chr1	178218378	178218578	+	1.12463	NA	intron (NM_024282, intron 1 of 4)	intron (NM_024282, intron 1 of 4)	31061	NM_024282	78825	Mm.440132	NM_024282	ENSMUSG00000026502	Desi2	5830417C01Rik|DeSI-2|Fam152a|Pppde1	desumoylating isopeptidase 2	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3636	chr17	83827861	83828061	+	1.12463	NA	Intergenic	Intergenic	18829	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding	0.005000	0.412935			-53(CTTTTCTAATGGAAAT,+,0.00),6(TTCTTTCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3054	chr15	97499161	97499361	+	1.12463	NA	Intergenic	MER57E1|LTR|ERV1	206561	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding	0.025000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-120	chr10	123403146	123403346	+	1.12463	NA	intron (NM_001252387, intron 1 of 4)	intron (NM_001252387, intron 1 of 4)	139170	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Tafa2	6330575M02|FAM19A2 TAFA-2|Fam19a2|Sam2|Tafa-2	TAFA chemokine like family member 2	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-324	chr1	119220125	119220325	+	1.12463	NA	Intergenic	MER45B|DNA|hAT-Tip100	-166606	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3798	chr18	38573603	38573803	+	1.12463	NA	Intergenic	Intergenic	27644	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty RTK signaling antagonist 4	protein-coding	0.040000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4120	chr19	52570915	52571115	+	1.12463	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	306718	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1869	chr12	104535797	104535997	+	1.12463	NA	Intergenic	Intergenic	-62661	NM_010351	14836	Mm.129	NM_010351	ENSMUSG00000021095	Gsc	-	goosecoid homeobox	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4796	chr2	171986582	171986782	+	1.12463	NA	Intergenic	B4|SINE|B4	-23883	NR_040509	75655	Mm.396203	NR_040509	ENSMUSG00000086823	1700028P15Rik	-	RIKEN cDNA 1700028P15 gene	ncRNA	0.020000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-137	chr1	47001074	47001274	+	1.12463	NA	Intergenic	Intergenic	-75398	NM_001356417	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|Zip10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7644	chr9	48586078	48586278	+	1.12463	NA	Intergenic	Intergenic	18945	NM_001311062	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7236	chr8	47694916	47695116	+	1.12463	NA	Intergenic	Intergenic	18915	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding	0.030000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-626	chr1	188398147	188398347	+	1.12463	NA	intron (NM_021408, intron 11 of 70)	intron (NM_021408, intron 11 of 70)	135409	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Ushrn	usherin	protein-coding	0.015000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2398	chr14	23529731	23529931	+	1.12463	NA	intron (NM_001253368, intron 7 of 28)	intron (NM_001253368, intron 7 of 28)	-435260	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	-	predicted gene 10248	ncRNA	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7617	chr9	39571616	39571816	+	1.12463	NA	TTS (NM_146508)	TTS (NM_146508)	1541	NM_146508	258501	Mm.156991	NM_146508	ENSMUSG00000059366	Olfr959	M34|MOR224-3|ORL583	olfactory receptor 959	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6293	chr6	7823088	7823288	+	1.12463	NA	Intergenic	Intergenic	-22036	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding	0.000000	0.437811			68(TTTTTCATAACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-268	chr1	92113866	92114066	+	1.12242	NA	intron (NM_207225, intron 2 of 26)	intron (NM_207225, intron 2 of 26)	66375	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2079	chr13	56712168	56712368	+	1.12242	NA	intron (NM_001164042, intron 1 of 6)	intron (NM_001164042, intron 1 of 6)	8600	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding	0.005000	0.437811			-89(ATATACATAACTAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6741	chr6	137946048	137946248	+	1.12237	NA	Intergenic	Intergenic	133768	NM_177787	277898	Mm.269823	NM_177787	ENSMUSG00000044378	Slc15a5	9830102E05Rik	solute carrier family 15, member 5	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1481	chr11	114345878	114346078	+	1.12236	NA	Intergenic	Intergenic	102882	NR_027643	319819	Mm.50754	NM_177008	ENSMUSG00000062391	4932435O22Rik	-	RIKEN cDNA 4932435O22 gene	ncRNA	0.010000	0.412935			-57(ATTTGCATGTGTAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-270	chr1	92707498	92707698	+	1.12236	NA	Intergenic	Intergenic	-58757	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding	0.005000	0.398010			25(TTTTACAACACAAAGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-264	chr13	103880362	103880562	+	1.12236	NA	intron (NM_001005868, intron 4 of 26)	L1M2|LINE|L1	40124	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding	0.000000	0.293532	-89(TATTAATAATTCATC,+,0.00),-89(TATTAATAATTCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2261	chr13	103880358	103880558	+	1.12236	NA	intron (NM_001005868, intron 4 of 26)	L1M2|LINE|L1	40128	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding	0.000000	0.288557	-85(TATTAATAATTCATC,+,0.00),-85(TATTAATAATTCATC,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-466	chr2	4783220	4783420	+	1.12202	NA	intron (NM_178663, intron 6 of 8)	intron (NM_178663, intron 6 of 8)	65489	NM_001190400	209645	Mm.149539	NM_178663	ENSMUSG00000048186	Bend7	1110017O21Rik|E130319B15Rik	BEN domain containing 7	protein-coding	0.005000	0.442786	30(TATTCATTATTTATA,+,0.00),30(TATTCATTATTTATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-81	chr1	26683157	26683357	+	1.12202	NA	exon (NM_001033764, exon 2 of 2)	exon (NM_001033764, exon 2 of 2)	4203	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2021	chr13	36200576	36200776	+	1.12202	NA	intron (NM_001039189, intron 1 of 5)	ORR1C2|LTR|ERVL-MaLR	83033	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.010000	0.422886			30(CCATTCTGATTCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1395	chr11	87854784	87854984	+	1.12202	NA	intron (NM_001039684, intron 2 of 17)	intron (NM_001039684, intron 2 of 17)	1669	NM_001039684	380718	Mm.24404	NM_001039684	ENSMUSG00000034121	Mks1	AK190930|B8d3|avc6	Meckel syndrome, type 1	protein-coding	0.015000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-632	chr4	85131287	85131487	+	1.12202	NA	3' UTR (NM_175275, exon 26 of 26)	3' UTR (NM_175275, exon 26 of 26)	-74069	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1190	chr11	22206230	22206430	+	1.12202	NA	intron (NM_153078, intron 5 of 24)	intron (NM_153078, intron 5 of 24)	80465	NM_153078	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2217	chr13	94490703	94490903	+	1.12202	NA	intron (NM_009680, intron 20 of 26)	intron (NM_009680, intron 20 of 26)	131843	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding	0.015000	0.417910	84(CATGAATTATGCATT,+,0.00),84(CATGAATTATGCATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2380	chr14	17978375	17978575	+	1.12202	NA	intron (NM_001113417, intron 4 of 9)	intron (NM_001113417, intron 4 of 9)	-3169	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7046	chr7	119988292	119988492	+	1.12193	NA	intron (NM_001370806, intron 40 of 60)	L1M6|LINE|L1	88281	NR_126475	73919	Mm.46381	NM_029610	ENSMUSG00000030922	Lyrm1	1110065L10Rik|2310004B22Rik|4930404J24Rik	LYR motif containing 1	protein-coding	0.010000	0.348259			27(ATTTAAATAATAATAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-804	chr7	102482615	102482815	+	1.12193	NA	Intergenic	MER2|DNA|TcMar-Tigger	-4813	NM_001011782	257947	Mm.376117	NM_001011782	ENSMUSG00000044814	Olfr543	MOR42-2	olfactory receptor 543	protein-coding	0.005000	0.293532			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-350	chr15	76799617	76799817	+	1.12193	NA	intron (NM_198420, intron 1 of 10)	intron (NM_198420, intron 1 of 10)	18449	NM_001168288	223666	Mm.322931	NM_198420	ENSMUSG00000033697	Arhgap39	9530053N22|AI843066|D15Wsu169e|Kiaa1688|Porf-2	Rho GTPase activating protein 39	protein-coding	0.005000	0.427861	32(TCTGAATAATTCATG,+,0.00),32(TCTGAATAATTCATG,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-265	chr13	104039996	104040196	+	1.12193	NA	intron (NM_029447, intron 9 of 12)	intron (NM_029447, intron 9 of 12)	69518	NM_029447	75805	Mm.127692	NM_029447	ENSMUSG00000021710	Nln	4930472G13Rik|C79345	neurolysin (metallopeptidase M3 family)	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6426	chr6	44900044	44900244	+	1.12121	NA	Intergenic	Intergenic	-159917	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3712	chr18	13742226	13742426	+	1.12121	NA	intron (NM_145492, intron 5 of 7)	intron (NM_145492, intron 5 of 7)	230407	NM_001360804	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3087	chr16	12078449	12078649	+	1.12121	NA	intron (NM_028277, intron 2 of 4)	intron (NM_028277, intron 2 of 4)	94436	NM_001174086	72555	Mm.310139	NM_028277	ENSMUSG00000022494	Shisa9	2700045P11Rik|Ckamp44	shisa family member 9	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-283	chr14	30561693	30561893	+	1.12091	NA	intron (NM_009388, intron 4 of 13)	intron (NM_009388, intron 4 of 13)	-10356	NR_037237	100526475		NR_037237	ENSMUSG00000093156	Mir3076	mir-3076|mmu-mir-3076	microRNA 3076	ncRNA	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-121	chr1	43115607	43115807	+	1.12070	NA	3' UTR (NM_133818, exon 4 of 4)	3' UTR (NM_133818, exon 4 of 4)	16997	NM_133818	98404	Mm.28817	NM_133818	ENSMUSG00000010290	AI597479	-	expressed sequence AI597479	protein-coding	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6248	chr5	146878102	146878302	+	1.12070	NA	Intergenic	Intergenic	33131	NM_026864	68895	Mm.266978	NM_026864	ENSMUSG00000029641	Rasl11a	1110065D03Rik|AI852031	RAS-like, family 11, member A	protein-coding	0.015000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-457	chr19	20915752	20915952	+	1.12070	NA	intron (NM_028953, intron 2 of 20)	B1_Mur1|SINE|Alu	38350	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding	0.000000	0.432836			9(GTCTGAAAAACAAAAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-300	chr14	77418497	77418697	+	1.11836	NA	intron (NM_172813, intron 4 of 18)	RMER1B|Other|Other	88271	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA	0.010000	0.467662			-42(ATCTCCATGACACAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1196	chr11	24484892	24485092	+	1.11836	NA	intron (NR_045857, intron 1 of 3)	intron (NR_045857, intron 1 of 3)	3083	NR_045857	71316	Mm.79162	NR_045857	ENSMUSG00000086892	4933430M04Rik	-	RIKEN cDNA 4933430M04 gene	ncRNA	0.005000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-85	chr10	29702915	29703115	+	1.11836	NA	Intergenic	Intergenic	-167148	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-605	chr1	185183856	185184056	+	1.11836	NA	Intergenic	Intergenic	-20212	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding	0.025000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7939	chrX	22898392	22898592	+	1.11749	NA	Intergenic	Intergenic	368310	NM_001310466	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3127	chr16	26546892	26547092	+	1.11749	NA	Intergenic	Intergenic	-20221	NM_001101640	100043057	Mm.295917	NM_001101640	ENSMUSG00000091972	Tmem207	Gm540	transmembrane protein 207	protein-coding	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4070	chr19	33264620	33264820	+	1.11749	NA	intron (NR_160911, intron 4 of 6)	RMER10A|LTR|ERVL	107608	NR_039552	100628575		NR_039552	ENSMUSG00000106278	Mir3970	mmu-mir-3970|mu-mir-3970	microRNA 3970	ncRNA	0.005000	0.482587			60(GCTTTGATATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2819	chr15	22815269	22815469	+	1.11749	NA	Intergenic	Lx6|LINE|L1	-100385	NM_001165971	545091	Mm.475598	NM_001165971		Hnrnpa1l2-ps2	EG545091|Gm5803	heterogeneous nuclear ribonucleoprotein A1-like 2, pseudogene 2	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6247	chr5	146338154	146338354	+	1.11749	NA	Intergenic	MamRep137|DNA|TcMar-Tigger	-46752	NM_145155	245880	Mm.472750	NM_145155	ENSMUSG00000029636	Wasf3	Scar3|Wave3	WAS protein family, member 3	protein-coding	0.035000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3392	chr16	94695005	94695205	+	1.11749	NA	3' UTR (NM_007890, exon 12 of 12)	3' UTR (NM_007890, exon 12 of 12)	83686	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding	0.005000	0.442786			-6(TGATTATCATGTTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7375	chr8	92895894	92896094	+	1.11749	NA	intron (NM_001357374, intron 9 of 11)	intron (NM_001357374, intron 9 of 11)	-5401	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1384	chr11	85188933	85189133	+	1.11749	NA	Intergenic	PB1D7|SINE|Alu	17937	NM_028589	73634	Mm.48850	NM_028589	ENSMUSG00000018479	1700125H20Rik	-	RIKEN cDNA 1700125H20 gene	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-172	chr1	59923165	59923365	+	1.11749	NA	intron (NM_001037725, intron 1 of 7)	intron (NM_001037725, intron 1 of 7)	10259	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6642	chr6	105493402	105493602	+	1.11749	NA	promoter-TSS (NR_040297)	promoter-TSS (NR_040297)	-834	NR_040297	100503536	Mm.366960	NR_040297	ENSMUSG00000108237	Gm19757	-	predicted gene, 19757	ncRNA	0.000000	0.373134			21(GCTTTATCATGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2655	chr14	101138566	101138766	+	1.11749	NA	Intergenic	Intergenic	61403	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding	0.000000	0.348259		5(AATGCTTATGTATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3238	chr16	55229230	55229430	+	1.11749	NA	intron (NM_178720, intron 10 of 11)	intron (NM_178720, intron 10 of 11)	53907	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7929	chrX	16967213	16967413	+	1.11749	NA	Intergenic	MER45B|DNA|hAT-Tip100	-55539	NM_010883	17986	Mm.5014	NM_010883	ENSMUSG00000040138	Ndp	ND|Ndph	Norrie disease (pseudoglioma) (human)	protein-coding	0.010000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4523	chr2	112571108	112571308	+	1.11749	NA	promoter-TSS (NR_149741)	promoter-TSS (NR_149741)	-405	NR_149741	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2850	chr15	31724360	31724560	+	1.11749	NA	Intergenic	Intergenic	122344	NM_026546	68073	Mm.119185	NM_026546	ENSMUSG00000039065	Atpsckmt	A930016P21Rik|AA987072|Fam173b|mFam173b	ATP synthase C subunit lysine N-methyltransferase	protein-coding	0.035000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6953	chr7	89051162	89051362	+	1.11749	NA	Intergenic	Intergenic	287525	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6158	chr5	114279447	114279647	+	1.11749	NA	Intergenic	Intergenic	-5786	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2922	chr15	52638194	52638394	+	1.11749	NA	Intergenic	Intergenic	-74151	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding	0.005000	0.283582			30(GCATTGTTATTTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5330	chr4	6873229	6873429	+	1.11749	NA	intron (NM_145711, intron 1 of 8)	intron (NM_145711, intron 1 of 8)	117394	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding	0.010000	0.417910			28(TTACTGTTTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2760	chr15	6080829	6081029	+	1.11749	NA	Intergenic	Intergenic	-36225	NR_155429	105245876	Mm.128197	NR_155428		Gm41259	-	predicted gene, 41259	ncRNA	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6384	chr6	33172636	33172836	+	1.11749	NA	Intergenic	Intergenic	-76392	NM_001347089	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding	0.005000	0.482587			-2(CCATTATCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7682	chr9	62017603	62017803	+	1.11749	NA	intron (NM_028748, intron 1 of 7)	intron (NM_028748, intron 1 of 7)	9087	NM_028748	74090	Mm.273267	NM_028748	ENSMUSG00000032278	Paqr5	0610010I15Rik|AV002411|BB115488|mPRg	progestin and adipoQ receptor family member V	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3332	chr16	78365675	78365875	+	1.11749	NA	intron (NM_001297747, intron 3 of 4)	intron (NM_001297747, intron 3 of 4)	10982	NR_002700	654432	Mm.458574	NR_002700		Gm7334	EG654432	B-cell translocation gene 3 pseudogene	pseudo	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2075	chr13	53364856	53365056	+	1.11749	NA	intron (NM_009269, intron 5 of 14)	intron (NM_009269, intron 5 of 14)	12405	NM_009269	268656	Mm.240336	NM_009269	ENSMUSG00000021468	Sptlc1	AW552086|C77762|E030036H05|Lcb1|SPT1	serine palmitoyltransferase, long chain base subunit 1	protein-coding	0.020000	0.412935			-19(CCTTTCTGTTGCAGAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7332	chr8	78219620	78219820	+	1.11749	NA	intron (NM_183096, intron 4 of 13)	intron (NM_183096, intron 4 of 13)	6378	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding	0.000000	0.318408		36(CATGCATATGTATG,+,0.00),36(CATGCATATGTATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1449	chr11	107209494	107209694	+	1.11749	NA	non-coding (NR_153311, exon 10 of 10)	non-coding (NR_153311, exon 10 of 10)	-20213	NM_133702	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding	0.025000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2741	chr14	122200667	122200867	+	1.11749	NA	intron (NM_029556, intron 1 of 7)	intron (NM_029556, intron 1 of 7)	19073	NM_029556	69634	Mm.34608	NM_029556	ENSMUSG00000025545	Clybl	0610033J05Rik|2310014M14Rik|AI256068|Clb	citrate lyase beta like	protein-coding	0.030000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3121	chr16	24767610	24767810	+	1.11749	NA	intron (NM_178665, intron 8 of 12)	intron (NM_178665, intron 8 of 12)	45855	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.010000	0.273632			-65(ATGTGAATAAAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6505	chr6	66386950	66387150	+	1.11749	NA	Intergenic	Intergenic	114545	NR_136927	102633773	Mm.272086	NR_136927	ENSMUSG00000107653	Gm31520	-	sterol-C5-desaturase pseudogene	pseudo	0.010000	0.353234			28(CTTTAAAAGAGAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8177	chrY	1244692	1244892	+	1.11749	NA	intron (NM_001326683, intron 2 of 26)	intron (NM_001326683, intron 2 of 26)	967	NM_001326683	22290	Mm.20477	NM_009484	ENSMUSG00000068457	Uty	Hydb|mKIAA4057	ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	protein-coding	0.020000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6000	chr5	66523993	66524193	+	1.11749	NA	intron (NM_001201413, intron 2 of 16)	intron (NM_001201413, intron 2 of 16)	94724	NM_001201413	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7739	chr9	76518762	76518962	+	1.11749	NA	intron (NM_001045518, intron 2 of 4)	intron (NM_001045518, intron 2 of 4)	48253	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	family with sequence similarity 83, member B	protein-coding	0.000000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5138	chr3	117121012	117121212	+	1.11749	NA	Intergenic	MTC|LTR|ERVL-MaLR	-43347	NR_038029	433646	Mm.158997	NR_038029	ENSMUSG00000028009	1700061I17Rik	-	RIKEN cDNA 1700061I17 gene	ncRNA	0.010000	0.507463	-68(AATGAATTATTGATG,+,0.00),-68(AATGAATTATTGATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1088	chr10	120027738	120027938	+	1.11749	NA	intron (NM_001358811, intron 15 of 23)	intron (NM_001358811, intron 15 of 23)	34916	NR_102387	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1553	chr12	15289712	15289912	+	1.11749	NA	Intergenic	Intergenic	-239423	NR_045960	73972	Mm.107680	NR_045960	ENSMUSG00000113644	4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA	0.005000	0.328358			-88(ATTTGTATAATAAGGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2383	chr14	19777000	19777200	+	1.11749	NA	intron (NM_008695, intron 4 of 20)	intron (NM_008695, intron 4 of 20)	25843	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding	0.020000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-572	chr1	177276885	177277085	+	1.11749	NA	Intergenic	Intergenic	-28218	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding	0.010000	0.323383		-20(TATCAATATGCAAG,-,0.00)	13(GCTCTTTTATGTATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5650	chr4	101244711	101244911	+	1.11749	NA	intron (NM_013567, intron 1 of 22)	intron (NM_013567, intron 1 of 22)	20412	NM_013567	16451	Mm.289657	NM_013567	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding	0.005000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6961	chr7	90843727	90843927	+	1.11749	NA	Intergenic	Intergenic	-246959	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs large MAGUK scaffold protein 2	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4502	chr2	107215704	107215904	+	1.11749	NA	Intergenic	Lx5|LINE|L1	-74785	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5230	chr3	138753372	138753572	+	1.11749	NA	intron (NR_121195, intron 1 of 7)	intron (NR_121195, intron 1 of 7)	11264	NR_121195	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding	0.025000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7701	chr9	66787948	66788148	+	1.11749	NA	intron (NM_177583, intron 4 of 5)	intron (NM_177583, intron 4 of 5)	7375	NM_177583	208117	Mm.41291	NM_177583	ENSMUSG00000032375	Aph1b	2310057K14Rik|Aph1c	aph1 homolog B, gamma secretase subunit	protein-coding	0.010000	0.378109			49(ATTTACAAGAAACATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2504	chr14	60525405	60525605	+	1.11749	NA	Intergenic	Intergenic	-109200	NM_001033272	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-859	chr10	66602054	66602254	+	1.11749	NA	Intergenic	Intergenic	318230	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6603	chr6	97526199	97526399	+	1.11749	NA	intron (NM_145148, intron 2 of 23)	intron (NM_145148, intron 2 of 23)	-38479	NM_001346637	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding	0.030000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7150	chr8	11036014	11036214	+	1.11749	NA	intron (NR_046017, intron 1 of 4)	intron (NR_046017, intron 1 of 4)	-27185	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1873	chr12	106185816	106186016	+	1.11749	NA	Intergenic	Intergenic	149376	NM_001364368	22367	Mm.2981	NM_011705	ENSMUSG00000021115	Vrk1	51PK	vaccinia related kinase 1	protein-coding	0.055000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5397	chr4	27225384	27225584	+	1.11749	NA	Intergenic	Intergenic	-520035	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5531	chr4	70527959	70528159	+	1.11749	NA	intron (NM_172694, intron 1 of 5)	intron (NM_172694, intron 1 of 5)	6869	NM_172694	230316	Mm.251188	NM_172694	ENSMUSG00000039270	Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7687	chr9	63215793	63215993	+	1.11749	NA	intron (NM_001364493, intron 18 of 20)	intron (NM_001364493, intron 18 of 20)	-66932	NM_001163758	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding	0.025000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5761	chr4	136325617	136325817	+	1.11749	NA	intron (NM_001355182, intron 5 of 10)	ID4_|SINE|ID	14119	NM_001355182	74326	Mm.31051	NM_028871	ENSMUSG00000066037	Hnrnpr	2610003J05Rik|2610528B01Rik|Hnrpr	heterogeneous nuclear ribonucleoprotein R	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7948	chrX	37809275	37809475	+	1.11749	NA	TTS (NM_008818)	TTS (NM_008818)	-17680	NM_008955	19202	Mm.10105	NM_008955	ENSMUSG00000006200	Rhox6	AV213605|AW548842|Psx1	reproductive homeobox 6	protein-coding	0.000000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2348	chr14	11084016	11084216	+	1.11749	NA	intron (NM_001360141, intron 2 of 9)	intron (NM_001360141, intron 2 of 9)	77919	NM_001308285	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding	0.015000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4096	chr19	43843158	43843358	+	1.11749	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	4455	NR_033472	100038628	Mm.212585	NR_033472	ENSMUSG00000025194	Gm10768	-	predicted gene 10768	ncRNA	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7542	chr9	16541163	16541363	+	1.11749	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-39209	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding	0.005000	0.412935			-26(ATTTACAACAGAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7569	chr9	27071125	27071325	+	1.11699	NA	intron (NM_178113, intron 23 of 35)	intron (NM_178113, intron 23 of 35)	41050	NM_178113	78658	Mm.251777	NM_178113	ENSMUSG00000035024	Ncapd3	2810487N22Rik|4632407J06Rik|AI195468|AU018739|B130055D15Rik|mKIAA0056	non-SMC condensin II complex, subunit D3	protein-coding	0.005000	0.343284			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-225	chr13	6587331	6587531	+	1.11683	NA	intron (NM_019703, intron 17 of 21)	MTE2a|LTR|ERVL-MaLR	39274	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1713	chr12	69725642	69725842	+	1.11683	NA	promoter-TSS (NM_145443)	promoter-TSS (NM_145443)	797	NM_001361691	68055	Mm.27844	NM_026536	ENSMUSG00000054894	Dmac2l	1110015E18Rik|ATPW|Atp5s	distal membrane arm assembly complex 2 like	protein-coding	0.005000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-600	chr3	156305336	156305536	+	1.11674	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	256251	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	ncRNA	0.000000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3114	chr16	22894177	22894377	+	1.11674	NA	intron (NM_001276449, intron 1 of 3)	intron (NM_001276449, intron 1 of 3)	109	NR_110508	102632430	Mm.474375	NR_110508	ENSMUSG00000116831	Gm30505	-	predicted gene, 30505	ncRNA	0.025000	0.592040			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-372	chr16	52251689	52251889	+	1.11674	NA	intron (NM_009655, intron 15 of 15)	intron (NM_009655, intron 15 of 15)	201292	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7645	chr9	48733933	48734133	+	1.11597	NA	intron (NM_001033324, intron 3 of 6)	intron (NM_001033324, intron 3 of 6)	101908	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-506	chr1	163104521	163104721	+	1.11597	NA	Intergenic	Intergenic	-18951	NM_030071	78258	Mm.78368	NM_030071	ENSMUSG00000071890	Mroh9	4921528O07Rik|Armc11	maestro heat-like repeat family member 9	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4963	chr3	59203915	59204115	+	1.11597	NA	intron (NM_177855, intron 15 of 43)	intron (NM_177855, intron 15 of 43)	6867	NM_028808	74191	Mm.90067	NM_028808	ENSMUSG00000036362	P2ry13	2010001L06Rik|GPCR1|GPR94|Gpr86|P2Y13|P2yr13|SP174	purinergic receptor P2Y, G-protein coupled 13	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2042	chr13	40673932	40674132	+	1.11597	NA	Intergenic	Intergenic	-53776	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA	0.015000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-267	chr13	106569764	106569964	+	1.11597	NA	Intergenic	Intergenic	367094	NM_001360897	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding	0.005000	0.328358			4(TTATTTGCATGAAAAT,+,0.00),6(ATTTGCATGAAAATGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-871	chr9	48733937	48734137	+	1.11597	NA	intron (NM_001033324, intron 3 of 6)	intron (NM_001033324, intron 3 of 6)	101904	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7492	chr8	127384918	127385118	+	1.11597	NA	intron (NM_001013580, intron 10 of 13)	intron (NM_001013580, intron 10 of 13)	85406	NM_001013581	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1960	chr13	15577075	15577275	+	1.11597	NA	intron (NM_008130, intron 3 of 14)	intron (NM_008130, intron 3 of 14)	113452	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-909	chrX	139058905	139059105	+	1.11597	NA	Intergenic	RLTR17|LTR|ERVK	26231	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3388	chr16	93826270	93826470	+	1.11597	NA	Intergenic	BGLII_A|LTR|ERVK	-5751	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding	0.030000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4544	chr2	116816861	116817061	+	1.11597	NA	Intergenic	Intergenic	-61730	NM_026104	67356	Mm.131623	NM_026104	ENSMUSG00000027355	Tmco5	1700095F04Rik|Tmco5a	transmembrane and coiled-coil domains 5	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5670	chr4	105171002	105171202	+	1.11597	NA	intron (NM_080555, intron 1 of 5)	intron (NM_080555, intron 1 of 5)	13755	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|PRG-2|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6304	chr6	10969951	10970151	+	1.11597	NA	Intergenic	Intergenic	4327	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	ncRNA	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1229	chr11	32020063	32020263	+	1.11597	NA	intron (NM_001290680, intron 3 of 4)	intron (NM_001290680, intron 3 of 4)	18886	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	P19	neuron specific gene family member 2	protein-coding	0.015000	0.512438			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-161	chr11	89038497	89038697	+	1.11597	NA	non-coding (NR_156181, exon 11 of 11)	non-coding (NR_156181, exon 11 of 11)	22151	NM_001362845	56077	Mm.153695	NM_019505	ENSMUSG00000000276	Dgke	C87606|DAGK6|DGK|DGK-epsilon	diacylglycerol kinase, epsilon	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7983	chrX	69858574	69858774	+	1.11597	NA	intron (NM_008032, intron 17 of 19)	intron (NM_008032, intron 17 of 19)	-86607	NM_029316	75509	Mm.233475	NM_029316	ENSMUSG00000059690	1700020N15Rik	-	RIKEN cDNA 1700020N15 gene	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-154	chr1	53022979	53023179	+	1.11597	NA	Intergenic	L2b|LINE|L2	-30422	NM_001368276	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6690	chr6	118785287	118785487	+	1.11592	NA	intron (NM_001256000, intron 3 of 46)	intron (NM_001256000, intron 3 of 46)	-27413	NM_001290335	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding	0.015000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-47	chr1	161147982	161148182	+	1.11592	NA	intron (NM_001368766, intron 2 of 7)	intron (NM_001368766, intron 2 of 7)	5370	NM_028664	73844	Mm.38830	NM_028664	ENSMUSG00000044835	Ankrd45	4933409K03Rik	ankyrin repeat domain 45	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6945	chr7	84681015	84681215	+	1.11592	NA	intron (NM_001360577, intron 1 of 7)	intron (NM_001360577, intron 1 of 7)	-1719	NM_001360580	65098	Mm.209349	NM_022985	ENSMUSG00000030629	Zfand6	3110005P07Rik|Awp1|Za20d3	zinc finger, AN1-type domain 6	protein-coding	0.000000	0.393035		-70(CATGAATATGGAGC,+,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-604	chr3	158850733	158850933	+	1.11592	NA	Intergenic	MTD|LTR|ERVL-MaLR	-225531	NR_040750	624759	Mm.491054	NR_040750	ENSMUSG00000106053	Gm20752	-	predicted gene, 20752	ncRNA	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2522	chr14	63523348	63523548	+	1.11592	NA	TTS (NM_177594)	TTS (NM_177594)	-14356	NM_021480	58865	Mm.354229	NM_021480	ENSMUSG00000021953	Tdh	-	L-threonine dehydrogenase	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1559	chr12	17193408	17193608	+	1.11471	NA	Intergenic	Intergenic	-16620	NM_201531	382571	Mm.40173	NM_201531	ENSMUSG00000051726	Kcnf1	Gm1182|Kv5.1	potassium voltage-gated channel, subfamily F, member 1	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3516	chr17	51695362	51695562	+	1.11471	NA	Intergenic	RLTR11A2|LTR|ERVK	116592	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1006	chr10	107340589	107340789	+	1.11471	NA	intron (NM_001039354, intron 2 of 5)	Charlie24|DNA|hAT-Charlie	68295	NM_001284329	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-466	chr1	153000577	153000777	+	1.11471	NA	intron (NM_175460, intron 1 of 10)	intron (NM_175460, intron 1 of 10)	45576	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.005000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7173	chr8	23922174	23922374	+	1.11471	NA	intron (NM_177086, intron 4 of 6)	intron (NM_177086, intron 4 of 6)	252613	NM_001277239	320158	Mm.121274	NM_177086	ENSMUSG00000037492	Zmat4	9630048M01Rik	zinc finger, matrin type 4	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3999	chr19	3744317	3744517	+	1.11471	NA	Intergenic	L1M4c|LINE|L1	-23004	NM_144871	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7098	chr7	134151309	134151509	+	1.11471	NA	intron (NM_007400, intron 2 of 22)	intron (NM_007400, intron 2 of 22)	73688	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1814	chr12	91808820	91809020	+	1.11471	NA	3' UTR (NM_011344, exon 21 of 21)	3' UTR (NM_011344, exon 21 of 21)	-22484	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-759	chr10	31334346	31334546	+	1.11471	NA	intron (NM_001359366, intron 4 of 4)	intron (NM_001359366, intron 4 of 4)	21041	NM_027168	69692	Mm.245537	NM_027168	ENSMUSG00000000295	Hddc2	2310057G13Rik	HD domain containing 2	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8051	chrX	104403538	104403738	+	1.11471	NA	intron (NM_009592, intron 1 of 15)	intron (NM_009592, intron 1 of 15)	10208	NM_009592	11306	Mm.426128	NM_009592	ENSMUSG00000031333	Abcb7	AA517758|AU019072|Abc7	ATP-binding cassette, sub-family B (MDR/TAP), member 7	protein-coding	0.005000	0.348259			3(ATTTACATTAGAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1584	chr12	31644645	31644845	+	1.11471	NA	intron (NM_028002, intron 4 of 6)	ORR1D1-int|LTR|ERVL-MaLR	10081	NM_028002	71916	Mm.62979	NM_028002	ENSMUSG00000020648	Dus4l	2310069P03Rik|2700089B10Rik|AI482040|Pp35	dihydrouridine synthase 4-like (S. cerevisiae)	protein-coding	0.005000	0.373134			4(TAACTCTTATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7312	chr8	73340985	73341185	+	1.11471	NA	intron (NM_001317391, intron 1 of 15)	intron (NM_001317391, intron 1 of 15)	12455	NM_001317391	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3862	chr18	54093440	54093640	+	1.11471	NA	Intergenic	Intergenic	231427	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5759	chr4	135229228	135229428	+	1.11471	NA	intron (NM_013885, intron 2 of 5)	intron (NM_013885, intron 2 of 5)	43432	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4603	chr2	128633973	128634173	+	1.11471	NA	intron (NM_008569, intron 32 of 47)	MER2|DNA|TcMar-Tigger	41732	NM_001310641	241634	Mm.297682	NM_001310641	ENSMUSG00000074812	Spdye4c	Gm355|SpeedyB3|SpyB3	speedy/RINGO cell cycle regulator family, member E4C	protein-coding	0.000000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6919	chr7	79393027	79393227	+	1.11471	NA	intron (NM_145946, intron 1 of 37)	intron (NM_145946, intron 1 of 37)	789	NM_145946	208836	Mm.349493	NM_145946	ENSMUSG00000039187	Fanci	-	Fanconi anemia, complementation group I	protein-coding	0.025000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7	chr1	4621301	4621501	+	1.11471	NA	Intergenic	Lx|LINE|L1	-124047	NM_001289464	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding	0.005000	0.432836			-29(CTTTTTTCTTGGATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5730	chr4	125021189	125021389	+	1.11471	NA	Intergenic	MER58B|DNA|hAT-Charlie	-8725	NM_145552	230737	Mm.90760	NM_145552	ENSMUSG00000028869	Gnl2	BC003262|HUMAUANTIG|Ngp-1	guanine nucleotide binding protein-like 2 (nucleolar)	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8057	chrX	106921842	106922042	+	1.11471	NA	intron (NM_175271, intron 1 of 2)	intron (NM_175271, intron 1 of 2)	1317	NM_175271	78134	Mm.90147	NM_175271	ENSMUSG00000049929	Lpar4	5730485F04Rik|Gpr23|LPA4|p2y9	lysophosphatidic acid receptor 4	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-149	chr1	51697367	51697567	+	1.11471	NA	Intergenic	Intergenic	-100749	NR_151621	100045066	Mm.404734	NR_151621		Gm17767	-	predicted gene, 17767	ncRNA	0.030000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4553	chr2	118743387	118743587	+	1.11471	NA	Intergenic	MER135|DNA|DNA	-2271	NM_001301269	100043272	Mm.398072	NM_001301269	ENSMUSG00000074918	Inafm2	5430417L22Rik	InaF motif containing 2	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8111	chrX	145329087	145329287	+	1.11471	NA	intron (NM_178358, intron 2 of 3)	B1F|SINE|Alu	19752	NM_178358	237091	Mm.135547	NM_178358	ENSMUSG00000041700	Lhfpl1	Lhfp	lipoma HMGIC fusion partner-like 1	protein-coding	0.005000	0.393035			85(ATCTCAAAGAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5475	chr4	53829822	53830022	+	1.11471	NA	intron (NM_028053, intron 1 of 5)	intron (NM_028053, intron 1 of 5)	3877	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding	0.010000	0.343284			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-311	chr14	98933422	98933622	+	1.11471	NA	Intergenic	Intergenic	112614	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding	0.005000	0.388060			30(TATTTGGTTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1341	chr11	71944829	71945029	+	1.11471	NA	Intergenic	Intergenic	-4807	NR_045942	73816	Mm.390391	NR_045942	ENSMUSG00000085528	4930401O10Rik	-	RIKEN cDNA 4930401O10 gene	ncRNA	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2645	chr14	98933474	98933674	+	1.11471	NA	Intergenic	Intergenic	112562	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding	0.005000	0.393035			-22(TATTTGGTTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6724	chr6	134774003	134774203	+	1.11471	NA	intron (NM_001048054, intron 1 of 6)	intron (NM_001048054, intron 1 of 6)	-18257	NR_151454	105242798	Mm.398227	NR_151454		1700055D16Rik	-	RIKEN cDNA 1700055D16 gene	ncRNA	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1383	chr11	84592902	84593102	+	1.11471	NA	Intergenic	Intergenic	67342	NR_038057	78365	Mm.260345	NR_038057	ENSMUSG00000087211	Lhx1os	1500016L03Rik|Lhx1as	LIM homeobox 1, opposite strand	ncRNA	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3068	chr16	4728221	4728421	+	1.11471	NA	intron (NM_001136066, intron 1 of 5)	intron (NM_001136066, intron 1 of 5)	1960	NM_001136066	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8012	chrX	88158125	88158325	+	1.11471	NA	Intergenic	Intergenic	-42277	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|IL1RAPL-1|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding	0.000000	0.472637			-47(ATTTGCATGGCCAATT,-,0.00),-31(GTTTGCATAACAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3012	chr15	89379621	89379821	+	1.11441	NA	promoter-TSS (NM_001013022)	promoter-TSS (NM_001013022)	-467	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding	0.030000	0.582090			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-683	chr5	72209692	72209892	+	1.11441	NA	intron (NR_003966, intron 1 of 22)	intron (NR_003966, intron 1 of 22)	6449	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding	0.015000	0.402985			76(CTATTGTCATGTATCT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6571	chr6	85942586	85942786	+	1.11441	NA	3' UTR (NM_028099, exon 9 of 9)	3' UTR (NM_028099, exon 9 of 9)	18981	NM_028099	72102	Mm.24007	NM_028099	ENSMUSG00000030002	Dusp11	2010300F21Rik|AI481497	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4609	chr2	130503654	130503854	+	1.11441	NA	intron (NM_008980, intron 2 of 21)	intron (NM_008980, intron 2 of 21)	53476	NM_008980	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4658	chr2	137229730	137229930	+	1.11441	NA	Intergenic	Intergenic	-113310	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4455	chr2	93252389	93252589	+	1.11441	NA	intron (NM_183180, intron 2 of 9)	intron (NM_183180, intron 2 of 9)	64941	NR_151503	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding	0.040000	0.606965			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1070	chr10	117349534	117349734	+	1.11441	NA	intron (NM_001310609, intron 9 of 9)	intron (NM_001310609, intron 9 of 9)	27339	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding	0.005000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-776	chr6	128790144	128790344	+	1.11441	NA	Intergenic	Intergenic	-1603	NM_001159904	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Klrb1b|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1b|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding	0.010000	0.313433		3(CATGAAAATGGATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6971	chr7	92404765	92404965	+	1.11441	NA	intron (NM_001243047, intron 4 of 10)	intron (NM_001243047, intron 4 of 10)	-156284	NM_001162918	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7128	chr7	143368067	143368267	+	1.11441	NA	intron (NM_008434, intron 15 of 15)	L1M5|LINE|L1	-37517	NR_045842	71153	Mm.398340	NR_045842	ENSMUSG00000101360	4933417O13Rik	-	RIKEN cDNA 4933417O13 gene	ncRNA	0.030000	0.412935			-29(ATTGTTTCATTCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-524	chr2	130503594	130503794	+	1.11441	NA	intron (NM_008980, intron 2 of 21)	intron (NM_008980, intron 2 of 21)	53416	NM_008980	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding	0.005000	0.313433			-96(AAATTATCATTTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-534	chr2	142660670	142660870	+	1.11441	NA	intron (NM_001355123, intron 25 of 26)	intron (NM_001355123, intron 25 of 26)	240694	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1870	chr12	105601569	105601769	+	1.11441	NA	Intergenic	Intergenic	-2422	NM_007539	12061	Mm.377078	NM_007539	ENSMUSG00000041347	Bdkrb1	B1BKR|B1R|BKR1|BRADYB1|Bdkrb	bradykinin receptor, beta 1	protein-coding	0.010000	0.542289			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-799	chr7	92404811	92405011	+	1.11441	NA	intron (NM_001243047, intron 4 of 10)	intron (NM_001243047, intron 4 of 10)	-156238	NM_001162918	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-886	chr9	92717081	92717281	+	1.11441	NA	Intergenic	Intergenic	-1535	NR_040770	331003	Mm.50805	NR_040770	ENSMUSG00000101734	4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	ncRNA	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7811	chr9	92717121	92717321	+	1.11441	NA	Intergenic	Intergenic	-1495	NR_040770	331003	Mm.50805	NR_040770	ENSMUSG00000101734	4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	ncRNA	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6021	chr5	72209748	72209948	+	1.11441	NA	intron (NR_003966, intron 1 of 22)	MIRb|SINE|MIR	6505	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding	0.015000	0.388060			20(CTATTGTCATGTATCT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-55	chr1	176153625	176153825	+	1.11441	NA	intron (NM_001357846, intron 1 of 8)	intron (NM_001357846, intron 1 of 8)	60217	NM_001357845	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding	0.005000	0.348259			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-860	chr9	18745897	18746097	+	1.11441	NA	Intergenic	Intergenic	9636	NM_146606	18322	Mm.246530	NM_146606	ENSMUSG00000054141	Olfr24	MOR132-1|MTPCR51	olfactory receptor 24	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6713	chr6	128790147	128790347	+	1.11441	NA	Intergenic	Intergenic	-1606	NM_001159904	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Klrb1b|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1b|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding	0.010000	0.318408		0(CATGAAAATGGATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2475	chr14	47829908	47830108	+	1.11432	NA	Intergenic	L1MB7|LINE|L1	-68856	NR_045959	73961	Mm.390702	NR_045959	ENSMUSG00000115609	4930447J18Rik	4930425M13Rik	RIKEN cDNA 4930447J18 gene	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5754	chr4	132182413	132182613	+	1.11432	NA	Intergenic	Intergenic	29743	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH N6-methyladenosine RNA binding protein 2	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1075	chr10	117780201	117780401	+	1.11432	NA	intron (NM_134010, intron 8 of 27)	B4A|SINE|B4	12404	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding	0.005000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-705	chr5	120894686	120894886	+	1.11193	NA	Intergenic	RLTR13B1|LTR|ERVK	-7173	NR_126529	23960	Mm.389688	NM_011852	ENSMUSG00000066861	Oas1g	AI449562|L2|Mmu-L|Mmu-L2|Oas1b|Oias-1|Oias1	2'-5' oligoadenylate synthetase 1G	protein-coding	0.000000	0.402985	12(ATTGCATTATTCATG,+,0.00),12(ATTGCATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4216	chr2	24260908	24261108	+	1.11193	NA	Intergenic	BGLII|LTR|ERVK	-15946	NM_001146087	54450	Mm.29261	NM_019451	ENSMUSG00000026983	Il1f5	AI413231|Fil1delta|IL-36Ra|IL36RN|Il-1h3|Il1hy1	interleukin 1 family, member 5 (delta)	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1189	chr11	22008378	22008578	+	1.11183	NA	intron (NM_153078, intron 23 of 24)	intron (NM_153078, intron 23 of 24)	-6827	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding	0.020000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-878	chr9	75673150	75673350	+	1.11183	NA	intron (NM_009130, intron 6 of 11)	intron (NM_009130, intron 6 of 11)	10806	NM_009130	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-90	chr1	29341648	29341848	+	1.11183	NA	Intergenic	Intergenic	-79740	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7735	chr9	75673113	75673313	+	1.11183	NA	intron (NM_009130, intron 6 of 11)	intron (NM_009130, intron 6 of 11)	10843	NM_009130	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding	0.010000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-109	chr10	111995924	111996124	+	1.11183	NA	intron (NM_028608, intron 1 of 5)	L1MA7|LINE|L1	1240	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding	0.015000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-782	chr6	146231060	146231260	+	1.11183	NA	intron (NM_019923, intron 41 of 56)	intron (NM_019923, intron 41 of 56)	271063	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4154	chr2	5676027	5676227	+	1.11161	NA	promoter-TSS (NM_001290376)	promoter-TSS (NM_001290376)	-81	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding	0.020000	0.467662			-82(CCTTTCTCTAGCAGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-508	chr2	104723177	104723377	+	1.11161	NA	intron (NM_144804, intron 6 of 8)	intron (NM_144804, intron 6 of 8)	-6987	NM_001033768	241593	Mm.423301	NM_001033768	ENSMUSG00000074997	Pin1rt1	Pin1-ps1|Pin1l	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1, retrogene 1	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2562	chr14	77239853	77240053	+	1.11161	NA	intron (NM_172813, intron 1 of 18)	intron (NM_172813, intron 1 of 18)	83190	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.000000	0.333333		-16(TATGCATATCCATG,+,0.00),-16(TATGCATATCCATG,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-135	chr11	24485041	24485241	+	1.11161	NA	intron (NR_045857, intron 1 of 3)	intron (NR_045857, intron 1 of 3)	3232	NR_045857	71316	Mm.79162	NR_045857	ENSMUSG00000086892	4933430M04Rik	-	RIKEN cDNA 4933430M04 gene	ncRNA	0.010000	0.343284			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-394	chr17	29786086	29786286	+	1.11130	NA	Intergenic	L1MB7|LINE|L1	-69169	NM_001163741	68597	Mm.390979	NM_026782	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding	0.005000	0.422886			22(CAATTGTTATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6614	chr6	100285826	100286026	+	1.11130	NA	intron (NM_019743, intron 2 of 4)	intron (NM_019743, intron 2 of 4)	1432	NM_019743	56353	Mm.321633	NM_019743	ENSMUSG00000072872	Rybp	2410018J24Rik|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5834	chr5	14543082	14543282	+	1.11130	NA	intron (NM_011995, intron 3 of 24)	intron (NM_011995, intron 3 of 24)	28264	NM_011995	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding	0.000000	0.268657		-95(TATACATATGTATA,+,0.00),-95(TATACATATGTATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3460	chr17	29786083	29786283	+	1.11130	NA	Intergenic	L1MB7|LINE|L1	-69166	NM_001163741	68597	Mm.390979	NM_026782	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding	0.005000	0.422886			25(CAATTGTTATTCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6212	chr5	136403637	136403837	+	1.11018	NA	intron (NM_001291233, intron 3 of 23)	intron (NM_001291233, intron 3 of 23)	-27934	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA	0.060000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-448	chr18	74104648	74104848	+	1.11018	NA	Intergenic	Intergenic	-39799	NM_172632	225724	Mm.254517	NM_172632	ENSMUSG00000024558	Mapk4	A330097D03Rik|Erk3|Prkm4|p63Mapk	mitogen-activated protein kinase 4	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3380	chr16	91582219	91582419	+	1.11018	NA	intron (NM_030018, intron 3 of 6)	intron (NM_030018, intron 3 of 6)	15361	NM_030018	77975	Mm.290341	NM_030018	ENSMUSG00000022964	Tmem50b	AU015466|AU019872|B230114J08Rik	transmembrane protein 50B	protein-coding	0.005000	0.422886			66(GTTTCCATGATAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7070	chr7	125878385	125878585	+	1.11018	NA	TTS (NM_001101488)	TTS (NM_001101488)	170615	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding	0.025000	0.407960		-59(CATGACTATTTATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4174	chr2	11340799	11340999	+	1.11018	NA	intron (NR_040369, intron 1 of 3)	RLTR13D3A|LTR|ERVK	1410	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	-	predicted gene 13293	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4801	chr2	173832808	173833008	+	1.10978	NA	Intergenic	Intergenic	95337	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding	0.015000	0.343284			-43(ATTTGCAATGGAAAAA,-,0.00),-16(TTTTTTTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1562	chr12	24916255	24916455	+	1.10827	NA	intron (NM_001083341, intron 3 of 11)	L1ME1|LINE|L1	-58577	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2830	chr15	25332117	25332317	+	1.10827	NA	Intergenic	Intergenic	81547	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1561	chr12	21256783	21256983	+	1.10827	NA	intron (NM_001135192, intron 24 of 28)	intron (NM_001135192, intron 24 of 28)	29401	NM_001355609	16413	Mm.273333	NM_008403	ENSMUSG00000062352	Itgb1bp1	AI449260|AU019480|Icap1	integrin beta 1 binding protein 1	protein-coding	0.010000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-288	chr14	43979546	43979746	+	1.10827	NA	Intergenic	Intergenic	22577	NM_007448	503844	Mm.24663	NM_007448	ENSMUSG00000053961	Ang5	-	angiogenin, ribonuclease A family, member 5	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-522	chr1	167021528	167021728	+	1.10827	NA	intron (NM_001160261, intron 1 of 2)	MTEb|LTR|ERVL-MaLR	20211	NM_001160261	226610	Mm.389217	NM_175461	ENSMUSG00000060568	Fam78b	C030014K22Rik|C030020L09Rik	family with sequence similarity 78, member B	protein-coding	0.005000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-335	chr15	25332155	25332355	+	1.10827	NA	Intergenic	Intergenic	81509	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding	0.030000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5121	chr3	110599254	110599454	+	1.10827	NA	Intergenic	Intergenic	-348355	NM_178891	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0.010000	0.442786		-87(CATCCATTTGCATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2569	chr14	77519727	77519927	+	1.10795	NA	intron (NM_172813, intron 7 of 18)	RLTR25A|LTR|ERVK	-12959	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA	0.000000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-189	chr12	55438733	55438933	+	1.10795	NA	Intergenic	Intergenic	40008	NM_011968	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding	0.020000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3804	chr18	39669154	39669354	+	1.10795	NA	Intergenic	MLTR25A|LTR|ERVK	-104243	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding	0.005000	0.417910			-60(ATAAGCAAAACAAAAC,-,0.00),-29(GAATTGATATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7335	chr8	78810189	78810389	+	1.10795	NA	intron (NM_001191004, intron 3 of 4)	intron (NM_001191004, intron 3 of 4)	10863	NM_030145	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.020000	0.527363			58(ATAAGCATTAGAATAT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-513	chr2	108794800	108795000	+	1.10795	NA	Intergenic	Intergenic	483390	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0.015000	0.328358			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-416	chr17	90717870	90718070	+	1.10795	NA	intron (NM_001346957, intron 3 of 18)	MLTR11A|LTR|ERVK	75506	NR_136930	102634634		NR_136930		Gm20491	-	enolase 1, alpha non-neuron pseudogene	pseudo	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2502	chr14	60365862	60366062	+	1.10795	NA	Intergenic	Intergenic	-11730	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1177	chr11	18576540	18576740	+	1.10795	NA	Intergenic	Intergenic	442329	NM_010789	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding	0.015000	0.497512			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-873	chr9	52149505	52149705	+	1.10795	NA	promoter-TSS (NM_001368810)	promoter-TSS (NM_001368810)	-242	NM_001368810	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5864	chr5	23624435	23624635	+	1.10795	NA	intron (NM_001359174, intron 2 of 16)	RSINE1|SINE|B4	-7964	NM_001359175	20817	Mm.288728	NM_009274	ENSMUSG00000062604	Srpk2	AW226533|AW492537|AW547358|Wbp6|mSRPK2	serine/arginine-rich protein specific kinase 2	protein-coding	0.005000	0.482587			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-745	chr6	57641807	57642007	+	1.10795	NA	intron (NM_025992, intron 13 of 22)	intron (NM_025992, intron 13 of 22)	50171	NM_025574	66459	Mm.44201	NM_025574	ENSMUSG00000043162	Pyurf	2610022G08Rik|AI847956|Prey	Pigy upstream reading frame	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-670	chr10	4006649	4006849	+	1.10795	NA	intron (NM_172308, intron 7 of 27)	intron (NM_172308, intron 7 of 27)	33674	NM_172308	270685	Mm.184752	NM_172308	ENSMUSG00000040675	Mthfd1l	2410004L15Rik|AI647056|Fthfsdc1	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-305	chr1	106290432	106290632	+	1.10795	NA	intron (NM_133821, intron 3 of 16)	B3|SINE|B2	118663	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6201	chr5	132198822	132199022	+	1.10795	NA	intron (NM_001363480, intron 2 of 19)	intron (NM_001363480, intron 2 of 19)	318653	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-177	chr12	5805119	5805319	+	1.10795	NA	Intergenic	Intergenic	429499	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA	0.005000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-565	chr3	84116139	84116339	+	1.10795	NA	intron (NM_029797, intron 5 of 7)	MIR|SINE|MIR	39547	NM_029797	76915	Mm.274829	NM_029797	ENSMUSG00000033752	Mnd1	2610034E18Rik|AI591601|Gaj	meiotic nuclear divisions 1	protein-coding	0.005000	0.333333			59(ATTAACAACAGAATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1525	chr12	5805104	5805304	+	1.10795	NA	Intergenic	Intergenic	429484	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6569	chr6	85027413	85027613	+	1.10795	NA	intron (NM_177077, intron 1 of 21)	RMER1B|Other|Other	42000	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding	0.010000	0.597015			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7654	chr9	52149479	52149679	+	1.10795	NA	promoter-TSS (NM_001368810)	promoter-TSS (NM_001368810)	-216	NM_001368810	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3119	chr16	23482344	23482544	+	1.10795	NA	intron (NM_001359083, intron 8 of 10)	intron (NM_001359083, intron 8 of 10)	38371	NM_001359083	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding	0.005000	0.542289			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-694	chr5	100436264	100436464	+	1.10729	NA	Intergenic	Intergenic	-6829	NR_034038	100503199	Mm.392282	NR_034038	ENSMUSG00000097772	5430416N02Rik	100041797|Adapt33|Gm3514	RIKEN cDNA 5430416N02 gene	ncRNA	0.010000	0.368159			-88(ATTTGAAAAAAAGTGT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-620	chr4	59108654	59108854	+	1.10729	NA	intron (NM_001370843, intron 4 of 27)	Lx4A|LINE|L1	30229	NM_001370843	100155	Mm.331636	NM_001033200	ENSMUSG00000038598	Shoc1	AI481877|Gm426|Mzip2	shortage in chiasmata 1	protein-coding	0.000000	0.393035			42(ATATGAATAACAACAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-821	chr10	52878210	52878410	+	1.10729	NA	intron (NM_178675, intron 1 of 7)	intron (NM_178675, intron 1 of 7)	187809	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	solute carrier family 35, member F1	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1779	chr12	83579185	83579385	+	1.10729	NA	intron (NM_183154, intron 2 of 11)	intron (NM_183154, intron 2 of 11)	-16825	NM_001359168	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding	0.000000	0.522388			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-558	chr3	60557054	60557254	+	1.10729	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	55975	NM_001253710	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind like splicing factor 1	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4128	chr19	57060088	57060288	+	1.10729	NA	intron (NM_178688, intron 14 of 24)	intron (NM_178688, intron 14 of 24)	-51613	NM_001177796	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-568	chr1	176153683	176153883	+	1.10729	NA	intron (NM_001357846, intron 1 of 8)	intron (NM_001357846, intron 1 of 8)	60159	NM_001357845	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1386	chr11	86473459	86473659	+	1.10729	NA	Intergenic	Intergenic	-11098	NM_029788	76892	Mm.262707	NM_029788	ENSMUSG00000020521	Rnft1	0610013E23Rik|AV007605	ring finger protein, transmembrane 1	protein-coding	0.005000	0.308458		74(TATGAATATTTAAA,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-199	chr12	83579107	83579307	+	1.10729	NA	intron (NM_183154, intron 2 of 11)	intron (NM_183154, intron 2 of 11)	-16747	NM_001359168	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding	0.000000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-277	chr14	16971011	16971211	+	1.10729	NA	intron (NM_001289760, intron 1 of 9)	intron (NM_001289760, intron 1 of 9)	111220	NM_001289761	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5887	chr5	30118293	30118493	+	1.10729	NA	TTS (NM_001167879)	TTS (NM_001167879)	-12307	NM_001256263	433868	Mm.450696	NM_001256263	ENSMUSG00000086815	3110082J24Rik	-	RIKEN cDNA 3110082J24 gene	protein-coding	0.000000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-890	chr9	103623638	103623838	+	1.10729	NA	intron (NM_178638, intron 2 of 5)	intron (NM_178638, intron 2 of 5)	66648	NR_040764	319215	Mm.425597	NR_040764	ENSMUSG00000099616	4932413F04Rik	-	RIKEN cDNA 4932413F04 gene	ncRNA	0.025000	0.482587			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-95	chr10	65540884	65541084	+	1.10729	NA	Intergenic	Intergenic	367255	NR_155764	102632897	Mm.183448	NR_155764	ENSMUSG00000112913	Gm30853	-	predicted gene, 30853	ncRNA	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4690	chr2	142660705	142660905	+	1.10729	NA	intron (NM_001355123, intron 25 of 26)	intron (NM_001355123, intron 25 of 26)	240659	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2545	chr14	74822985	74823185	+	1.10729	NA	intron (NM_001033439, intron 4 of 19)	intron (NM_001033439, intron 4 of 19)	90788	NM_001285423	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding	0.015000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-178	chr12	11694664	11694864	+	1.10729	NA	Intergenic	Intergenic	188135	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	tubulin, beta 2a, pseudogene 2	pseudo	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1931	chr13	5448898	5449098	+	1.10729	NA	Intergenic	Intergenic	409094	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7560	chr9	24316927	24317127	+	1.10729	NA	TTS (NM_175678)	TTS (NM_175678)	186113	NM_001359948	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5493	chr4	59108708	59108908	+	1.10729	NA	intron (NM_001370843, intron 4 of 27)	intron (NM_001370843, intron 4 of 27)	30175	NM_001370843	100155	Mm.331636	NM_001033200	ENSMUSG00000038598	Shoc1	AI481877|Gm426|Mzip2	shortage in chiasmata 1	protein-coding	0.005000	0.368159			-12(ATATGAATAACAACAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-321	chr14	117337469	117337669	+	1.10720	NA	intron (NM_001079844, intron 2 of 9)	intron (NM_001079844, intron 2 of 9)	412272	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1726	chr12	71725688	71725888	+	1.10686	NA	Intergenic	Intergenic	-105280	NM_026102	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6528	chr6	72748822	72749022	+	1.10686	NA	intron (NM_009332, intron 3 of 11)	intron (NM_009332, intron 3 of 11)	40123	NM_009332	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding	0.015000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1914	chr12	118564392	118564592	+	1.10644	NA	Intergenic	Intergenic	-34299	NR_045947	100384890	Mm.484658	NR_045947	ENSMUSG00000113875	D230030E09Rik	Npe	Riken cDNA D230030E09 gene	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7912	chrX	6427648	6427848	+	1.10644	NA	intron (NM_001313764, intron 1 of 8)	intron (NM_001313764, intron 1 of 8)	12006	NM_001313764	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6060	chr5	82931988	82932188	+	1.10644	NA	Intergenic	Intergenic	-133023	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mir-1187|mmu-mir-1187	microRNA 1187	ncRNA	0.000000	0.308458	12(GCTGAATAATGTATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-625	chr1	188368616	188368816	+	1.10644	NA	intron (NM_021408, intron 8 of 70)	intron (NM_021408, intron 8 of 70)	105878	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Ushrn	usherin	protein-coding	0.000000	0.293532			-79(TTTCAGTTATGCATAT,+,0.00),70(TTATACCCATGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1365	chr11	77259333	77259533	+	1.10644	NA	intron (NM_177710, intron 1 of 14)	intron (NM_177710, intron 1 of 14)	43008	NM_177710	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot protein phosphatase 2	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6465	chr6	57551369	57551569	+	1.10644	NA	Intergenic	Intergenic	-15982	NR_156746	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2C-kappa|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1361	chr11	75717018	75717218	+	1.10644	NA	Intergenic	B2_Mm2|SINE|B2	-15769	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding	0.015000	0.442786	34(AATACATAAATCATA,+,0.00),34(AATACATAAATCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5352	chr4	13875208	13875408	+	1.10644	NA	intron (NM_009822, intron 8 of 10)	intron (NM_009822, intron 8 of 10)	90526	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	RUNX1 translocation partner 1	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7712	chr9	69758686	69758886	+	1.10644	NA	3' UTR (NM_022378, exon 2 of 2)	3' UTR (NM_022378, exon 2 of 2)	2154	NM_022378	64290	Mm.440890	NM_022378	ENSMUSG00000059246	Foxb1	C43|Fkh5|Foxb1a|Foxb1b|Hfh-e5.1|Mf3|Twh	forkhead box B1	protein-coding	0.045000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4773	chr2	164512729	164512929	+	1.10644	NA	Intergenic	Intergenic	15304	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1587	chr12	31849223	31849423	+	1.10644	NA	intron (NM_001163126, intron 14 of 22)	RMER1B|Other|Other	100922	NM_177993	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3763	chr18	28705151	28705351	+	1.10644	NA	intron (NR_045398, intron 2 of 4)	intron (NR_045398, intron 2 of 4)	145087	NR_045398	320624	Mm.50107	NR_045398	ENSMUSG00000117473	4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA	0.005000	0.348259			-72(ATTTTCATAACTGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5364	chr4	18529944	18530144	+	1.10644	NA	Intergenic	Intergenic	592506	NM_001371269									0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3554	chr17	63639674	63639874	+	1.10644	NA	Intergenic	Intergenic	-139194	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding	0.005000	0.288557		86(TATACATATGCAAA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5188	chr3	130858256	130858456	+	1.10644	NA	Intergenic	Intergenic	-127958	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding	0.020000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1624	chr12	43115960	43116160	+	1.10644	NA	Intergenic	MTD|LTR|ERVL-MaLR	-81843	NR_148724	102636207		NR_148724		Gm33340	Gm40882	predicted gene, 33340	ncRNA	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6734	chr6	137483096	137483296	+	1.10644	NA	intron (NM_007945, intron 20 of 21)	intron (NM_007945, intron 20 of 21)	36699	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0.025000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-184	chr1	63274185	63274385	+	1.10644	NA	intron (NM_001267872, intron 1 of 5)	intron (NM_001267872, intron 1 of 5)	1016	NM_028673	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding	0.035000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7695	chr9	65273918	65274118	+	1.10644	NA	intron (NM_001364527, intron 8 of 10)	L2|LINE|L2	8838	NM_001364527	214425	Mm.138455	NM_173385	ENSMUSG00000042254	Cilp	9830114D16|C130036G17Rik|CILP-1	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4877	chr3	25402786	25402986	+	1.10644	NA	Intergenic	Lx9|LINE|L1	-618880	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding	0.000000	0.318408		-42(CATTCATATTCACA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5142	chr3	117849485	117849685	+	1.10644	NA	intron (NM_029655, intron 1 of 8)	intron (NM_029655, intron 1 of 8)	19351	NM_029655	76561	Mm.33824	NM_029655	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4539	chr2	116096192	116096392	+	1.10644	NA	Intergenic	Intergenic	-20196	NR_033447	69974	Mm.440293	NR_033447		2810405F15Rik	-	RIKEN cDNA 2810405F15 gene	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4863	chr3	18524588	18524788	+	1.10644	NA	Intergenic	Intergenic	-44211	NR_040544	73959	Mm.60616	NR_040544	ENSMUSG00000102699	4930433B08Rik	-	RIKEN cDNA 4930433B08 gene	ncRNA	0.000000	0.437811			-16(TTTAACATGACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3379	chr16	90275331	90275531	+	1.10644	NA	intron (NM_001346799, intron 1 of 19)	B1F|SINE|Alu	9055	NM_001346799	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding	0.000000	0.427861			-3(ATCTGAATTACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3913	chr18	67513123	67513323	+	1.10644	NA	intron (NM_194355, intron 8 of 16)	intron (NM_194355, intron 8 of 16)	35950	NM_176832	68166	Mm.208723	NM_176832	ENSMUSG00000024533	Spire1	6030430B19Rik|AI415299|AU022898|AW550622|Spir-1	spire type actin nucleation factor 1	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8040	chrX	101805570	101805770	+	1.10644	NA	Intergenic	B3A|SINE|B2	11014	NM_001359671	382231	Mm.328112	NM_001359671	ENSMUSG00000046774	8030474K03Rik	Gm1142	RIKEN cDNA 8030474K03 gene	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4596	chr2	126768317	126768517	+	1.10644	NA	intron (NM_029163, intron 6 of 6)	B2_Mm2|SINE|B2	15043	NM_029163	75083	Mm.389373	NM_029163	ENSMUSG00000027364	Usp50	1700086G18Rik|4930511O11Rik	ubiquitin specific peptidase 50	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-33	chr1	12807105	12807305	+	1.10644	NA	intron (NM_172294, intron 6 of 21)	intron (NM_172294, intron 6 of 21)	88660	NM_172294	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding	0.020000	0.432836			-18(ATTAGCAAGTCAAACG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2539	chr14	71606414	71606614	+	1.10644	NA	Intergenic	Intergenic	-250195	NR_046274	74667	Mm.159286	NR_046274	ENSMUSG00000115304	4930434J06Rik	-	RIKEN cDNA 4930434J06 gene	ncRNA	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5567	chr4	82643098	82643298	+	1.10644	NA	Intergenic	Intergenic	135209	NR_137202	102635783	Mm.41666	NR_137202		Gm11266	-	predicted gene 11266	ncRNA	0.005000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7526	chr9	13965361	13965561	+	1.10644	NA	Intergenic	RLTR18B|LTR|ERVK	137745	NM_176836	72826	Mm.246174	NM_176836	ENSMUSG00000037808	Fam76b	2810485I05Rik|C78303	family with sequence similarity 76, member B	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4600	chr2	128312191	128312391	+	1.10644	NA	intron (NR_028589, intron 2 of 2)	intron (NR_028589, intron 2 of 2)	117060	NR_028589	100043424	Mm.297222	NR_028589		Morrbid	Gm14005|Mir4435-2hg	myeloid RNA regulator of BCL2L11 induced cell death	ncRNA	0.010000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-807	chr10	46433676	46433876	+	1.10644	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	189028	NR_028274	100302593		NR_028274	ENSMUSG00000095118	Snord14d	Gm23710	small nucleolar RNA, C/D box 14D	snoRNA	0.005000	0.358209			1(GTTTGAATAAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1533	chr12	8656618	8656818	+	1.10644	NA	Intergenic	Intergenic	-17416	NM_001160221	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding	0.015000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-942	chr10	92633710	92633910	+	1.10644	NA	Intergenic	Intergenic	88608	NM_008682	17997	Mm.2998	NM_008682	ENSMUSG00000019988	Nedd1	-	neural precursor cell expressed, developmentally down-regulated gene 1	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2895	chr15	43982843	43983043	+	1.10644	NA	Intergenic	BGLII|LTR|ERVK	-112914	NM_175502	239408	Mm.41219	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding	0.000000	0.437811			15(CCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3541	chr17	58615307	58615507	+	1.10644	NA	Intergenic	Intergenic	375968	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	Pdzph1	2610034M16Rik|AV114557	PDZ and pleckstrin homology domains 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1530	chr12	8229820	8230020	+	1.10644	NA	intron (NR_157106, intron 3 of 5)	L1MCb|LINE|L1	21727	NM_001364260	68832	Mm.25608	NM_172401	ENSMUSG00000037669	Ldah	1110057K04Rik|mLDAH	lipid droplet associated hydrolase	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6106	chr5	99546220	99546420	+	1.10644	NA	intron (NR_030692, intron 2 of 3)	intron (NR_030692, intron 2 of 3)	182740	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA	0.025000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1307	chr11	60960221	60960421	+	1.10644	NA	Intergenic	L1MC5|LINE|L1	28267	NR_157293	26397	Mm.18494	NM_008928	ENSMUSG00000018932	Map2k3	AW212142|MAPKK 3|MEK3|MKK3|MKK3b|Prkmk3	mitogen-activated protein kinase kinase 3	protein-coding	0.005000	0.373134			-85(TTTAAAATGACAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2025	chr13	36339913	36340113	+	1.10644	NA	intron (NM_001039189, intron 3 of 5)	intron (NM_001039189, intron 3 of 5)	222370	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6191	chr5	130947431	130947631	+	1.10644	NA	intron (NM_145218, intron 6 of 10)	intron (NM_145218, intron 6 of 10)	359991	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Galnt17	AA388321|E330012B09Rik|Galnt19|Gcap8|Wbscr17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-228	chr1	83219589	83219789	+	1.10644	NA	Intergenic	Intergenic	59927	NR_027636	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5321	chr4	3953437	3953637	+	1.10644	NA	Intergenic	Intergenic	14113	NR_104356	66433	Mm.27406	NM_181391	ENSMUSG00000042198	Chchd7	1810049H20Rik	coiled-coil-helix-coiled-coil-helix domain containing 7	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3970	chr18	84051116	84051316	+	1.10644	NA	intron (NM_001364993, intron 1 of 1)	intron (NM_001364993, intron 1 of 1)	35249	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|teashirt1	teashirt zinc finger family member 1	protein-coding	0.025000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-281	chr1	96383916	96384116	+	1.10644	NA	Intergenic	Intergenic	278557	NR_040478	75159	Mm.243854	NR_040478	ENSMUSG00000100589	4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	ncRNA	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5821	chr5	8850233	8850433	+	1.10644	NA	intron (NM_011075, intron 23 of 27)	intron (NM_011075, intron 23 of 27)	-43388	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7171	chr8	22978076	22978276	+	1.10644	NA	intron (NM_001277280, intron 1 of 42)	intron (NM_001277280, intron 1 of 42)	3340	NM_001277280	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding	0.015000	0.398010			-6(TTTTTTTTTTTTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3882	chr18	57748139	57748339	+	1.10644	NA	Intergenic	Intergenic	31756	NR_152224	100503033	Mm.381112	NR_152224	ENSMUSG00000118391	Gm19519	-	predicted gene, 19519	ncRNA	0.015000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7762	chr9	80360156	80360356	+	1.10644	NA	intron (NM_022016, intron 12 of 16)	intron (NM_022016, intron 12 of 16)	105182	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0.000000	0.452736			44(CTGTAGTCATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4668	chr2	139551934	139552134	+	1.10644	NA	intron (NM_175467, intron 5 of 12)	intron (NM_175467, intron 5 of 12)	58121	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2947	chr15	59025898	59026098	+	1.10644	NA	intron (NM_001146180, intron 3 of 13)	intron (NM_001146180, intron 3 of 13)	56028	NM_144800	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	MTSS I-BAR domain containing 1	protein-coding	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4138	chr19	59466023	59466223	+	1.10644	NA	TTS (NM_010132)	TTS (NM_010132)	7433	NM_010132	13797	Mm.245394	NM_010132	ENSMUSG00000043969	Emx2	Pdo	empty spiracles homeobox 2	protein-coding	0.025000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3404	chr17	3443122	3443322	+	1.10644	NA	intron (NM_011878, intron 9 of 26)	intron (NM_011878, intron 9 of 26)	-39093	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2754	chr15	4035133	4035333	+	1.10644	NA	intron (NM_024188, intron 1 of 16)	intron (NM_024188, intron 1 of 16)	-7827	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5789	chr4	149496695	149496895	+	1.10644	NA	TTS (NM_001356322)	TTS (NM_001356322)	11529	NM_026963	69151	Mm.464434	NM_026963	ENSMUSG00000028990	Lzic	1810030J04Rik|AW047580	leucine zipper and CTNNBIP1 domain containing	protein-coding	0.005000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7330	chr8	77564316	77564516	+	1.10644	NA	intron (NM_001363465, intron 6 of 11)	intron (NM_001363465, intron 6 of 11)	15019	NM_001363465	102182	Mm.197630	NM_178903	ENSMUSG00000037134	Prmt9	AI931714|Prmt10	protein arginine methyltransferase 9	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3023	chr15	91502700	91502900	+	1.10644	NA	intron (NM_001033633, intron 2 of 9)	MER5B|DNA|hAT-Charlie	70461	NM_001033633	239606	Mm.360596	NM_001033633	ENSMUSG00000036298	Slc2a13	6530403A04|A630029G22Rik|AI505012|Gm308	solute carrier family 2 (facilitated glucose transporter), member 13	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6463	chr6	55588338	55588538	+	1.10644	NA	Intergenic	Intergenic	92825	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding	0.000000	0.368159			72(GTATTGTTAAGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1231	chr11	32399405	32399605	+	1.10644	NA	intron (NM_177364, intron 6 of 12)	intron (NM_177364, intron 6 of 12)	51665	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4903	chr3	32577835	32578035	+	1.10644	NA	TTS (NM_001348104)	TTS (NM_001348104)	38232	NM_001348062	14696	Mm.139192	NM_013531	ENSMUSG00000027669	Gnb4	6720453A21Rik|G(beta)4	guanine nucleotide binding protein (G protein), beta 4	protein-coding	0.015000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-747	chr6	59358613	59358813	+	1.10608	NA	intron (NM_183183, intron 1 of 1)	intron (NM_183183, intron 1 of 1)	67593	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1411	chr11	92804981	92805181	+	1.10608	NA	Intergenic	Intergenic	-293285	NM_001361707	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2997	chr15	76119313	76119513	+	1.10608	NA	TTS (NM_001142968)	TTS (NM_001142968)	782	NM_144848	223650	Mm.259929	NM_144848		Eppk1	6230424I18Rik|EPIPL|EPIPL1|EPPK	epiplakin 1	protein-coding	0.005000	0.537313			70(GTTTGCAAGGGAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6472	chr6	59358605	59358805	+	1.10608	NA	intron (NM_183183, intron 1 of 1)	intron (NM_183183, intron 1 of 1)	67601	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6558	chr6	83428617	83428817	+	1.10608	NA	intron (NM_183138, intron 2 of 10)	intron (NM_183138, intron 2 of 10)	12961	NM_183138	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4256	chr2	35877506	35877706	+	1.10570	NA	intron (NM_029774, intron 6 of 9)	intron (NM_029774, intron 6 of 9)	58416	NR_040618	77665	Mm.400558	NR_040618	ENSMUSG00000086449	9030204H09Rik	-	RIKEN cDNA 9030204H09 gene	ncRNA	0.020000	0.497512			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-141	chr11	36020105	36020305	+	1.10570	NA	intron (NM_011856, intron 27 of 28)	intron (NM_011856, intron 27 of 28)	-39678	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra	WW, C2 and coiled-coil domain containing 1	protein-coding	0.005000	0.467662		-23(TATAAATATGCAAA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3569	chr17	67617642	67617842	+	1.10570	NA	intron (NR_155516, intron 2 of 2)	intron (NR_155516, intron 2 of 2)	11590	NR_155516	102640031	Mm.421441	NR_155516	ENSMUSG00000117029	Gm36201	-	predicted gene, 36201	ncRNA	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4258	chr2	36077305	36077505	+	1.10570	NA	intron (NM_029309, intron 4 of 4)	intron (NM_029309, intron 4 of 4)	26655	NM_001083127	16874	Mm.12881	NM_008500	ENSMUSG00000026890	Lhx6	Lhx6.1	LIM homeobox protein 6	protein-coding	0.015000	0.542289			-50(CATCTGTGATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1933	chr13	5797076	5797276	+	1.10570	NA	Intergenic	L2b|LINE|L2	60916	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA	0.005000	0.407960			65(ATTATCATTACAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1238	chr11	36020097	36020297	+	1.10570	NA	intron (NM_011856, intron 27 of 28)	intron (NM_011856, intron 27 of 28)	-39670	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra	WW, C2 and coiled-coil domain containing 1	protein-coding	0.005000	0.467662		-15(TATAAATATGCAAA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6061	chr5	82933969	82934169	+	1.10570	NA	Intergenic	Intergenic	-135004	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mir-1187|mmu-mir-1187	microRNA 1187	ncRNA	0.025000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4479	chr2	102212203	102212403	+	1.10570	NA	Intergenic	Intergenic	-25843	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6051	chr5	80956098	80956298	+	1.10570	NA	Intergenic	Intergenic	-64373	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.363184			13(ATTATCATAACAAAAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4611	chr2	130752473	130752673	+	1.10570	NA	intron (NM_029432, intron 20 of 36)	L1M4|LINE|L1	51528	NR_024097	100043766	Mm.447040	NR_024097		Gm14057	-	Ppp1r14c pseudogene	pseudo	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-382	chr1	131365854	131366054	+	1.10570	NA	intron (NM_001081011, intron 4 of 22)	ORR1E|LTR|ERVL-MaLR	-86391	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-E|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding	0.005000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-684	chr5	80956105	80956305	+	1.10570	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-64366	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.363184			6(ATTATCATAACAAAAT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-486	chr2	61084300	61084500	+	1.10570	NA	Intergenic	Intergenic	-109249	NR_045335	100038493	Mm.388076	NR_045335	ENSMUSG00000075325	Gm13582	-	predicted gene 13582	ncRNA	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-412	chr1	139317023	139317223	+	1.10570	NA	intron (NM_133239, intron 4 of 11)	RLTR25B|LTR|ERVK	59953	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5127	chr3	113988320	113988520	+	1.10570	NA	Intergenic	Intergenic	-42120	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4531	chr2	115398240	115398440	+	1.10570	NA	Intergenic	Intergenic	-54060	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	ncRNA	0.000000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-316	chr14	105348874	105349074	+	1.10570	NA	Intergenic	Intergenic	-78585	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-802	chr10	45054580	45054780	+	1.10570	NA	Intergenic	Intergenic	-12536	NM_011156	19072	Mm.37294	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PE|PEP|Pop	prolyl endopeptidase	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1418	chr11	95305054	95305254	+	1.10570	NA	intron (NM_001195003, intron 2 of 14)	intron (NM_001195003, intron 2 of 14)	5092	NM_177619	217127	Mm.90213	NM_177619	ENSMUSG00000038909	Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7717	chr9	71355804	71356004	+	1.10570	NA	Intergenic	Intergenic	129054	NM_001164793	28015	Mm.21094	NM_178602	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4612	chr2	130827516	130827716	+	1.10570	NA	intron (NM_029432, intron 1 of 36)	intron (NM_029432, intron 1 of 36)	12071	NM_001311147	228602	Mm.271990	NM_028367	ENSMUSG00000027309	4930402H24Rik	2810487F15Rik|AI413763|C78926	RIKEN cDNA 4930402H24 gene	protein-coding	0.000000	0.447761			-43(TCTTTGGTTTGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6137	chr5	107040291	107040491	+	1.10570	NA	Intergenic	Intergenic	75830	NM_001271566	12545	Mm.20842	NM_009863	ENSMUSG00000029283	Cdc7	AI597260|Cdc7l1|muCdc7	cell division cycle 7 (S. cerevisiae)	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6043	chr5	78680876	78681076	+	1.10570	NA	Intergenic	L1MA6|LINE|L1	1215488	NR_131050	69370	Mm.426881	NR_131050	ENSMUSG00000107232	1700017L05Rik	-	RIKEN cDNA 1700017L05 gene	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3768	chr18	30698076	30698276	+	1.10570	NA	Intergenic	RLTR13D6|LTR|ERVK	425311	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7726	chr9	73574048	73574248	+	1.10570	NA	intron (NM_001081153, intron 19 of 31)	intron (NM_001081153, intron 19 of 31)	394889	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C	protein-coding	0.000000	0.373134			-69(CATTGCATAACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2641	chr14	98048383	98048583	+	1.10570	NA	intron (NM_001038610, intron 1 of 10)	intron (NM_001038610, intron 1 of 10)	121282	NM_007826	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund family transcription factor 1	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2675	chr14	105348898	105349098	+	1.10570	NA	Intergenic	Intergenic	-78561	NR_045859	71362	Mm.410781	NR_045859	ENSMUSG00000115548	5430440P10Rik	-	RIKEN cDNA 5430440P10 gene	ncRNA	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1119	chr10	125175019	125175219	+	1.10570	NA	Intergenic	Intergenic	133697	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.010000	0.363184			-14(CTATTCTCATATAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2492	chr14	56565848	56566048	+	1.10570	NA	intron (NM_001014996, intron 1 of 16)	intron (NM_001014996, intron 1 of 16)	5898	NM_001014996	219103	Mm.212525	NM_001014996	ENSMUSG00000064128	Cenpj	4932437H03Rik|CPAP|Gm81|LAP|LIP1|Sas4	centromere protein J	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6034	chr5	75066831	75067031	+	1.10570	NA	Intergenic	Intergenic	-8670	NM_133256	14843	Mm.218752	NM_133256	ENSMUSG00000035946	Gsx2	Gsh-2|Gsh2	GS homeobox 2	protein-coding	0.020000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4672	chr2	140023950	140024150	+	1.10570	NA	intron (NR_110352, intron 3 of 12)	intron (NR_110352, intron 3 of 12)	42755	NM_001289611	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-381	chr1	131365605	131365805	+	1.10570	NA	intron (NM_001081011, intron 4 of 22)	intron (NM_001081011, intron 4 of 22)	-86142	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-E|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4054	chr19	23776090	23776290	+	1.10570	NA	intron (NM_177034, intron 1 of 12)	intron (NM_177034, intron 1 of 12)	17314	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3350	chr16	84045252	84045452	+	1.10570	NA	Intergenic	RLTR28|LTR|ERVL	-325791	NR_040567	75247	Mm.417813	NR_040567	ENSMUSG00000116907	4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5690	chr4	111305730	111305930	+	1.10523	NA	intron (NM_001284190, intron 5 of 12)	intron (NM_001284190, intron 5 of 12)	-109176	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0.010000	0.422886			-6(TTGTAAATGACAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6382	chr6	32373398	32373598	+	1.10523	NA	intron (NM_175750, intron 3 of 31)	L1MB3|LINE|L1	-137643	NR_040277	319849	Mm.440860	NR_040277	ENSMUSG00000086763	Plxna4os1	B230378P21Rik	plexin A4, opposite strand 1	ncRNA	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-254	chr1	88668937	88669137	+	1.10523	NA	Intergenic	Intergenic	33154	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding	0.010000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-649	chr4	111305696	111305896	+	1.10523	NA	intron (NM_001284190, intron 5 of 12)	intron (NM_001284190, intron 5 of 12)	-109210	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0.010000	0.427861			28(TTGTAAATGACAATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-714	chr5	138703106	138703306	+	1.10523	NA	Intergenic	Intergenic	-51875	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding	0.000000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-661	chr5	13659870	13660070	+	1.10251	NA	Intergenic	Intergenic	-131649	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding	0.000000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-553	chr3	16085805	16086005	+	1.10251	NA	Intergenic	RLTR13D3A|LTR|ERVK	-79573	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding	0.005000	0.388060	45(ATTGTATTATTCATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7895	chr9	115805437	115805637	+	1.10251	NA	Intergenic	Intergenic	-103918	NM_028638	73748	Mm.485018	NM_028638	ENSMUSG00000056880	Gadl1	1110027M19Rik|ADC|CSADC	glutamate decarboxylase-like 1	protein-coding	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-697	chr10	12383568	12383768	+	1.10208	NA	3' UTR (NM_011682, exon 74 of 74)	3' UTR (NM_011682, exon 74 of 74)	478067	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding	0.000000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2045	chr13	40982876	40983076	+	1.10107	NA	intron (NR_155347, intron 1 of 4)	intron (NR_155347, intron 1 of 4)	-18034	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding	0.005000	0.482587			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-686	chr5	81061455	81061655	+	1.10102	NA	intron (NM_198702, intron 1 of 27)	intron (NM_198702, intron 1 of 27)	39962	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.412935		1(AATGCATTTGCATT,+,0.00),1(AATGCATTTGCATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6717	chr6	132656799	132656999	+	1.10059	NA	promoter-TSS (NM_207023)	promoter-TSS (NM_207023)	-58	NM_207023	387348	Mm.377910	NM_207023	ENSMUSG00000059382	Tas2r120	T2R20|Tas2r20|mGR20|mt2r47	taste receptor, type 2, member 120	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-755	chr10	29702842	29703042	+	1.10059	NA	Intergenic	Intergenic	-167075	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7026	chr7	112497461	112497661	+	1.10059	NA	intron (NM_020606, intron 1 of 12)	Tigger7|DNA|TcMar-Tigger	38122	NR_154466	102636183	Mm.446701	NR_154466		Parvaos	A230071N21Rik	parvin, alpha, opposite strand	ncRNA	0.015000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1577	chr12	28776523	28776723	+	1.10059	NA	intron (NM_201357, intron 3 of 8)	intron (NM_201357, intron 3 of 8)	24795	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Eipr1	D12Ertd604e|Tssc1	EARP complex and GARP complex interacting protein 1	protein-coding	0.000000	0.363184			-9(TTATTCTCTTTAAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-849	chr8	103122768	103122968	+	1.10059	NA	Intergenic	Intergenic	224666	NR_036588	69794	Mm.396139	NR_036588	ENSMUSG00000110340	1600027J07Rik	-	RIKEN cDNA 1600027J07 gene	ncRNA	0.005000	0.338308			70(ATATAAATAGCAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7421	chr8	103122764	103122964	+	1.10059	NA	Intergenic	Intergenic	224670	NR_036588	69794	Mm.396139	NR_036588	ENSMUSG00000110340	1600027J07Rik	-	RIKEN cDNA 1600027J07 gene	ncRNA	0.005000	0.338308			74(ATATAAATAGCAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3596	chr17	75603795	75603995	+	1.10059	NA	Intergenic	Intergenic	-51949	NM_001357860	72722	Mm.24641	NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	family with sequence similarity 98, member A	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2969	chr15	66485885	66486085	+	1.10059	NA	intron (NM_019457, intron 2 of 11)	intron (NM_019457, intron 2 of 11)	14925	NM_019457	54562	Mm.244890	NM_019457	ENSMUSG00000022375	Lrrc6	LRTP	leucine rich repeat containing 6 (testis)	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-818	chr10	52028276	52028476	+	1.10051	NA	TTS (NM_153786)	TTS (NM_153786)	5874	NM_001300957	215031	Mm.87237	NM_153786	ENSMUSG00000049641	Vgll2	C130057C21Rik|VITO-1|Vito1|vgl-2	vestigial like family member 2	protein-coding	0.010000	0.363184			-38(ATTTCCAAAACAGAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7353	chr8	81472127	81472327	+	1.10051	NA	intron (NM_001297593, intron 1 of 23)	intron (NM_001297593, intron 1 of 23)	129665	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding	0.000000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-17	chr1	47307050	47307250	+	1.10051	NA	Intergenic	BGLII|LTR|ERVK	159975	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA	0.000000	0.407960			-43(TCTTTATTTTACAAAT,+,0.00),82(CTATCCATAACAATGC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-13	chr1	35243425	35243625	+	1.10051	NA	Intergenic	Intergenic	393536	NM_001357425	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding	0.015000	0.467662	29(TCTGAATTATTAATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-252	chr1	87378026	87378226	+	1.10051	NA	intron (NM_146112, intron 6 of 28)	intron (NM_146112, intron 6 of 28)	16603	NM_001110227	100040591	Mm.443539	NM_001110227	ENSMUSG00000079436	Kcnj13	-	potassium inwardly-rectifying channel, subfamily J, member 13	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7662	chr9	55482120	55482320	+	1.10051	NA	intron (NM_145615, intron 9 of 11)	intron (NM_145615, intron 9 of 11)	30023	NM_145615	110842	Mm.290853	NM_145615	ENSMUSG00000032314	Etfa	2010200I21Rik|D9Ertd394e	electron transferring flavoprotein, alpha polypeptide	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-449	chr1	150740922	150741122	+	1.10051	NA	intron (NM_001024720, intron 25 of 106)	intron (NM_001024720, intron 25 of 106)	252413	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5431	chr4	36216977	36217177	+	1.10051	NA	intron (NM_001166000, intron 4 of 8)	intron (NM_001166000, intron 4 of 8)	-371873	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8090	chrX	134762528	134762728	+	1.10051	NA	Intergenic	Intergenic	4997	NR_106061	102466805		NR_106061	ENSMUSG00000099272	Mir7093	Gm27453|mmu-mir-7093	microRNA 7093	ncRNA	0.010000	0.383085			0(ATTTTTTTTTGCTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1458	chr11	109544372	109544572	+	1.10051	NA	intron (NM_001361978, intron 1 of 3)	intron (NM_001361978, intron 1 of 3)	761	NM_001166177	74008	Mm.482224	NM_028710	ENSMUSG00000020604	Arsg	6330406P08Rik|AI846872|ASG	arylsulfatase G	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4184	chr2	16423149	16423349	+	1.10051	NA	intron (NM_026162, intron 1 of 13)	B3A|SINE|B2	66945	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0.025000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-125	chr10	125220222	125220422	+	1.10051	NA	3' UTR (NM_001358915, exon 6 of 6)	3' UTR (NM_001358915, exon 6 of 6)	88494	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.005000	0.358209			34(ATTACCAAAACAATTC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-857	chr9	13512867	13513067	+	1.10051	NA	Intergenic	Intergenic	81606	NR_028271	18689	Mm.41972	NM_008835	ENSMUSG00000031802	Phxr4	Sp5	per-hexamer repeat gene 4	ncRNA	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2107	chr13	63609304	63609504	+	1.10051	NA	Intergenic	Intergenic	-35944	NM_001328514	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes|wig	patched 1	protein-coding	0.005000	0.422886			-20(ATTTACAAGCCAAACT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7264	chr8	56616247	56616447	+	1.10051	NA	Intergenic	Intergenic	65193	NM_001368348	50753	Mm.251174	NM_015791	ENSMUSG00000038206	Fbxo8	Fbx8	F-box protein 8	protein-coding	0.025000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-373	chr16	53227294	53227494	+	1.10051	NA	Intergenic	Intergenic	-411650	NR_040495	73820	Mm.60493	NR_040495	ENSMUSG00000116611	4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA	0.015000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-908	chrX	134762534	134762734	+	1.10051	NA	Intergenic	Intergenic	5003	NR_106061	102466805		NR_106061	ENSMUSG00000099272	Mir7093	Gm27453|mmu-mir-7093	microRNA 7093	ncRNA	0.010000	0.373134			-6(ATTTTTTTTTGCTTAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1501	chr11	120183285	120183485	+	1.10051	NA	Intergenic	Intergenic	6471	NR_030682	100042332	Mm.269766	NR_030682		2810410L24Rik	-	RIKEN cDNA 2810410L24 gene	ncRNA	0.000000	0.527363			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-875	chr9	55482055	55482255	+	1.10051	NA	intron (NM_145615, intron 9 of 11)	intron (NM_145615, intron 9 of 11)	30088	NM_145615	110842	Mm.290853	NM_145615	ENSMUSG00000032314	Etfa	2010200I21Rik|D9Ertd394e	electron transferring flavoprotein, alpha polypeptide	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4522	chr2	112512944	112513144	+	1.10051	NA	intron (NM_028844, intron 1 of 5)	intron (NM_028844, intron 1 of 5)	20080	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7804	chr9	89335247	89335447	+	1.10051	NA	Intergenic	Intergenic	123963	NM_001359993	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding	0.000000	0.358209			19(TTTTTTTTTTGTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5309	chr3	156305415	156305615	+	1.09945	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	256172	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	ncRNA	0.005000	0.467662			50(ATTTACAGGACAAGAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2192	chr13	90358784	90358984	+	1.09945	NA	Intergenic	Intergenic	269217	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7338	chr8	79224491	79224691	+	1.09919	NA	intron (NM_026315, intron 2 of 5)	ORR1E-int|LTR|ERVL-MaLR	23992	NM_026315	67687	Mm.178707	NM_026315	ENSMUSG00000031682	1700011L22Rik	-	RIKEN cDNA 1700011L22 gene	protein-coding	0.025000	0.472637			-18(TTCCTGTCATTCTAAT,+,0.00),-12(TCATTCTAATGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-840	chr8	79224462	79224662	+	1.09919	NA	intron (NM_026315, intron 2 of 5)	ORR1E-int|LTR|ERVL-MaLR	24021	NM_026315	67687	Mm.178707	NM_026315	ENSMUSG00000031682	1700011L22Rik	-	RIKEN cDNA 1700011L22 gene	protein-coding	0.025000	0.472637			11(TTCCTGTCATTCTAAT,+,0.00),17(TCATTCTAATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7566	chr9	25267683	25267883	+	1.09919	NA	intron (NM_001359738, intron 2 of 12)	ORR1D2|LTR|ERVL-MaLR	14891	NM_001359738	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding	0.005000	0.467662			40(TGTTTGTGATTCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2684	chr14	105859281	105859481	+	1.09902	NA	Intergenic	RMER10A|LTR|ERVL	37438	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty RTK signaling antagonist 2	protein-coding	0.005000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-241	chr13	44751824	44752024	+	1.09822	NA	intron (NM_021878, intron 2 of 18)	intron (NM_021878, intron 2 of 18)	20653	NM_001360281	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6165	chr5	120894674	120894874	+	1.09748	NA	Intergenic	RLTR13B1|LTR|ERVK	-7161	NR_126529	23960	Mm.389688	NM_011852	ENSMUSG00000066861	Oas1g	AI449562|L2|Mmu-L|Mmu-L2|Oas1b|Oias-1|Oias1	2'-5' oligoadenylate synthetase 1G	protein-coding	0.000000	0.402985	24(ATTGCATTATTCATG,+,0.00),24(ATTGCATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-967	chr10	97245675	97245875	+	1.09748	NA	Intergenic	Intergenic	-177703	NR_039547	100628616		NR_039547	ENSMUSG00000105557	Mir3966	mmu-mir-3966|mu-mir-3966	microRNA 3966	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2066	chr13	49376868	49377068	+	1.09744	NA	intron (NM_029791, intron 3 of 7)	intron (NM_029791, intron 3 of 7)	35419	NM_029791	76895	Mm.197387	NM_029791	ENSMUSG00000037933	Bicd2	-	BICD cargo adaptor 2	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1254	chr11	40568480	40568680	+	1.09744	NA	Intergenic	RLTR45|LTR|ERVK	124102	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding	0.010000	0.502488			-79(TCTTTGTTTTGGAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4557	chr2	120243038	120243238	+	1.09744	NA	intron (NM_001363090, intron 1 of 20)	intron (NM_001363090, intron 1 of 20)	2197	NM_177845	329502	Mm.330505	NM_177845	ENSMUSG00000050211	Pla2g4e	2310026J01Rik|C230096D22|Pla2epsilon	phospholipase A2, group IVE	protein-coding	0.005000	0.552239			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-32	chr1	119806111	119806311	+	1.09744	NA	intron (NM_019933, intron 1 of 26)	intron (NM_019933, intron 1 of 26)	30860	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6162	chr5	118280832	118281032	+	1.09744	NA	Intergenic	RLTR11A|LTR|ERVK	35705	NM_001081236	76792	Mm.103428	NM_001081236	ENSMUSG00000032840	2410131K14Rik	-	RIKEN cDNA 2410131K14 gene	protein-coding	0.010000	0.452736			-51(GTATTCTAATGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3979	chr18	85010831	85011031	+	1.09744	NA	Intergenic	L1_Mur3|LINE|L1	58815	NM_001367965	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8120	chrX	152074502	152074702	+	1.09744	NA	Intergenic	L1MDa|LINE|L1	58174	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4364	chr2	66162441	66162641	+	1.09744	NA	Intergenic	L1ME5|LINE|L1	-37748	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.010000	0.333333			41(TTTTCAATGACAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7345	chr8	79828135	79828335	+	1.09744	NA	Intergenic	Intergenic	116386	NM_001357235	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5790	chr4	149710599	149710799	+	1.09744	NA	Intergenic	Intergenic	-9070	NM_001029837	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta	protein-coding	0.020000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4497	chr2	106868329	106868529	+	1.09744	NA	TTS (NM_001143683)	TTS (NM_001143683)	101962	NM_173750	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding	0.020000	0.432836			42(GGTTTGTTTTTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2076	chr13	53717652	53717852	+	1.09744	NA	Intergenic	Intergenic	69167	NR_131010	75252	Mm.401989	NR_131010	ENSMUSG00000113329	4930555G21Rik	-	RIKEN cDNA 4930555G21 gene	ncRNA	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5935	chr5	48320553	48320753	+	1.09744	NA	Intergenic	Intergenic	-51739	NM_025755	66768	Mm.29409	NM_025755	ENSMUSG00000029089	Pacrgl	4933428G09Rik	PARK2 co-regulated-like	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7916	chrX	7867315	7867515	+	1.09744	NA	intron (NM_001290537, intron 3 of 9)	intron (NM_001290537, intron 3 of 9)	-10891	NM_138606	18715	Mm.347478	NM_138606	ENSMUSG00000031155	Pim2	DXCch3|Pim-2	proviral integration site 2	protein-coding	0.000000	0.482587			-66(CTTTACAACACAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5934	chr5	48161551	48161751	+	1.09744	NA	intron (NR_111900, intron 4 of 35)	intron (NR_111900, intron 4 of 35)	-62291	NR_029798	723822		NR_029798	ENSMUSG00000065603	Mir218-1	Mirn218-1|mir-218-1	microRNA 218-1	ncRNA	0.005000	0.308458			-54(ATTTAAAAAATAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6615	chr6	100645387	100645587	+	1.09744	NA	intron (NM_181590, intron 6 of 10)	intron (NM_181590, intron 6 of 10)	25670	NM_181590	72171	Mm.256022	NM_181590	ENSMUSG00000035378	Shq1	2810403P18Rik|Grim-1	SHQ1 homolog (S. cerevisiae)	protein-coding	0.020000	0.407960			-22(ATCTGAATAAGAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7157	chr8	12545693	12545893	+	1.09744	NA	Intergenic	Intergenic	-27243	NM_024279	78634	Mm.116871	NM_024279	ENSMUSG00000010435	Spaca7	1700094C09Rik	sperm acrosome associated 7	protein-coding	0.005000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-577	chr3	119415281	119415481	+	1.09744	NA	intron (NM_170778, intron 21 of 22)	intron (NM_170778, intron 21 of 22)	368007	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-294	chr1	104210428	104210628	+	1.09744	NA	Intergenic	L1MC|LINE|L1	-557992	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.000000	0.338308			16(ATTTGCAAGAAATAAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-331	chr15	11457372	11457572	+	1.09744	NA	Intergenic	Intergenic	-57814	NM_033074	110960	Mm.286061	NM_033074	ENSMUSG00000022241	Tars	D15Wsu59e|ThrRS	threonyl-tRNA synthetase	protein-coding	0.035000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7520	chr9	12653906	12654106	+	1.09744	NA	Intergenic	Intergenic	451849	NR_040755	78219	Mm.414868	NR_040755	ENSMUSG00000111830	4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	ncRNA	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5465	chr4	53115961	53116161	+	1.09744	NA	intron (NM_013454, intron 5 of 49)	intron (NM_013454, intron 5 of 49)	43834	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding	0.010000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4192	chr2	17704598	17704798	+	1.09744	NA	intron (NM_028757, intron 2 of 6)	intron (NM_028757, intron 2 of 6)	26436	NR_156123	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-408	chr1	139000736	139000936	+	1.09744	NA	intron (NM_181347, intron 1 of 20)	intron (NM_181347, intron 1 of 20)	23179	NR_108103	78229	Mm.437838	NR_108103	ENSMUSG00000104900	4930596I21Rik	-	RIKEN cDNA 4930596I21 gene	ncRNA	0.015000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-327	chr1	119806121	119806321	+	1.09744	NA	intron (NM_019933, intron 1 of 26)	intron (NM_019933, intron 1 of 26)	30850	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-489	chr2	66162505	66162705	+	1.09744	NA	Intergenic	L1ME5|LINE|L1	-37812	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.010000	0.323383			-23(TTTTCAATGACAAATA,-,0.00),76(ATTAGCAAAAGAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7670	chr9	57988276	57988476	+	1.09744	NA	Intergenic	Intergenic	-9648	NM_001346787	13070	Mm.302865	NM_019779	ENSMUSG00000032323	Cyp11a1	Cyp11a|Cypxia1|D9Ertd411e|P450scc|Scc|cscc	cytochrome P450, family 11, subfamily a, polypeptide 1	protein-coding	0.005000	0.447761			-14(TATTTGACTTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3891	chr18	61966585	61966785	+	1.09744	NA	intron (NM_172628, intron 2 of 16)	intron (NM_172628, intron 2 of 16)	13610	NM_172628	225608	Mm.262320	NM_172628	ENSMUSG00000045629	Sh3tc2	D430044G18Rik	SH3 domain and tetratricopeptide repeats 2	protein-coding	0.030000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6132	chr5	105911107	105911307	+	1.09744	NA	intron (NR_030777, intron 8 of 9)	(TATTG)n|Simple_repeat|Simple_repeat	34639	NR_030777	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding	0.010000	0.323383			50(ATTTAAATTACAAGTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-283	chr1	96736444	96736644	+	1.09701	NA	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-73971	NR_040478	75159	Mm.243854	NR_040478	ENSMUSG00000100589	4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	ncRNA	0.005000	0.457711			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-859	chr9	14246575	14246775	+	1.09701	NA	Intergenic	Intergenic	-29626	NM_030261	75747	Mm.325126	NM_030261	ENSMUSG00000032009	Sesn3	5630400E15Rik|BC003348|SEST3	sestrin 3	protein-coding	0.020000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2786	chr15	10672888	10673088	+	1.09701	NA	intron (NM_030690, intron 2 of 17)	intron (NM_030690, intron 2 of 17)	40552	NM_030690	75646	Mm.212395	NM_030690	ENSMUSG00000022246	Rai14	1700008J19Rik|1700020L11Rik|Ankycorbin|Norpeg|mKIAA1334	retinoic acid induced 14	protein-coding	0.005000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-185	chr12	36612847	36613047	+	1.09701	NA	intron (NM_178629, intron 9 of 9)	intron (NM_178629, intron 9 of 9)	197331	NR_037309	100499526		NR_037309	ENSMUSG00000092917	Mir3472	mmu-mir-3472	microRNA 3472	ncRNA	0.000000	0.348259			-92(GCATTGTTATGAAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-26	chr1	96736487	96736687	+	1.09701	NA	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-74014	NR_040478	75159	Mm.243854	NR_040478	ENSMUSG00000100589	4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-504	chr1	162224819	162225019	+	1.09701	NA	non-coding (NR_002870, exon 1 of 1)	non-coding (NR_002870, exon 1 of 1)	1551	NR_029796	387210		NR_029796	ENSMUSG00000065516	Mir214	Mirn214|mir-214|mmu-mir-214	microRNA 214	ncRNA	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4860	chr3	16085835	16086035	+	1.09701	NA	Intergenic	RLTR13D3A|LTR|ERVK	-79603	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding	0.005000	0.368159	15(ATTGTATTATTCATG,+,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-619	chr4	52543070	52543270	+	1.09701	NA	Intergenic	RMER13A2|LTR|ERVK	-53104	NM_026652	68274	Mm.85045	NM_026652	ENSMUSG00000028314	Toporsl	4930547C10Rik	topoisomerase I binding, arginine/serine-rich like	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3940	chr18	76338976	76339176	+	1.09664	NA	Intergenic	Intergenic	76631	NM_001311070	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1224	chr11	29656851	29657051	+	1.09664	NA	Intergenic	Intergenic	-35947	NM_194053	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7293	chr8	64658595	64658795	+	1.09664	NA	intron (NM_013494, intron 1 of 8)	intron (NM_013494, intron 1 of 8)	34414	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|NF-alpha1|R74677|fat	carboxypeptidase E	protein-coding	0.010000	0.373134			-24(ATCTGCATAGGAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7032	chr7	114584726	114584926	+	1.09664	NA	Intergenic	L1MC|LINE|L1	-21854	NM_177382	244209	Mm.108037	NM_177382	ENSMUSG00000030670	Cyp2r1	-	cytochrome P450, family 2, subfamily r, polypeptide 1	protein-coding	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1774	chr12	82433404	82433604	+	1.09664	NA	intron (NM_001167983, intron 18 of 23)	intron (NM_001167983, intron 18 of 23)	122155	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6219	chr5	138096255	138096455	+	1.09664	NA	intron (NM_029869, intron 3 of 3)	intron (NM_029869, intron 3 of 3)	11271	NM_029869	74570	Mm.213114	NM_029869	ENSMUSG00000029729	Zkscan1	5930429A01Rik|9130423L19Rik|9230118B16Rik|AI646829|AI788588|C87323|KOX18|PHZ-37|ZNF139	zinc finger with KRAB and SCAN domains 1	protein-coding	0.010000	0.442786		-50(TCTGCATTTGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3471	chr17	32805685	32805885	+	1.09664	NA	intron (NM_183177, intron 1 of 3)	B3|SINE|B2	4146	NM_001267583	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5023	chr3	76348588	76348788	+	1.09664	NA	intron (NM_178673, intron 4 of 15)	Lx2B2|LINE|L1	273105	NM_001253719	213262	Mm.379337	NM_178673	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6458	chr6	54478902	54479102	+	1.09664	NA	intron (NM_001167861, intron 2 of 7)	intron (NM_001167861, intron 2 of 7)	-48781	NR_033635	100042056	Mm.448157	NM_198118	ENSMUSG00000073067	9130019P16Rik	6430501H15Rik	RIKEN cDNA 9130019P16 gene	ncRNA	0.000000	0.343284			-97(TCTTTTTTTTTTAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2165	chr13	80723123	80723323	+	1.09664	NA	Intergenic	RLTR9A3B|LTR|ERVK	-160161	NR_153410	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5514	chr4	64676013	64676213	+	1.09664	NA	Intergenic	Intergenic	-399510	NR_151546	102633436	Mm.411637	NR_151546		Gm11217	-	predicted gene 11217	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-727	chr10	21533729	21533929	+	1.09664	NA	Intergenic	Intergenic	-59316	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA	0.000000	0.308458			40(TCATTCCTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6164	chr5	120475960	120476160	+	1.09664	NA	promoter-TSS (NM_145565)	promoter-TSS (NM_145565)	-487	NM_145565	231691	Mm.28685	NM_145565	ENSMUSG00000029597	Sds	4432411H13Rik|SDH	serine dehydratase	protein-coding	0.025000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6577	chr6	88639708	88639908	+	1.09664	NA	Intergenic	Intergenic	-12379	NM_001278671	74589	Mm.196226	NM_029013	ENSMUSG00000033182	Kbtbd12	4833415F11Rik|4933428M03Rik|Klhdc6	kelch repeat and BTB (POZ) domain containing 12	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7121	chr7	139843243	139843443	+	1.09664	NA	intron (NM_177469, intron 3 of 7)	intron (NM_177469, intron 3 of 7)	9169	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding	0.020000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2944	chr15	58767282	58767482	+	1.09664	NA	Intergenic	Intergenic	56045	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding	0.000000	0.447761			-89(AAATTGCCTTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7764	chr9	80526607	80526807	+	1.09664	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-61269	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0.000000	0.368159			-46(ATTTGCATGACTAATT,-,0.00),6(GTTTGAATAAGAGTAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4226	chr2	27038699	27038899	+	1.09664	NA	Intergenic	Intergenic	-10801	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2393	chr14	21690974	21691174	+	1.09664	NA	intron (NM_001013826, intron 2 of 3)	intron (NM_001013826, intron 2 of 3)	23502	NM_001013826	435391	Mm.295860	NM_001013826	ENSMUSG00000063821	Dupd1	EG435391	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding	0.005000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5316	chr3	158320500	158320700	+	1.09664	NA	intron (NM_001291452, intron 4 of 26)	RMER1B|Other|Other	241161	NM_001370781	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding	0.000000	0.402985			-100(TTCTTTTCATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-806	chr10	45851836	45852036	+	1.09664	NA	TTS (NR_040624)	TTS (NR_040624)	44232	NR_040624	320363	Mm.123343	NR_040624	ENSMUSG00000110874	D030045P18Rik	-	RIKEN cDNA D030045P18 gene	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2995	chr15	75821973	75822173	+	1.09664	NA	intron (NM_172121, intron 3 of 11)	intron (NM_172121, intron 3 of 11)	19835	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding	0.020000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1768	chr12	80804491	80804691	+	1.09664	NA	intron (NM_178682, intron 1 of 5)	B1_Mur3|SINE|Alu	14059	NM_178682	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3010	chr15	86517451	86517651	+	1.09664	NA	Intergenic	Lx9|LINE|L1	239876	NM_001358062	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3124	chr16	25426319	25426519	+	1.09664	NA	Intergenic	Intergenic	139602	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3914	chr18	67606189	67606389	+	1.09664	NA	intron (NM_194355, intron 1 of 16)	intron (NM_194355, intron 1 of 16)	4617	NM_194355	68166	Mm.208723	NM_176832	ENSMUSG00000024533	Spire1	6030430B19Rik|AI415299|AU022898|AW550622|Spir-1	spire type actin nucleation factor 1	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4246	chr2	31503157	31503357	+	1.09664	NA	intron (NR_002687, intron 12 of 15)	intron (NR_002687, intron 12 of 15)	32949	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo	0.020000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5820	chr5	8407553	8407753	+	1.09664	NA	intron (NM_013726, intron 6 of 11)	intron (NM_013726, intron 6 of 11)	15063	NM_001190717	27214	Mm.292470	NM_013726	ENSMUSG00000002297	Dbf4	AA545217|Ask	DBF4 zinc finger	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2155	chr13	77448369	77448569	+	1.09664	NA	intron (NM_001145676, intron 19 of 19)	intron (NM_001145676, intron 19 of 19)	-260221	NM_001163420	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding	0.005000	0.328358			-16(TCTTAGTCATTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3528	chr17	53512365	53512565	+	1.09664	NA	intron (NM_173449, intron 2 of 2)	intron (NM_173449, intron 2 of 2)	26986	NM_173449	110332	Mm.444633	NM_173449	ENSMUSG00000044957	Pp2d1	4921523A10Rik	protein phosphatase 2C-like domain containing 1	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2404	chr14	25660774	25660974	+	1.09664	NA	intron (NM_183208, intron 22 of 23)	intron (NM_183208, intron 22 of 23)	-33296	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding	0.045000	0.636816			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1195	chr11	23587817	23588017	+	1.09664	NA	intron (NM_027860, intron 16 of 21)	intron (NM_027860, intron 16 of 21)	-29075	NR_004857	100134990	Mm.247328	NR_004857	ENSMUSG00000085415	Selenok-ps1	Gm12060	selenoprotein K, pseudogene 1	pseudo	0.000000	0.313433			13(ATTAGCATGTCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2723	chr14	119820650	119820850	+	1.09664	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	71523	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA	0.015000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7065	chr7	124627834	124628034	+	1.09626	NA	intron (NR_045907, intron 2 of 3)	intron (NR_045907, intron 2 of 3)	81001	NR_045907	73076	Mm.417827	NR_045907	ENSMUSG00000086254	3100003L05Rik	-	RIKEN cDNA 3100003L05 gene	ncRNA	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7190	chr8	32405418	32405618	+	1.09626	NA	Intergenic	Intergenic	253623	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	ncRNA	0.005000	0.432836		12(TATGAATATGAATG,+,0.00),12(TATGAATATGAATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7568	chr9	27070944	27071144	+	1.09626	NA	intron (NM_178113, intron 23 of 35)	intron (NM_178113, intron 23 of 35)	40869	NM_178113	78658	Mm.251777	NM_178113	ENSMUSG00000035024	Ncapd3	2810487N22Rik|4632407J06Rik|AI195468|AU018739|B130055D15Rik|mKIAA0056	non-SMC condensin II complex, subunit D3	protein-coding	0.020000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-811	chr7	124627801	124628001	+	1.09626	NA	intron (NR_045907, intron 2 of 3)	intron (NR_045907, intron 2 of 3)	81034	NR_045907	73076	Mm.417827	NR_045907	ENSMUSG00000086254	3100003L05Rik	-	RIKEN cDNA 3100003L05 gene	ncRNA	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7334	chr8	78719795	78719995	+	1.09443	NA	intron (NM_029736, intron 10 of 11)	intron (NM_029736, intron 10 of 11)	101257	NM_030145	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.010000	0.487562			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-755	chr6	82640227	82640427	+	1.09443	NA	intron (NM_001370295, intron 3 of 3)	intron (NM_001370295, intron 3 of 3)	12538	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-25	chr1	92707431	92707631	+	1.09443	NA	Intergenic	L1MB8|LINE|L1	-58690	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6554	chr6	82640196	82640396	+	1.09443	NA	intron (NM_001370295, intron 3 of 3)	intron (NM_001370295, intron 3 of 3)	12569	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding	0.005000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-447	chr18	72484533	72484733	+	1.09443	NA	Intergenic	Intergenic	-133564	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0.005000	0.303483			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-900	chrX	82809283	82809483	+	1.09429	NA	Intergenic	Lx9|LINE|L1	-139487	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding	0.010000	0.427861			
merged_common	chr5	84007862	84008062	+	1.09429	NA	Intergenic	Intergenic	409420	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0.000000	0.353234			41(CCATTTTTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3651	chr17	86977416	86977616	+	1.09429	NA	intron (NM_145491, intron 2 of 4)	B1_Mur1|SINE|Alu	14405	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding	0.015000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-395	chr17	38011392	38011592	+	1.09429	NA	Intergenic	MMSAT4|Satellite|Satellite	48292	NM_146327	258324	Mm.329044	NM_146327	ENSMUSG00000081724	Olfr129	MOR263-9	olfactory receptor 129	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-212	chr1	76136915	76137115	+	1.09429	NA	Intergenic	Intergenic	-352118	NR_038012	620079	Mm.378379	NR_038012	ENSMUSG00000100553	Gm17751	-	predicted gene, 17751	ncRNA	0.000000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-341	chr15	35028648	35028848	+	1.09429	NA	intron (NM_019635, intron 6 of 10)	intron (NM_019635, intron 6 of 10)	127058	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding	0.000000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-519	chr2	120441313	120441513	+	1.09429	NA	intron (NM_172672, intron 14 of 23)	intron (NM_172672, intron 14 of 23)	-22180	NM_007601	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2858	chr15	35028655	35028855	+	1.09429	NA	intron (NM_019635, intron 6 of 10)	intron (NM_019635, intron 6 of 10)	127051	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7998	chrX	82809278	82809478	+	1.09429	NA	Intergenic	Lx9|LINE|L1	-139492	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4218	chr2	24479819	24480019	+	1.09429	NA	Intergenic	Intergenic	-4320	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding	0.000000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5284	chr3	149567188	149567388	+	1.09396	NA	Intergenic	Intergenic	292551	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.000000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-279	chr14	17978410	17978610	+	1.09356	NA	intron (NM_001113417, intron 4 of 9)	B3A|SINE|B2	-3134	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4270	chr2	43245322	43245522	+	1.09356	NA	Intergenic	Intergenic	-309903	NM_001289593	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5118	chr3	110238445	110238645	+	1.09356	NA	Intergenic	Intergenic	12454	NR_024139	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3597	chr17	76118418	76118618	+	1.09356	NA	Intergenic	RLTR13B4|LTR|ERVK	257495	NR_033456	100043885	Mm.127562	NR_033456	ENSMUSG00000117539	Gm4710	-	predicted gene 4710	ncRNA	0.005000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-442	chr18	63040668	63040868	+	1.09356	NA	intron (NM_001039485, intron 40 of 53)	intron (NM_001039485, intron 40 of 53)	62852	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding	0.015000	0.368159		-62(AATGATTATTCATG,+,0.00),-62(AATGATTATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6941	chr7	84403459	84403659	+	1.09356	NA	intron (NM_007488, intron 1 of 18)	intron (NM_007488, intron 1 of 18)	6479	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4850	chr3	13370902	13371102	+	1.09356	NA	Intergenic	LTR78B|LTR|ERV1	-100653	NM_001357035	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6567	chr6	84796963	84797163	+	1.09356	NA	intron (NM_177077, intron 18 of 21)	intron (NM_177077, intron 18 of 21)	-203155	NM_001177713	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5941	chr5	49882420	49882620	+	1.09356	NA	Intergenic	Intergenic	176476	NM_133911	70693	Mm.272974	NM_133911	ENSMUSG00000029090	Adgra3	3830613O22Rik|AU044632|Gpr125|Tem5-like	adhesion G protein-coupled receptor A3	protein-coding	0.005000	0.363184			-76(TTCGTGTTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4228	chr2	28159864	28160064	+	1.09356	NA	Intergenic	L1MB2|LINE|L1	-33129	NM_001038613	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7602	chr9	33343777	33343977	+	1.09356	NA	Intergenic	Intergenic	-414911	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3320	chr16	75870195	75870395	+	1.09356	NA	intron (NM_023380, intron 7 of 7)	intron (NM_023380, intron 7 of 7)	38971	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding	0.005000	0.358209			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-236	chr13	36947799	36947999	+	1.09356	NA	intron (NM_028784, intron 6 of 14)	intron (NM_028784, intron 6 of 14)	101314	NM_028784	74145	Mm.235105	NM_028784	ENSMUSG00000039109	F13a1	1200014I03Rik|AI462306|F13a	coagulation factor XIII, A1 subunit	protein-coding	0.005000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-796	chr7	84403446	84403646	+	1.09356	NA	intron (NM_007488, intron 1 of 18)	intron (NM_007488, intron 1 of 18)	6492	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1745	chr12	75907574	75907774	+	1.09356	NA	intron (NM_001005510, intron 14 of 115)	intron (NM_001005510, intron 14 of 115)	-1429	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6395	chr6	35758954	35759154	+	1.09356	NA	Intergenic	Intergenic	-219166	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2483	chr14	49074408	49074608	+	1.09356	NA	intron (NM_001360070, intron 2 of 8)	MLT1F1|LTR|ERVL-MaLR	-7841	NM_207214	105504	Mm.31607	NM_207214	ENSMUSG00000061244	Exoc5	AI447711|AI448003|Gm76|PRO1912|SEC10|Sec10l1	exocyst complex component 5	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5418	chr4	34327358	34327558	+	1.09356	NA	Intergenic	Intergenic	-223157	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4300	chr2	51431678	51431878	+	1.09356	NA	intron (NR_130155, intron 2 of 2)	intron (NR_130155, intron 2 of 2)	6122	NR_130155	73375	Mm.396227	NR_130155	ENSMUSG00000086007	1700057H21Rik	-	RIKEN cDNA 1700057H21 gene	ncRNA	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6204	chr5	132229741	132229941	+	1.09356	NA	intron (NM_001363480, intron 2 of 19)	intron (NM_001363480, intron 2 of 19)	313379	NM_001363480	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3077	chr16	10524270	10524470	+	1.09356	NA	intron (NM_001243761, intron 17 of 18)	intron (NM_001243761, intron 17 of 18)	18684	NM_021428	58239	Mm.353006	NM_021428	ENSMUSG00000038055	Dexi	1810029J14Rik|AI836170|AW413143|D16Bwg0586e|Myle	dexamethasone-induced transcript	protein-coding	0.005000	0.383085	-12(AATGAATATTTCATC,+,0.00),-12(AATGAATATTTCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3657	chr17	89654290	89654490	+	1.09345	NA	Intergenic	Intergenic	275149	NR_045952	100043904	Mm.396198	NR_045952	ENSMUSG00000117524	Gm4719	-	predicted gene 4719	ncRNA	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6557	chr6	82998588	82998788	+	1.09345	NA	intron (NM_033079, intron 4 of 9)	intron (NM_033079, intron 4 of 9)	34783	NM_001291799	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding	0.030000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1152	chr11	8472646	8472846	+	1.09345	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	191789	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding	0.030000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4696	chr2	142818292	142818492	+	1.09345	NA	intron (NM_001355123, intron 12 of 26)	intron (NM_001355123, intron 12 of 26)	83072	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-45	chr1	16183986	16184186	+	1.09345	NA	Intergenic	Intergenic	78204	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6052	chr5	81061431	81061631	+	1.09325	NA	intron (NM_198702, intron 1 of 27)	intron (NM_198702, intron 1 of 27)	39938	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.388060		25(AATGCATTTGCATT,+,0.00),25(AATGCATTTGCATT,-,0.00)	-89(CCATTATTATTTAAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-573	chr3	118299831	118300031	+	1.09304	NA	Intergenic	Intergenic	-133926	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5145	chr3	118299849	118300049	+	1.09304	NA	Intergenic	Intergenic	-133908	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA	0.015000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-421	chr18	13742190	13742390	+	1.09304	NA	intron (NM_145492, intron 5 of 7)	intron (NM_145492, intron 5 of 7)	230443	NM_001360804	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding	0.005000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-879	chr9	78844701	78844901	+	1.09304	NA	Intergenic	Intergenic	229255	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6790	chr7	12966958	12967158	+	1.09194	NA	intron (NM_001362140, intron 1 of 2)	B3A|SINE|B2	1220	NM_001362140	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding	0.010000	0.452736			70(TTTTGAAAGACAATCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7890	chr9	113876922	113877122	+	1.09177	NA	intron (NM_001081960, intron 18 of 33)	intron (NM_001081960, intron 18 of 33)	-53912	NM_001083319	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1149	chr11	7283114	7283314	+	1.09163	NA	Intergenic	Intergenic	-69291	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding	0.005000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6488	chr6	63440817	63441017	+	1.09163	NA	intron (NM_001370966, intron 1 of 15)	MTE2b-int|LTR|ERVL-MaLR	184911	NM_001370966									0.000000	0.263682			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-784	chr7	12967050	12967250	+	1.09119	NA	intron (NM_001362140, intron 1 of 2)	intron (NM_001362140, intron 1 of 2)	1312	NM_001362140	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding	0.005000	0.467662			-22(TTTTGAAAGACAATCT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-762	chr6	96373409	96373609	+	1.09086	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	-207304	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	Npap60|Nup50	nucleoporin 50 pseudogene	pseudo	0.005000	0.388060			-6(ATATTCTCTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6600	chr6	96373415	96373615	+	1.09086	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	-207310	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	Npap60|Nup50	nucleoporin 50 pseudogene	pseudo	0.005000	0.383085			-12(ATATTCTCTTTTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-244	chr13	58011467	58011667	+	1.09055	NA	intron (NM_001362415, intron 12 of 14)	intron (NM_001362415, intron 12 of 14)	11633	NR_030544	100124491		NR_030544	ENSMUSG00000077962	Mir874	Mirn874|mir-874|mmu-mir-874	microRNA 874	ncRNA	0.005000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-347	chr15	69202173	69202373	+	1.09055	NA	Intergenic	Intergenic	-68260	NR_130983	75076		NR_130983	ENSMUSG00000116167	4930504C09Rik	-	RIKEN cDNA 4930504C09 gene	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-329	chr1	120139006	120139206	+	1.08985	NA	intron (NM_001172074, intron 1 of 4)	intron (NM_001172074, intron 1 of 4)	17919	NM_001172074	73103	Mm.271602	NM_028439	ENSMUSG00000026388	3110009E18Rik	-	RIKEN cDNA 3110009E18 gene	protein-coding	0.010000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7207	chr8	36923044	36923244	+	1.08985	NA	intron (NM_001194940, intron 2 of 17)	intron (NM_001194940, intron 2 of 17)	29298	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding	0.015000	0.373134			37(ATTTTAAAGAAAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4932	chr3	47549273	47549473	+	1.08985	NA	Intergenic	RLTR16B_MM|LTR|ERVK	477386	NR_040408	666202	Mm.465057	NR_040408	ENSMUSG00000103257	Gm7977	EG666202	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene	pseudo	0.015000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4053	chr19	23694346	23694546	+	1.08985	NA	exon (NM_028208, exon 2 of 7)	exon (NM_028208, exon 2 of 7)	7046	NM_028208	72351	Mm.474795	NM_028208	ENSMUSG00000074925	Ptar1	1700084D09Rik|2010013L17Rik|4930428J16Rik|AI449677	protein prenyltransferase alpha subunit repeat containing 1	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5396	chr4	26586646	26586846	+	1.08985	NA	Intergenic	Intergenic	118703	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	ncRNA	0.005000	0.388060			28(CTTTTATTCTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6027	chr5	73559294	73559494	+	1.08985	NA	non-coding (NR_153313, exon 10 of 10)	non-coding (NR_153313, exon 10 of 10)	68368	NM_001190733	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding	0.015000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-332	chr1	120978440	120978640	+	1.08985	NA	Intergenic	Intergenic	-108865	NR_110450	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA	0.010000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7392	chr8	97365234	97365434	+	1.08985	NA	Intergenic	Intergenic	-1476933	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding	0.010000	0.348259			36(TTTAAAATAACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7281	chr8	61757272	61757472	+	1.08985	NA	intron (NM_001293772, intron 2 of 21)	intron (NM_001293772, intron 2 of 21)	2717	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3391	chr16	94657146	94657346	+	1.08985	NA	intron (NM_001113389, intron 2 of 11)	intron (NM_001113389, intron 2 of 11)	45827	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7473	chr8	120136434	120136634	+	1.08985	NA	intron (NM_001163762, intron 1 of 7)	intron (NM_001163762, intron 1 of 7)	-8395	NM_001163760	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding	0.005000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1851	chr12	100814745	100814945	+	1.08985	NA	intron (NM_001361020, intron 2 of 13)	intron (NM_001361020, intron 2 of 13)	35788	NM_001361020	217830	Mm.218590	NM_145448	ENSMUSG00000021185	Dglucy	9030617O03Rik	D-glutamate cyclase	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7255	chr8	53236513	53236713	+	1.08985	NA	Intergenic	Intergenic	-275089	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-416	chr1	140451513	140451713	+	1.08985	NA	intron (NM_001081027, intron 13 of 27)	intron (NM_001081027, intron 13 of 27)	204789	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA	0.015000	0.393035			-75(CATTTCTCTTGAAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6246	chr5	146290954	146291154	+	1.08985	NA	intron (NM_001359991, intron 6 of 12)	intron (NM_001359991, intron 6 of 12)	59804	NM_001359990	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2639	chr14	97780685	97780885	+	1.08985	NA	Intergenic	MT2A|LTR|ERVL	388980	NM_007826	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund family transcription factor 1	protein-coding	0.000000	0.298507			10(CTTTTAATAACAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4350	chr2	63359892	63360092	+	1.08985	NA	Intergenic	Intergenic	-175705	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding	0.005000	0.278607			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2041	chr13	40673597	40673797	+	1.08985	NA	Intergenic	Intergenic	-54111	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6325	chr6	16747131	16747331	+	1.08985	NA	Intergenic	Intergenic	-30293	NR_157239	102640655		NR_157239	ENSMUSG00000107022	Gm36669	-	predicted gene, 36669	ncRNA	0.005000	0.328358	64(TATGTATTATTCAAG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6081	chr5	89919434	89919634	+	1.08985	NA	Intergenic	Intergenic	-36200	NM_177872	330119	Mm.133062	NM_177872	ENSMUSG00000043635	Adamts3	1100001H14Rik|6330442E02Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 3	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-330	chr1	120139073	120139273	+	1.08985	NA	intron (NM_001172074, intron 1 of 4)	intron (NM_001172074, intron 1 of 4)	17986	NM_001172074	73103	Mm.271602	NM_028439	ENSMUSG00000026388	3110009E18Rik	-	RIKEN cDNA 3110009E18 gene	protein-coding	0.015000	0.502488			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-827	chr8	53236512	53236712	+	1.08985	NA	Intergenic	Intergenic	-275090	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1098	chr10	121958952	121959152	+	1.08985	NA	intron (NM_001081037, intron 1 of 21)	intron (NM_001081037, intron 1 of 21)	88263	NM_001081037	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.015000	0.353234			46(CTATTTTAATTCAAAT,+,0.00),79(TTTTTTTTTTTTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-162	chr11	92804909	92805109	+	1.08961	NA	Intergenic	Intergenic	-293357	NM_001361707	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2556	chr14	76419452	76419652	+	1.08961	NA	intron (NM_207652, intron 1 of 2)	intron (NM_207652, intron 1 of 2)	3731	NM_207652	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding	0.020000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-115	chr10	117824327	117824527	+	1.08961	NA	intron (NM_024457, intron 2 of 7)	ID_B1|SINE|B4	21547	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6094	chr5	93131635	93131835	+	1.08875	NA	intron (NM_001009818, intron 1 of 9)	intron (NM_001009818, intron 1 of 9)	38319	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding	0.005000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-293	chr14	64306513	64306713	+	1.08833	NA	intron (NM_001253714, intron 1 of 4)	intron (NM_001253714, intron 1 of 4)	110343	NM_001253716	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding	0.005000	0.527363			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-422	chr18	16713517	16713717	+	1.08833	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	95629	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding	0.005000	0.398010			16(ATTTGAATGTCCAAAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-156	chr11	72953051	72953251	+	1.08833	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	-8018	NM_001163336	53313	Mm.6306	NM_016745	ENSMUSG00000020788	Atp2a3	SERCA3b|Serca3	ATPase, Ca++ transporting, ubiquitous	protein-coding	0.000000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5455	chr4	49720149	49720349	+	1.08833	NA	intron (NM_001033351, intron 3 of 8)	intron (NM_001033351, intron 3 of 8)	-38266	NM_001004025	19059	Mm.46125	NM_001004025	ENSMUSG00000028310	Ppp3r2	CaNB2|CnB2	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type II)	protein-coding	0.000000	0.462687			-42(GTATGGTTTTTCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3	chr1	7497420	7497620	+	1.08833	NA	Intergenic	Intergenic	408600	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.000000	0.313433			-89(ATTTTGTCTTGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2523	chr14	64306545	64306745	+	1.08833	NA	intron (NM_001253714, intron 1 of 4)	intron (NM_001253714, intron 1 of 4)	110311	NM_001253716	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding	0.005000	0.527363			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-906	chrX	113888744	113888944	+	1.08833	NA	Intergenic	RLTR13D4|LTR|ERVK	-585489	NM_172781	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding	0.000000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-774	chr6	119057492	119057692	+	1.08800	NA	intron (NM_009781, intron 1 of 46)	intron (NM_009781, intron 1 of 46)	50903	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6695	chr6	119057512	119057712	+	1.08800	NA	intron (NM_009781, intron 1 of 46)	intron (NM_009781, intron 1 of 46)	50883	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7110	chr7	136430693	136430893	+	1.08800	NA	Intergenic	Intergenic	-81378	NR_040459	330664	Mm.127762	NR_040459	ENSMUSG00000109633	C230079O03Rik	C230079O03	RIKEN cDNA C230079O03 gene	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2955	chr15	61496953	61497153	+	1.08786	NA	Intergenic	MER2|DNA|TcMar-Tigger	277398	NR_040350	432956	Mm.404918	NR_040350	ENSMUSG00000116031	D030024E09Rik	-	RIKEN cDNA D030024E09 gene	ncRNA	0.000000	0.318408			13(ATTTACATAGCAATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5875	chr5	27029029	27029229	+	1.08786	NA	intron (NM_001198886, intron 1 of 25)	intron (NM_001198886, intron 1 of 25)	-20070	NM_207282	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0.000000	0.442786			-34(CTATTCCTATGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3595	chr17	75465434	75465634	+	1.08786	NA	promoter-TSS (NM_207246)	promoter-TSS (NM_207246)	-4	NM_207246	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding	0.040000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1919	chr12	119396692	119396892	+	1.08786	NA	Intergenic	Lx9|LINE|L1	-46618	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding	0.005000	0.358209		-82(CTTGCATATGTATG,+,0.00),-82(CTTGCATATGTATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6175	chr5	125447947	125448147	+	1.08786	NA	intron (NM_029752, intron 1 of 2)	intron (NM_029752, intron 1 of 2)	6479	NM_029752	76809	Mm.290720	NM_029752	ENSMUSG00000037905	Bri3bp	2410150I18Rik|AI841257|AW742481	Bri3 binding protein	protein-coding	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4147	chr2	3230075	3230275	+	1.08786	NA	Intergenic	Intergenic	-54037	NM_008708	18108	Mm.65021	NM_008708	ENSMUSG00000026643	Nmt2	A930001K02Rik|AI605445|AU044698|hNMT-2	N-myristoyltransferase 2	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3184	chr16	41742417	41742617	+	1.08786	NA	intron (NM_001361281, intron 3 of 8)	intron (NM_001361281, intron 3 of 8)	209691	NM_001347236	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Gm29907|Lam|Lamp	limbic system-associated membrane protein	protein-coding	0.005000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-668	chr10	3420844	3421044	+	1.08786	NA	intron (NM_133485, intron 1 of 3)	intron (NM_133485, intron 1 of 3)	54794	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory inhibitor subunit 14C	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3527	chr17	52978666	52978866	+	1.08786	NA	3' UTR (NM_001031811, exon 16 of 16)	3' UTR (NM_001031811, exon 16 of 16)	376057	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding	0.020000	0.447761			74(TATTTGCCATGTAAAT,+,0.00),82(ATGTAAATGAAAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4269	chr2	42736176	42736376	+	1.08786	NA	Intergenic	Intergenic	-82678	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4209	chr2	22213689	22213889	+	1.08786	NA	Intergenic	Intergenic	-13714	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6732	chr6	137206154	137206354	+	1.08786	NA	Intergenic	Intergenic	-35758	NM_181988	232441	Mm.46233	NM_181988	ENSMUSG00000030222	Rerg	-	RAS-like, estrogen-regulated, growth-inhibitor	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4235	chr2	29448679	29448879	+	1.08786	NA	intron (NM_001290489, intron 2 of 6)	intron (NM_001290489, intron 2 of 6)	26515	NR_105753	102465170		NR_105753	ENSMUSG00000098539	Mir133c	Gm27865|mmu-mir-133c	microRNA 133c	ncRNA	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3951	chr18	80069427	80069627	+	1.08786	NA	intron (NM_053117, intron 1 of 2)	L1MB7|LINE|L1	22632	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 family cell polarity regulator gamma	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6425	chr6	44444144	44444344	+	1.08786	NA	Intergenic	Intergenic	-615817	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3713	chr18	13924615	13924815	+	1.08786	NA	intron (NM_145492, intron 3 of 7)	intron (NM_145492, intron 3 of 7)	48018	NM_001360804	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding	0.015000	0.398010	-67(TATGTTTAATGCATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1272	chr11	45032386	45032586	+	1.08786	NA	Intergenic	Intergenic	84442	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-544	chr1	172907574	172907774	+	1.08786	NA	Intergenic	Intergenic	-12620	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3051	chr15	96830806	96831006	+	1.08786	NA	Intergenic	Intergenic	-131178	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding	0.030000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3796	chr18	38459840	38460040	+	1.08786	NA	intron (NM_022996, intron 6 of 7)	intron (NM_022996, intron 6 of 7)	41033	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4648	chr2	135747091	135747291	+	1.08786	NA	intron (NM_001355153, intron 2 of 38)	intron (NM_001355153, intron 2 of 38)	-17647	NM_001355154	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2978	chr15	68241286	68241486	+	1.08786	NA	intron (NR_152182, intron 1 of 13)	intron (NR_152182, intron 1 of 13)	17470	NM_198644	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding	0.005000	0.432836		76(CATACATATGCACA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2591	chr14	80250059	80250259	+	1.08786	NA	Intergenic	L2c|LINE|L2	249857	NM_001351947	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5416	chr4	33982894	33983094	+	1.08786	NA	Intergenic	Intergenic	56614	NM_001365881	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1A|CB1B|CB1R	cannabinoid receptor 1 (brain)	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-922	chr10	88057058	88057258	+	1.08786	NA	Intergenic	Intergenic	-33914	NM_029971	110312	Mm.391436	NM_029971	ENSMUSG00000035383	Pmch	A230109K23Rik	pro-melanin-concentrating hormone	protein-coding	0.025000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7887	chr9	113190585	113190785	+	1.08786	NA	Intergenic	Intergenic	396467	NR_040760	102688	Mm.394901	NR_040760	ENSMUSG00000109890	AU023762	-	expressed sequence AU023762	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3191	chr16	42910119	42910319	+	1.08786	NA	intron (NM_001285805, intron 1 of 10)	intron (NM_001285805, intron 1 of 10)	1851	NR_040402	100503040	Mm.490721	NR_040402	ENSMUSG00000116903	Gm19522	-	predicted gene, 19522	ncRNA	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-836	chr10	57526196	57526396	+	1.08786	NA	intron (NM_019760, intron 2 of 8)	intron (NM_019760, intron 2 of 8)	6233	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-555	chr1	175448198	175448398	+	1.08786	NA	intron (NM_001357129, intron 2 of 15)	intron (NM_001357129, intron 2 of 15)	44247	NM_001199003	24012	Mm.7956	NM_011880	ENSMUSG00000026527	Rgs7	-	regulator of G protein signaling 7	protein-coding	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7756	chr9	79745104	79745304	+	1.08786	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	14649	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit 7A2	protein-coding	0.005000	0.472637			-61(GTTTGAATAAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4020	chr19	16293323	16293523	+	1.08786	NA	intron (NM_008139, intron 2 of 6)	B1F|SINE|Alu	21581	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7471	chr8	118801980	118802180	+	1.08786	NA	intron (NM_019707, intron 4 of 13)	intron (NM_019707, intron 4 of 13)	518469	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-499	chr1	161379822	161380022	+	1.08786	NA	Intergenic	Lx8|LINE|L1	-15516	NM_009452	22164	Mm.4994	NM_009452	ENSMUSG00000026700	Tnfsf4	Ath-1|Ath1|CD134L|OX-40L|Ox40l|TXGP1|Tnlg2b|Txgp1l|gp34	tumor necrosis factor (ligand) superfamily, member 4	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3458	chr17	29199509	29199709	+	1.08786	NA	intron (NM_001360239, intron 9 of 21)	intron (NM_001360239, intron 9 of 21)	38181	NM_001360239	240058	Mm.39905	NM_153166	ENSMUSG00000024008	Cpne5	A830083G22Rik	copine V	protein-coding	0.020000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6631	chr6	102334789	102334989	+	1.08786	NA	intron (NM_008779, intron 4 of 21)	intron (NM_008779, intron 4 of 21)	68789	NR_131017	75893	Mm.2968	NR_131017	ENSMUSG00000107563	4930587E11Rik	4930523E13Rik|Gm44188	RIKEN cDNA 4930587E11 gene	ncRNA	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2787	chr15	10702163	10702363	+	1.08786	NA	intron (NM_001166408, intron 1 of 17)	intron (NM_001166408, intron 1 of 17)	11277	NM_030690	75646	Mm.212395	NM_030690	ENSMUSG00000022246	Rai14	1700008J19Rik|1700020L11Rik|Ankycorbin|Norpeg|mKIAA1334	retinoic acid induced 14	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2136	chr13	71969183	71969383	+	1.08786	NA	Intergenic	Intergenic	-5560	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois homeobox 1	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4783	chr2	167727210	167727410	+	1.08786	NA	Intergenic	Intergenic	36133	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA	0.045000	0.656716			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4366	chr2	66189850	66190050	+	1.08786	NA	intron (NM_001047604, intron 26 of 28)	L1MC5|LINE|L1	-65157	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2688	chr14	110112513	110112713	+	1.08786	NA	Intergenic	Intergenic	642536	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	SLIT and NTRK-like family, member 6	protein-coding	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5985	chr5	63034184	63034384	+	1.08786	NA	Intergenic	MLT-int|LTR|ERVL-MaLR	222628	NM_001170705	100322896		NM_001170705	ENSMUSG00000090326	Dthd1	Gm17384	death domain containing 1	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8158	chrX	166265196	166265396	+	1.08786	NA	intron (NM_023122, intron 1 of 6)	ID_B1|SINE|B4	26353	NM_023122	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-875	chr10	69343955	69344155	+	1.08786	NA	intron (NM_007659, intron 4 of 7)	intron (NM_007659, intron 4 of 7)	8857	NM_007659	12534	Mm.68442	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding	0.000000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5040	chr3	83541735	83541935	+	1.08786	NA	Intergenic	Intergenic	32283	NR_036591	69460	Mm.389464	NR_036591	ENSMUSG00000101334	1700028M03Rik	-	RIKEN cDNA 1700028M03 gene	ncRNA	0.015000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3492	chr17	44588106	44588306	+	1.08786	NA	intron (NR_073425, intron 5 of 5)	intron (NR_073425, intron 5 of 5)	147970	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding	0.005000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6001	chr5	66854023	66854223	+	1.08724	NA	intron (NM_001001980, intron 1 of 25)	intron (NM_001001980, intron 1 of 25)	-3346	NM_001368863	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding	0.015000	0.398010			23(ATTTGAATGATTCAGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-122	chr10	124631022	124631222	+	1.08718	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	162048	NR_028310	75030	Mm.159403	NR_028310	ENSMUSG00000112364	4930503E24Rik	-	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1650	chr12	50709382	50709582	+	1.08706	NA	Intergenic	Intergenic	-60259	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding	0.015000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-461	chr19	49734868	49735068	+	1.08706	NA	Intergenic	Lx6|LINE|L1	943678	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4304	chr2	52661927	52662127	+	1.08706	NA	intron (NM_001037099, intron 2 of 13)	intron (NM_001037099, intron 2 of 13)	13832	NM_001285428	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding	0.010000	0.338308			-17(TTTTACATAAAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6716	chr6	128996425	128996625	+	1.08706	NA	intron (NR_015455, intron 1 of 2)	RMER17C-int|LTR|ERVK	3564	NR_015455	408064	Mm.172429	NR_015455		BC064078	-	cDNA sequence BC064078	ncRNA	0.000000	0.467662			-65(AATAGCAAGAGAATGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-637	chr4	96089944	96090144	+	1.08706	NA	Intergenic	RLTR13G|LTR|ERVK	-12497	NM_001346540	230459	Mm.268175	NM_145548	ENSMUSG00000028571	Cyp2j13	-	cytochrome P450, family 2, subfamily j, polypeptide 13	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2175	chr13	83570345	83570545	+	1.08706	NA	intron (NM_001347581, intron 1 of 9)	L2b|LINE|L2	-3162	NM_001347577	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3163	chr16	33770258	33770458	+	1.08706	NA	Intergenic	Intergenic	-23679	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding	0.000000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-309	chr14	89651221	89651421	+	1.08706	NA	Intergenic	Intergenic	-244903	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	poly(A)-binding protein, cytoplasmic pseudogene	pseudo	0.015000	0.298507	-61(AATGCATTATGAATC,+,0.00),-61(AATGCATTATGAATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1551	chr12	14765786	14765986	+	1.08706	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	284503	NR_045960	73972	Mm.107680	NR_045960	ENSMUSG00000113644	4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7806	chr9	90710841	90711041	+	1.08706	NA	Intergenic	Intergenic	-440172	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5850	chr5	19906774	19906974	+	1.08706	NA	promoter-TSS (NM_001170745)	promoter-TSS (NM_001170745)	-644	NM_001170745	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding	0.005000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5515	chr4	64943608	64943808	+	1.08706	NA	Intergenic	Intergenic	-180466	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding	0.000000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-626	chr4	64943593	64943793	+	1.08706	NA	Intergenic	Intergenic	-180481	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1519	chr12	4662087	4662287	+	1.08675	NA	intron (NM_011365, intron 22 of 38)	intron (NM_011365, intron 22 of 38)	69179	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-387	chr16	91582168	91582368	+	1.08675	NA	intron (NM_030018, intron 3 of 6)	B1_Mur2|SINE|Alu	15412	NM_030018	77975	Mm.290341	NM_030018	ENSMUSG00000022964	Tmem50b	AU015466|AU019872|B230114J08Rik	transmembrane protein 50B	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2357	chr14	11555985	11556185	+	1.08675	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	2532	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding	0.025000	0.512438			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-654	chr4	137487436	137487636	+	1.08675	NA	intron (NM_008305, intron 1 of 96)	intron (NM_008305, intron 1 of 96)	18733	NM_008305	15530	Mm.273662	NM_008305	ENSMUSG00000028763	Hspg2	AI852380|HSPG|Pcn|Plc|per	perlecan (heparan sulfate proteoglycan 2)	protein-coding	0.015000	0.587065			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-643	chr4	103068379	103068579	+	1.08602	NA	intron (NM_146254, intron 8 of 16)	L1MC1|LINE|L1	-41208	NM_001290648	23919	Mm.100163	NM_011831	ENSMUSG00000066090	Insl5	RIF2	insulin-like 5	protein-coding	0.000000	0.447761			-35(ATTTACATGAGAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5043	chr3	83583065	83583265	+	1.08585	NA	Intergenic	Intergenic	-9047	NR_036591	69460	Mm.389464	NR_036591	ENSMUSG00000101334	1700028M03Rik	-	RIKEN cDNA 1700028M03 gene	ncRNA	0.015000	0.467662			3(ATCAAAATGACAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3821	chr18	44364874	44365074	+	1.08498	NA	Intergenic	Intergenic	-15526	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding	0.020000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2231	chr13	96680987	96681187	+	1.08461	NA	Intergenic	Intergenic	-10151	NM_001360166	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding	0.000000	0.308458			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-545	chr2	173832818	173833018	+	1.08364	NA	Intergenic	Intergenic	95347	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding	0.015000	0.368159			-53(ATTTGCAATGGAAAAA,-,0.00),-26(TTTTTTTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-620	chr1	187787444	187787644	+	1.08288	NA	intron (NM_001357535, intron 1 of 7)	intron (NM_001357535, intron 1 of 7)	135303	NM_001357535	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding	0.015000	0.383085			-25(TATTTGTAATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4641	chr2	135214878	135215078	+	1.08282	NA	intron (NR_040517, intron 1 of 5)	intron (NR_040517, intron 1 of 5)	638	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-321	chr1	113533672	113533872	+	1.08282	NA	Intergenic	RLTR17|LTR|ERVK	-1116854	NR_157044	102635484		NR_157044		Gm32810	Gm18406	predicted gene, 32810	ncRNA	0.000000	0.358209			-11(ATTACCATCAAAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5509	chr4	62944532	62944732	+	1.08282	NA	Intergenic	RMER1A|Other|Other	-20935	NM_001369118	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding	0.000000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-700	chr10	12912300	12912500	+	1.08282	NA	Intergenic	Intergenic	10727	NR_038028	320273	Mm.417706	NR_038027	ENSMUSG00000097378	B230208H11Rik	-	RIKEN cDNA B230208H11 gene	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4067	chr19	32295693	32295893	+	1.08282	NA	intron (NM_001362423, intron 2 of 9)	L1MA4A|LINE|L1	53523	NM_001168525	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding	0.020000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-322	chr14	118193865	118194065	+	1.08282	NA	Intergenic	Intergenic	-42267	NR_131970	105245869	Mm.460408	NR_131969	ENSMUSG00000090534	LOC105245869	-	uncharacterized LOC105245869	ncRNA	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-477	chr1	155491723	155491923	+	1.08282	NA	Intergenic	Intergenic	35288	NR_132128	433367	Mm.359304	NR_132128	ENSMUSG00000073535	Gm5532	EG433367	predicted gene 5532	ncRNA	0.035000	0.462687	56(TTTCAATTATTCATG,+,0.00),56(TTTCAATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4703	chr2	144240267	144240467	+	1.08282	NA	Intergenic	Intergenic	25835	NR_030762	100313519	Mm.453538	NR_030762	ENSMUSG00000077714	Snord17	MBI-43	small nucleolar RNA, C/D box 17	snoRNA	0.000000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7176	chr8	25011474	25011674	+	1.08282	NA	intron (NM_007404, intron 1 of 22)	intron (NM_007404, intron 1 of 22)	5348	NM_001270996	11502	Mm.28908	NM_007404	ENSMUSG00000031555	Adam9	AU020942|MDC9|Mltng|mKIAA0021	a disintegrin and metallopeptidase domain 9 (meltrin gamma)	protein-coding	0.005000	0.412935			-7(AATTACAAGACAAACA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3797	chr18	38564977	38565177	+	1.08282	NA	Intergenic	BGLII|LTR|ERVK	36270	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty RTK signaling antagonist 4	protein-coding	0.015000	0.432836			31(ATTAGCATTACTAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6289	chr6	6583279	6583479	+	1.08282	NA	Intergenic	Intergenic	-4721	NM_009169	20422	Mm.2469	NM_009169	ENSMUSG00000042541	Sem1	DSS1|Shfdg1|Shfg|Shfm1	SEM1, 26S proteasome complex subunit	protein-coding	0.005000	0.308458			-77(ATTTGCATGCCCAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4594	chr2	126071788	126071988	+	1.08282	NA	intron (NM_008008, intron 2 of 3)	intron (NM_008008, intron 2 of 3)	37230	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2718	chr14	118193859	118194059	+	1.08282	NA	Intergenic	Intergenic	-42273	NR_131970	105245869	Mm.460408	NR_131969	ENSMUSG00000090534	LOC105245869	-	uncharacterized LOC105245869	ncRNA	0.005000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-624	chr4	62944508	62944708	+	1.08282	NA	Intergenic	RMER1A|Other|Other	-20959	NM_001369118	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding	0.000000	0.557214			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-794	chr7	79668441	79668641	+	1.08280	NA	intron (NM_029835, intron 3 of 21)	intron (NM_029835, intron 3 of 21)	8345	NM_029835	77011	Mm.28132	NM_029835	ENSMUSG00000046591	Ticrr	5730590G19Rik|BC028450|Lrrk1	TOPBP1-interacting checkpoint and replication regulator	protein-coding	0.000000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-179	chr12	24916120	24916320	+	1.08280	NA	intron (NM_001083341, intron 3 of 11)	L1ME1|LINE|L1	-58712	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding	0.010000	0.368159			-26(GTTTTCTTGTGCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6921	chr7	79668430	79668630	+	1.08280	NA	intron (NM_029835, intron 3 of 21)	intron (NM_029835, intron 3 of 21)	8334	NM_029835	77011	Mm.28132	NM_029835	ENSMUSG00000046591	Ticrr	5730590G19Rik|BC028450|Lrrk1	TOPBP1-interacting checkpoint and replication regulator	protein-coding	0.000000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-93	chr10	58950143	58950343	+	1.08280	NA	intron (NM_172788, intron 1 of 9)	intron (NM_172788, intron 1 of 9)	136884	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding	0.025000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7003	chr7	102482697	102482897	+	1.08280	NA	Intergenic	MER2|DNA|TcMar-Tigger	-4895	NM_001011782	257947	Mm.376117	NM_001011782	ENSMUSG00000044814	Olfr543	MOR42-2	olfactory receptor 543	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-369	chr1	128459317	128459517	+	1.08270	NA	Intergenic	Intergenic	-42001	NM_145507	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding	0.010000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8066	chrX	113888630	113888830	+	1.08270	NA	Intergenic	RLTR13D4|LTR|ERVK	-585603	NM_172781	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding	0.000000	0.353234			-55(ATTTAAAAGAGAAGCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4100	chr19	46645256	46645456	+	1.08270	NA	intron (NM_146099, intron 2 of 3)	intron (NM_146099, intron 2 of 3)	21955	NM_001177813	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding	0.010000	0.497512			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-467	chr2	5675984	5676184	+	1.08270	NA	promoter-TSS (NM_001290376)	promoter-TSS (NM_001290376)	-38	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding	0.020000	0.507463			-39(CCTTTCTCTAGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3338	chr16	79611021	79611221	+	1.08270	NA	Intergenic	Intergenic	-388255	NM_030146	78654		NM_030146		1700066C05Rik	-	RIKEN cDNA 1700066C05 gene	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-470	chr1	153321888	153322088	+	1.08270	NA	intron (NM_010683, intron 1 of 27)	intron (NM_010683, intron 1 of 27)	10798	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding	0.020000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6108	chr5	100436218	100436418	+	1.08096	NA	Intergenic	Intergenic	-6783	NR_034038	100503199	Mm.392282	NR_034038	ENSMUSG00000097772	5430416N02Rik	100041797|Adapt33|Gm3514	RIKEN cDNA 5430416N02 gene	ncRNA	0.005000	0.373134			-42(ATTTGAAAAAAAGTGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3240	chr16	55512882	55513082	+	1.08096	NA	Intergenic	Intergenic	18251	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA	0.000000	0.393035			-19(CTATTGACTTGCAAAT,+,0.00),40(CCTTTAGTATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1930	chr13	5448763	5448963	+	1.08096	NA	Intergenic	Intergenic	409229	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA	0.000000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-127	chr10	125901901	125902101	+	1.08096	NA	Intergenic	Intergenic	-64218	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5019	chr3	75711426	75711626	+	1.08096	NA	Intergenic	L1_Mur3|LINE|L1	-55795	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3663	chr17	90504377	90504577	+	1.08096	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	-48597	NM_001346960	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.005000	0.298507			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-463	chr19	57060093	57060293	+	1.08096	NA	intron (NM_178688, intron 14 of 24)	intron (NM_178688, intron 14 of 24)	-51618	NM_001177796	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-641	chr1	192325237	192325437	+	1.08096	NA	intron (NM_010600, intron 6 of 10)	MIRc|SINE|MIR	134560	NM_010600	16510	Mm.4489	NM_010600	ENSMUSG00000058248	Kcnh1	EAG1|Kv10.1|M-eag	potassium voltage-gated channel, subfamily H (eag-related), member 1	protein-coding	0.010000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5271	chr3	148595684	148595884	+	1.08096	NA	Intergenic	Intergenic	358851	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.010000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-785	chr7	34246873	34247073	+	1.08061	NA	intron (NM_172741, intron 8 of 12)	intron (NM_172741, intron 8 of 12)	-16637	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding	0.000000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-753	chr6	72748581	72748781	+	1.08052	NA	intron (NM_009332, intron 3 of 11)	intron (NM_009332, intron 3 of 11)	40364	NM_009332	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding	0.005000	0.492537			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-892	chr9	107769612	107769812	+	1.08052	NA	intron (NR_153191, intron 1 of 23)	intron (NR_153191, intron 1 of 23)	1290	NR_153191	83486	Mm.259197	NM_148930	ENSMUSG00000032580	Rbm5	D030069N10Rik	RNA binding motif protein 5	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3846	chr18	50457970	50458170	+	1.07991	NA	Intergenic	Intergenic	110629	NM_026108	67365	Mm.158150	NM_026108	ENSMUSG00000048875	Pudp	1700121L12Rik|GS1|Hdhd1|Hdhd1a	pseudouridine 5-phosphatase	protein-coding	0.010000	0.348259	62(TATGAATTAATCATG,+,0.00),62(TATGAATTAATCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-354	chr1	126287513	126287713	+	1.07991	NA	intron (NM_172484, intron 3 of 14)	B3A|SINE|B2	205314	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding	0.005000	0.412935		4(TATACATATGCACA,+,0.00),4(TATACATATGCACA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4408	chr2	76992802	76993002	+	1.07991	NA	Intergenic	L1MC2|LINE|L1	-10355	NM_011652	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1652	chr12	51039707	51039907	+	1.07991	NA	intron (NR_126468, intron 2 of 4)	Eulor6A|DNA?|DNA?	34651	NR_126468	75494	Mm.416848	NR_126468	ENSMUSG00000111986	1700008C04Rik	-	RIKEN cDNA 1700008C04 gene	ncRNA	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-736	chr10	24447990	24448190	+	1.07991	NA	intron (NR_163910, intron 3 of 4)	intron (NR_163910, intron 3 of 4)	-147352	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ccn2	Ctgf|Fisp12|Hcs24|fisp-12	cellular communication network factor 2	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2344	chr14	10158111	10158311	+	1.07991	NA	intron (NM_001308286, intron 2 of 6)	L1MC2|LINE|L1	274116	NR_030680	100042415	Mm.235938	NR_030680	ENSMUSG00000089686	Mnd1-ps	Gm3833	Mnd1 retrotransposed pseudogene	pseudo	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7719	chr9	72019420	72019620	+	1.07991	NA	intron (NM_001253862, intron 3 of 19)	intron (NM_001253862, intron 3 of 19)	91681	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding	0.000000	0.383085			-93(CTTCTGTTTTGTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-173	chr11	119429028	119429228	+	1.07991	NA	intron (NM_001040005, intron 20 of 67)	intron (NM_001040005, intron 20 of 67)	38656	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA	0.005000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6007	chr5	67789400	67789600	+	1.07991	NA	intron (NM_001038999, intron 5 of 36)	MER2|DNA|TcMar-Tigger	57931	NM_001038999	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3047	chr15	96330176	96330376	+	1.07991	NA	intron (NM_175251, intron 3 of 20)	L1MB5|LINE|L1	42754	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|BAF200|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5768	chr4	139093109	139093309	+	1.07991	NA	promoter-TSS (NM_008675)	promoter-TSS (NM_008675)	-239	NM_008675	17965	Mm.9404	NM_008675	ENSMUSG00000041120	Nbl1	D4H1S1733E|DAN|Dana|NO3	NBL1, DAN family BMP antagonist	protein-coding	0.080000	0.661692			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-764	chr10	32752800	32753000	+	1.07991	NA	intron (NM_001013411, intron 1 of 6)	intron (NM_001013411, intron 1 of 6)	137015	NM_001013411	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding	0.005000	0.338308			7(CCTTTGTGGTTCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-15	chr1	6939793	6939993	+	1.07991	NA	Intergenic	Intergenic	-149027	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8055	chrX	105916304	105916504	+	1.07991	NA	intron (NM_009530, intron 1 of 34)	Tigger9b|DNA|TcMar-Tigger	12968	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	ATRX, chromatin remodeler	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6320	chr6	15428601	15428801	+	1.07991	NA	intron (NM_212435, intron 16 of 16)	RLTR17B_Mm|LTR|ERVK	243195	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding	0.000000	0.363184			50(CCTTTCACATGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4936	chr3	50392593	50392793	+	1.07991	NA	intron (NM_011990, intron 6 of 11)	RMER15|LTR|ERVL	50920	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6896	chr7	70625456	70625656	+	1.07991	NA	Intergenic	Intergenic	-258810	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding	0.060000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4482	chr2	103089561	103089761	+	1.07991	NA	intron (NM_001355474, intron 4 of 5)	intron (NM_001355474, intron 4 of 5)	15986	NM_001355473	56369	Mm.24772	NM_019735	ENSMUSG00000010911	Apip	APIP2|CGI-29|Mmrp19	APAF1 interacting protein	protein-coding	0.020000	0.472637			-56(CTTTTGTCCTTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7194	chr8	32667945	32668145	+	1.07991	NA	Intergenic	RLTR13D6|LTR|ERVK	281981	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-502	chr1	162076573	162076773	+	1.07991	NA	intron (NM_001038619, intron 16 of 20)	intron (NM_001038619, intron 16 of 20)	71704	NR_040562	72753	Mm.452125	NR_040562	ENSMUSG00000090260	2810442N19Rik	-	RIKEN cDNA 2810442N19 gene	ncRNA	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3832	chr18	46811774	46811974	+	1.07991	NA	Intergenic	RLTR13D3|LTR|ERVK	-38165	NM_029008	74574	Mm.26379	NM_029008	ENSMUSG00000024481	Lvrn	4833403I15Rik|APQ|Aqpep	laeverin	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2220	chr13	95739708	95739908	+	1.07991	NA	intron (NM_027711, intron 5 of 35)	intron (NM_027711, intron 5 of 35)	42888	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3105	chr16	19064949	19065149	+	1.07991	NA	Intergenic	Intergenic	188299	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|Tuple1	histone cell cycle regulator	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-471	chr1	153665427	153665627	+	1.07991	NA	promoter-TSS (NM_001347115)	promoter-TSS (NM_001347115)	-146	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding	0.025000	0.641791			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2152	chr13	76317815	76318015	+	1.07991	NA	Intergenic	Intergenic	-45971	NM_001370926	238726	Mm.71912	NM_001370926	ENSMUSG00000109228	Fam81b	Gm276	family with sequence similarity 81, member B	protein-coding	0.000000	0.373134			83(CCATTGTTATGTAATA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6353	chr6	23252804	23253004	+	1.07991	NA	Intergenic	Intergenic	-4640	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding	0.030000	0.442786			-44(ATTTGCATGTTAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7865	chr9	105681963	105682163	+	1.07991	NA	intron (NM_001081309, intron 15 of 19)	PB1D9|SINE|Alu	39068	NM_001081309	75669	Mm.274830	NM_029380	ENSMUSG00000032571	Pik3r4	2210010O15Rik|C730038E05Rik|C85833|D9Ertd418e|Vps15|p150	phosphoinositide-3-kinase regulatory subunit 4	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1915	chr12	118908978	118909178	+	1.07991	NA	intron (NM_029961, intron 16 of 27)	intron (NM_029961, intron 16 of 27)	57343	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1046	chr10	114141009	114141209	+	1.07991	NA	Intergenic	Lx4A|LINE|L1	660261	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-592	chr1	181950110	181950310	+	1.07991	NA	intron (NM_010135, intron 3 of 14)	intron (NM_010135, intron 3 of 14)	69770	NM_001083121	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	ENAH actin regulator	protein-coding	0.000000	0.432836			-4(TCTGTCCTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8113	chrX	145428804	145429004	+	1.07991	NA	Intergenic	Intergenic	58735	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3026	chr15	92349008	92349208	+	1.07991	NA	intron (NR_153785, intron 1 of 3)	intron (NR_153785, intron 1 of 3)	4749	NR_153785	105246020	Mm.352910	NR_153785		Gm26760	-	predicted gene, 26760	ncRNA	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1866	chr12	103567203	103567403	+	1.07991	NA	intron (NM_028980, intron 3 of 24)	intron (NM_028980, intron 3 of 24)	34738	NM_028980	74521	Mm.248619	NM_028980	ENSMUSG00000021209	Ppp4r4	8430415E04Rik|mKIAA1622	protein phosphatase 4, regulatory subunit 4	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5580	chr4	85750787	85750987	+	1.07991	NA	Intergenic	Intergenic	-303028	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2365	chr14	13914793	13914993	+	1.07991	NA	Intergenic	Intergenic	46420	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-646	chr1	192790578	192790778	+	1.07991	NA	Intergenic	B3|SINE|B2	-19459	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6598	chr6	96219763	96219963	+	1.07991	NA	intron (NM_182808, intron 2 of 4)	L1MB3|LINE|L1	-53658	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	Npap60|Nup50	nucleoporin 50 pseudogene	pseudo	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4197	chr2	18588032	18588232	+	1.07991	NA	Intergenic	Intergenic	-84303	NM_147778	12238	Mm.249586	NM_147778	ENSMUSG00000051154	Commd3	AW550818|Bup|D2Ertd542e	COMM domain containing 3	protein-coding	0.050000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1754	chr12	79007920	79008120	+	1.07991	NA	promoter-TSS (NM_178745)	promoter-TSS (NM_178745)	-743	NM_178745	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding	0.010000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-393	chr17	29018640	29018840	+	1.07874	NA	Intergenic	B3|SINE|B2	-10745	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding	0.030000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-89	chr1	29341466	29341666	+	1.07874	NA	Intergenic	Intergenic	-79922	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA	0.005000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-685	chr5	81061266	81061466	+	1.07786	NA	intron (NM_198702, intron 1 of 27)	intron (NM_198702, intron 1 of 27)	39773	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.358209	-80(GATGAAATATTCATG,+,0.00),-80(GATGAAATATTCATG,-,0.00)		76(CCATTATTATTTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4601	chr2	128413079	128413279	+	1.07785	NA	intron (NR_028591, intron 1 of 1)	intron (NR_028591, intron 1 of 1)	16172	NR_028589	100043424	Mm.297222	NR_028589		Morrbid	Gm14005|Mir4435-2hg	myeloid RNA regulator of BCL2L11 induced cell death	ncRNA	0.035000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7527	chr9	14246562	14246762	+	1.07785	NA	Intergenic	Intergenic	-29639	NM_030261	75747	Mm.325126	NM_030261	ENSMUSG00000032009	Sesn3	5630400E15Rik|BC003348|SEST3	sestrin 3	protein-coding	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2457	chr14	39053855	39054055	+	1.07785	NA	intron (NM_001190187, intron 1 of 9)	Lx8|LINE|L1	155653	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2999	chr15	76799625	76799825	+	1.07785	NA	intron (NM_198420, intron 1 of 10)	intron (NM_198420, intron 1 of 10)	18441	NM_001168288	223666	Mm.322931	NM_198420	ENSMUSG00000033697	Arhgap39	9530053N22|AI843066|D15Wsu169e|Kiaa1688|Porf-2	Rho GTPase activating protein 39	protein-coding	0.000000	0.417910	24(TCTGAATAATTCATG,+,0.00),24(TCTGAATAATTCATG,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-605	chr4	8730389	8730589	+	1.07785	NA	intron (NM_001277149, intron 1 of 37)	intron (NM_001277149, intron 1 of 37)	-20835	NM_001355382	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding	0.030000	0.532338			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-274	chr14	11376690	11376890	+	1.07785	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	94313	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5464	chr4	52543078	52543278	+	1.07785	NA	Intergenic	RMER13A2|LTR|ERVK	-53096	NM_026652	68274	Mm.85045	NM_026652	ENSMUSG00000028314	Toporsl	4930547C10Rik	topoisomerase I binding, arginine/serine-rich like	protein-coding	0.000000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-38	chr1	135714952	135715152	+	1.07735	NA	Intergenic	Intergenic	-5011	NM_001360782	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding	0.000000	0.522388			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-193	chr12	72708462	72708662	+	1.07735	NA	Intergenic	Intergenic	-43734	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2134	chr13	71750215	71750415	+	1.07735	NA	Intergenic	RLTR25A|LTR|ERVK	213408	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois homeobox 1	protein-coding	0.000000	0.373134			1(GGATTGTCATGTAAAA,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-707	chr5	128041715	128041915	+	1.07735	NA	intron (NM_172885, intron 3 of 8)	intron (NM_172885, intron 3 of 8)	391262	NM_172885	243274	Mm.447698	NM_172885	ENSMUSG00000034310	Tmem132d	C630028F04Rik	transmembrane protein 132D	protein-coding	0.005000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-365	chr16	30916849	30917049	+	1.07735	NA	Intergenic	Intergenic	164483	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6166	chr5	120895189	120895389	+	1.07735	NA	TTS (NM_145211)	TTS (NM_145211)	-7676	NR_126529	23960	Mm.389688	NM_011852	ENSMUSG00000066861	Oas1g	AI449562|L2|Mmu-L|Mmu-L2|Oas1b|Oias-1|Oias1	2'-5' oligoadenylate synthetase 1G	protein-coding	0.010000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-462	chr19	54584831	54585031	+	1.07735	NA	Intergenic	Intergenic	514546	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT-1|GPAT1|P90	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6731	chr6	136532121	136532321	+	1.07735	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	13370	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding	0.005000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-297	chr14	75967174	75967374	+	1.07735	NA	intron (NM_026816, intron 4 of 7)	intron (NM_026816, intron 4 of 7)	12271	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding	0.005000	0.278607			16(ATTTACAACAAAAGAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4058	chr19	28337364	28337564	+	1.07735	NA	intron (NM_175459, intron 6 of 10)	intron (NM_175459, intron 6 of 10)	-326298	NM_001166414	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4125	chr19	54584826	54585026	+	1.07735	NA	Intergenic	Intergenic	514551	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT-1|GPAT1|P90	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1259	chr11	42562887	42563087	+	1.07735	NA	intron (NM_001362646, intron 6 of 9)	intron (NM_001362646, intron 6 of 9)	141786	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding	0.020000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-349	chr15	76119414	76119614	+	1.07735	NA	TTS (NM_001142968)	TTS (NM_001142968)	681	NM_144848	223650	Mm.259929	NM_144848		Eppk1	6230424I18Rik|EPIPL|EPIPL1|EPPK	epiplakin 1	protein-coding	0.020000	0.532338			-31(GTTTGCAAGGGAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1544	chr12	12708868	12709068	+	1.07735	NA	Intergenic	Intergenic	-39051	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA	0.025000	0.477612			43(GCTTTGTCCTGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6992	chr7	99953776	99953976	+	1.07630	NA	intron (NM_175388, intron 2 of 5)	intron (NM_175388, intron 2 of 5)	-20984	NR_163856									0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-549	chr1	173737545	173737745	+	1.07630	NA	intron (NM_001204910, intron 1 of 7)	intron (NM_001204910, intron 1 of 7)	4164	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A|pyhinA	interferon activated gene 207	protein-coding	0.000000	0.273632			-33(ATTTTAATGACAATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5749	chr4	129554749	129554949	+	1.07630	NA	intron (NM_001162432, intron 9 of 12)	intron (NM_001162432, intron 9 of 12)	2962	NR_106199	102465997		NR_106199	ENSMUSG00000099070	Mir8119	Gm27567|mmu-mir-8119	microRNA 8119	ncRNA	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2080	chr13	56760228	56760428	+	1.07630	NA	Intergenic	MER2|DNA|TcMar-Tigger	56660	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6466	chr6	57641906	57642106	+	1.07630	NA	intron (NM_025992, intron 13 of 22)	intron (NM_025992, intron 13 of 22)	50072	NM_025574	66459	Mm.44201	NM_025574	ENSMUSG00000043162	Pyurf	2610022G08Rik|AI847956|Prey	Pigy upstream reading frame	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3166	chr16	34457246	34457446	+	1.07630	NA	intron (NM_177357, intron 1 of 59)	intron (NM_177357, intron 1 of 59)	56681	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding	0.010000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-443	chr18	63400856	63401056	+	1.07630	NA	Intergenic	Intergenic	-13773	NM_001039485	667742	Mm.158720	NM_172629	ENSMUSG00000041482	Piezo2	5930434P17|9030411M15Rik|9430028L06Rik|Fam38b|Fam38b2	piezo-type mechanosensitive ion channel component 2	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2378	chr14	17675234	17675434	+	1.07630	NA	intron (NM_001113417, intron 1 of 9)	intron (NM_001113417, intron 1 of 9)	14374	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0.000000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4689	chr2	142399583	142399783	+	1.07630	NA	Intergenic	Intergenic	501781	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.000000	0.432836			-76(CTTTGCAAAGGAATAA,-,0.00),-28(ATCTGCAAAACACAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6142	chr5	107601645	107601845	+	1.07630	NA	exon (NM_001359916, exon 3 of 13)	exon (NM_001359916, exon 3 of 13)	3784	NM_001359917	231571	Mm.482420	NM_144911	ENSMUSG00000033773	Rpap2	AW060207	RNA polymerase II associated protein 2	protein-coding	0.015000	0.442786			-35(ACTTTCTCATTAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3902	chr18	63400886	63401086	+	1.07630	NA	Intergenic	Intergenic	-13803	NM_001039485	667742	Mm.158720	NM_172629	ENSMUSG00000041482	Piezo2	5930434P17|9030411M15Rik|9430028L06Rik|Fam38b|Fam38b2	piezo-type mechanosensitive ion channel component 2	protein-coding	0.005000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-733	chr6	30196136	30196336	+	1.07624	NA	Intergenic	Intergenic	19613	NR_038124	100463519	Mm.361139	NR_038124		BB283400	BF465573|Rncr4	expressed sequence BB283400	ncRNA	0.020000	0.587065			-65(CATTTCCCTTGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7671	chr9	58916147	58916347	+	1.07521	NA	intron (NM_001042752, intron 13 of 27)	intron (NM_001042752, intron 13 of 27)	93298	NM_001081192	330953	Mm.151967	NM_001081192	ENSMUSG00000032338	Hcn4	Bcng3|Hcn3	hyperpolarization-activated, cyclic nucleotide-gated K+ 4	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4227	chr2	27347133	27347333	+	1.07521	NA	intron (NR_133905, intron 1 of 29)	RLTR11A|LTR|ERVK	80375	NM_009500	22325	Mm.179011	NM_009500	ENSMUSG00000009621	Vav2	2810040F13Rik|AI847175|Vav-2	vav 2 oncogene	protein-coding	0.000000	0.527363		-24(TATGCATTGTCATG,-,0.00)	-21(GCATTGTCATGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3817	chr18	43309064	43309264	+	1.07521	NA	intron (NM_178749, intron 8 of 12)	MLTR25A|LTR|ERVK	64108	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5146	chr3	119143089	119143289	+	1.07521	NA	intron (NM_170778, intron 16 of 22)	intron (NM_170778, intron 16 of 22)	581009	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DHPDHase|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8149	chrX	163927762	163927962	+	1.07521	NA	3' UTR (NM_026887, exon 5 of 5)	3' UTR (NM_026887, exon 5 of 5)	18845	NM_001290378	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6057	chr5	81960912	81961112	+	1.07521	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	163701	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA	0.000000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-438	chr18	43308944	43309144	+	1.07521	NA	intron (NM_178749, intron 8 of 12)	MLTR25A|LTR|ERVK	64228	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2337	chr14	7934284	7934484	+	1.07521	NA	intron (NM_001081427, intron 39 of 45)	intron (NM_001081427, intron 39 of 45)	-22916	NM_001371278									0.020000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-771	chr10	36520395	36520595	+	1.07311	NA	intron (NM_001081208, intron 1 of 3)	intron (NM_001081208, intron 1 of 3)	13688	NM_001081208	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0.010000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-16	chr1	44645387	44645587	+	1.07311	NA	intron (NM_028450, intron 1 of 10)	L1M4|LINE|L1	93816	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding	0.000000	0.283582			40(TCTTTATTATGGAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-175	chr12	4662221	4662421	+	1.07311	NA	intron (NM_011365, intron 22 of 38)	intron (NM_011365, intron 22 of 38)	69313	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding	0.005000	0.373134			10(TCTTACCCTTTCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-894	chr9	113876939	113877139	+	1.07311	NA	intron (NM_001081960, intron 18 of 33)	intron (NM_001081960, intron 18 of 33)	-53895	NM_001083319	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding	0.025000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-401	chr17	60396477	60396677	+	1.07299	NA	Intergenic	Intergenic	-1383255	NM_001368393	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.010000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3820	chr18	44364776	44364976	+	1.07294	NA	Intergenic	Intergenic	-15624	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7988	chrX	74141354	74141554	+	1.07266	NA	intron (NM_008106, intron 4 of 5)	Lx7|LINE|L1	13988	NM_008106	14539	Mm.284825	NM_008106	ENSMUSG00000031394	Opn1mw	Gcp	opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan)	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3084	chr16	11624329	11624529	+	1.07266	NA	intron (NM_028964, intron 15 of 20)	intron (NM_028964, intron 15 of 20)	-155273	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA	0.000000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5812	chr5	4500758	4500958	+	1.07266	NA	Intergenic	Intergenic	257358	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7637	chr9	46482512	46482712	+	1.07266	NA	Intergenic	Intergenic	-162626	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding	0.020000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1836	chr12	98404295	98404495	+	1.07266	NA	Intergenic	Intergenic	-119449	NR_136759	105245437	Mm.446375	NR_136759	ENSMUSG00000113613	Gm40893	-	predicted gene, 40893	ncRNA	0.010000	0.383085			29(TCTTTGTGTTGCTATT,+,0.00),41(TATTTGTTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4430	chr2	82826626	82826826	+	1.07266	NA	Intergenic	L1M2|LINE|L1	-116908	NM_001370266	241516	Mm.302516	NM_001370266	ENSMUSG00000075249	Fsip2	-	fibrous sheath-interacting protein 2	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4212	chr2	22940885	22941085	+	1.07266	NA	TTS (NM_019501)	TTS (NM_019501)	45463	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7866	chr9	105767674	105767874	+	1.07266	NA	intron (NM_001102607, intron 8 of 36)	intron (NM_001102607, intron 8 of 36)	41874	NM_172927	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding	0.010000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3682	chr18	5060037	5060237	+	1.07266	NA	intron (NM_001347449, intron 6 of 30)	intron (NM_001347449, intron 6 of 30)	13548	NM_001347449	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1155	chr11	10518853	10519053	+	1.07266	NA	Intergenic	Intergenic	-595063	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3381	chr16	91669734	91669934	+	1.07266	NA	intron (NM_178880, intron 6 of 11)	intron (NM_178880, intron 6 of 11)	18066	NM_001370901	102640710		NM_001370901		Gm36712	-	predicted gene, 36712	protein-coding	0.015000	0.378109			-41(AAATTGTAATGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6347	chr6	21147647	21147847	+	1.07266	NA	Intergenic	Intergenic	-67599	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121	potassium voltage-gated channel, Shal-related family, member 2	protein-coding	0.010000	0.298507			39(ATTTGAATAAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6383	chr6	32982697	32982897	+	1.07266	NA	intron (NM_025336, intron 3 of 7)	MIRb|SINE|MIR	77463	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177|Micos19	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding	0.005000	0.373134			-11(TATTTCTCATAAAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1011	chr10	107971844	107972044	+	1.07266	NA	intron (NR_131147, intron 5 of 5)	intron (NR_131147, intron 5 of 5)	25299	NR_131147	628877	Mm.363120	NR_131147	ENSMUSG00000112910	Gm29685	-	predicted gene, 29685	ncRNA	0.000000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-237	chr13	38080104	38080304	+	1.07266	NA	Intergenic	Intergenic	43215	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7778	chr9	83320619	83320819	+	1.07266	NA	Intergenic	Intergenic	-110828	NR_102437	100039186	Mm.212721	NR_102437	ENSMUSG00000099718	Gm2087	-	predicted gene 2087	ncRNA	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7765	chr9	80559568	80559768	+	1.07266	NA	Intergenic	Intergenic	-94230	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0.000000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-728	chr10	22976136	22976336	+	1.07266	NA	Intergenic	ORR1D2-int|LTR|ERVL-MaLR	-156093	NM_011545	21412	Mm.16497	NM_011545	ENSMUSG00000045680	Tcf21	Pod-1|Pod1|bHLHa23|capsulin|epc|epicardin	transcription factor 21	protein-coding	0.000000	0.467662			-66(ATTTGCAGTAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6065	chr5	84019176	84019376	+	1.07266	NA	Intergenic	RLTR13C3|LTR|ERVK	398106	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2668	chr14	104473150	104473350	+	1.07266	NA	Intergenic	CpG	-5251	NM_011143	18996	Mm.246550	NM_011143	ENSMUSG00000048349	Pou4f1	Brn-3|Brn-3.0|Brn3|Brn3.0|Brn3a|E130119J07Rik	POU domain, class 4, transcription factor 1	protein-coding	0.075000	0.626866			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5104	chr3	107823268	107823468	+	1.07266	NA	Intergenic	Intergenic	-53862	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-718	chr10	19630326	19630526	+	1.07266	NA	intron (NM_178258, intron 3 of 4)	intron (NM_178258, intron 3 of 4)	8398	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3129	chr16	26750548	26750748	+	1.07266	NA	intron (NR_105063, intron 1 of 2)	Lx7|LINE|L1	4854	NR_105063	100504628	Mm.393275	NR_105063	ENSMUSG00000092545	Gm20319	-	predicted gene, 20319	ncRNA	0.000000	0.368159			-23(ATGAGAATGACAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5435	chr4	40161995	40162195	+	1.07266	NA	intron (NM_007386, intron 1 of 20)	ORR1A1|LTR|ERVL-MaLR	18830	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4738	chr2	154963970	154964170	+	1.07266	NA	Intergenic	MTC|LTR|ERVL-MaLR	-49500	NM_015770	50518	Mm.315593	NM_015770	ENSMUSG00000027596	a	A<y>|ASIP|ASP|As	nonagouti	protein-coding	0.010000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5682	chr4	108976562	108976762	+	1.07266	NA	Intergenic	Intergenic	-4585	NR_040664	77173	Mm.402545	NR_040664	ENSMUSG00000086483	8030443G20Rik	-	RIKEN cDNA 8030443G20 gene	ncRNA	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6151	chr5	111175613	111175813	+	1.07266	NA	intron (NM_001267622, intron 5 of 22)	intron (NM_001267622, intron 5 of 22)	-154984	NM_019640	56305	Mm.200516	NM_019640	ENSMUSG00000050017	Pitpnb	PI-TP-beta	phosphatidylinositol transfer protein, beta	protein-coding	0.040000	0.597015			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-185	chr1	63741068	63741268	+	1.07266	NA	intron (NM_172422, intron 7 of 11)	L1MB1|LINE|L1	10543	NM_172422	75619	Mm.30965	NM_172422	ENSMUSG00000025962	Fastkd2	2810421I24Rik	FAST kinase domains 2	protein-coding	0.005000	0.393035			15(TCTTTGTTGTGTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2064	chr13	48245497	48245697	+	1.07266	NA	intron (NR_102303, intron 1 of 2)	intron (NR_102303, intron 1 of 2)	-15519	NM_031166	15904	Mm.458006	NM_031166	ENSMUSG00000021379	Id4	Idb4|bHLHb27	inhibitor of DNA binding 4	protein-coding	0.000000	0.482587			-5(ATTTACAAGGCAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6406	chr6	38764205	38764405	+	1.07266	NA	intron (NM_001294144, intron 2 of 14)	intron (NM_001294144, intron 2 of 14)	73006	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-375	chr1	129710254	129710454	+	1.07227	NA	intron (NM_172485, intron 7 of 27)	intron (NM_172485, intron 7 of 27)	437050	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding	0.000000	0.417910			-76(ATCAGCATAACTATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6833	chr7	40618050	40618250	+	1.07227	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-56587	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA	0.000000	0.477612			-28(GTTTGAATAGGAATGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-50	chr1	170492622	170492822	+	1.07227	NA	intron (NR_154593, intron 2 of 9)	Tigger18a|DNA|TcMar-Tigger	64388	NR_154593	70729	Mm.409310	NM_027528	ENSMUSG00000038473	Nos1ap	6330408P19Rik|Capon	nitric oxide synthase 1 (neuronal) adaptor protein	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2551	chr14	75967104	75967304	+	1.07227	NA	intron (NM_026816, intron 4 of 7)	intron (NM_026816, intron 4 of 7)	12201	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding	0.025000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-788	chr7	40618048	40618248	+	1.07227	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-56589	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA	0.000000	0.482587			-26(GTTTGAATAGGAATGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-131	chr11	5383379	5383579	+	1.07227	NA	intron (NM_001080924, intron 1 of 8)	intron (NM_001080924, intron 1 of 8)	-1739	NM_001290501	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5075	chr3	98108619	98108819	+	1.07211	NA	intron (NM_010928, intron 12 of 33)	intron (NM_010928, intron 12 of 33)	-51915	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding	0.005000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-89	chr10	39452101	39452301	+	1.07087	NA	intron (NM_001122892, intron 2 of 12)	intron (NM_001122892, intron 2 of 12)	82402	NM_001122892	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7252	chr8	53057943	53058143	+	1.07021	NA	Intergenic	Intergenic	-453659	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0.000000	0.248756			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5158	chr3	121703948	121704148	+	1.07021	NA	Intergenic	L1ME3A|LINE|L1	-19489	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding	0.010000	0.437811	14(TCTCCATTATGCATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5067	chr3	93506769	93506969	+	1.07021	NA	Intergenic	B1_Mur4|SINE|Alu	-13627	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding	0.045000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3319	chr16	74995906	74996106	+	1.07021	NA	intron (NM_001358491, intron 1 of 27)	intron (NM_001358491, intron 1 of 27)	96764	NM_001358493	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding	0.010000	0.318408	-11(CATGAAAAATTCATT,+,0.00),-11(CATGAAAAATTCATT,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-870	chr9	43210079	43210279	+	1.07021	NA	Intergenic	Intergenic	-4424	NM_011139	18988	Mm.436650	NM_011139	ENSMUSG00000032015	Pou2f3	Epoc-1|Oct-11a|Oct11|Otf-11|Otf11|Skin|Skin-1a|Skn-1a|Skn-li	POU domain, class 2, transcription factor 3	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7630	chr9	43210080	43210280	+	1.07021	NA	Intergenic	Intergenic	-4425	NM_011139	18988	Mm.436650	NM_011139	ENSMUSG00000032015	Pou2f3	Epoc-1|Oct-11a|Oct11|Otf-11|Otf11|Skin|Skin-1a|Skn-1a|Skn-li	POU domain, class 2, transcription factor 3	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2628	chr14	92826692	92826892	+	1.07021	NA	Intergenic	RSINE1|SINE|B4	1063877	NM_001081377	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding	0.000000	0.398010		-77(TGTGCATATGAATG,-,0.00)	24(GCTTTGACTTGCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2519	chr14	63022325	63022525	+	1.07021	NA	Intergenic	Intergenic	10654	NM_001039121	654458	Mm.390737	NM_001039121	ENSMUSG00000075572	Defb43	BD-43|EG654458|mBD-43	defensin beta 43	protein-coding	0.020000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5773	chr4	141751562	141751762	+	1.07021	NA	intron (NM_001081408, intron 2 of 6)	intron (NM_001081408, intron 2 of 6)	4987	NM_001081408	75986	Mm.30032	NM_001081408	ENSMUSG00000040706	Agmat	5033405N08Rik	agmatine ureohydrolase (agmatinase)	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2879	chr15	41288740	41288940	+	1.07021	NA	Intergenic	Intergenic	115139	NR_151516	100418302		NR_151516		4930555K19Rik	-	leucine rich repeat and sterile alpha motif containing 1 pseudogene	pseudo	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5723	chr4	124048509	124048709	+	1.07021	NA	Intergenic	Intergenic	131176	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding	0.025000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6868	chr7	56900109	56900309	+	1.07021	NA	intron (NM_008074, intron 5 of 9)	intron (NM_008074, intron 5 of 9)	487006	NM_008074	14407	Mm.322667	NM_008074	ENSMUSG00000055026	Gabrg3	6330406O05Rik|B230362M20Rik|Gabrg-3	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7507	chr9	7070890	7071090	+	1.07021	NA	intron (NM_029851, intron 59 of 88)	intron (NM_029851, intron 59 of 88)	-105600	NM_001357484	76863	Mm.27293	NM_029775	ENSMUSG00000032002	Dcun1d5	3110001A18Rik|4833420K19Rik|AW060460|D430047L21Rik	DCN1, defective in cullin neddylation 1, domain containing 5 (S. cerevisiae)	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7522	chr9	13512759	13512959	+	1.07021	NA	Intergenic	Intergenic	81498	NR_028271	18689	Mm.41972	NM_008835	ENSMUSG00000031802	Phxr4	Sp5	per-hexamer repeat gene 4	ncRNA	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6086	chr5	91179573	91179773	+	1.07021	NA	Intergenic	Intergenic	40074	NM_009704	11839	Mm.8039	NM_009704	ENSMUSG00000029378	Areg	AR|Mcub|Sdgf	amphiregulin	protein-coding	0.000000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-314	chr14	103948453	103948653	+	1.07021	NA	Intergenic	Intergenic	78589	NR_045953	73877	Mm.399172	NR_045953	ENSMUSG00000115727	4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	ncRNA	0.005000	0.402985	-100(TATAAATTATGTATG,+,0.00),-100(TATAAATTATGTATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5620	chr4	96089439	96089639	+	1.06979	NA	Intergenic	RLTR13G|LTR|ERVK	-11992	NM_001346540	230459	Mm.268175	NM_145548	ENSMUSG00000028571	Cyp2j13	-	cytochrome P450, family 2, subfamily j, polypeptide 13	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7246	chr8	50425845	50426045	+	1.06979	NA	Intergenic	Intergenic	57833	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-704	chr10	13225688	13225888	+	1.06979	NA	intron (NM_001359294, intron 10 of 11)	intron (NM_001359294, intron 10 of 11)	-32651	NM_181470	353258	Mm.117581	NM_181470	ENSMUSG00000019814	Ltv1	2610020N02Rik	LTV1 ribosome biogenesis factor	protein-coding	0.005000	0.388060		65(GATGCTTATGCATG,+,0.00),65(GATGCTTATGCATG,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-210	chr12	99819560	99819760	+	1.06979	NA	intron (NM_030172, intron 5 of 5)	intron (NM_030172, intron 5 of 5)	63782	NM_030172	78767	Mm.235920	NM_030172	ENSMUSG00000021176	Efcab11	2610021K21Rik|2610110A13Rik	EF-hand calcium binding domain 11	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6104	chr5	98986109	98986309	+	1.06979	NA	intron (NM_008926, intron 6 of 18)	intron (NM_008926, intron 6 of 18)	50870	NM_008926	19092	Mm.263002	NM_008926	ENSMUSG00000029334	Prkg2	AW212535|CGKII|Prkgr2|cGK-II	protein kinase, cGMP-dependent, type II	protein-coding	0.015000	0.497512		75(AATGCTTTTTCATG,-,0.00)	78(GCTTTTTCATGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7690	chr9	64703082	64703282	+	1.06979	NA	intron (NM_001134399, intron 23 of 24)	intron (NM_001134399, intron 23 of 24)	34574	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding	0.005000	0.537313			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-167	chr11	107946595	107946795	+	1.06979	NA	intron (NM_011101, intron 16 of 16)	intron (NM_011101, intron 16 of 16)	-31640	NM_001199301	140723	Mm.87663	NM_080644	ENSMUSG00000040373	Cacng5	-	calcium channel, voltage-dependent, gamma subunit 5	protein-coding	0.005000	0.338308			84(TTATTATTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-752	chr10	28818351	28818551	+	1.06979	NA	intron (NM_001305663, intron 5 of 5)	MTB|LTR|ERVL-MaLR	150091	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-739	chr10	24885927	24886127	+	1.06936	NA	intron (NM_001166416, intron 11 of 29)	B1F1|SINE|Alu	16041	NM_027347	70208	Mm.28020	NM_027347	ENSMUSG00000019984	Med23	130kDa|3000002A17Rik|Crsp3|ESTM7|Sur2|X83317|mKIAA1216	mediator complex subunit 23	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4425	chr2	80173011	80173211	+	1.06869	NA	Intergenic	Intergenic	-43453	NM_001355141	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding	0.000000	0.338308			-29(TCTTTATTTTACAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-498	chr2	80172950	80173150	+	1.06869	NA	Intergenic	Intergenic	-43392	NM_001355141	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding	0.005000	0.378109			32(TCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2358	chr14	11556139	11556339	+	1.06858	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	2686	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding	0.030000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3938	chr18	74104706	74104906	+	1.06858	NA	Intergenic	Intergenic	-39857	NM_172632	225724	Mm.254517	NM_172632	ENSMUSG00000024558	Mapk4	A330097D03Rik|Erk3|Prkm4|p63Mapk	mitogen-activated protein kinase 4	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5993	chr5	64647235	64647435	+	1.06858	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	-36636	NR_045078	100042198	Mm.25191	NR_045078	ENSMUSG00000105402	Gm3716	Gm1683	predicted gene 3716	ncRNA	0.045000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6229	chr5	141388456	141388656	+	1.06813	NA	intron (NM_177879, intron 1 of 44)	intron (NM_177879, intron 1 of 44)	147022	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding	0.005000	0.427861			-79(AAATTGTCATTGAAAA,+,0.00),-4(GACTTCTCAGGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-715	chr5	141388451	141388651	+	1.06813	NA	intron (NM_177879, intron 1 of 44)	intron (NM_177879, intron 1 of 44)	147017	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding	0.005000	0.422886			-74(AAATTGTCATTGAAAA,+,0.00),1(GACTTCTCAGGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5783	chr4	144994097	144994297	+	1.06766	NA	intron (NM_001276465, intron 67 of 69)	intron (NM_001276465, intron 67 of 69)	101060	NM_001357274	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6249	chr5	146878267	146878467	+	1.06744	NA	Intergenic	Intergenic	33296	NM_026864	68895	Mm.266978	NM_026864	ENSMUSG00000029641	Rasl11a	1110065D03Rik|AI852031	RAS-like, family 11, member A	protein-coding	0.010000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5	chr1	16184030	16184230	+	1.06744	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	78248	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding	0.005000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-816	chr7	136430638	136430838	+	1.06744	NA	Intergenic	Intergenic	-81323	NR_040459	330664	Mm.127762	NR_040459	ENSMUSG00000109633	C230079O03Rik	C230079O03	RIKEN cDNA C230079O03 gene	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5657	chr4	103068305	103068505	+	1.06697	NA	intron (NM_146254, intron 8 of 16)	intron (NM_146254, intron 8 of 16)	-41134	NM_001290648	23919	Mm.100163	NM_011831	ENSMUSG00000066090	Insl5	RIF2	insulin-like 5	protein-coding	0.000000	0.407960			39(ATTTACATGAGAATCC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1470	chr11	111397719	111397919	+	1.06631	NA	Intergenic	RLTR11A2|LTR|ERVK	331655	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2869	chr15	38418905	38419105	+	1.06602	NA	Intergenic	MIR|SINE|MIR	71542	NR_105916	102465574		NR_105916	ENSMUSG00000099110	Mir6951	Gm27765|mmu-mir-6951	microRNA 6951	ncRNA	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3547	chr17	61444415	61444615	+	1.06602	NA	Intergenic	Lx7|LINE|L1	1436802	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0.015000	0.412935			-80(ATTAGAAAGACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7572	chr9	28198404	28198604	+	1.06602	NA	Intergenic	Intergenic	-205824	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6329	chr6	17403191	17403391	+	1.06602	NA	Intergenic	Intergenic	-60666	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5969	chr5	55984051	55984251	+	1.06602	NA	Intergenic	Lx4B|LINE|L1	1634159	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13	predicted gene 10440	ncRNA	0.000000	0.323383			-53(TCTTTATATTGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1758	chr12	79481996	79482196	+	1.06602	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	184745	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1313	chr11	62005104	62005304	+	1.06602	NA	intron (NM_001310526, intron 1 of 7)	intron (NM_001310526, intron 1 of 7)	48441	NM_001281818	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7018	chr7	109758601	109758801	+	1.06602	NA	3' UTR (NM_020610, exon 7 of 7)	3' UTR (NM_020610, exon 7 of 7)	-6438	NM_020050	56786	Mm.240668	NM_020050	ENSMUSG00000031021	Tmem9b	2310004K06Rik|AW539847|D7H11orf15|ICRFP703B1614Q5.3	TMEM9 domain family, member B	protein-coding	0.005000	0.378109			17(ATAAACAAAACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2817	chr15	21153033	21153233	+	1.06602	NA	intron (NM_001008420, intron 1 of 11)	intron (NM_001008420, intron 1 of 11)	41681	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7504	chr9	4191610	4191810	+	1.06602	NA	Intergenic	RMER6A|LTR|ERVK	117784	NR_136940	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding	0.000000	0.368159			-15(ATCTGAAAAATAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7134	chr8	4267715	4267915	+	1.06602	NA	intron (NM_011592, intron 5 of 12)	intron (NM_011592, intron 5 of 12)	8090	NM_011592	21856	Mm.195249	NM_011592	ENSMUSG00000002949	Timm44	0710005E20Rik|D8Ertd118e|Mimt44|Tim44	translocase of inner mitochondrial membrane 44	protein-coding	0.035000	0.651741			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-290	chr14	56565894	56566094	+	1.06602	NA	intron (NM_001014996, intron 1 of 16)	intron (NM_001014996, intron 1 of 16)	5852	NM_001014996	219103	Mm.212525	NM_001014996	ENSMUSG00000064128	Cenpj	4932437H03Rik|CPAP|Gm81|LAP|LIP1|Sas4	centromere protein J	protein-coding	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7583	chr9	29773407	29773607	+	1.06602	NA	intron (NM_001357597, intron 1 of 8)	intron (NM_001357597, intron 1 of 8)	189762	NM_001357598	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2974	chr15	67502814	67503014	+	1.06602	NA	Intergenic	Intergenic	276145	NR_045140	69334	Mm.63770	NR_045140	ENSMUSG00000102069	1700012I11Rik	-	RIKEN cDNA 1700012I11 gene	ncRNA	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4635	chr2	134381837	134382037	+	1.06602	NA	Intergenic	Lx6|LINE|L1	172415	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	hydroxyacid oxidase 1, liver	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6174	chr5	124881414	124881614	+	1.06602	NA	intron (NM_001081750, intron 2 of 3)	intron (NM_001081750, intron 2 of 3)	18809	NM_001081750	269704	Mm.138617	NM_001081750	ENSMUSG00000079215	Zfp664	AW060232|D930038J03Rik|ZFOC1|Znf664	zinc finger protein 664	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5438	chr4	43384052	43384252	+	1.06602	NA	intron (NM_001369199, intron 1 of 10)	intron (NM_001369199, intron 1 of 10)	2083	NM_001369198	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1927	chr13	4825903	4826103	+	1.06602	NA	Intergenic	RLTR13D6|LTR|ERVK	-216839	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding	0.000000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6	chr1	20259258	20259458	+	1.06602	NA	intron (NM_153179, intron 52 of 66)	intron (NM_153179, intron 52 of 66)	-97096	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6356	chr6	23840082	23840282	+	1.06602	NA	promoter-TSS (NM_001252106)	promoter-TSS (NM_001252106)	-761	NM_001252110	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding	0.040000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3988	chr18	86394749	86394949	+	1.06602	NA	promoter-TSS (NM_144946)	promoter-TSS (NM_144946)	-103	NM_001360910	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0.025000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2713	chr14	117579240	117579440	+	1.06602	NA	intron (NM_001079844, intron 3 of 9)	intron (NM_001079844, intron 3 of 9)	374507	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA	0.010000	0.303483			-17(TTATTGTCGTGTTAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5281	chr3	149274153	149274353	+	1.06602	NA	promoter-TSS (NR_040591)	promoter-TSS (NR_040591)	-484	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5053	chr3	85971512	85971712	+	1.06602	NA	Intergenic	Intergenic	30919	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding	0.035000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3192	chr16	43096109	43096309	+	1.06602	NA	intron (NM_001285805, intron 2 of 10)	intron (NM_001285805, intron 2 of 10)	140629	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1590	chr12	33303365	33303565	+	1.06583	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	950	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding	0.030000	0.487562			27(ATTTGCATGGCTAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5672	chr4	105323488	105323688	+	1.06466	NA	Intergenic	Intergenic	166241	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|PRG-2|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3546	chr17	60866639	60866839	+	1.06466	NA	Intergenic	Intergenic	-1853417	NM_001368393	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.010000	0.318408	56(CATGAATAATTCAGG,+,0.00),56(CATGAATAATTCAGG,-,0.00)		-95(TCTTTTTCTTGAAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2638	chr14	97638181	97638381	+	1.06466	NA	Intergenic	Intergenic	531484	NM_007826	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund family transcription factor 1	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-606	chr1	185184010	185184210	+	1.06466	NA	Intergenic	Intergenic	-20058	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding	0.020000	0.512438			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-663	chr5	22479774	22479974	+	1.06466	NA	Intergenic	Intergenic	49156	NR_004442	100042049	Mm.21724	NR_004442		Gm15421	-	ribosomal protein L22 like 1 pseudogene	pseudo	0.005000	0.323383			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-20	chr1	76136953	76137153	+	1.06466	NA	Intergenic	Intergenic	-352080	NR_038012	620079	Mm.378379	NR_038012	ENSMUSG00000100553	Gm17751	-	predicted gene, 17751	ncRNA	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3142	chr16	28902788	28902988	+	1.06466	NA	intron (NM_177718, intron 1 of 1)	intron (NM_177718, intron 1 of 1)	26810	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4948	chr3	53169837	53170037	+	1.06451	NA	intron (NM_175386, intron 2 of 3)	intron (NM_175386, intron 2 of 3)	128390	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968|Lhfpl6	lipoma HMGIC fusion partner	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5577	chr4	85131101	85131301	+	1.06451	NA	3' UTR (NM_175275, exon 26 of 26)	3' UTR (NM_175275, exon 26 of 26)	-74255	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7959	chrX	46677969	46678169	+	1.06451	NA	Intergenic	Intergenic	349062	NM_028514	73360	Mm.60929	NM_028514	ENSMUSG00000046615	Actrt1	1700061J02Rik|Arp-T1	actin-related protein T1	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-116	chr1	39911607	39911807	+	1.06451	NA	intron (NM_001252200, intron 2 of 31)	intron (NM_001252200, intron 2 of 31)	10794	NM_001252202	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3270	chr16	62798934	62799134	+	1.06451	NA	intron (NM_026577, intron 9 of 9)	ORR1E-int|LTR|ERVL-MaLR	-12318	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7761	chr9	80205995	80206195	+	1.06451	NA	intron (NM_001039546, intron 1 of 32)	intron (NM_001039546, intron 1 of 32)	41061	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Myo6<rsv>|Tlc|rsv|sv	myosin VI	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7481	chr8	124217164	124217364	+	1.06451	NA	Intergenic	B1F2|SINE|Alu	-14130	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.000000	0.517413			-34(TTGTTGTCATGCAGAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2030	chr13	36947788	36947988	+	1.06451	NA	intron (NM_028784, intron 6 of 14)	intron (NM_028784, intron 6 of 14)	101325	NM_028784	74145	Mm.235105	NM_028784	ENSMUSG00000039109	F13a1	1200014I03Rik|AI462306|F13a	coagulation factor XIII, A1 subunit	protein-coding	0.005000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-75	chr10	3383532	3383732	+	1.06435	NA	intron (NM_133485, intron 1 of 3)	intron (NM_133485, intron 1 of 3)	17482	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory inhibitor subunit 14C	protein-coding	0.000000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-472	chr2	24260919	24261119	+	1.06429	NA	Intergenic	BGLII|LTR|ERVK	-15935	NM_001146087	54450	Mm.29261	NM_019451	ENSMUSG00000026983	Il1f5	AI413231|Fil1delta|IL-36Ra|IL36RN|Il-1h3|Il1hy1	interleukin 1 family, member 5 (delta)	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7749	chr9	78844688	78844888	+	1.06429	NA	Intergenic	Intergenic	229242	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-647	chr1	192870470	192870670	+	1.06424	NA	Intergenic	Intergenic	-14818	NM_198247	214791	Mm.22806	NM_198247	ENSMUSG00000016262	Sertad4	4833404A09|C130018M11Rik	SERTA domain containing 4	protein-coding	0.010000	0.398010			-26(TTAGTGTTATGCAAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-102	chr10	96410278	96410478	+	1.06424	NA	Intergenic	Intergenic	184171	NR_110448	74881	Mm.410819	NR_110448	ENSMUSG00000112762	4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA	0.010000	0.378109			6(TCTTAGCTATGGAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-166	chr11	103292452	103292652	+	1.06424	NA	Intergenic	Intergenic	-25151	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding	0.010000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-609	chr4	20194730	20194930	+	1.06351	NA	intron (NM_001290410, intron 4 of 5)	intron (NM_001290410, intron 4 of 5)	152778	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7909	chr9	123477775	123477975	+	1.06282	NA	promoter-TSS (NM_013860)	promoter-TSS (NM_013860)	-826	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding	0.000000	0.402985			-57(ATTTGCATAACATTTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6714	chr6	128992980	128993180	+	1.06282	NA	non-coding (NR_015455, exon 1 of 3)	non-coding (NR_015455, exon 1 of 3)	119	NR_015455	408064	Mm.172429	NR_015455		BC064078	-	cDNA sequence BC064078	ncRNA	0.005000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-820	chr8	32405425	32405625	+	1.06068	NA	Intergenic	Intergenic	253630	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	ncRNA	0.005000	0.422886		5(TATGAATATGAATG,+,0.00),5(TATGAATATGAATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-392	chr1	135714916	135715116	+	1.06007	NA	Intergenic	Intergenic	-5047	NM_001360782	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding	0.000000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4427	chr2	80554082	80554282	+	1.05988	NA	intron (NM_001355410, intron 5 of 31)	intron (NM_001355410, intron 5 of 31)	27000	NM_016965	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6149	chr5	110357617	110357817	+	1.05988	NA	Intergenic	Intergenic	12987	NM_001310709	381667	Mm.332572	NM_001033459	ENSMUSG00000072754	Lrcol1	Clpsl3|Gm1679	leucine rich colipase-like 1	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5087	chr3	100791764	100791964	+	1.05988	NA	Intergenic	Intergenic	-33595	NM_178594	242122	Mm.137467	NM_178594	ENSMUSG00000051076	Vtcn1	B7h4|B7s1|B7x|BC032925	V-set domain containing T cell activation inhibitor 1	protein-coding	0.005000	0.417910			72(ATCTACATAAAAAGGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8001	chrX	84443095	84443295	+	1.05988	NA	intron (NM_007868, intron 50 of 78)	RLTR11A|LTR|ERVK	-605100	NM_001314037	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding	0.005000	0.472637			38(CTTAGCATTACAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2735	chr14	121152931	121153131	+	1.05988	NA	intron (NM_134082, intron 2 of 26)	intron (NM_134082, intron 2 of 26)	-95675	NR_155502	320268	Mm.435974	NR_155502		B930095G15Rik	-	RIKEN cDNA B930095G15 gene	ncRNA	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3906	chr18	65510426	65510626	+	1.05988	NA	intron (NR_105742, intron 3 of 6)	intron (NR_105742, intron 3 of 6)	-69704	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4341	chr2	61084477	61084677	+	1.05988	NA	Intergenic	Intergenic	-109426	NR_045335	100038493	Mm.388076	NR_045335	ENSMUSG00000075325	Gm13582	-	predicted gene 13582	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-926	chr10	88833997	88834197	+	1.05988	NA	Intergenic	Intergenic	-7283	NM_175158	70683	Mm.29631	NM_175158	ENSMUSG00000004356	Utp20	3830408P06Rik|AA617408|Drim|mDRIM|mDRIN	UTP20 small subunit processome component	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3396	chr16	96201652	96201852	+	1.05988	NA	intron (NM_015825, intron 1 of 7)	intron (NM_015825, intron 1 of 7)	1282	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding	0.020000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6814	chr7	35084487	35084687	+	1.05988	NA	Intergenic	L2a|LINE|L2	-28021	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-877	chr10	69968020	69968220	+	1.05988	NA	intron (NM_146005, intron 29 of 42)	intron (NM_146005, intron 29 of 42)	42588	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4016	chr19	15617674	15617874	+	1.05988	NA	Intergenic	Intergenic	306848	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding	0.015000	0.422886			21(TTTTGGTAATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5673	chr4	105444454	105444654	+	1.05988	NA	Intergenic	Intergenic	287207	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|PRG-2|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding	0.020000	0.427861			-94(CAGTTTTCATTTAAAT,+,0.00),-86(ATTTAAATGAAAATAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3601	chr17	78257574	78257774	+	1.05988	NA	intron (NM_015800, intron 2 of 16)	intron (NM_015800, intron 2 of 16)	57426	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding	0.000000	0.383085		-50(CATACATATGCATA,+,0.00),-50(CATACATATGCATA,-,0.00),-21(CATACATATGCACA,+,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-786	chr7	35084471	35084671	+	1.05988	NA	Intergenic	L2a|LINE|L2	-28005	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding	0.010000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2792	chr15	11457414	11457614	+	1.05988	NA	Intergenic	Intergenic	-57856	NM_033074	110960	Mm.286061	NM_033074	ENSMUSG00000022241	Tars	D15Wsu59e|ThrRS	threonyl-tRNA synthetase	protein-coding	0.030000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-358	chr16	11558878	11559078	+	1.05988	NA	intron (NM_028964, intron 14 of 20)	intron (NM_028964, intron 14 of 20)	153330	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2310	chr13	113345111	113345311	+	1.05988	NA	Intergenic	Lx9|LINE|L1	135552	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding	0.005000	0.383085			-5(TTATTTTTTTGCAATT,+,0.00),71(CAACTCTCTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3762	chr18	28479736	28479936	+	1.05988	NA	Intergenic	Intergenic	-80328	NR_045398	320624	Mm.50107	NR_045398	ENSMUSG00000117473	4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA	0.015000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5592	chr4	89360375	89360575	+	1.05988	NA	intron (NR_132431, intron 2 of 9)	intron (NR_132431, intron 2 of 9)	-49443	NM_007670	12579	Mm.423094	NM_007670	ENSMUSG00000073802	Cdkn2b	AV083695|INK4b|MTS2|p15|p15(INK4b)|p15INK4b	cyclin dependent kinase inhibitor 2B	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6123	chr5	103288928	103289128	+	1.05979	NA	intron (NR_040699, intron 1 of 6)	intron (NR_040699, intron 1 of 6)	10001	NR_040699	74624	Mm.389662	NR_040699	ENSMUSG00000104956	4930429D17Rik	-	RIKEN cDNA 4930429D17 gene	ncRNA	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3722	chr18	16713593	16713793	+	1.05979	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	95553	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding	0.005000	0.437811			-60(ATTTGAATGTCCAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6244	chr5	144263906	144264106	+	1.05979	NA	TTS (NM_025833)	TTS (NM_025833)	8781	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding	0.020000	0.606965			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3450	chr17	27621798	27621998	+	1.05979	NA	intron (NM_019837, intron 1 of 4)	intron (NM_019837, intron 1 of 4)	1066	NM_001291046	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2235	chr13	97668887	97669087	+	1.05979	NA	Intergenic	Intergenic	78424	NR_152141	403201	Mm.110162	NR_152140		5330416C01Rik	Gm532	RIKEN cDNA 5330416C01 gene	ncRNA	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3980	chr18	85403757	85403957	+	1.05979	NA	Intergenic	Intergenic	451741	NM_001367965	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding	0.005000	0.383085			-58(ATTTACAAGGGAATTG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-865	chr10	67998250	67998450	+	1.05916	NA	intron (NM_001359318, intron 3 of 11)	intron (NM_001359318, intron 3 of 11)	18780	NM_001359319	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding	0.035000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6972	chr7	92404986	92405186	+	1.05916	NA	intron (NM_001243047, intron 4 of 10)	intron (NM_001243047, intron 4 of 10)	-156063	NM_001162918	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3591	chr17	75097474	75097674	+	1.05916	NA	intron (NM_019919, intron 3 of 33)	intron (NM_019919, intron 3 of 33)	-81207	NM_001331237	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding	0.010000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-896	chr9	116284249	116284449	+	1.05916	NA	Intergenic	Intergenic	95169	NR_152204	100043817	Mm.404276	NR_152204		Gm4668	-	predicted gene 4668	ncRNA	0.000000	0.393035			-89(ATTTGTTAGACAAAGA,-,0.00),17(TATTTCTCATGGAGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-409	chr17	75097393	75097593	+	1.05916	NA	intron (NM_019919, intron 3 of 33)	intron (NM_019919, intron 3 of 33)	-81288	NM_001331237	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding	0.015000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1667	chr12	54303594	54303794	+	1.05916	NA	Intergenic	Intergenic	70079	NR_108033	73592	Mm.416874	NR_108033	ENSMUSG00000112821	1700104L18Rik	-	RIKEN cDNA 1700104L18 gene	ncRNA	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-323	chr1	119179244	119179444	+	1.05916	NA	Intergenic	Intergenic	-125725	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6439	chr6	49168077	49168277	+	1.05916	NA	intron (NM_023670, intron 3 of 14)	intron (NM_023670, intron 3 of 14)	46777	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding	0.010000	0.378109			-19(TATTTGTCTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7160	chr8	13695235	13695435	+	1.05916	NA	Intergenic	Lx9|LINE|L1	-10554	NM_001101519	403185	Mm.252143	NM_001101519	ENSMUSG00000090336	Cfap97d2	4932443I19Rik|A230061C02Rik|Gm1106	CFAP97 domain containing 2	protein-coding	0.015000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2983	chr15	68819755	68819955	+	1.05916	NA	Intergenic	Intergenic	-58460	NR_155443	105245971	Mm.380365	NR_155443	ENSMUSG00000069996	Gm41341	-	predicted gene, 41341	ncRNA	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6120	chr5	103002423	103002623	+	1.05916	NA	intron (NM_001310685, intron 2 of 11)	MT2A|LTR|ERVL	55869	NM_001310686	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.015000	0.522388			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-882	chr9	81712874	81713074	+	1.05916	NA	Intergenic	L1MA5|LINE|L1	-79142	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	5-HT-1B	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding	0.010000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-276	chr14	16200908	16201108	+	1.05916	NA	Intergenic	Intergenic	42323	NM_001359883	71147	Mm.197960	NM_027695	ENSMUSG00000021786	Oxsm	4933425A18Rik|C80494	3-oxoacyl-ACP synthase, mitochondrial	protein-coding	0.020000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2370	chr14	16200651	16200851	+	1.05916	NA	Intergenic	Intergenic	42580	NM_001359883	71147	Mm.197960	NM_027695	ENSMUSG00000021786	Oxsm	4933425A18Rik|C80494	3-oxoacyl-ACP synthase, mitochondrial	protein-coding	0.010000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2588	chr14	79905642	79905842	+	1.05910	NA	Intergenic	Intergenic	-36566	NR_033535	100038734	Mm.387484	NR_033535	ENSMUSG00000095959	Gm10845	-	predicted gene 10845	ncRNA	0.000000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-82	chr10	22612379	22612579	+	1.05842	NA	Intergenic	RLTR24|LTR|ERV1	-32532	NM_178934	353169	Mm.473705	NM_178934	ENSMUSG00000037490	Slc2a12	GLUT-12|Glut12	solute carrier family 2 (facilitated glucose transporter), member 12	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1955	chr13	13831170	13831370	+	1.05842	NA	Intergenic	Intergenic	46963	NM_010317	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1346	chr11	72953316	72953516	+	1.05842	NA	Intergenic	Intergenic	-7753	NM_001163336	53313	Mm.6306	NM_016745	ENSMUSG00000020788	Atp2a3	SERCA3b|Serca3	ATPase, Ca++ transporting, ubiquitous	protein-coding	0.015000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-903	chrX	92640569	92640769	+	1.05842	NA	Intergenic	Intergenic	-41097	NM_173783	215641	Mm.327999	NM_173783	ENSMUSG00000067649	Mageb18	B430216B18Rik	melanoma antigen family B, 18	protein-coding	0.005000	0.437811			-35(ACATTGCTTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1861	chr12	103056935	103057135	+	1.05842	NA	intron (NM_001081017, intron 11 of 48)	intron (NM_001081017, intron 11 of 48)	108176	NM_001081017	217843	Mm.387073	NM_177621	ENSMUSG00000021198	Unc79	9030205A07Rik|Mlca3	unc-79 homolog	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6177	chr5	126104973	126105173	+	1.05842	NA	Intergenic	Intergenic	-255172	NM_001370875	231736		NM_001370875		Gm4868	EG231736	predicted gene 4868	protein-coding	0.005000	0.462687			55(TCTTTGAGATGCAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-423	chr18	16763115	16763315	+	1.05842	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	46031	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4577	chr2	124473055	124473255	+	1.05689	NA	intron (NM_001290997, intron 4 of 20)	intron (NM_001290997, intron 4 of 20)	-137141	NM_199238	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding	0.005000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-758	chr6	83467795	83467995	+	1.05661	NA	Intergenic	Intergenic	-11503	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-361	chr16	22894127	22894327	+	1.05607	NA	intron (NM_001276449, intron 1 of 3)	intron (NM_001276449, intron 1 of 3)	159	NR_110508	102632430	Mm.474375	NR_110508	ENSMUSG00000116831	Gm30505	-	predicted gene, 30505	ncRNA	0.020000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4911	chr3	39318643	39318843	+	1.05607	NA	Intergenic	Intergenic	431803	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding	0.000000	0.363184			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-773	chr6	115647963	115648163	+	1.05588	NA	intron (NM_001356333, intron 1 of 17)	intron (NM_001356333, intron 1 of 17)	27825	NM_001356334	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|cRaf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1733	chr12	72708492	72708692	+	1.05517	NA	Intergenic	Intergenic	-43764	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7789	chr9	85469358	85469558	+	1.05517	NA	Intergenic	Intergenic	-142308	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Tent5a	BAP014|D930050G01Rik|Fam46a	terminal nucleotidyltransferase 5A	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4976	chr3	63814403	63814603	+	1.05517	NA	intron (NM_001370984, intron 3 of 23)	intron (NM_001370984, intron 3 of 23)	36782	NM_001177733	269437	Mm.316391	NM_183191	ENSMUSG00000036834	Plch1	BC042549|PLC-eta-1|PLCeta1|Plcl3	phospholipase C, eta 1	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6317	chr6	14505322	14505522	+	1.05517	NA	Intergenic	Intergenic	249852	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory subunit 3A	protein-coding	0.010000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4785	chr2	168912435	168912635	+	1.05517	NA	promoter-TSS (NM_001370946)	promoter-TSS (NM_001370946)	68	NM_001370946	22722	Mm.2095	NM_009564	ENSMUSG00000027551	Zfp64	Gm38422	zinc finger protein 64	protein-coding	0.105000	0.686567			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1591	chr12	34048626	34048826	+	1.05517	NA	3' UTR (NM_001271386, exon 28 of 28)	3' UTR (NM_001271386, exon 28 of 28)	91055	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding	0.000000	0.398010		-70(TATACATATACATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7610	chr9	36887371	36887571	+	1.05420	NA	Intergenic	BGLII_A|LTR|ERVK	53897	NM_001357611	235180	Mm.5264	NM_183171	ENSMUSG00000032118	Fez1	UNC-76|UNC76	fasciculation and elongation protein zeta 1 (zygin I)	protein-coding	0.005000	0.447761			-91(GTATTTTGATGCTAAT,+,0.00),-1(ATTTGTAAAATAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5764	chr4	137487267	137487467	+	1.05420	NA	intron (NM_008305, intron 1 of 96)	intron (NM_008305, intron 1 of 96)	18564	NM_008305	15530	Mm.273662	NM_008305	ENSMUSG00000028763	Hspg2	AI852380|HSPG|Pcn|Plc|per	perlecan (heparan sulfate proteoglycan 2)	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2600	chr14	85935188	85935388	+	1.05420	NA	Intergenic	Intergenic	-310682	NR_040457	75155	Mm.399239	NR_040457	ENSMUSG00000115271	4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6159	chr5	115078899	115079099	+	1.05420	NA	intron (NM_029012, intron 3 of 10)	intron (NM_029012, intron 3 of 10)	28963	NM_001271591	100502825	Mm.361657	NM_001271590		Rpl37rt	EyeLinc4|Gm13826|Rpl37	ribosomal protein L37, retrotransposed	protein-coding	0.010000	0.402985			-91(TTTTTCTTAGGTTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-287	chr14	39053761	39053961	+	1.05420	NA	intron (NM_001190187, intron 1 of 9)	Lx8|LINE|L1	155559	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA	0.000000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-306	chr14	85935225	85935425	+	1.05420	NA	Intergenic	Intergenic	-310645	NR_040457	75155	Mm.399239	NR_040457	ENSMUSG00000115271	4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA	0.005000	0.338308			80(ATTTGCATAAAATTTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4475	chr2	102087442	102087642	+	1.05420	NA	intron (NM_178886, intron 2 of 5)	intron (NM_178886, intron 2 of 5)	98918	NM_001290784	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2105	chr13	63524109	63524309	+	1.05419	NA	intron (NM_008957, intron 17 of 23)	intron (NM_008957, intron 17 of 23)	41526	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes|wig	patched 1	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6107	chr5	99738014	99738214	+	1.05419	NA	intron (NR_131054, intron 5 of 11)	MER5A1|DNA|hAT-Charlie	-9054	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1391	chr11	87310868	87311068	+	1.05419	NA	intron (NM_177167, intron 1 of 6)	intron (NM_177167, intron 1 of 6)	48026	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4560	chr2	120770515	120770715	+	1.05419	NA	intron (NM_001024857, intron 9 of 14)	intron (NM_001024857, intron 9 of 14)	-39098	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6085	chr5	91076743	91076943	+	1.05419	NA	intron (NM_007950, intron 1 of 4)	intron (NM_007950, intron 1 of 4)	2226	NM_007950	13874	Mm.4791	NM_007950	ENSMUSG00000029377	Ereg	EPR	epiregulin	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6090	chr5	92208465	92208665	+	1.05419	NA	Intergenic	Intergenic	6843	NR_033483	57425	Mm.2548	NM_020562	ENSMUSG00000029409	U90926	-	cDNA sequence U90926	ncRNA	0.005000	0.457711			7(GTTTAAATCACAATTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7254	chr8	53145992	53146192	+	1.05419	NA	Intergenic	Intergenic	-365610	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1999	chr13	29554445	29554645	+	1.05419	NA	intron (NR_131896, intron 9 of 16)	intron (NR_131896, intron 9 of 16)	301128	NM_144536	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding	0.020000	0.407960			-17(TGGTTGTCATGTAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1963	chr13	16109942	16110142	+	1.05419	NA	Intergenic	Intergenic	-86619	NR_155430	100503142	Mm.359204	NR_155430		B230303A05Rik	B230303A05|EG328191	U1 small nuclear ribonucleoprotein 1C pseudogene	pseudo	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5668	chr4	104673586	104673786	+	1.05419	NA	intron (NM_001369049, intron 7 of 19)	intron (NM_001369049, intron 7 of 19)	-92631	NM_133882	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-482	chr1	157114550	157114750	+	1.05419	NA	Intergenic	Intergenic	-5970	NM_001305063	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-569	chr1	176823007	176823207	+	1.05419	NA	intron (NR_151682, intron 1 of 16)	intron (NR_151682, intron 1 of 16)	8447	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding	0.010000	0.417910			-11(TCCTTGTCATGCTAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5689	chr4	111232608	111232808	+	1.05419	NA	intron (NM_001284190, intron 5 of 12)	intron (NM_001284190, intron 5 of 12)	-182298	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0.000000	0.353234	44(AATGTATTATGTATA,+,0.00),44(AATGTATTATGTATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7684	chr9	62640254	62640454	+	1.05419	NA	Intergenic	Intergenic	-37501	NM_176922	319480	Mm.34883	NM_176922	ENSMUSG00000032243	Itga11	4732459H24Rik	integrin alpha 11	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-982	chr10	102895516	102895716	+	1.05419	NA	Intergenic	Intergenic	133161	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding	0.005000	0.358209			28(ATTATCATGAGAATCT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-700	chr5	106825474	106825674	+	1.05419	NA	Intergenic	Intergenic	100316	NM_001252516	330149	Mm.121664	NM_177873	ENSMUSG00000043410	Hfm1	A330009G12Rik|Gm1046|Mer3|Sec63d1	HFM1, ATP-dependent DNA helicase homolog	protein-coding	0.055000	0.616915			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3175	chr16	38241064	38241264	+	1.05419	NA	3' UTR (NM_019827, exon 11 of 11)	3' UTR (NM_019827, exon 11 of 11)	53660	NM_001098404	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding	0.005000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-853	chr8	127144914	127145114	+	1.05412	NA	intron (NM_001363431, intron 1 of 24)	intron (NM_001363431, intron 1 of 24)	80958	NM_033620	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-531	chr2	137229619	137229819	+	1.05412	NA	Intergenic	Intergenic	-113199	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5614	chr4	94472188	94472388	+	1.05412	NA	Intergenic	Intergenic	84508	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-832	chr8	66448892	66449092	+	1.05412	NA	intron (NM_175188, intron 6 of 7)	intron (NM_175188, intron 6 of 7)	37538	NM_001357208	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6799	chr7	24889709	24889909	+	1.05412	NA	TTS (NM_001360116)	TTS (NM_001360116)	4896	NM_001360115	20085	Mm.300281	NM_023133	ENSMUSG00000040952	Rps19	Dsk3	ribosomal protein S19	protein-coding	0.015000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-503	chr2	95967812	95968012	+	1.05412	NA	Intergenic	Intergenic	-350257	NM_001363048	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding	0.000000	0.333333			16(ATTTAAATGGTAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7061	chr7	123644951	123645151	+	1.05412	NA	Intergenic	MER2|DNA|TcMar-Tigger	-144425	NM_001081329	210162	Mm.135397	NM_175435	ENSMUSG00000030757	Zkscan2	9430065N20Rik|AW493225|Zfp694	zinc finger with KRAB and SCAN domains 2	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7343	chr8	79679079	79679279	+	1.05412	NA	Intergenic	Intergenic	32561	NR_152614	24015	Mm.5831	NM_015751	ENSMUSG00000058355	Abce1	C79080|Oabp|RLI|RNS41|RNS4I|Rnaseli	ATP-binding cassette, sub-family E (OABP), member 1	protein-coding	0.010000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6739	chr6	137565984	137566184	+	1.05412	NA	intron (NM_001271588, intron 1 of 20)	intron (NM_001271588, intron 1 of 20)	4925	NM_001271587	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0.005000	0.512438			8(CTCTGCATGAGAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5272	chr3	148595899	148596099	+	1.05412	NA	Intergenic	Intergenic	358636	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding	0.010000	0.363184		-30(CTTTAATATTCATC,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5296	chr3	153260563	153260763	+	1.05412	NA	intron (NM_011372, intron 3 of 4)	intron (NM_011372, intron 3 of 4)	37986	NR_126464	75489	Mm.443252	NR_126464	ENSMUSG00000105023	1700012D16Rik	-	RIKEN cDNA 1700012D16 gene	ncRNA	0.000000	0.348259			45(CTTTGAATTACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1842	chr12	99819651	99819851	+	1.05412	NA	intron (NM_030172, intron 5 of 5)	intron (NM_030172, intron 5 of 5)	63691	NM_030172	78767	Mm.235920	NM_030172	ENSMUSG00000021176	Efcab11	2610021K21Rik|2610110A13Rik	EF-hand calcium binding domain 11	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5300	chr3	154509360	154509560	+	1.05412	NA	Intergenic	Intergenic	-87251	NM_009968	12972	Mm.374855	NM_009968	ENSMUSG00000028199	Cryz	Sez9	crystallin, zeta	protein-coding	0.020000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7299	chr8	66448871	66449071	+	1.05412	NA	intron (NM_175188, intron 6 of 7)	intron (NM_175188, intron 6 of 7)	37559	NM_001357208	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6560	chr6	83467854	83468054	+	1.05331	NA	Intergenic	Intergenic	-11562	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4776	chr2	165664619	165664819	+	1.05323	NA	intron (NM_010165, intron 1 of 15)	intron (NM_010165, intron 1 of 15)	9421	NM_010165	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1937	chr13	6587195	6587395	+	1.05323	NA	intron (NM_019703, intron 17 of 21)	intron (NM_019703, intron 17 of 21)	39138	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5656	chr4	103068194	103068394	+	1.05307	NA	intron (NM_146254, intron 8 of 16)	ERVL-E-int|LTR|ERVL	-41023	NM_001290648	23919	Mm.100163	NM_011831	ENSMUSG00000066090	Insl5	RIF2	insulin-like 5	protein-coding	0.000000	0.373134			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-706	chr5	120895164	120895364	+	1.05222	NA	TTS (NM_145211)	TTS (NM_145211)	-7651	NR_126529	23960	Mm.389688	NM_011852	ENSMUSG00000066861	Oas1g	AI449562|L2|Mmu-L|Mmu-L2|Oas1b|Oias-1|Oias1	2'-5' oligoadenylate synthetase 1G	protein-coding	0.010000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-791	chr7	58668764	58668964	+	1.05222	NA	intron (NM_009728, intron 1 of 20)	intron (NM_009728, intron 1 of 20)	10662	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6871	chr7	58668740	58668940	+	1.05222	NA	intron (NM_009728, intron 1 of 20)	intron (NM_009728, intron 1 of 20)	10638	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding	0.000000	0.432836			-100(CTTTAAAAAAAAAAAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-822	chr8	37570375	37570575	+	1.05222	NA	intron (NM_145841, intron 4 of 7)	Lx8|LINE|L1	-546237	NR_126063	414128	Mm.450976	NR_126063	ENSMUSG00000110242	G630064G18Rik	-	RIKEN cDNA G630064G18 gene	ncRNA	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2260	chr13	103880252	103880452	+	1.05222	NA	intron (NM_001005868, intron 4 of 26)	intron (NM_001005868, intron 4 of 26)	40234	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding	0.000000	0.313433	21(TATTAATAATTCATC,+,0.00),21(TATTAATAATTCATC,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-207	chr12	93669536	93669736	+	1.05191	NA	Intergenic	MLTR25A|LTR|ERVK	-224813	NR_126436	75295	Mm.243878	NR_126436	ENSMUSG00000113164	4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-666	chr10	3383365	3383565	+	1.05137	NA	intron (NM_133485, intron 1 of 3)	intron (NM_133485, intron 1 of 3)	17315	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory inhibitor subunit 14C	protein-coding	0.010000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-74	chr10	3383332	3383532	+	1.05137	NA	intron (NM_133485, intron 1 of 3)	intron (NM_133485, intron 1 of 3)	17282	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory inhibitor subunit 14C	protein-coding	0.015000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-391	chr17	28431202	28431402	+	1.05077	NA	intron (NM_010220, intron 3 of 10)	intron (NM_010220, intron 3 of 10)	54847	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding	0.020000	0.393035			-19(GTTTACATTATAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-198	chr1	69178592	69178792	+	1.05077	NA	Intergenic	Intergenic	-70633	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6024	chr5	72558651	72558851	+	1.05077	NA	intron (NM_001359837, intron 2 of 4)	intron (NM_001359837, intron 2 of 4)	894	NM_001359837	100978	Mm.187453	NM_133921	ENSMUSG00000072889	Nfxl1	1700012H24Rik|AW538212|D430033A06Rik|DNABF|GCF|Gm1058|TCF9	nuclear transcription factor, X-box binding-like 1	protein-coding	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4333	chr2	59645467	59645667	+	1.05077	NA	intron (NM_198294, intron 1 of 26)	intron (NM_198294, intron 1 of 26)	-1202	NM_001290659	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5848	chr5	19154048	19154248	+	1.05077	NA	Intergenic	ORR1D-int|LTR|ERVL-MaLR	72407	NR_102341	70832	Mm.398993	NR_102341	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	ncRNA	0.000000	0.383085			-3(TTAGTCTCATGCACAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1387	chr11	86624222	86624422	+	1.05077	NA	intron (NM_029478, intron 7 of 11)	intron (NM_029478, intron 7 of 11)	-40164	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA	0.015000	0.432836			-63(ATCTACATGACAAGAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4474	chr2	102087193	102087393	+	1.05077	NA	intron (NM_178886, intron 2 of 5)	intron (NM_178886, intron 2 of 5)	99167	NM_001290784	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.015000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4417	chr2	78928477	78928677	+	1.05077	NA	non-coding (NR_151458, exon 7 of 7)	non-coding (NR_151458, exon 7 of 7)	58899	NM_001356395	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding	0.005000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6939	chr7	83821114	83821314	+	1.05017	NA	Intergenic	Intergenic	-26375	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	Cfap161	1700026D08Rik|AW047638|AW551802	cilia and flagella associated protein 161	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4324	chr2	57303360	57303560	+	1.05017	NA	intron (NM_001145820, intron 3 of 16)	intron (NM_001145820, intron 3 of 16)	65078	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding	0.010000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-711	chr5	136403487	136403687	+	1.05017	NA	intron (NM_001291233, intron 3 of 23)	intron (NM_001291233, intron 3 of 23)	-27784	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA	0.045000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4674	chr2	140274889	140275089	+	1.05017	NA	intron (NM_001033296, intron 5 of 19)	intron (NM_001033296, intron 5 of 19)	104343	NM_027093	69487	Mm.287921	NM_027093	ENSMUSG00000027384	Ndufaf5	2310003L22Rik	NADH:ubiquinone oxidoreductase complex assembly factor 5	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4733	chr2	153140132	153140332	+	1.05016	NA	intron (NM_001172117, intron 10 of 12)	L2c|LINE|L2	-21069	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-740	chr10	24886124	24886324	+	1.05016	NA	intron (NM_001166416, intron 11 of 29)	intron (NM_001166416, intron 11 of 29)	16238	NM_027347	70208	Mm.28020	NM_027347	ENSMUSG00000019984	Med23	130kDa|3000002A17Rik|Crsp3|ESTM7|Sur2|X83317|mKIAA1216	mediator complex subunit 23	protein-coding	0.030000	0.567164			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-83	chr10	24886129	24886329	+	1.05016	NA	intron (NM_001166416, intron 11 of 29)	intron (NM_001166416, intron 11 of 29)	16243	NM_027347	70208	Mm.28020	NM_027347	ENSMUSG00000019984	Med23	130kDa|3000002A17Rik|Crsp3|ESTM7|Sur2|X83317|mKIAA1216	mediator complex subunit 23	protein-coding	0.030000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3456	chr17	29018446	29018646	+	1.04970	NA	Intergenic	B1F|SINE|Alu	-10551	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding	0.005000	0.442786			-33(CCTCACTCTTGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1780	chr12	83579354	83579554	+	1.04936	NA	intron (NM_183154, intron 2 of 11)	intron (NM_183154, intron 2 of 11)	-16994	NM_001359168	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding	0.010000	0.532338			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-157	chr11	79827614	79827814	+	1.04936	NA	Intergenic	Intergenic	101314	NR_029959	723853		NR_029959	ENSMUSG00000065489	Mir365-2	Mirn365-2|mir-365-2	microRNA 365-2	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5484	chr4	56864118	56864318	+	1.04936	NA	intron (NM_018761, intron 1 of 18)	intron (NM_018761, intron 1 of 18)	993	NM_018761	54366	Mm.218891	NM_018761	ENSMUSG00000038816	Ctnnal1	ACRP|AI616177|AW545119|C86009|Catnal1	catenin (cadherin associated protein), alpha-like 1	protein-coding	0.015000	0.442786			68(ACTTTTTTTTTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1371	chr11	79827471	79827671	+	1.04936	NA	Intergenic	Intergenic	101171	NR_029959	723853		NR_029959	ENSMUSG00000065489	Mir365-2	Mirn365-2|mir-365-2	microRNA 365-2	ncRNA	0.000000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1537	chr12	11694707	11694907	+	1.04936	NA	Intergenic	Intergenic	188092	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	tubulin, beta 2a, pseudogene 2	pseudo	0.010000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6936	chr7	83774740	83774940	+	1.04894	NA	TTS (NM_029335)	TTS (NM_029335)	19999	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	Cfap161	1700026D08Rik|AW047638|AW551802	cilia and flagella associated protein 161	protein-coding	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6962	chr7	90882146	90882346	+	1.04894	NA	Intergenic	Intergenic	-208540	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5182	chr3	128347855	128348055	+	1.04894	NA	Intergenic	Intergenic	-116350	NR_045704	402774	Mm.209170	NR_045704	ENSMUSG00000105816	D030025E07Rik	-	RIKEN cDNA D030025E07 gene	ncRNA	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-553	chr1	174703519	174703719	+	1.04894	NA	intron (NM_019445, intron 13 of 17)	intron (NM_019445, intron 13 of 17)	201794	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3842	chr18	49998302	49998502	+	1.04894	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	18975	NM_001177760	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding	0.000000	0.363184			17(ATCTGAATAAAAATAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8107	chrX	143683823	143684023	+	1.04894	NA	intron (NM_001195049, intron 4 of 17)	intron (NM_001195049, intron 4 of 17)	-9364	NM_001195046	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 (RAC1) activated kinase 3	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-905	chr10	83079302	83079502	+	1.04894	NA	intron (NM_021439, intron 1 of 2)	intron (NM_021439, intron 1 of 2)	93905	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2036	chr13	39516219	39516419	+	1.04894	NA	Intergenic	Intergenic	-555440	NM_001170431	108652	Mm.255506	NM_134060	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	solute carrier family 35, member B3	protein-coding	0.025000	0.557214			41(CCTCTGTTAAGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6809	chr7	30844704	30844904	+	1.04894	NA	Intergenic	Intergenic	11374	NM_001033316	233080	Mm.291167	NM_001033316	ENSMUSG00000019429	Ffar3	Gm478|Gpr41	free fatty acid receptor 3	protein-coding	0.010000	0.467662	32(CATACATTATGCAAA,+,0.00),32(CATACATTATGCAAA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5344	chr4	12069870	12070070	+	1.04894	NA	intron (NR_110955, intron 9 of 28)	intron (NR_110955, intron 9 of 28)	17987	NR_161254	329795	Mm.475125	NM_177861	ENSMUSG00000049488	Tmem67	5330408M12Rik|B230117O07|b2b1163.1Clo|b2b1291.1Clo	transmembrane protein 67	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7603	chr9	33620581	33620781	+	1.04894	NA	Intergenic	Intergenic	-421690	NR_040744	77119	Mm.367930	NR_040744	ENSMUSG00000098758	7630403G23Rik	TH-cre|Tg(Th-cre)1Tmd	RIKEN cDNA 7630403G23 gene	ncRNA	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6670	chr6	113031349	113031549	+	1.04894	NA	Intergenic	Intergenic	-14853	NM_001355266	14911	Mm.781	NM_008188	ENSMUSG00000030264	Thumpd3	AW556087|Gt(ROSA)26asSor|Gtrosa26as	THUMP domain containing 3	protein-coding	0.010000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-933	chr10	90373563	90373763	+	1.04894	NA	intron (NM_001359241, intron 12 of 25)	MTEb|LTR|ERVL-MaLR	-202064	NM_001177397	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1|AIDA-1b|C030032C09Rik|E530015N03Rik|EB-1|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-356	chr1	126691375	126691575	+	1.04894	NA	intron (NM_001081756, intron 2 of 16)	MIR|SINE|MIR	139157	NM_176957	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3367	chr16	87578976	87579176	+	1.04894	NA	intron (NM_144854, intron 3 of 4)	B3|SINE|B2	25746	NM_144854	224419	Mm.194466	NM_144854	ENSMUSG00000025610	Map3k7cl	C21orf7|ORF63|Tak1l	Map3k7 C-terminal like	protein-coding	0.030000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4825	chr3	5829752	5829952	+	1.04894	NA	Intergenic	RLTR13D6|LTR|ERVK	-253604	NM_001267715	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0.020000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-251	chr1	87355235	87355435	+	1.04894	NA	intron (NM_146112, intron 3 of 28)	intron (NM_146112, intron 3 of 28)	28337	NM_146112	227331	Mm.23065	NM_146112	ENSMUSG00000048000	Gigyf2	2610016F01Rik|A830080H02Rik|AI852361|AW259676|BC006835|Tnrc15|mKIAA0642	GRB10 interacting GYF protein 2	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3052	chr15	97236970	97237170	+	1.04894	NA	Intergenic	Intergenic	-10037	NM_172293	239647	Mm.130036	NM_172293	ENSMUSG00000044250	Pced1b	Fam113b	PC-esterase domain containing 1B	protein-coding	0.030000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1535	chr12	10013577	10013777	+	1.04894	NA	Intergenic	L1MD1|LINE|L1	-356294	NM_001310582	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB|cN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2465	chr14	45142698	45142898	+	1.04894	NA	intron (NM_172597, intron 18 of 20)	intron (NM_172597, intron 18 of 20)	76627	NM_001310534	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7746	chr9	77849352	77849552	+	1.04894	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-67913	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-456	chr1	152254414	152254614	+	1.04894	NA	Intergenic	Tigger5|DNA|TcMar-Tigger	132168	NM_025677	66637	Mm.379120	NM_025677	ENSMUSG00000014980	Tsen15	5730449L18Rik|AL023077|Sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.025000	0.388060		-75(AATCCATATGCAAA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1943	chr13	9646222	9646422	+	1.04894	NA	intron (NM_001081426, intron 31 of 36)	intron (NM_001081426, intron 31 of 36)	117488	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5643	chr4	100393613	100393813	+	1.04894	NA	intron (NM_013845, intron 4 of 8)	intron (NM_013845, intron 4 of 8)	-85154	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding	0.020000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-70	chr1	23893359	23893559	+	1.04894	NA	intron (NM_028534, intron 1 of 9)	intron (NM_028534, intron 1 of 9)	16277	NM_001290683	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding	0.005000	0.393035			3(TTTTTCCTATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1465	chr11	110866565	110866765	+	1.04894	NA	Intergenic	Intergenic	-101368	NM_001252207	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2901	chr15	45076666	45076866	+	1.04894	NA	Intergenic	Intergenic	38168	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding	0.000000	0.258706			63(ATTTTGTCATGCTTAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2623	chr14	90057249	90057449	+	1.04894	NA	Intergenic	Intergenic	-69542	NR_045712	74967	Mm.390704	NR_045712	ENSMUSG00000115001	4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA	0.000000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3859	chr18	53974817	53975017	+	1.04894	NA	Intergenic	Intergenic	112804	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding	0.005000	0.398010		24(TGTGCATATGCAAA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2157	chr13	77545175	77545375	+	1.04894	NA	intron (NM_001145676, intron 19 of 19)	intron (NM_001145676, intron 19 of 19)	-163415	NM_001163420	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding	0.005000	0.358209			0(ATATTCTCATGCAGTT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3560	chr17	66048871	66049071	+	1.04894	NA	intron (NM_001025572, intron 3 of 12)	ORR1C1|LTR|ERVL-MaLR	28075	NM_001025572	106585	Mm.34706	NM_001025572	ENSMUSG00000034647	Ankrd12	2900001A12Rik|AI447928|ANCO-2|AV347965|GAC-1|mKIAA0874	ankyrin repeat domain 12	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2091	chr13	59351604	59351804	+	1.04894	NA	Intergenic	B3|SINE|B2	192747	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding	0.020000	0.507463			24(ATCTAAATAACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2733	chr14	121107651	121107851	+	1.04894	NA	intron (NM_134082, intron 2 of 26)	intron (NM_134082, intron 2 of 26)	72177	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding	0.025000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7891	chr9	114501231	114501431	+	1.04894	NA	Intergenic	Intergenic	-4787	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2043	chr13	40744879	40745079	+	1.04894	NA	Intergenic	Intergenic	-10059	NM_001301674	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding	0.040000	0.517413			-22(TTTCTGCCATGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1715	chr12	69752101	69752301	+	1.04894	NA	intron (NM_183294, intron 7 of 9)	intron (NM_183294, intron 7 of 9)	11743	NR_030450	751538		NR_030450	ENSMUSG00000076065	Mir681	Mirn681|mmu-mir-681	microRNA 681	ncRNA	0.010000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4059	chr19	28383986	28384186	+	1.04894	NA	intron (NM_175459, intron 4 of 10)	intron (NM_175459, intron 4 of 10)	-294138	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-867	chr10	68268177	68268377	+	1.04894	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	10449	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1997	chr13	28661002	28661202	+	1.04894	NA	intron (NR_045054, intron 5 of 7)	intron (NR_045054, intron 5 of 7)	49771	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3963	chr18	82780361	82780561	+	1.04894	NA	Intergenic	Intergenic	-21422	NR_045389	76961	Mm.396392	NR_045389	ENSMUSG00000101773	2210420H20Rik	-	RIKEN cDNA 2210420H20 gene	ncRNA	0.020000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4444	chr2	90469377	90469577	+	1.04894	NA	intron (NM_008982, intron 4 of 23)	intron (NM_008982, intron 4 of 23)	9697	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding	0.005000	0.358209	-43(TATGTATTATGCATA,+,0.00),-43(TATGTATTATGCATA,-,0.00),-30(TATGTATTATGCAAA,+,0.00),-30(TATGTATTATGCAAA,-,0.00)	-55(ATTGCATATTTATA,+,0.00),-36(TATGCATATGTATT,+,0.00),-36(TATGCATATGTATT,-,0.00)	-30(TATGTATTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2499	chr14	60116140	60116340	+	1.04894	NA	Intergenic	Intergenic	-29326	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding	0.010000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7766	chr9	80571230	80571430	+	1.04894	NA	Intergenic	Intergenic	-105892	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3402	chr16	97657737	97657937	+	1.04894	NA	Intergenic	Intergenic	-46642	NM_015775	50528	Mm.276145	NM_015775	ENSMUSG00000000385	Tmprss2	D16Ertd61e	transmembrane protease, serine 2	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8151	chrX	164720359	164720559	+	1.04894	NA	Intergenic	MER99|DNA|hAT?	222556	NM_027027	69299	Mm.79031	NM_027027	ENSMUSG00000031384	Asb9	1700011M07Rik	ankyrin repeat and SOCS box-containing 9	protein-coding	0.005000	0.288557		37(AATAAATATTCATA,+,0.00),37(AATAAATATTCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5839	chr5	16654789	16654989	+	1.04894	NA	Intergenic	Intergenic	100988	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3025	chr15	92190192	92190392	+	1.04894	NA	intron (NM_001358051, intron 3 of 25)	intron (NM_001358051, intron 3 of 25)	28935	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8044	chrX	102623541	102623741	+	1.04894	NA	intron (NM_173021, intron 5 of 31)	L1M2|LINE|L1	20605	NM_173021	18679	Mm.212889	NM_008832	ENSMUSG00000034055	Phka1	5330411D17|9830108K24Rik|Phka	phosphorylase kinase alpha 1	protein-coding	0.005000	0.338308		54(TATACATATGCATG,+,0.00),54(TATACATATGCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-42	chr1	15026775	15026975	+	1.04894	NA	Intergenic	L1M4b|LINE|L1	-108013	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2061	chr13	46817532	46817732	+	1.04894	NA	intron (NM_010617, intron 9 of 37)	intron (NM_010617, intron 9 of 37)	-89783	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2853	chr15	32480987	32481187	+	1.04894	NA	intron (NM_009154, intron 5 of 22)	intron (NM_009154, intron 5 of 22)	236274	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding	0.000000	0.328358			47(TTATTTTTATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4403	chr2	76446239	76446439	+	1.04894	NA	intron (NM_145525, intron 1 of 26)	intron (NM_145525, intron 1 of 26)	39831	NM_001290733	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3204	chr16	45392148	45392348	+	1.04894	NA	exon (NM_001358443, exon 4 of 5)	exon (NM_001358443, exon 4 of 5)	16805	NM_001358443	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding	0.015000	0.358209		-100(CATCAATATTTATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7933	chrX	20161783	20161983	+	1.04894	NA	intron (NM_177353, intron 10 of 16)	intron (NM_177353, intron 10 of 16)	102313	NM_021715	60322	Mm.44827	NM_021715	ENSMUSG00000037347	Chst7	2600013M07Rik|C6ST-2|GST5|Gn6st-4|glcNAc6ST-4	carbohydrate (N-acetylglucosamino) sulfotransferase 7	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4121	chr19	52676578	52676778	+	1.04894	NA	Intergenic	Intergenic	-246503	NR_030678	100043450	Mm.145594	NR_030678	ENSMUSG00000117896	AA387883	-	expressed sequence AA387883	ncRNA	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1127	chr10	125636881	125637081	+	1.04894	NA	Intergenic	Intergenic	-308018	NM_001358496	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding	0.020000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7414	chr8	101767106	101767306	+	1.04894	NA	Intergenic	Intergenic	1017905	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding	0.000000	0.353234			-29(ATTATCAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4002	chr19	6685375	6685575	+	1.04894	NA	Intergenic	Intergenic	-142405	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding	0.020000	0.472637		-5(GCTAAATATGCATT,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6459	chr6	54586260	54586460	+	1.04894	NA	intron (NM_153573, intron 2 of 3)	intron (NM_153573, intron 2 of 3)	6814	NM_001363793	231997	Mm.274693	NM_153573	ENSMUSG00000038074	Fkbp14	BC029109|FKBP-14|FKBP22	FK506 binding protein 14	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1469	chr11	111256007	111256207	+	1.04894	NA	Intergenic	Intergenic	189943	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding	0.010000	0.407960			1(CAATGTTTATGTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4542	chr2	116737038	116737238	+	1.04894	NA	Intergenic	Intergenic	-141553	NM_026104	67356	Mm.131623	NM_026104	ENSMUSG00000027355	Tmco5	1700095F04Rik|Tmco5a	transmembrane and coiled-coil domains 5	protein-coding	0.005000	0.273632			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7977	chrX	63204944	63205144	+	1.04894	NA	Intergenic	MLTR25A|LTR|ERVK	-678033	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	Tslrn1	1700019B21Rik	testis specific long noncoding RNA 1	ncRNA	0.000000	0.368159			5(TAATTATCATGTAATT,+,0.00),68(ACATTATTATGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5837	chr5	16062433	16062633	+	1.04894	NA	intron (NM_001110843, intron 3 of 38)	intron (NM_001110843, intron 3 of 38)	127842	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding	0.000000	0.328358	-79(AATGAATAATTCATC,+,0.00),-79(AATGAATAATTCATC,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5598	chr4	91340518	91340718	+	1.04894	NA	intron (NM_001347149, intron 1 of 7)	intron (NM_001347149, intron 1 of 7)	31437	NM_010486	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV like RNA binding protein 1	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5055	chr3	86107681	86107881	+	1.04894	NA	intron (NM_001082414, intron 7 of 14)	B1_Mm|SINE|Alu	23347	NM_001082414	27059	Mm.2454	NM_012059	ENSMUSG00000028082	Sh3d19	AW011754|Kryn	SH3 domain protein D19	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6331	chr6	17516037	17516237	+	1.04894	NA	intron (NM_008591, intron 4 of 21)	intron (NM_008591, intron 4 of 21)	52180	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5510	chr4	63982525	63982725	+	1.04894	NA	intron (NM_001369214, intron 10 of 20)	intron (NM_001369214, intron 10 of 20)	64311	NM_001369212	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding	0.025000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6927	chr7	81016771	81016971	+	1.04894	NA	intron (NM_178707, intron 2 of 9)	RLTR11A2|LTR|ERVK	23187	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	A730014M16Rik|Znf592	zinc finger protein 592	protein-coding	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6543	chr6	80503839	80504039	+	1.04894	NA	intron (NM_001134743, intron 2 of 2)	intron (NM_001134743, intron 2 of 2)	484296	NM_001347261	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0.005000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2611	chr14	87266433	87266633	+	1.04894	NA	Intergenic	Intergenic	-125309	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|p134MDia2	diaphanous related formin 3	protein-coding	0.030000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4036	chr19	19005192	19005392	+	1.04894	NA	intron (NM_001043354, intron 1 of 9)	MER5A|DNA|hAT-Charlie	-4175	NM_001289921	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding	0.015000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1402	chr11	89038631	89038831	+	1.04888	NA	non-coding (NR_156181, exon 11 of 11)	non-coding (NR_156181, exon 11 of 11)	22017	NM_001362845	56077	Mm.153695	NM_019505	ENSMUSG00000000276	Dgke	C87606|DAGK6|DGK|DGK-epsilon	diacylglycerol kinase, epsilon	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6171	chr5	122448047	122448247	+	1.04888	NA	Intergenic	Intergenic	25703	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding	0.035000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4716	chr2	149493240	149493440	+	1.04888	NA	Intergenic	Intergenic	88091	NM_021405	58214	Mm.117117	NM_021405	ENSMUSG00000033156	Cst10	DD72	cystatin 10 (chondrocytes)	protein-coding	0.000000	0.378109			-80(ATCTCCATGATAAACT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-595	chr3	149498651	149498851	+	1.04888	NA	Intergenic	Intergenic	224014	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.000000	0.293532			-94(GAATTCTCATGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3420	chr17	12300285	12300485	+	1.04888	NA	intron (NM_001357722, intron 1 of 25)	intron (NM_001357722, intron 1 of 25)	18275	NM_011948	26407	Mm.28587	NM_011948	ENSMUSG00000014426	Map3k4	D17Rp17|D17Rp17e|MAPKKK4|MEKK 4|MTK1|Mek4b|Mekk4|RP17|Rp17a|Tas|mKIAA0213	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.020000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4803	chr2	174257386	174257586	+	1.04888	NA	Intergenic	Intergenic	9639	NR_029646	723906		NR_029646	ENSMUSG00000065521	Mir296	Mirn296|mir-296|mmu-mir-296	microRNA 296	ncRNA	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5508	chr4	62944411	62944611	+	1.04888	NA	Intergenic	RMER1A|Other|Other	-21056	NM_001369118	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding	0.010000	0.527363			-35(CCTGTGTCATGGAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5189	chr3	130880716	130880916	+	1.04888	NA	Intergenic	Intergenic	-150418	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding	0.015000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1825	chr12	94546430	94546630	+	1.04888	NA	Intergenic	Intergenic	619192	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA	0.005000	0.348259			67(CTTTACATATCAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1617	chr12	40258585	40258785	+	1.04888	NA	Intergenic	Intergenic	35321	NR_045157	629820	Mm.435540	NR_045157	ENSMUSG00000035983	Gm7008	EG629820	predicted gene 7008	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5304	chr3	155849899	155850099	+	1.04888	NA	Intergenic	L1M5|LINE|L1	-126355	NR_040553	329780	Mm.119000	NR_040553	ENSMUSG00000104553	9330178D15Rik	9330178D15	RIKEN cDNA 9330178D15 gene	ncRNA	0.005000	0.288557			-13(AATTGCTTATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-395	chr1	136339921	136340121	+	1.04888	NA	intron (NM_001347110, intron 1 of 16)	intron (NM_001347110, intron 1 of 16)	6083	NM_001347110	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding	0.005000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-319	chr14	105859084	105859284	+	1.04708	NA	Intergenic	Intergenic	37635	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty RTK signaling antagonist 2	protein-coding	0.020000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-802	chr7	97804553	97804753	+	1.04657	NA	intron (NM_001357364, intron 1 of 14)	intron (NM_001357364, intron 1 of 14)	16112	NM_001357365	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 (RAC1) activated kinase 1	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-541	chr1	172177603	172177803	+	1.04657	NA	intron (NM_001357204, intron 6 of 13)	intron (NM_001357204, intron 6 of 13)	29101	NM_001329869	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1811	chr12	90976155	90976355	+	1.04657	NA	Intergenic	Intergenic	-69593	NR_045858	71349	Mm.442093	NR_045858	ENSMUSG00000085004	5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6989	chr7	97804549	97804749	+	1.04657	NA	intron (NM_001357364, intron 1 of 14)	intron (NM_001357364, intron 1 of 14)	16108	NM_001357365	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 (RAC1) activated kinase 1	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2462	chr14	43979473	43979673	+	1.04657	NA	Intergenic	Intergenic	22504	NM_007448	503844	Mm.24663	NM_007448	ENSMUSG00000053961	Ang5	-	angiogenin, ribonuclease A family, member 5	protein-coding	0.010000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-206	chr12	90976167	90976367	+	1.04657	NA	Intergenic	Intergenic	-69581	NR_045858	71349	Mm.442093	NR_045858	ENSMUSG00000085004	5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3723	chr18	16762612	16762812	+	1.04657	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	46534	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding	0.005000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-591	chr3	144411207	144411407	+	1.04629	NA	Intergenic	Intergenic	158909	NM_001355234	23908	Mm.12863	NM_011828	ENSMUSG00000040151	Hs2st1	2OST|AW214369|Hs2st|mKIAA0448	heparan sulfate 2-O-sulfotransferase 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3689	chr18	6466466	6466666	+	1.04629	NA	intron (NM_007935, intron 1 of 13)	intron (NM_007935, intron 1 of 13)	24080	NR_035446	100316773		NR_035446	ENSMUSG00000084514	Mir1893	Mirn1893|mmu-mir-1893	microRNA 1893	ncRNA	0.010000	0.437811			-95(TTCTGAATAAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5711	chr4	118625121	118625321	+	1.04629	NA	intron (NM_026932, intron 7 of 8)	intron (NM_026932, intron 7 of 8)	-1183	NR_029469	100041290	Mm.472885	NR_029469		D4Ertd617e	-	DNA segment, Chr 4, ERATO Doi 617, expressed	ncRNA	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4579	chr2	124731531	124731731	+	1.04629	NA	Intergenic	L1ME2|LINE|L1	78050	NM_199239	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1437	chr11	103292375	103292575	+	1.04629	NA	Intergenic	Intergenic	-25074	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3737	chr18	21128797	21128997	+	1.04629	NA	3' UTR (NM_001033445, exon 6 of 6)	3' UTR (NM_001033445, exon 6 of 6)	56553	NM_008586	17288	Mm.2682	NM_008586	ENSMUSG00000024313	Mep1b	Mep-1b	meprin 1 beta	protein-coding	0.015000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-263	chr13	96681067	96681267	+	1.04628	NA	Intergenic	Intergenic	-10231	NM_001360166	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding	0.000000	0.333333	54(GATGAATCATTTATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1269	chr11	44805290	44805490	+	1.04486	NA	intron (NM_001362579, intron 7 of 16)	intron (NM_001362579, intron 7 of 16)	185162	NM_001362569	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1573	chr12	26299822	26300022	+	1.04486	NA	Intergenic	Intergenic	-46788	NR_130981	75243	Mm.444753	NR_130981	ENSMUSG00000114048	4930549C15Rik	-	RIKEN cDNA 4930549C15 gene	ncRNA	0.005000	0.487562			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-414	chr17	86549777	86549977	+	1.04486	NA	intron (NM_011104, intron 10 of 14)	L1MB1|LINE|L1	-203987	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.020000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1320	chr11	64531913	64532113	+	1.04486	NA	Intergenic	Intergenic	-95339	NR_028445	654805	Mm.436132	NR_028445		F930015N05Rik	-	RIKEN cDNA F930015N05 gene	ncRNA	0.005000	0.447761			24(ATGATCATGAGAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1182	chr11	20004558	20004758	+	1.04486	NA	intron (NM_033523, intron 2 of 5)	intron (NM_033523, intron 2 of 5)	80216	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related EVH1 domain containing 2	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7456	chr8	114805884	114806084	+	1.04486	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	366332	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding	0.020000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-509	chr2	105719706	105719906	+	1.04486	NA	intron (NM_023876, intron 9 of 9)	intron (NM_023876, intron 9 of 9)	37343	NM_001310146	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding	0.010000	0.358209			-4(TTTTAAATGAAAATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-876	chr9	58916170	58916370	+	1.04486	NA	intron (NM_001042752, intron 13 of 27)	intron (NM_001042752, intron 13 of 27)	93321	NM_001081192	330953	Mm.151967	NM_001081192	ENSMUSG00000032338	Hcn4	Bcng3|Hcn3	hyperpolarization-activated, cyclic nucleotide-gated K+ 4	protein-coding	0.005000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-304	chr14	79905584	79905784	+	1.04399	NA	Intergenic	Intergenic	-36508	NR_033535	100038734	Mm.387484	NR_033535	ENSMUSG00000095959	Gm10845	-	predicted gene 10845	ncRNA	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7361	chr8	84441927	84442127	+	1.04392	NA	intron (NM_001252060, intron 1 of 47)	intron (NM_001252060, intron 1 of 47)	26663	NM_001252061	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding	0.000000	0.582090			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6437	chr6	49055587	49055787	+	1.04392	NA	exon (NM_053110, exon 10 of 11)	exon (NM_053110, exon 10 of 11)	-18108	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.010000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-242	chr13	52636266	52636466	+	1.04392	NA	intron (NM_001198977, intron 9 of 13)	intron (NM_001198977, intron 9 of 13)	39484	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding	0.010000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-287	chr1	97622701	97622901	+	1.04392	NA	Intergenic	Intergenic	38875	NM_001355073	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6750	chr6	140310291	140310491	+	1.04392	NA	Intergenic	Intergenic	-113708	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5524	chr4	67977861	67978061	+	1.04392	NA	Intergenic	Intergenic	344000	NR_151548	102633975		NR_151548		Gm12911	-	predicted gene 12911	ncRNA	0.005000	0.388060			59(ATAATCAAGACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5999	chr5	66385808	66386008	+	1.04392	NA	intron (NM_001201413, intron 9 of 16)	MLT1H|LTR|ERVL-MaLR	-48243	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-758	chr10	30551910	30552110	+	1.04392	NA	intron (NM_028604, intron 11 of 12)	Lx7|LINE|L1	48690	NM_028604	73681	Mm.294503	NM_028604	ENSMUSG00000019792	Trmt11	2410075D05Rik|3110045I18Rik|AW213713	tRNA methyltransferase 11	protein-coding	0.005000	0.378109			-71(CTATTCTTTTGCATAT,+,0.00),1(TTATTTTTTTTTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-734	chr6	30491562	30491762	+	1.04392	NA	intron (NM_178625, intron 10 of 14)	intron (NM_178625, intron 10 of 14)	18111	NM_001347087	72649	Mm.45418	NM_178625	ENSMUSG00000029782	Tmem209	2700094F01Rik|AI428435	transmembrane protein 209	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4802	chr2	173833708	173833908	+	1.04392	NA	Intergenic	Intergenic	96237	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding	0.015000	0.572139			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-895	chr9	115828637	115828837	+	1.04392	NA	Intergenic	MYSERV6-int|LTR|ERVK	-80718	NM_028638	73748	Mm.485018	NM_028638	ENSMUSG00000056880	Gadl1	1110027M19Rik|ADC|CSADC	glutamate decarboxylase-like 1	protein-coding	0.000000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-27	chr1	97622692	97622892	+	1.04392	NA	Intergenic	Intergenic	38884	NM_001355073	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7172	chr8	23289125	23289325	+	1.04392	NA	Intergenic	RMER1B|Other|Other	-32145	NM_020585	57437	Mm.196269	NM_020585	ENSMUSG00000015341	Golga7	AB041568|C130038N16Rik|GCP16|GOLGA3AP1|HSPC041|R75586	golgi autoantigen, golgin subfamily a, 7	protein-coding	0.005000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-829	chr8	56616364	56616564	+	1.04392	NA	Intergenic	B3A|SINE|B2	65310	NM_001368348	50753	Mm.251174	NM_015791	ENSMUSG00000038206	Fbxo8	Fbx8	F-box protein 8	protein-coding	0.020000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2411	chr14	27837316	27837516	+	1.04392	NA	intron (NM_177814, intron 3 of 15)	intron (NM_177814, intron 3 of 15)	215009	NM_001347497	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0.000000	0.437811			-4(ATCTGCAAAACAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4072	chr19	34120065	34120265	+	1.04392	NA	intron (NM_023903, intron 9 of 9)	intron (NM_023903, intron 9 of 9)	19222	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7273	chr8	58223650	58223850	+	1.04392	NA	intron (NM_175032, intron 4 of 11)	intron (NM_175032, intron 4 of 11)	477046	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	-	predicted gene 15881	protein-coding	0.010000	0.353234			-64(ATAAACATAAGAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4136	chr19	59072399	59072599	+	1.04392	NA	intron (NM_175172, intron 1 of 14)	intron (NM_175172, intron 1 of 14)	3570	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Shootin1|mKIAA1598	shootin 1	protein-coding	0.005000	0.373134			-22(TTTTCCAAGAGAATTC,-,0.00),57(ATATGCATCGGAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2218	chr13	95332484	95332684	+	1.04392	NA	intron (NM_001302539, intron 1 of 1)	L1M2|LINE|L1	1973	NR_034043	100217450	Mm.442313	NR_034043	ENSMUSG00000088108	Snora47	MBI-115	small nucleolar RNA, H/ACA box 47	snoRNA	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7068	chr7	125785510	125785710	+	1.04392	NA	intron (NM_001358287, intron 5 of 26)	intron (NM_001358287, intron 5 of 26)	77740	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7232	chr8	44899507	44899707	+	1.04392	NA	Intergenic	Intergenic	-50601	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding	0.030000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4637	chr2	135067656	135067856	+	1.04392	NA	intron (NM_001145830, intron 3 of 31)	L1M4|LINE|L1	147860	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1821	chr12	93669587	93669787	+	1.04385	NA	Intergenic	MLTR25A|LTR|ERVK	-224864	NR_126436	75295	Mm.243878	NR_126436	ENSMUSG00000113164	4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-873	chr10	68537093	68537293	+	1.04385	NA	intron (NM_028491, intron 1 of 7)	intron (NM_028491, intron 1 of 7)	4682	NM_028491	73287	Mm.141830	NM_028491	ENSMUSG00000019945	Cabcoco1	1700040L02Rik	ciliary associated calcium binding coiled-coil 1	protein-coding	0.020000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3544	chr17	60396433	60396633	+	1.04375	NA	Intergenic	Intergenic	-1383211	NM_001368393	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.005000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3433	chr17	15885842	15886042	+	1.04348	NA	Intergenic	Intergenic	-59356	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding	0.005000	0.348259			19(CCTTTGTGCTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3724	chr18	17418956	17419156	+	1.04348	NA	Intergenic	Intergenic	161934	NR_045374	75162	Mm.60874	NR_045374	ENSMUSG00000117615	4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3206	chr16	45938273	45938473	+	1.04348	NA	Intergenic	Intergenic	-7233	NR_152227	100503378	Mm.387133	NR_152226	ENSMUSG00000085826	Gm15638	Gm41457	predicted gene 15638	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5949	chr5	51677716	51677916	+	1.04348	NA	Intergenic	Intergenic	-110091	NR_132764	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding	0.005000	0.402985			-3(ATTTACATGTGAATTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5775	chr4	142005387	142005587	+	1.04348	NA	intron (NM_177868, intron 1 of 31)	intron (NM_177868, intron 1 of 31)	6164	NM_177868	329977	Mm.252019	NM_028429	ENSMUSG00000051435	Fhad1	2900090M10Rik|B230311F11	forkhead-associated (FHA) phosphopeptide binding domain 1	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2477	chr14	47931172	47931372	+	1.04348	NA	intron (NR_045959, intron 2 of 3)	L1_Mur3|LINE|L1	32408	NR_045959	73961	Mm.390702	NR_045959	ENSMUSG00000115609	4930447J18Rik	4930425M13Rik	RIKEN cDNA 4930447J18 gene	ncRNA	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8029	chrX	96915034	96915234	+	1.04348	NA	Intergenic	RLTR13D|LTR|ERVK	-157462	NM_001033361	245526	Mm.336164	NM_001033361	ENSMUSG00000031212	Pgr15l	-	G protein-coupled receptor 15-like	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2640	chr14	97784241	97784441	+	1.04348	NA	Intergenic	Lx6|LINE|L1	385424	NM_007826	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund family transcription factor 1	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7148	chr8	10840136	10840336	+	1.04348	NA	Intergenic	Intergenic	42218	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1546	chr12	13456239	13456439	+	1.04348	NA	intron (NM_027706, intron 40 of 51)	intron (NM_027706, intron 40 of 51)	171307	NR_136761	102639399	Mm.122052	NR_136761	ENSMUSG00000113666	Gm35725	-	predicted gene, 35725	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2124	chr13	69691233	69691433	+	1.04348	NA	Intergenic	Intergenic	48564	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding	0.010000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7441	chr8	109012925	109013125	+	1.04348	NA	Intergenic	Intergenic	-62197	NR_126329	628686	Mm.203332	NR_126329	ENSMUSG00000097393	D030068K23Rik	-	RIKEN cDNA D030068K23 gene	ncRNA	0.025000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3466	chr17	30679972	30680172	+	1.04348	NA	intron (NM_013811, intron 18 of 92)	intron (NM_013811, intron 18 of 92)	53136	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding	0.005000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5036	chr3	82365237	82365437	+	1.04348	NA	intron (NM_001356457, intron 4 of 13)	intron (NM_001356457, intron 4 of 13)	7150	NM_001356457	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4792	chr2	170266424	170266624	+	1.04348	NA	Intergenic	B3|SINE|B2	-72471	NR_157067	100502923	Mm.44078	NR_157067	ENSMUSG00000097514	Gm17619	-	predicted gene, 17619	ncRNA	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2687	chr14	109180071	109180271	+	1.04348	NA	Intergenic	Intergenic	-265932	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6235	chr5	141880127	141880327	+	1.04348	NA	intron (NM_177879, intron 5 of 44)	MTD|LTR|ERVL-MaLR	-521270	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|Gm10868|Mnf	forkhead box K1	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4728	chr2	151720491	151720691	+	1.04348	NA	intron (NM_212446, intron 5 of 6)	intron (NM_212446, intron 5 of 6)	18583	NM_001160363	108832	Mm.103494	NM_001160363	ENSMUSG00000044364	Tmem74b	5430405G05Rik	transmembrane protein 74B	protein-coding	0.000000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5037	chr3	82652346	82652546	+	1.04348	NA	Intergenic	Intergenic	-104361	NM_008731	18167	Mm.1433	NM_008731	ENSMUSG00000028004	Npy2r	NPY2-R	neuropeptide Y receptor Y2	protein-coding	0.000000	0.427861			40(ATTTCCAAAAGCAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5114	chr3	109582726	109582926	+	1.04348	NA	intron (NM_020505, intron 19 of 26)	intron (NM_020505, intron 19 of 26)	8819	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding	0.000000	0.348259			-29(TTTATATCATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6948	chr7	87354114	87354314	+	1.04348	NA	intron (NM_001285833, intron 14 of 19)	intron (NM_001285833, intron 14 of 19)	107565	NM_001285835	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8080	chrX	131132550	131132750	+	1.04348	NA	Intergenic	Intergenic	1382908	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2852	chr15	32382681	32382881	+	1.04348	NA	intron (NM_009154, intron 2 of 22)	intron (NM_009154, intron 2 of 22)	137968	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding	0.010000	0.417910		-5(AATTCATATGCAAG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3718	chr18	15447907	15448107	+	1.04348	NA	Intergenic	Intergenic	-37025	NM_001308641	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding	0.005000	0.358209	6(CATGAATTATTTATT,+,0.00),6(CATGAATTATTTATT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7364	chr8	86726025	86726225	+	1.04348	NA	intron (NM_009172, intron 1 of 1)	intron (NM_009172, intron 1 of 1)	-19574	NR_027829	666945	Mm.391806	NR_027829		Gm10638	-	predicted gene 10638	ncRNA	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5772	chr4	141158808	141159008	+	1.04348	NA	intron (NM_172518, intron 1 of 9)	PB1D9|SINE|Alu	10986	NM_172518	213499	Mm.28865	NM_172518	ENSMUSG00000028920	Fbxo42	6720460I06Rik|mKIAA1332	F-box protein 42	protein-coding	0.000000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-584	chr1	179330309	179330509	+	1.04348	NA	intron (NM_027188, intron 5 of 11)	intron (NM_027188, intron 5 of 11)	187632	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3475	chr17	36303071	36303271	+	1.04348	NA	Intergenic	RMER19B|LTR|ERVK	-16750	NM_177923	333715	Mm.246798	NM_177923	ENSMUSG00000023083	H2-M10.2	4.7H	histocompatibility 2, M region locus 10.2	protein-coding	0.010000	0.432836			21(GCATACTCATGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4820	chr2	181764680	181764880	+	1.04348	NA	intron (NM_001171615, intron 1 of 22)	intron (NM_001171615, intron 1 of 22)	1448	NM_001171615	17932	Mm.458718	NM_008665	ENSMUSG00000010505	Myt1	Nzf2|Nzf2a|Nzf2b|Nztf2	myelin transcription factor 1	protein-coding	0.045000	0.597015			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6243	chr5	144040763	144040963	+	1.04348	NA	intron (NM_033039, intron 1 of 4)	intron (NM_033039, intron 1 of 4)	9746	NM_033039	18261	Mm.270533	NM_033039	ENSMUSG00000029618	Ocm	-	oncomodulin	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7623	chr9	42437912	42438112	+	1.04348	NA	intron (NM_001357656, intron 6 of 7)	intron (NM_001357656, intron 6 of 7)	19587	NM_001357657	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7279	chr8	61117794	61117994	+	1.04348	NA	intron (NM_175089, intron 28 of 32)	RMER1B|Other|Other	-106277	NM_021506	59009	Mm.27949	NM_021506	ENSMUSG00000031642	Sh3rf1	2200003J05Rik|Posh|R75531|Sh3md2	SH3 domain containing ring finger 1	protein-coding	0.000000	0.363184			81(ATTAAAATAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-550	chr1	173965348	173965548	+	1.04348	NA	intron (NM_011940, intron 5 of 6)	intron (NM_011940, intron 5 of 6)	17396	NM_011940	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-26	chr1	9572179	9572379	+	1.04348	NA	intron (NM_001357376, intron 12 of 12)	L1MB4|LINE|L1	24331	NM_001357377	76187	Mm.28514	NM_175236	ENSMUSG00000025911	Adhfe1	6330565B14Rik|AI043035|Adh8|HOT	alcohol dehydrogenase, iron containing, 1	protein-coding	0.000000	0.432836			9(ATTAACAACACAAAGG,-,0.00),64(CCATTGTTTTTATAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6497	chr6	65137715	65137915	+	1.04348	NA	intron (NM_019455, intron 2 of 5)	intron (NM_019455, intron 2 of 5)	6915	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5862	chr5	23466340	23466540	+	1.04348	NA	intron (NM_026984, intron 4 of 25)	intron (NM_026984, intron 4 of 25)	31976	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5861	chr5	23151139	23151339	+	1.04348	NA	intron (NM_029990, intron 2 of 2)	L1MB2|LINE|L1	283114	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2343	chr14	9297892	9298092	+	1.04348	NA	Intergenic	MERVL_2A-int|LTR|ERVL	-586103	NR_030680	100042415	Mm.235938	NR_030680	ENSMUSG00000089686	Mnd1-ps	Gm3833	Mnd1 retrotransposed pseudogene	pseudo	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3056	chr15	99746839	99747039	+	1.04348	NA	intron (NM_028015, intron 3 of 9)	intron (NM_028015, intron 3 of 9)	21321	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding	0.025000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4620	chr2	132593958	132594158	+	1.04348	NA	Intergenic	B2_Mm1t|SINE|B2	-4138	NR_033469	767814	Mm.371752	NR_033468	ENSMUSG00000074783	AU019990	-	expressed sequence AU019990	ncRNA	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1446	chr11	105460034	105460234	+	1.04348	NA	Intergenic	Intergenic	-3399	NM_172568	632687	Mm.121570	NM_172568	ENSMUSG00000078627	March10	4933417C16Rik|AV039223|Rnf190	membrane-associated ring finger (C3HC4) 10	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5572	chr4	83392002	83392202	+	1.04348	NA	Intergenic	MTC|LTR|ERVL-MaLR	-1434	NR_045450	790913	Mm.406752	NR_045450	ENSMUSG00000086321	Gm11413	-	predicted gene 11413	ncRNA	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5549	chr4	76849509	76849709	+	1.04348	NA	intron (NR_160919, intron 8 of 39)	intron (NR_160919, intron 8 of 39)	-505366	NM_001352630	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6004	chr5	67621491	67621691	+	1.04348	NA	3' UTR (NM_009727, exon 36 of 36)	3' UTR (NM_009727, exon 36 of 36)	13708	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding	0.025000	0.462687			6(ATGTACATGACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7242	chr8	48299420	48299620	+	1.04348	NA	intron (NM_011857, intron 15 of 28)	intron (NM_011857, intron 15 of 28)	189507	NM_001161515	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding	0.020000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3042	chr15	95388323	95388523	+	1.04348	NA	intron (NM_001289653, intron 10 of 20)	intron (NM_001289653, intron 10 of 20)	139591	NM_001356951	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2461	chr14	40827671	40827871	+	1.04348	NA	intron (NM_177816, intron 6 of 7)	ID_B1|SINE|B4	65543	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3586	chr17	72429827	72430027	+	1.04348	NA	intron (NM_007439, intron 1 of 28)	intron (NM_007439, intron 1 of 28)	174380	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7720	chr9	72359483	72359683	+	1.04348	NA	intron (NM_146224, intron 20 of 21)	intron (NM_146224, intron 20 of 21)	50284	NR_152222	100502819	Mm.392319	NR_152222	ENSMUSG00000097211	BC065403	A930005F02Rik	cDNA sequence BC065403	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6905	chr7	73743328	73743528	+	1.04257	NA	intron (NM_001162532, intron 1 of 2)	intron (NM_001162532, intron 1 of 2)	3121	NM_001162532	100038347	Mm.425464	NM_001162532	ENSMUSG00000078670	Fam174b	-	family with sequence similarity 174, member B	protein-coding	0.025000	0.452736			-31(TTTAGCAAAAGAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-674	chr10	4653127	4653327	+	1.04257	NA	intron (NM_007956, intron 1 of 8)	intron (NM_007956, intron 1 of 8)	41238	NR_126357	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding	0.005000	0.323383	34(CATGAAAAATGCATG,+,0.00),34(CATGAAAAATGCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6176	chr5	126104688	126104888	+	1.04257	NA	Intergenic	Intergenic	-254887	NM_001370875	231736		NM_001370875		Gm4868	EG231736	predicted gene 4868	protein-coding	0.010000	0.477612			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-224	chr13	6066328	6066528	+	1.04257	NA	Intergenic	Intergenic	204939	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3258	chr16	57736428	57736628	+	1.04257	NA	intron (NM_007739, intron 1 of 3)	intron (NM_007739, intron 1 of 3)	18209	NM_007739	12837	Mm.130388	NM_007739	ENSMUSG00000068196	Col8a1	Col8a-1	collagen, type VIII, alpha 1	protein-coding	0.000000	0.328358			-87(ATTAGAAAAAGAAATG,-,0.00),33(ATTTGCTTAAAAAATA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-243	chr13	56712193	56712393	+	1.04257	NA	intron (NM_001164042, intron 1 of 6)	intron (NM_001164042, intron 1 of 6)	8625	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding	0.005000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8019	chrX	92640543	92640743	+	1.04256	NA	Intergenic	Intergenic	-41071	NM_173783	215641	Mm.327999	NM_173783	ENSMUSG00000067649	Mageb18	B430216B18Rik	melanoma antigen family B, 18	protein-coding	0.000000	0.393035			-9(ACATTGCTTTGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7305	chr8	68727683	68727883	+	1.04256	NA	intron (NM_001364256, intron 1 of 10)	intron (NM_001364256, intron 1 of 10)	7302	NM_001364256	234356	Mm.334569	NM_172753	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.005000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3747	chr18	24043314	24043514	+	1.04256	NA	Intergenic	B4A|SINE|B4	-22601	NM_021559	59057	Mm.417427	NM_021559	ENSMUSG00000051469	Zfp24	3526401F17Rik|5033419P20Rik|AI480505|AI642085|AL024422|KOX17|ZF-12|Zfp191|Znf24	zinc finger protein 24	protein-coding	0.005000	0.487562			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-833	chr8	68727676	68727876	+	1.04256	NA	intron (NM_001364256, intron 1 of 10)	intron (NM_001364256, intron 1 of 10)	7309	NM_001364256	234356	Mm.334569	NM_172753	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2674	chr14	105257873	105258073	+	1.04256	NA	promoter-TSS (NM_029561)	promoter-TSS (NM_029561)	-650	NM_029561	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3619	chr17	80782839	80783039	+	1.04256	NA	Intergenic	Intergenic	-54914	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-433	chr1	143852937	143853137	+	1.04149	NA	Intergenic	Intergenic	75759	NM_001159866	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding	0.005000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4734	chr2	153140412	153140612	+	1.04149	NA	intron (NM_001172117, intron 10 of 12)	intron (NM_001172117, intron 10 of 12)	-20789	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8075	chrX	129645326	129645526	+	1.04149	NA	Intergenic	Intergenic	-104316	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2427	chr14	31775218	31775418	+	1.04149	NA	intron (NM_001024604, intron 2 of 27)	L1MB8|LINE|L1	55097	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding	0.000000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6973	chr7	92580611	92580811	+	1.04104	NA	intron (NM_001162918, intron 7 of 7)	B3|SINE|B2	19562	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding	0.020000	0.482587			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-246	chr13	63915604	63915804	+	1.04068	NA	Intergenic	Intergenic	100464	NM_001361124	76251	Mm.186610	NM_023507	ENSMUSG00000021470	Ercc6l2	0610007P08Rik|1700019D06Rik|9330134C04Rik|Rad26l|Sr278	excision repair cross-complementing rodent repair deficiency, complementation group 6 like 2	protein-coding	0.000000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-130	chr11	5009832	5010032	+	1.04058	NA	intron (NM_001355659, intron 2 of 22)	intron (NM_001355659, intron 2 of 22)	23108	NM_001243044	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4456	chr2	93252780	93252980	+	1.04058	NA	intron (NM_183180, intron 2 of 9)	MIRc|SINE|MIR	65332	NR_151503	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding	0.020000	0.388060			-71(ATTTGCAAAATAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7562	chr9	24839843	24840043	+	1.04058	NA	Intergenic	L1MC|LINE|L1	-65640	NM_020496	57246	Mm.31452	NM_020496	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7152	chr8	11807063	11807263	+	1.04058	NA	intron (NM_001113518, intron 8 of 20)	intron (NM_001113518, intron 8 of 20)	-33358	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding	0.000000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-864	chr9	27616890	27617090	+	1.04058	NA	Intergenic	Intergenic	219778	NM_001305058	75469	Mm.45824	NM_029299	ENSMUSG00000031991	Spata19	1700001L23Rik|AV047838|spergen-1	spermatogenesis associated 19	protein-coding	0.005000	0.358209			27(AAATGCTCATGCTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-813	chr7	129026135	129026335	+	1.04058	NA	Intergenic	Intergenic	-230859	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7879	chr9	110405134	110405334	+	1.04058	NA	intron (NM_001081043, intron 1 of 24)	URR1B|DNA|hAT-Charlie	2976	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3141	chr16	28902410	28902610	+	1.04058	NA	intron (NM_177718, intron 1 of 1)	intron (NM_177718, intron 1 of 1)	27188	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1174	chr11	16607909	16608109	+	1.04058	NA	Intergenic	RLTR13D6|LTR|ERVK	-99525	NM_001109971	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2903	chr15	45222040	45222240	+	1.03925	NA	Intergenic	L1M2|LINE|L1	-107206	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding	0.000000	0.308458			41(ATTTCAATAATAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2951	chr15	59598936	59599136	+	1.03925	NA	intron (NM_026746, intron 6 of 6)	intron (NM_026746, intron 6 of 6)	-49618	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding	0.010000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3167	chr16	34457577	34457777	+	1.03925	NA	intron (NM_177357, intron 1 of 59)	intron (NM_177357, intron 1 of 59)	56350	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6257	chr5	148857569	148857769	+	1.03925	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	70978	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding	0.010000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4981	chr3	65101604	65101804	+	1.03925	NA	intron (NM_001357358, intron 1 of 13)	L1MB1|LINE|L1	-7310	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding	0.000000	0.303483			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-691	chr5	91179634	91179834	+	1.03925	NA	Intergenic	Intergenic	40135	NM_009704	11839	Mm.8039	NM_009704	ENSMUSG00000029378	Areg	AR|Mcub|Sdgf	amphiregulin	protein-coding	0.000000	0.378109	65(CATAAATTTTGCATA,+,0.00),65(CATAAATTTTGCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4548	chr2	118208695	118208895	+	1.03925	NA	intron (NM_027759, intron 10 of 10)	intron (NM_027759, intron 10 of 10)	48171	NM_027759	71313	Mm.85046	NM_027759	ENSMUSG00000027344	Fsip1	1700012M13Rik|4933432K11Rik	fibrous sheath-interacting protein 1	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1347	chr11	72954387	72954587	+	1.03925	NA	Intergenic	Intergenic	-6682	NM_001163336	53313	Mm.6306	NM_016745	ENSMUSG00000020788	Atp2a3	SERCA3b|Serca3	ATPase, Ca++ transporting, ubiquitous	protein-coding	0.010000	0.502488			-34(ATTTCCAAGGCAAATC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4201	chr2	20448374	20448574	+	1.03925	NA	intron (NM_001081006, intron 2 of 21)	intron (NM_001081006, intron 2 of 21)	-61573	NM_178059	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7153	chr8	11930401	11930601	+	1.03925	NA	Intergenic	Intergenic	89980	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding	0.010000	0.452736			-33(CCATTATCTTGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6375	chr6	30491437	30491637	+	1.03925	NA	intron (NM_178625, intron 10 of 14)	intron (NM_178625, intron 10 of 14)	18236	NM_001347087	72649	Mm.45418	NM_178625	ENSMUSG00000029782	Tmem209	2700094F01Rik|AI428435	transmembrane protein 209	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4922	chr3	42240200	42240400	+	1.03925	NA	Intergenic	Intergenic	497682	NM_001099785	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6453	chr6	53075006	53075206	+	1.03925	NA	Intergenic	Intergenic	-6482	NM_173406	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding	0.025000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2361	chr14	12294104	12294304	+	1.03925	NA	intron (NM_178141, intron 3 of 4)	Tigger7|DNA|TcMar-Tigger	10001	NM_001284386	218734	Mm.44068	NM_146051	ENSMUSG00000033111	3830406C13Rik	-	RIKEN cDNA 3830406C13 gene	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-715	chr10	18999614	18999814	+	1.03925	NA	Intergenic	RLTR13G|LTR|ERVK	12249	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5074	chr3	96427375	96427575	+	1.03925	NA	Intergenic	Intergenic	-12642	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA	0.015000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-367	chr16	34457525	34457725	+	1.03925	NA	intron (NM_177357, intron 1 of 59)	intron (NM_177357, intron 1 of 59)	56402	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3666	chr17	90717921	90718121	+	1.03925	NA	intron (NM_001346957, intron 3 of 18)	MLTR11A|LTR|ERVK	75455	NR_136930	102634634		NR_136930		Gm20491	-	enolase 1, alpha non-neuron pseudogene	pseudo	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3982	chr18	85503966	85504166	+	1.03925	NA	Intergenic	RLTR13D6|LTR|ERVK	551950	NM_001367965	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding	0.015000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-261	chr13	92896686	92896886	+	1.03925	NA	Intergenic	RLTR13D2|LTR|ERVK	52018	NM_001162945	382793	Mm.296770	NM_001162945	ENSMUSG00000021704	Mtx3	4930470O13Rik|AA409304|AI853833|AU067765|EG624619|Gm1194|Gm6514	metaxin 3	protein-coding	0.000000	0.407960	-56(CATGAATAATGCAAT,+,0.00),-56(CATGAATAATGCAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1976	chr13	20600332	20600532	+	1.03925	NA	intron (NM_080288, intron 21 of 21)	intron (NM_080288, intron 21 of 21)	127442	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.025000	0.452736			18(GTTACCATAACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-241	chr1	84847698	84847898	+	1.03925	NA	intron (NM_025386, intron 1 of 3)	intron (NM_025386, intron 1 of 3)	7957	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding	0.015000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7388	chr8	96047794	96047994	+	1.03925	NA	Intergenic	Intergenic	-159493	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding	0.010000	0.512438			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-548	chr2	181244865	181245065	+	1.03872	NA	Intergenic	Intergenic	-2938	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2246	chr13	100103020	100103220	+	1.03872	NA	intron (NM_001081061, intron 1 of 38)	intron (NM_001081061, intron 1 of 38)	950	NM_001081061	544971	Mm.288546	NM_001081061	ENSMUSG00000049658	Bdp1	AI662220|AW049390|AW456745|B130055N23Rik|G630013P12Rik|TAF3B1|TFC5|TFIIIB150|TFIIIB90|Tfnr|mKIAA1241	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding	0.025000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2521	chr14	63523110	63523310	+	1.03872	NA	TTS (NM_177594)	TTS (NM_177594)	-14118	NM_021480	58865	Mm.354229	NM_021480	ENSMUSG00000021953	Tdh	-	L-threonine dehydrogenase	protein-coding	0.030000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1632	chr12	44091731	44091931	+	1.03872	NA	Intergenic	Lx8|LINE|L1	118237	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding	0.000000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1792	chr12	86673472	86673672	+	1.03843	NA	Intergenic	Intergenic	-5128	NM_177354	238328	Mm.216101	NM_177354	ENSMUSG00000021256	Vash1	AI834978|D930046M13Rik|G630009D10Rik|TTCP 1	vasohibin 1	protein-coding	0.015000	0.472637	19(TATTCATAATTAATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6878	chr7	65082220	65082420	+	1.03843	NA	intron (NM_183087, intron 1 of 9)	L1MB4|LINE|L1	74208	NM_183087	70638	Mm.441986	NM_183087	ENSMUSG00000030518	Fam189a1	5730507A09Rik|AW047451	family with sequence similarity 189, member A1	protein-coding	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5413	chr4	32418710	32418910	+	1.03843	NA	intron (NM_001109661, intron 1 of 4)	intron (NM_001109661, intron 1 of 4)	1375	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding	0.020000	0.412935			-91(ATGTTGTCATGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2032	chr13	37428530	37428730	+	1.03843	NA	Intergenic	Intergenic	83285	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4311	chr2	54158868	54159068	+	1.03843	NA	Intergenic	Intergenic	-73416	NM_023396	67874	Mm.27086	NM_023396	ENSMUSG00000075334	Rprm	2410012A13Rik|Reprimo	reprimo, TP53 dependent G2 arrest mediator candidate	protein-coding	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3357	chr16	85393590	85393790	+	1.03843	NA	Intergenic	RMER20A|LTR|ERVK	156683	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5538	chr4	74280142	74280342	+	1.03843	NA	intron (NM_001356561, intron 2 of 20)	intron (NM_001356561, intron 2 of 20)	28363	NM_001356561	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1732	chr12	72373181	72373381	+	1.03843	NA	intron (NM_153457, intron 1 of 8)	intron (NM_153457, intron 1 of 8)	35773	NM_153457	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7366	chr8	88011447	88011647	+	1.03843	NA	Intergenic	Intergenic	-51952	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6853	chr7	52732276	52732476	+	1.03843	NA	Intergenic	RLTR13D6|LTR|ERVK	-716660	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0.000000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2725	chr14	120353152	120353352	+	1.03843	NA	intron (NM_001360380, intron 2 of 7)	intron (NM_001360380, intron 2 of 7)	46800	NM_001360376	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind like splicing factor 2	protein-coding	0.015000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6153	chr5	111681392	111681592	+	1.03843	NA	Intergenic	Intergenic	80236	NR_045832	269683	Mm.136946	NM_207252	ENSMUSG00000085271	E130006D01Rik	Gm16018|Gm681	RIKEN cDNA E130006D01 gene	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8071	chrX	127631876	127632076	+	1.03843	NA	Intergenic	RMER15|LTR|ERVL	104578	NM_001281537	73934	Mm.159093	NM_001281537	ENSMUSG00000043569	Cldn34c4	4930412D23Rik	claudin 34C4	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7901	chr9	117581217	117581417	+	1.03843	NA	intron (NM_001172121, intron 1 of 14)	Charlie16a|DNA|hAT-Charlie	48596	NM_001172121	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding	0.030000	0.467662			-85(GCTTTGTCTTACTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-293	chr1	100381935	100382135	+	1.03843	NA	intron (NM_172851, intron 17 of 23)	RLTR25B|LTR|ERVK	609634	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6192	chr5	131039171	131039371	+	1.03843	NA	intron (NM_145218, intron 5 of 10)	intron (NM_145218, intron 5 of 10)	268251	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Galnt17	AA388321|E330012B09Rik|Galnt19|Gcap8|Wbscr17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.020000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4145	chr19	61118720	61118920	+	1.03843	NA	exon (NM_001309216, exon 4 of 4)	exon (NM_001309216, exon 4 of 4)	22020	NR_131955	414758	Mm.100056	NM_001001737	ENSMUSG00000074733	Zfp950	5830428H23Rik|AU016073|BC055757|Gm34518|Zfp826|mszf84	zinc finger protein 950	protein-coding	0.000000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1838	chr12	98779252	98779452	+	1.03843	NA	intron (NM_029334, intron 11 of 16)	intron (NM_029334, intron 11 of 16)	8330	NM_001160108	75553	Mm.25549	NM_029334	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding	0.010000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2753	chr15	3666972	3667172	+	1.03843	NA	Intergenic	Intergenic	-83720	NM_010284	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3446	chr17	26110176	26110376	+	1.03843	NA	Intergenic	Intergenic	-3040	NM_021793	60455	Mm.304656	NM_021793	ENSMUSG00000024180	Tmem8	AW490096|GPI-PLA2|M83|Pgap6|Rxylt1|Tmem8a	transmembrane protein 8	protein-coding	0.010000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1474	chr11	112412867	112413067	+	1.03843	NA	Intergenic	Intergenic	298389	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2351	chr14	11348291	11348491	+	1.03843	NA	Intergenic	MYSERV6-int|LTR|ERVK	65914	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA	0.000000	0.308458			47(CTACTTTTTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7740	chr9	77455871	77456071	+	1.03843	NA	intron (NM_172528, intron 7 of 13)	B3|SINE|B2	-56555	NR_040378	70487	Mm.58958	NR_040378	ENSMUSG00000099170	5730403I07Rik	-	RIKEN cDNA 5730403I07 gene	ncRNA	0.025000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6728	chr6	136117507	136117707	+	1.03843	NA	intron (NM_001363750, intron 3 of 14)	B3A|SINE|B2	55938	NM_001363750	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|GluRepsilon2|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding	0.000000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5135	chr3	116256742	116256942	+	1.03843	NA	Intergenic	Intergenic	-3358	NM_022427	64378	Mm.40025	NM_022427	ENSMUSG00000068696	Gpr88	AW061286|Strg	G-protein coupled receptor 88	protein-coding	0.005000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3306	chr16	70836856	70837056	+	1.03843	NA	Intergenic	Intergenic	220531	NR_040474	52645	Mm.188475	NR_040474	ENSMUSG00000116792	D16Ertd519e	-	DNA segment, Chr 16, ERATO Doi 519, expressed	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7797	chr9	87419484	87419684	+	1.03843	NA	Intergenic	Intergenic	-164052	NM_199316	382090	Mm.335338	NM_199316	ENSMUSG00000056919	Cep162	4922501C03Rik|mKIAA1009	centrosomal protein 162	protein-coding	0.025000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6542	chr6	80491092	80491292	+	1.03843	NA	intron (NM_001134743, intron 2 of 2)	intron (NM_001134743, intron 2 of 2)	471549	NM_001347261	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0.005000	0.318408			64(TCATTCTCATTCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6762	chr6	145061666	145061866	+	1.03843	NA	intron (NM_007532, intron 1 of 10)	RMER16B2|LTR|ERVK	-12954	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5894	chr5	32472632	32472832	+	1.03843	NA	intron (NM_172707, intron 1 of 7)	ORR1C2-int|LTR|ERVL-MaLR	13762	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1 catalytic subunit beta	protein-coding	0.010000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-52	chr1	19427448	19427648	+	1.03843	NA	Intergenic	Intergenic	215494	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5251	chr3	145980314	145980514	+	1.03843	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-7456	NM_001166064	214804	Mm.268854	NM_001166064	ENSMUSG00000036863	Syde2	C430017H16Rik	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	protein-coding	0.015000	0.517413			-81(GTTTGAATAAAAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2717	chr14	118087537	118087737	+	1.03843	NA	Intergenic	Intergenic	-35391	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding	0.020000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3960	chr18	81797014	81797214	+	1.03843	NA	Intergenic	Intergenic	194966	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA	0.030000	0.631841			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6970	chr7	92235721	92235921	+	1.03843	NA	intron (NM_001243047, intron 1 of 10)	(GGGAGA)n|Simple_repeat|Simple_repeat	851	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs large MAGUK scaffold protein 2	protein-coding	0.030000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4178	chr2	12760085	12760285	+	1.03843	NA	Intergenic	Intergenic	-163856	NM_001305436	19212	Mm.229322	NM_008961	ENSMUSG00000026730	Pter	AI790318|Mpr56-1	phosphotriesterase related	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3758	chr18	26635490	26635690	+	1.03843	NA	Intergenic	Intergenic	-881433	NM_001362332	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding	0.005000	0.298507			-50(GTTTTCTAATGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3674	chr17	94247404	94247604	+	1.03843	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	502515	NM_001357136	76781	Mm.139146	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-162	chr1	55666367	55666567	+	1.03843	NA	intron (NM_001114663, intron 1 of 5)	intron (NM_001114663, intron 1 of 5)	260521	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding	0.015000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5022	chr3	76114640	76114840	+	1.03843	NA	intron (NM_001253719, intron 1 of 15)	intron (NM_001253719, intron 1 of 15)	39157	NM_001253719	213262	Mm.379337	NM_178673	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0.000000	0.263682			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6023	chr5	72411778	72411978	+	1.03843	NA	intron (NM_016869, intron 5 of 21)	intron (NM_016869, intron 5 of 21)	92330	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin, serine peptidase	protein-coding	0.020000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1304	chr11	60346628	60346828	+	1.03843	NA	intron (NM_001359810, intron 1 of 12)	MER5A|DNA|hAT-Charlie	6177	NM_153080	216810	Mm.218875	NM_153080	ENSMUSG00000000538	Tom1l2	2900016I08Rik|A730055F12Rik|AU042072|Srebf1	target of myb1-like 2 (chicken)	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2413	chr14	28475197	28475397	+	1.03843	NA	intron (NM_001347497, intron 19 of 19)	Lx6|LINE|L1	-30176	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding	0.010000	0.447761		3(TATGCATATGAATG,+,0.00),3(TATGCATATGAATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6258	chr5	148970668	148970868	+	1.03843	NA	Intergenic	RLTR11A|LTR|ERVK	20518	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA	0.010000	0.412935			-34(ATTAACATTATAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5569	chr4	82872267	82872467	+	1.03843	NA	Intergenic	Intergenic	-12694	NR_149737	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding	0.000000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8129	chrX	157368835	157369035	+	1.03843	NA	intron (NM_011077, intron 5 of 21)	intron (NM_011077, intron 5 of 21)	46351	NM_011077	18675	Mm.2529	NM_011077	ENSMUSG00000057457	Phex	Gy|HPDR|HPDR1|Hyp|PEX	phosphate regulating endopeptidase homolog, X-linked	protein-coding	0.005000	0.333333			-23(ATTTGAAAGACAATCT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-489	chr1	159286112	159286312	+	1.03843	NA	intron (NM_011931, intron 10 of 19)	intron (NM_011931, intron 10 of 19)	-7561	NR_144489	100846986		NR_144489		Pou5f1-rs1	Gm21053|Oct4P2|Otf-3rs|Otf3-rs1|Otf3a	POU domain, class 5, transcription factor 1, related sequence 1	pseudo	0.005000	0.293532			-22(GATTTCTTATTTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3568	chr17	67412551	67412751	+	1.03843	NA	Intergenic	Intergenic	-58160	NM_001357625	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding	0.015000	0.393035		-82(GCTGCATATTCATG,+,0.00),-82(GCTGCATATTCATG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6777	chr6	148337799	148337999	+	1.03843	NA	intron (NM_198967, intron 5 of 19)	RLTR11A2|LTR|ERVK	-16757	NR_003634	66184	Mm.391542	NM_025405	ENSMUSG00000063171	Rps4l	1110033J19Rik|AA407494|Rps4y2	ribosomal protein S4-like	pseudo	0.000000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8125	chrX	153696688	153696888	+	1.03843	NA	promoter-TSS (NM_175429)	promoter-TSS (NM_175429)	-508	NM_175429	207474	Mm.271572	NM_175429	ENSMUSG00000041633	Kctd12b	9530071H11Rik|B430319H24Rik	potassium channel tetramerisation domain containing 12b	protein-coding	0.000000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7151	chr8	11089475	11089675	+	1.03843	NA	Intergenic	Intergenic	-80646	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding	0.030000	0.616915			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7549	chr9	21871085	21871285	+	1.03843	NA	Intergenic	Intergenic	-18550	NM_177030	319899	Mm.128153	NM_177030	ENSMUSG00000032198	Dock6	2410095B20Rik|4931431C02Rik|C330023D02Rik|mKIAA1395	dedicator of cytokinesis 6	protein-coding	0.040000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1009	chr10	107947937	107948137	+	1.03843	NA	intron (NR_131147, intron 1 of 5)	MLT1B|LTR|ERVL-MaLR	1392	NR_131147	628877	Mm.363120	NR_131147	ENSMUSG00000112910	Gm29685	-	predicted gene, 29685	ncRNA	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-701	chr10	13035301	13035501	+	1.03843	NA	Intergenic	Intergenic	26951	NM_175102	66125	Mm.29743	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	splicing factor 3b, subunit 5	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5232	chr3	139022698	139022898	+	1.03843	NA	intron (NM_001356388, intron 2 of 13)	intron (NM_001356388, intron 2 of 13)	52403	NM_001286759	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding	0.015000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5641	chr4	99663460	99663660	+	1.03843	NA	Intergenic	Intergenic	7261	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding	0.045000	0.597015			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3736	chr18	21089007	21089207	+	1.03843	NA	intron (NM_008586, intron 8 of 14)	intron (NM_008586, intron 8 of 14)	16763	NM_008586	17288	Mm.2682	NM_008586	ENSMUSG00000024313	Mep1b	Mep-1b	meprin 1 beta	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4423	chr2	79908755	79908955	+	1.03843	NA	promoter-TSS (NM_001009979)	promoter-TSS (NM_001009979)	-456	NM_001009978	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2711	chr14	117073562	117073762	+	1.03843	NA	intron (NM_001079844, intron 1 of 9)	intron (NM_001079844, intron 1 of 9)	148365	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding	0.020000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-292	chr14	61161686	61161886	+	1.03816	NA	intron (NM_172809, intron 2 of 9)	intron (NM_172809, intron 2 of 9)	23329	NM_015788	50720	Mm.440703	NM_015788	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik	sacsin	protein-coding	0.020000	0.457711			-19(CCTTTCTAATGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5193	chr3	131190567	131190767	+	1.03816	NA	intron (NM_001276402, intron 5 of 9)	intron (NM_001276402, intron 5 of 9)	77876	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding	0.010000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-655	chr4	144994157	144994357	+	1.03770	NA	intron (NM_001276465, intron 67 of 69)	intron (NM_001276465, intron 67 of 69)	101120	NM_001357274	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6095	chr5	93131847	93132047	+	1.03668	NA	intron (NM_001009818, intron 1 of 9)	intron (NM_001009818, intron 1 of 9)	38531	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding	0.005000	0.417910			36(ATTTTTGCATGGAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-517	chr2	115230116	115230316	+	1.03668	NA	Intergenic	Intergenic	114064	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	ncRNA	0.005000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3111	chr16	22434810	22435010	+	1.03651	NA	intron (NM_001358428, intron 5 of 12)	intron (NM_001358428, intron 5 of 12)	3458	NM_001358428	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding	0.015000	0.497512			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-477	chr2	42184376	42184576	+	1.03651	NA	intron (NM_053011, intron 2 of 90)	RLTR21|LTR|ERVK	263092	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7079	chr7	129026074	129026274	+	1.03651	NA	Intergenic	Intergenic	-230920	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding	0.005000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-520	chr1	165609587	165609787	+	1.03651	NA	intron (NM_001001880, intron 1 of 4)	intron (NM_001001880, intron 1 of 4)	24854	NM_001347128	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding	0.020000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-759	chr6	84796695	84796895	+	1.03651	NA	intron (NM_177077, intron 18 of 21)	intron (NM_177077, intron 18 of 21)	-202887	NM_001177713	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4268	chr2	42184352	42184552	+	1.03651	NA	intron (NM_053011, intron 2 of 90)	RLTR21|LTR|ERVK	263116	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA	0.000000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-17	chr1	7263891	7264091	+	1.03651	NA	Intergenic	ORR1C2-int|LTR|ERVL-MaLR	175071	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4661	chr2	137939629	137939829	+	1.03651	NA	Intergenic	MER2|DNA|TcMar-Tigger	-316855	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding	0.010000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-716	chr5	144263897	144264097	+	1.03651	NA	TTS (NM_025833)	TTS (NM_025833)	8772	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding	0.025000	0.616915			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-198	chr12	79704857	79705057	+	1.03651	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	219776	NR_131075	77290	Mm.395042	NR_131073	ENSMUSG00000112765	9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA	0.005000	0.373134			-15(GCTTTGACATGGTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-617	chr4	49720188	49720388	+	1.03651	NA	intron (NM_001033351, intron 3 of 8)	intron (NM_001033351, intron 3 of 8)	-38305	NM_001004025	19059	Mm.46125	NM_001004025	ENSMUSG00000028310	Ppp3r2	CaNB2|CnB2	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type II)	protein-coding	0.005000	0.477612			-81(GTATGGTTTTTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6410	chr6	39373245	39373445	+	1.03651	NA	intron (NM_001361617, intron 1 of 16)	L2|LINE|L2	4090	NR_155076	72144	Mm.482167	NM_028123	ENSMUSG00000029924	Slc37a3	2610507O21Rik|AU044904	solute carrier family 37 (glycerol-3-phosphate transporter), member 3	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-697	chr5	103288972	103289172	+	1.03651	NA	intron (NR_040699, intron 1 of 6)	B1_Mur2|SINE|Alu	9957	NR_040699	74624	Mm.389662	NR_040699	ENSMUSG00000104956	4930429D17Rik	-	RIKEN cDNA 4930429D17 gene	ncRNA	0.000000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-402	chr17	60866583	60866783	+	1.03651	NA	Intergenic	Intergenic	-1853361	NM_001368393	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.010000	0.308458			-86(ATTTCAATTACAATAA,-,0.00),-39(TCTTTTTCTTGAAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1764	chr12	79704828	79705028	+	1.03651	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	219805	NR_131075	77290	Mm.395042	NR_131073	ENSMUSG00000112765	9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA	0.010000	0.402985			14(GCTTTGACATGGTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-660	chr1	194593510	194593710	+	1.03555	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-26219	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding	0.010000	0.437811			-44(ATTTGAATAGGAATGC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-439	chr18	44364792	44364992	+	1.03555	NA	Intergenic	Intergenic	-15608	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding	0.015000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-746	chr6	59358496	59358696	+	1.03555	NA	intron (NM_183183, intron 1 of 1)	intron (NM_183183, intron 1 of 1)	67710	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0.005000	0.353234			-13(TTTTTGTTTTTCACAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-542	chr2	165558276	165558476	+	1.03553	NA	Intergenic	Intergenic	-36652	NM_001271963	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.000000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6742	chr6	137946182	137946382	+	1.03542	NA	Intergenic	Intergenic	133634	NM_177787	277898	Mm.269823	NM_177787	ENSMUSG00000044378	Slc15a5	9830102E05Rik	solute carrier family 15, member 5	protein-coding	0.015000	0.427861		51(TATAAATATACATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6429	chr6	45988324	45988524	+	1.03542	NA	intron (NM_001004357, intron 4 of 23)	intron (NM_001004357, intron 4 of 23)	928363	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.005000	0.298507	56(AATGCATTTTTCATA,+,0.00),56(AATGCATTTTTCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5333	chr4	8730343	8730543	+	1.03504	NA	intron (NM_001277149, intron 1 of 37)	intron (NM_001277149, intron 1 of 37)	-20881	NM_001355382	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding	0.030000	0.522388			-99(TGCTTTTCATGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7896	chr9	115805637	115805837	+	1.03504	NA	Intergenic	Intergenic	-103718	NM_028638	73748	Mm.485018	NM_028638	ENSMUSG00000056880	Gadl1	1110027M19Rik|ADC|CSADC	glutamate decarboxylase-like 1	protein-coding	0.005000	0.412935			-25(ATTTCCATAACAATAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-767	chr6	106455449	106455649	+	1.03504	NA	intron (NM_001109749, intron 8 of 25)	intron (NM_001109749, intron 8 of 25)	293488	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding	0.005000	0.363184			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-87	chr10	36520432	36520632	+	1.03504	NA	intron (NM_001081208, intron 1 of 3)	intron (NM_001081208, intron 1 of 3)	13725	NM_001081208	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0.005000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1396	chr11	88394636	88394836	+	1.03486	NA	intron (NM_054043, intron 8 of 13)	intron (NM_054043, intron 8 of 13)	41963	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA	0.025000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4435	chr2	84919111	84919311	+	1.03486	NA	Intergenic	ID_B1|SINE|B4	-17435	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding	0.000000	0.482587			-31(TAAATGTTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4970	chr3	60957372	60957572	+	1.03486	NA	Intergenic	Intergenic	-45313	NM_001282016	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	purinergic receptor P2Y, G-protein coupled 1	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2647	chr14	99107979	99108179	+	1.03486	NA	intron (NM_029320, intron 4 of 17)	intron (NM_029320, intron 4 of 17)	-8309	NM_028315	72662	Mm.163339	NM_028315	ENSMUSG00000033166	Dis3	2810028N01Rik	DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease	protein-coding	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6128	chr5	104229127	104229327	+	1.03486	NA	Intergenic	L1MDa|LINE|L1	26610	NM_016779	13406	Mm.199008	NM_016779	ENSMUSG00000029307	Dmp1	AG1|AV020965|DMP-1|Dmp|PP	dentin matrix protein 1	protein-coding	0.005000	0.358209			-2(ATTTAAAAAACAACTA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3424	chr17	14211400	14211600	+	1.03486	NA	Intergenic	Intergenic	-7669	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding	0.020000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-880	chr9	80205968	80206168	+	1.03486	NA	intron (NM_001039546, intron 1 of 32)	intron (NM_001039546, intron 1 of 32)	41034	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Myo6<rsv>|Tlc|rsv|sv	myosin VI	protein-coding	0.010000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-312	chr14	99107925	99108125	+	1.03486	NA	intron (NM_029320, intron 4 of 17)	intron (NM_029320, intron 4 of 17)	-8255	NM_028315	72662	Mm.163339	NM_028315	ENSMUSG00000033166	Dis3	2810028N01Rik	DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-891	chr10	73836733	73836933	+	1.03486	NA	intron (NM_001142747, intron 1 of 26)	intron (NM_001142747, intron 1 of 26)	14966	NM_001142742	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding	0.000000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-559	chr3	60957389	60957589	+	1.03486	NA	Intergenic	Intergenic	-45296	NM_001282016	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	purinergic receptor P2Y, G-protein coupled 1	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7197	chr8	34372745	34372945	+	1.03486	NA	Intergenic	Intergenic	-206133	NR_105820	102465211		NR_105820	ENSMUSG00000098785	Mir6395	Gm27561|mmu-mir-6395	microRNA 6395	ncRNA	0.020000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-754	chr6	80760773	80760973	+	1.03486	NA	intron (NM_001134743, intron 2 of 2)	intron (NM_001134743, intron 2 of 2)	741230	NM_001347261	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0.005000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-602	chr3	157348546	157348746	+	1.03486	NA	Intergenic	Intergenic	185444	NR_152231	381498	Mm.402095	NR_152231	ENSMUSG00000105834	4930592C13Rik	Gm1657|Gm43159	RIKEN cDNA 4930592C13 gene	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3164	chr16	34195277	34195477	+	1.03486	NA	intron (NM_177357, intron 25 of 59)	intron (NM_177357, intron 25 of 59)	-228339	NM_001348087	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1651	chr12	50765609	50765809	+	1.03486	NA	Intergenic	Intergenic	-116486	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5502	chr4	62607343	62607543	+	1.03486	NA	intron (NM_019492, intron 6 of 19)	intron (NM_019492, intron 6 of 19)	-12229	NM_001081650	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding	0.030000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3800	chr18	38918655	38918855	+	1.03372	NA	promoter-TSS (NM_010197)	promoter-TSS (NM_010197)	-56	NM_010197	14164	Mm.241282	NM_010197	ENSMUSG00000036585	Fgf1	Dffrx|Fam|Fgf-1|Fgfa	fibroblast growth factor 1	protein-coding	0.030000	0.656716			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4297	chr2	50724838	50725038	+	1.03372	NA	Intergenic	Intergenic	-184746	NR_033595	227885	Mm.301654	NR_033595	ENSMUSG00000083270	Gm13498	-	heat shock protein 90 alpha (cytosolic), class B member 1 pseudogene	pseudo	0.000000	0.253731			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7995	chrX	77568050	77568250	+	1.03372	NA	intron (NM_020601, intron 1 of 15)	intron (NM_020601, intron 1 of 15)	56923	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding	0.005000	0.482587			69(CTATTGTCGTGCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1420	chr11	96319163	96319363	+	1.03372	NA	intron (NM_010459, intron 1 of 1)	intron (NM_010459, intron 1 of 1)	996	NM_010459	15412	Mm.3546	NM_010459	ENSMUSG00000038692	Hoxb4	Hox-2.6	homeobox B4	protein-coding	0.075000	0.621891			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-624	chr1	187943770	187943970	+	1.03372	NA	intron (NM_001357534, intron 2 of 7)	intron (NM_001357534, intron 2 of 7)	-53957	NM_001357536	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7888	chr9	113528621	113528821	+	1.03372	NA	intron (NR_040760, intron 1 of 4)	intron (NR_040760, intron 1 of 4)	58431	NR_040760	102688	Mm.394901	NR_040760	ENSMUSG00000109890	AU023762	-	expressed sequence AU023762	ncRNA	0.005000	0.477612	-58(TGTGCATTATGAATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6708	chr6	122519528	122519728	+	1.03372	NA	intron (NM_015776, intron 3 of 9)	intron (NM_015776, intron 3 of 9)	6044	NM_015776	50530	Mm.41931	NM_015776	ENSMUSG00000030116	Mfap5	MAGP-2|MFAP-5	microfibrillar associated protein 5	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4737	chr2	154350946	154351146	+	1.03372	NA	intron (NM_025876, intron 9 of 13)	intron (NM_025876, intron 9 of 13)	21673	NM_025876	66971	Mm.289427	NM_025876	ENSMUSG00000027487	Cdk5rap1	2310066P17Rik	CDK5 regulatory subunit associated protein 1	protein-coding	0.010000	0.368159			-11(TCAATCTTATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6167	chr5	121009455	121009655	+	1.03372	NA	promoter-TSS (NM_011286)	promoter-TSS (NM_011286)	-17	NM_011286	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding	0.070000	0.686567			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7469	chr8	118685852	118686052	+	1.03372	NA	intron (NM_019707, intron 3 of 13)	ORR1D2|LTR|ERVL-MaLR	402341	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2914	chr15	51621610	51621810	+	1.03372	NA	Intergenic	Intergenic	-226100	NR_045092	100502643	Mm.131987	NR_045092	ENSMUSG00000115654	Gm19303	-	predicted gene, 19303	ncRNA	0.015000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5291	chr3	152223790	152223990	+	1.03372	NA	intron (NM_001355373, intron 16 of 19)	intron (NM_001355373, intron 16 of 19)	13468	NM_001355366	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding	0.005000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6766	chr6	146268338	146268538	+	1.03372	NA	intron (NM_019923, intron 37 of 56)	intron (NM_019923, intron 37 of 56)	233785	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding	0.005000	0.348259			-21(GCATTATCATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1750	chr12	76937733	76937933	+	1.03372	NA	3' UTR (NM_008558, exon 5 of 5)	3' UTR (NM_008558, exon 5 of 5)	24415	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding	0.030000	0.497512			-88(TCATTCAGATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7582	chr9	29773181	29773381	+	1.03372	NA	intron (NM_001357597, intron 1 of 8)	intron (NM_001357597, intron 1 of 8)	189988	NM_001357598	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0.015000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-954	chr10	95677798	95677998	+	1.03372	NA	Intergenic	Tigger12|DNA|TcMar-Tigger	-113752	NM_001358996	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP-2|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding	0.025000	0.587065			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6841	chr7	49462370	49462570	+	1.03372	NA	intron (NM_001111016, intron 10 of 38)	intron (NM_001111016, intron 10 of 38)	174365	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding	0.025000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7030	chr7	114090302	114090502	+	1.03372	NA	intron (NM_025846, intron 1 of 5)	intron (NM_025846, intron 1 of 5)	27379	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding	0.005000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8172	chrX	168646172	168646372	+	1.03372	NA	Intergenic	Intergenic	26753	NM_001370793	17692	Mm.24248	NM_010832	ENSMUSG00000031358	Msl3	AU018931|Msl31|Msl3l1	MSL complex subunit 3	protein-coding	0.005000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-290	chr1	97929607	97929807	+	1.03372	NA	intron (NM_001357127, intron 5 of 25)	intron (NM_001357127, intron 5 of 25)	118086	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA	0.005000	0.442786			-65(ATTTAAATGAGTAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1668	chr12	54377209	54377409	+	1.03372	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	14009	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA	0.000000	0.417910			-73(ATTAACATGAAACAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1148	chr11	6840822	6841022	+	1.03372	NA	Intergenic	Intergenic	-120885	NR_046025	626419	Mm.390334	NR_046025	ENSMUSG00000086808	Gm11981	-	predicted gene 11981	ncRNA	0.000000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-491	chr1	159676048	159676248	+	1.03372	NA	intron (NM_022312, intron 1 of 22)	MLT1B|LTR|ERVL-MaLR	152379	NM_022312	21960	Mm.44701	NM_022312	ENSMUSG00000015829	Tnr	J1-tenascin|TN-R|janusin|restrictin	tenascin R	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-780	chr10	39124981	39125181	+	1.03372	NA	intron (NM_001359442, intron 2 of 4)	intron (NM_001359442, intron 2 of 4)	8819	NM_001359442	66337	Mm.45187	NM_183254	ENSMUSG00000051736	Fam229b	1700025K23Rik	family with sequence similarity 229, member B	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5905	chr5	36340082	36340282	+	1.03372	NA	intron (NM_030889, intron 1 of 26)	intron (NM_030889, intron 1 of 26)	38612	NR_106162	102465792		NR_106162	ENSMUSG00000098884	Mir7689	Gm27434|mmu-mir-7689	microRNA 7689	ncRNA	0.025000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2557	chr14	76528345	76528545	+	1.03372	NA	Intergenic	Intergenic	-7590	NR_045660	75789	Mm.159571	NR_045660	ENSMUSG00000097172	4930444M15Rik	-	RIKEN cDNA 4930444M15 gene	ncRNA	0.010000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7676	chr9	59978721	59978921	+	1.03372	NA	intron (NM_172444, intron 10 of 11)	intron (NM_172444, intron 10 of 11)	27527	NM_001101600	665389	Mm.335214	NM_001101600		Gm7616	EG665389	predicted gene 7616	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8000	chrX	84414357	84414557	+	1.03372	NA	intron (NM_007868, intron 48 of 78)	(CAAAA)n|Simple_repeat|Simple_repeat	-633838	NM_001314037	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding	0.010000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2006	chr13	29995366	29995566	+	1.03372	NA	Intergenic	Intergenic	-9403	NM_010093	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding	0.000000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3584	chr17	71947490	71947690	+	1.03372	NA	intron (NM_007439, intron 11 of 28)	intron (NM_007439, intron 11 of 28)	165643	NM_030179	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding	0.035000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7741	chr9	77535911	77536111	+	1.03372	NA	intron (NM_001146048, intron 1 of 13)	intron (NM_001146048, intron 1 of 13)	8048	NM_172528	214345	Mm.28534	NM_172528	ENSMUSG00000032352	Lrrc1	A430093J20Rik|AU016091|D030059I21|mKIAA4018	leucine rich repeat containing 1	protein-coding	0.015000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-493	chr2	72881617	72881817	+	1.03368	NA	Intergenic	Intergenic	-68000	NR_102349	76218	Mm.75260	NR_102348	ENSMUSG00000085427	6430710C18Rik	5033406J01Rik	RIKEN cDNA 6430710C18 gene	ncRNA	0.005000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-144	chr11	42562835	42563035	+	1.03263	NA	intron (NM_001362646, intron 6 of 9)	intron (NM_001362646, intron 6 of 9)	141734	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding	0.025000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4815	chr2	180727713	180727913	+	1.03263	NA	intron (NM_183161, intron 1 of 12)	intron (NM_183161, intron 1 of 12)	2474	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5722	chr4	123625565	123625765	+	1.03263	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	9245	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-866	chr10	68240217	68240417	+	1.03263	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	38409	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding	0.000000	0.407960			-77(ATTTTCAAGACCAAAC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7	chr1	20471253	20471453	+	1.03263	NA	intron (NM_153179, intron 35 of 66)	intron (NM_153179, intron 35 of 66)	114899	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-673	chr10	4652988	4653188	+	1.03223	NA	intron (NM_007956, intron 1 of 8)	intron (NM_007956, intron 1 of 8)	41099	NR_126357	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding	0.000000	0.268657			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2265	chr13	105754220	105754420	+	1.03223	NA	Intergenic	Intergenic	310627	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0.000000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-266	chr13	105754242	105754442	+	1.03223	NA	Intergenic	Intergenic	310649	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0.000000	0.358209			79(TAATTGTAATGCAATT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-397	chr17	50525221	50525421	+	1.03200	NA	intron (NM_013880, intron 1 of 5)	Charlie24|DNA|hAT-Charlie	15774	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding	0.020000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7262	chr8	56478538	56478738	+	1.03151	NA	intron (NR_131020, intron 1 of 2)	Lx6|LINE|L1	6330	NR_131020	75123	Mm.72666	NR_131020	ENSMUSG00000110310	4930518J21Rik	-	RIKEN cDNA 4930518J21 gene	ncRNA	0.005000	0.432836			-25(TTGTTTTTATTTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-248	chr13	68597766	68597966	+	1.03151	NA	intron (NM_027035, intron 1 of 2)	intron (NM_027035, intron 1 of 2)	427	NM_027035	69315	Mm.272795	NM_027035	ENSMUSG00000021534	1700001L19Rik	-	RIKEN cDNA 1700001L19 gene	protein-coding	0.035000	0.606965			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-828	chr8	56478529	56478729	+	1.03151	NA	intron (NR_131020, intron 1 of 2)	Lx6|LINE|L1	6339	NR_131020	75123	Mm.72666	NR_131020	ENSMUSG00000110310	4930518J21Rik	-	RIKEN cDNA 4930518J21 gene	ncRNA	0.005000	0.427861			-16(TTGTTTTTATTTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-852	chr8	125498616	125498816	+	1.03071	NA	intron (NM_001357372, intron 2 of 21)	intron (NM_001357372, intron 2 of 21)	-5883	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding	0.025000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6502	chr6	66207920	66208120	+	1.03071	NA	Intergenic	Intergenic	-64485	NR_136927	102633773	Mm.272086	NR_136927	ENSMUSG00000107653	Gm31520	-	sterol-C5-desaturase pseudogene	pseudo	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4928	chr3	44925193	44925393	+	1.03071	NA	Intergenic	Intergenic	452967	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	ncRNA	0.000000	0.308458			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-818	chr8	13695197	13695397	+	1.03071	NA	Intergenic	Lx9|LINE|L1	-10592	NM_001101519	403185	Mm.252143	NM_001101519	ENSMUSG00000090336	Cfap97d2	4932443I19Rik|A230061C02Rik|Gm1106	CFAP97 domain containing 2	protein-coding	0.015000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7485	chr8	125498628	125498828	+	1.03071	NA	intron (NM_001357372, intron 2 of 21)	intron (NM_001357372, intron 2 of 21)	-5895	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding	0.020000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3218	chr16	49545907	49546107	+	1.03071	NA	Intergenic	Lx9|LINE|L1	-153287	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5696	chr4	114568577	114568777	+	1.03071	NA	intron (NM_001085549, intron 2 of 6)	intron (NM_001085549, intron 2 of 6)	161953	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat	TraB domain containing 2B	protein-coding	0.015000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3990	chr18	86488613	86488813	+	1.03071	NA	intron (NM_001360910, intron 5 of 8)	intron (NM_001360910, intron 5 of 8)	93761	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0.005000	0.388060			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-615	chr4	36217424	36217624	+	1.03071	NA	intron (NM_001166000, intron 4 of 8)	intron (NM_001166000, intron 4 of 8)	-372320	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.005000	0.353234			-36(ATCAGAATAACAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-102	chr1	35243357	35243557	+	1.03071	NA	Intergenic	Intergenic	393468	NM_001357425	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding	0.020000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5432	chr4	36217347	36217547	+	1.03071	NA	intron (NM_001166000, intron 4 of 8)	intron (NM_001166000, intron 4 of 8)	-372243	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.005000	0.368159			-92(ATTTAAAGGAAAATAG,-,0.00),41(ATCAGAATAACAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5746	chr4	128695029	128695229	+	1.03071	NA	intron (NM_018774, intron 1 of 14)	intron (NM_018774, intron 1 of 14)	6391	NM_018774	54383	Mm.473738	NM_018774	ENSMUSG00000028796	Phc2	A3galt2|AA415044|D130050K19Rik|D4Ertd810e|Edr2|Mph2|p36	polyhomeotic 2	protein-coding	0.025000	0.467662			0(TATCTGTTTTGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5785	chr4	145156072	145156272	+	1.03071	NA	exon (NM_001276502, exon 18 of 69)	exon (NM_001276502, exon 18 of 69)	34494	NM_001276502	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding	0.020000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5578	chr4	85131340	85131540	+	1.03071	NA	3' UTR (NM_175275, exon 26 of 26)	3' UTR (NM_175275, exon 26 of 26)	-74016	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3159	chr16	33545470	33545670	+	1.02932	NA	intron (NM_001083902, intron 3 of 11)	intron (NM_001083902, intron 3 of 11)	27035	NM_001083902	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7266	chr8	57409175	57409375	+	1.02932	NA	Intergenic	Lx5c|LINE|L1	-46648	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1421	chr11	96351441	96351641	+	1.02932	NA	promoter-TSS (NM_134032)	promoter-TSS (NM_134032)	-91	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding	0.040000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5462	chr4	52110537	52110737	+	1.02932	NA	Intergenic	ORR1C2-int|LTR|ERVL-MaLR	-59527	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	ncRNA	0.005000	0.393035			34(CCATTCTTATTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2299	chr13	111296288	111296488	+	1.02932	NA	Intergenic	Intergenic	41375	NM_175497	238880	Mm.107293	NM_175497	ENSMUSG00000055194	Actbl2	4732495G21Rik	actin, beta-like 2	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-39	chr1	13457120	13457320	+	1.02932	NA	Intergenic	LTRIS2|LTR|ERV1	-83137	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0.015000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3076	chr16	10303508	10303708	+	1.02932	NA	intron (NM_007929, intron 1 of 4)	intron (NM_007929, intron 1 of 4)	10360	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2023	chr13	36282069	36282269	+	1.02932	NA	intron (NM_001039189, intron 3 of 5)	intron (NM_001039189, intron 3 of 5)	164526	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5303	chr3	155194509	155194709	+	1.02932	NA	TTS (NM_028938)	TTS (NM_028938)	101175	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7663	chr9	56195023	56195223	+	1.02932	NA	Intergenic	Intergenic	-34053	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding	0.015000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-74	chr1	24231657	24231857	+	1.02932	NA	intron (NM_001290691, intron 25 of 31)	intron (NM_001290691, intron 25 of 31)	36554	NM_001290691	12839	Mm.154662	NM_007740	ENSMUSG00000026147	Col9a1	Col9a-1	collagen, type IX, alpha 1	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-209	chr1	75804526	75804726	+	1.02932	NA	Intergenic	Intergenic	258164	NM_001357150	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding	0.010000	0.447761			-2(GCATTTGCATGTAAAT,+,0.00),0(ATTTGCATGTAAATCA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-831	chr10	56788287	56788487	+	1.02932	NA	Intergenic	Intergenic	356406	NR_152768	102640560	Mm.417249	NR_152768		Gm36595	-	predicted gene, 36595	ncRNA	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4503	chr2	107345546	107345746	+	1.02932	NA	Intergenic	MLTR11B|LTR|ERVK	55057	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding	0.015000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1497	chr11	119428939	119429139	+	1.02932	NA	intron (NM_001040005, intron 20 of 67)	intron (NM_001040005, intron 20 of 67)	38567	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA	0.035000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2186	chr13	85912102	85912302	+	1.02932	NA	Intergenic	L1_Mur2|LINE|L1	134593	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit 7C	protein-coding	0.010000	0.363184			-88(ATTAACATCAAAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5102	chr3	106535526	106535726	+	1.02932	NA	intron (NM_001357818, intron 2 of 8)	MER3|DNA|hAT-Charlie	7520	NM_001357819	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding	0.005000	0.308458			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3799	chr18	38610617	38610817	+	1.02932	NA	Intergenic	Intergenic	-9370	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty RTK signaling antagonist 4	protein-coding	0.020000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4943	chr3	51833242	51833442	+	1.02932	NA	intron (NM_001004176, intron 2 of 4)	L2c|LINE|L2	172163	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.025000	0.432836			-7(ATTAGAAAGAAAACGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7873	chr9	108409445	108409645	+	1.02932	NA	intron (NM_001135198, intron 5 of 6)	RLTR28|LTR|ERVL	16711	NM_053216	112418	Mm.78287	NM_053216	ENSMUSG00000032611	1700102P08Rik	AI593206	RIKEN cDNA 1700102P08 gene	protein-coding	0.010000	0.422886			-65(ATATACATAAAAGAAA,-,0.00),-39(ATTAAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2034	chr13	38080208	38080408	+	1.02932	NA	Intergenic	Intergenic	43319	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1	protein-coding	0.035000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6898	chr7	71192967	71193167	+	1.02932	NA	Intergenic	Intergenic	-716628	NR_130995	78156	Mm.243818	NR_130995	ENSMUSG00000108669	4930441H08Rik	-	RIKEN cDNA 4930441H08 gene	ncRNA	0.020000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2185	chr13	85911961	85912161	+	1.02932	NA	Intergenic	BGLII|LTR|ERVK	134734	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit 7C	protein-coding	0.005000	0.432836			-42(CCTTTATTTTACAAAT,+,0.00),53(ATTAACATCAAAATAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6523	chr6	71851521	71851721	+	1.02932	NA	intron (NM_001362137, intron 3 of 13)	intron (NM_001362137, intron 3 of 13)	20301	NM_001253688	76614	Mm.235123	NM_029673	ENSMUSG00000052337	Immt	1700082C19Rik|D830041H16Rik|HMP|Micos60|P87|P87/89|P89	inner membrane protein, mitochondrial	protein-coding	0.000000	0.293532			73(CTTTAAAAAAGAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3997	chr18	90122286	90122486	+	1.02932	NA	Intergenic	RLTR22_Mur|LTR|ERVK	-352846	NM_001039173	623279	Mm.447164	NM_001039173	ENSMUSG00000073514	Dok6	Dok-6	docking protein 6	protein-coding	0.010000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2537	chr14	71557254	71557454	+	1.02932	NA	Intergenic	Intergenic	-299355	NR_046274	74667	Mm.159286	NR_046274	ENSMUSG00000115304	4930434J06Rik	-	RIKEN cDNA 4930434J06 gene	ncRNA	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1385	chr11	85509246	85509446	+	1.02932	NA	intron (NM_138681, intron 15 of 25)	intron (NM_138681, intron 15 of 25)	156182	NM_001166642	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding	0.005000	0.398010			-35(CTATTCTTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3852	chr18	52677175	52677375	+	1.02932	NA	Intergenic	Intergenic	-16404	NM_010293	14625	Mm.32242	NM_010293	ENSMUSG00000053624	Gykl1	AI449806|Gk-rs1	glycerol kinase-like 1	protein-coding	0.010000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7201	chr8	35614096	35614296	+	1.02932	NA	intron (NR_157105, intron 1 of 3)	L1ME1|LINE|L1	-25176	NR_040376	100504714	Mm.381744	NR_040376	ENSMUSG00000097357	Gm16793	-	predicted gene, 16793	ncRNA	0.010000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1239	chr11	36063641	36063841	+	1.02932	NA	intron (NM_011856, intron 18 of 28)	intron (NM_011856, intron 18 of 28)	-83214	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra	WW, C2 and coiled-coil domain containing 1	protein-coding	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1144	chr11	5269936	5270136	+	1.02932	NA	Intergenic	Intergenic	-8426	NM_032396	84035	Mm.209989	NM_032396	ENSMUSG00000020393	Kremen1	AV002070|Kremen|Krm1	kringle containing transmembrane protein 1	protein-coding	0.010000	0.462687			-34(TCATTCTCATGGTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4441	chr2	87393259	87393459	+	1.02932	NA	Intergenic	BGLII|LTR|ERVK	5652	NM_147031	259033	Mm.377798	NM_147031	ENSMUSG00000047594	Olfr1122	MOR264-1	olfactory receptor 1122	protein-coding	0.005000	0.402985			7(ATTTGTAAAATAAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5958	chr5	53598567	53598767	+	1.02932	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	8181	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4140	chr19	59891167	59891367	+	1.02932	NA	Intergenic	Intergenic	52097	NM_001033172	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5083	chr3	100578831	100579031	+	1.02932	NA	intron (NM_010763, intron 11 of 12)	RLTR13B1|LTR|ERVK	-89739	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Tent5c	4930431B09Rik|AI449797|Fam46c	terminal nucleotidyltransferase 5C	protein-coding	0.020000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3016	chr15	90483776	90483976	+	1.02932	NA	Intergenic	Intergenic	130166	NR_155426	102640415	Mm.394352	NR_155426	ENSMUSG00000116204	Gm36480	-	predicted gene, 36480	ncRNA	0.000000	0.258706			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1684	chr12	59736514	59736714	+	1.02932	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-517131	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-173	chr1	60421481	60421681	+	1.02932	NA	intron (NM_001198570, intron 1 of 11)	L1MA9|LINE|L1	11962	NM_001198570	329165	Mm.212066	NM_198127	ENSMUSG00000026782	Abi2	8430425M24Rik|AI839867|AblBP3|ArgBP1|C130078H13	abl-interactor 2	protein-coding	0.005000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-359	chr1	127575332	127575532	+	1.02902	NA	intron (NM_028135, intron 2 of 7)	intron (NM_028135, intron 2 of 7)	102589	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|A-cre|Act-Cre|SV31|Tg(ACTB-cre)2Mrt|actin-cre|cre<actin>	transmembrane protein 163	protein-coding	0.010000	0.427861			-95(TTTAAAATGAGAAAAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-424	chr18	19730559	19730759	+	1.02902	NA	Intergenic	Intergenic	271438	NM_001291809	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0.000000	0.358209			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4771	chr2	163493171	163493371	+	1.02893	NA	TTS (NR_027970)	TTS (NR_027970)	953	NM_001099331	100043899	Mm.442535	NM_001099331	ENSMUSG00000078949	R3hdml	-	R3H domain containing-like	protein-coding	0.005000	0.532338			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1145	chr11	5383455	5383655	+	1.02893	NA	intron (NM_001080924, intron 1 of 8)	intron (NM_001080924, intron 1 of 8)	-1815	NM_001290501	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding	0.005000	0.358209		46(TATGCATATGTATG,+,0.00),46(TATGCATATGTATG,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-735	chr6	32373077	32373277	+	1.02893	NA	intron (NM_175750, intron 3 of 31)	intron (NM_175750, intron 3 of 31)	-137964	NR_040277	319849	Mm.440860	NR_040277	ENSMUSG00000086763	Plxna4os1	B230378P21Rik	plexin A4, opposite strand 1	ncRNA	0.010000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1694	chr12	64849039	64849239	+	1.02893	NA	Intergenic	Intergenic	-68772	NM_001025605	217648	Mm.341586	NM_001025605	ENSMUSG00000047227	Gm527	-	predicted gene 527	protein-coding	0.015000	0.363184			-13(ATTTCAATAATAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2697	chr14	114002082	114002282	+	1.02893	NA	Intergenic	Intergenic	-829783	NR_045661	75822	Mm.410813	NR_045661	ENSMUSG00000115320	4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	ncRNA	0.000000	0.323383			-50(TCTTTTACATGCAAAC,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-99	chr10	75098307	75098507	+	1.02893	NA	intron (NM_001081412, intron 1 of 22)	intron (NM_001081412, intron 1 of 22)	37511	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-880	chr10	71193471	71193671	+	1.02893	NA	Intergenic	Intergenic	-8174	NR_131003	78638	Mm.71171	NR_131003	ENSMUSG00000112028	1700113B09Rik	-	RIKEN cDNA 1700113B09 gene	ncRNA	0.000000	0.388060	-11(GATAAATTATTCATA,+,0.00),-11(GATAAATTATTCATA,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-535	chr2	142818347	142818547	+	1.02893	NA	intron (NM_001355123, intron 12 of 26)	intron (NM_001355123, intron 12 of 26)	83017	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4912	chr3	40058760	40058960	+	1.02812	NA	Intergenic	Intergenic	464052	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA	0.030000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-551	chr3	12677286	12677486	+	1.02812	NA	Intergenic	Intergenic	-794269	NM_001357035	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0.000000	0.417910			60(CTTTGAATGACAGAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7828	chr9	94816588	94816788	+	1.02812	NA	intron (NM_177909, intron 5 of 15)	MER33|DNA|hAT-Charlie	64859	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA	0.010000	0.388060			10(TTTAAAATAACAATAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-420	chr18	6466419	6466619	+	1.02812	NA	intron (NM_007935, intron 1 of 13)	intron (NM_007935, intron 1 of 13)	24127	NR_035446	100316773		NR_035446	ENSMUSG00000084514	Mir1893	Mirn1893|mmu-mir-1893	microRNA 1893	ncRNA	0.010000	0.417910			-48(TTCTGAATAAGAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5248	chr3	144411076	144411276	+	1.02812	NA	Intergenic	Intergenic	159040	NM_001355234	23908	Mm.12863	NM_011828	ENSMUSG00000040151	Hs2st1	2OST|AW214369|Hs2st|mKIAA0448	heparan sulfate 2-O-sulfotransferase 1	protein-coding	0.010000	0.502488			16(ATTTGCAAGGCAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-959	chr10	96410304	96410504	+	1.02812	NA	Intergenic	Intergenic	184197	NR_110448	74881	Mm.410819	NR_110448	ENSMUSG00000112762	4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA	0.010000	0.402985			-20(TCTTAGCTATGGAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5504	chr4	62666005	62666205	+	1.02793	NA	intron (NM_134257, intron 10 of 15)	L1M|LINE|L1	-7869	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5042	chr3	83582750	83582950	+	1.02750	NA	Intergenic	Intergenic	-8732	NR_036591	69460	Mm.389464	NR_036591	ENSMUSG00000101334	1700028M03Rik	-	RIKEN cDNA 1700028M03 gene	ncRNA	0.000000	0.378109			-63(TTTCTTTCATGCTTAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-800	chr7	92580598	92580798	+	1.02750	NA	intron (NM_001162918, intron 7 of 7)	B3|SINE|B2	19549	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7001	chr7	101985905	101986105	+	1.02677	NA	intron (NM_133947, intron 2 of 24)	intron (NM_133947, intron 2 of 24)	16162	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7564	chr9	24840140	24840340	+	1.02677	NA	Intergenic	B3|SINE|B2	-65937	NM_020496	57246	Mm.31452	NM_020496	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-295	chr14	74822702	74822902	+	1.02677	NA	intron (NM_001033439, intron 4 of 19)	intron (NM_001033439, intron 4 of 19)	90505	NM_001285423	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding	0.010000	0.353234			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-862	chr9	24840147	24840347	+	1.02677	NA	Intergenic	B3|SINE|B2	-65944	NM_020496	57246	Mm.31452	NM_020496	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding	0.010000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-803	chr7	101985920	101986120	+	1.02677	NA	intron (NM_133947, intron 2 of 24)	intron (NM_133947, intron 2 of 24)	16177	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding	0.010000	0.477612			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-555	chr3	21973095	21973295	+	1.02677	NA	Intergenic	Intergenic	-103457	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.000000	0.338308	50(TATGAATAAGTTATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5239	chr3	141250554	141250754	+	1.02677	NA	Intergenic	L1MA5|LINE|L1	-38299	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.005000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7574	chr9	28255692	28255892	+	1.02677	NA	Intergenic	Intergenic	-148536	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0.020000	0.363184		-34(TATGCAAATTTATG,-,0.00)	-78(ATTTGAAAGACAGGAC,-,0.00),-41(TAATTATTATGCAAAT,+,0.00),50(AATTTGTAATGCAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4968	chr3	60557116	60557316	+	1.02677	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	56037	NM_001253710	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind like splicing factor 1	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5521	chr4	66947979	66948179	+	1.02677	NA	Intergenic	Intergenic	120528	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0.005000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-953	chr10	95563378	95563578	+	1.02677	NA	intron (NM_001358996, intron 1 of 4)	CpG	668	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP-2|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding	0.065000	0.547264			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4870	chr3	21973122	21973322	+	1.02677	NA	Intergenic	Intergenic	-103430	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.000000	0.308458	23(TATGAATAAGTTATT,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3021	chr15	91252688	91252888	+	1.02677	NA	Intergenic	Intergenic	-60781	NM_001358967	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1071	chr10	117349735	117349935	+	1.02677	NA	intron (NM_001310609, intron 9 of 9)	intron (NM_001310609, intron 9 of 9)	27138	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding	0.005000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7651	chr9	50746285	50746485	+	1.02677	NA	intron (NM_025865, intron 1 of 3)	intron (NM_025865, intron 1 of 3)	142	NM_025865	66952	Mm.273375	NM_025865	ENSMUSG00000032062	2310030G06Rik	2610024D04Rik|AV017521	RIKEN cDNA 2310030G06 gene	protein-coding	0.050000	0.611940			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6154	chr5	112341627	112341827	+	1.02677	NA	intron (NM_001359388, intron 1 of 6)	intron (NM_001359388, intron 1 of 6)	1313	NR_153106	70118	Mm.172947	NM_027323	ENSMUSG00000029346	Srrd	2810002G02Rik|Srr1	SRR1 domain containing	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5144	chr3	118299626	118299826	+	1.02660	NA	Intergenic	Intergenic	-134131	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7077	chr7	128671856	128672056	+	1.02593	NA	intron (NM_178641, intron 9 of 19)	L1M5|LINE|L1	-16914	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding	0.010000	0.333333			-43(ATGTACAATACAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1116	chr10	124630883	124631083	+	1.02590	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	161909	NR_028310	75030	Mm.159403	NR_028310	ENSMUSG00000112364	4930503E24Rik	-	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo	0.000000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6784	chr7	5072000	5072200	+	1.02539	NA	intron (NM_133671, intron 7 of 11)	ID4_|SINE|ID	-8135	NM_010147	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding	0.005000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-893	chr9	110054183	110054383	+	1.02539	NA	intron (NM_001311164, intron 1 of 9)	intron (NM_001311164, intron 1 of 9)	2262	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding	0.005000	0.427861			72(ATTTAAAACACAAATT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4305	chr2	52700494	52700694	+	1.02539	NA	intron (NM_019667, intron 12 of 13)	intron (NM_019667, intron 12 of 13)	-23985	NM_001037099	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding	0.010000	0.497512			-84(ATCACCATGAGAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6956	chr7	89606514	89606714	+	1.02518	NA	Intergenic	Intergenic	-26204	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding	0.005000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-968	chr10	97247272	97247472	+	1.02518	NA	Intergenic	Intergenic	-176106	NR_039547	100628616		NR_039547	ENSMUSG00000105557	Mir3966	mmu-mir-3966|mu-mir-3966	microRNA 3966	ncRNA	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1112	chr10	123505196	123505396	+	1.02518	NA	intron (NR_153334, intron 2 of 6)	intron (NR_153334, intron 2 of 6)	241220	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Tafa2	6330575M02|FAM19A2 TAFA-2|Fam19a2|Sam2|Tafa-2	TAFA chemokine like family member 2	protein-coding	0.015000	0.412935			74(TTTTTGTCTTTTAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6573	chr6	86758291	86758491	+	1.02518	NA	intron (NM_013471, intron 3 of 12)	intron (NM_013471, intron 3 of 12)	16723	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding	0.010000	0.398010			-36(ATTTAAAAAAAAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3823	chr18	44586442	44586642	+	1.02518	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-75123	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-101	chr1	34994800	34995000	+	1.02518	NA	Intergenic	L1MA4|LINE|L1	144911	NM_001357425	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding	0.025000	0.442786			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-12	chr1	34994790	34994990	+	1.02518	NA	Intergenic	L1MA4|LINE|L1	144901	NM_001357425	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding	0.025000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1211	chr11	27095639	27095839	+	1.02518	NA	Intergenic	RLTR13D6|LTR|ERVK	310631	NR_002890	654472	Mm.347777	NR_002890		Gm12070	-	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5052	chr3	85658877	85659077	+	1.02518	NA	Intergenic	Intergenic	84848	NM_144896	229487	Mm.52275	NM_144896	ENSMUSG00000028085	Gatb	9430026F02Rik|Pet112|Pet112l	glutamyl-tRNA(Gln) amidotransferase, subunit B	protein-coding	0.000000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5767	chr4	139048673	139048873	+	1.02518	NA	intron (NM_029857, intron 14 of 16)	intron (NM_029857, intron 14 of 16)	26016	NM_021358	15565	Mm.291096	NM_021358	ENSMUSG00000028747	Htr6	5-HT6	5-hydroxytryptamine (serotonin) receptor 6	protein-coding	0.010000	0.442786		79(TATGAATATGCATA,+,0.00),79(TATGAATATGCATA,-,0.00),85(TATGCATAAGTATT,+,0.00)	66(ATTTACATAAGAATAT,-,0.00),84(ATATGCATAAGTATTT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2543	chr14	74646471	74646671	+	1.02518	NA	intron (NM_172812, intron 2 of 2)	intron (NM_172812, intron 2 of 2)	5697	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	5-HT-2|5-HT-2A|E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding	0.020000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2828	chr15	25060713	25060913	+	1.02518	NA	Intergenic	Intergenic	352951	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding	0.000000	0.338308			60(ATAATCATGAAAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5904	chr5	36339383	36339583	+	1.02518	NA	intron (NM_030889, intron 1 of 26)	intron (NM_030889, intron 1 of 26)	37913	NR_106162	102465792		NR_106162	ENSMUSG00000098884	Mir7689	Gm27434|mmu-mir-7689	microRNA 7689	ncRNA	0.005000	0.492537		17(CCTAAATATTCATA,+,0.00)	73(ATTTAAAACACAAAGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-607	chr1	185231240	185231440	+	1.02518	NA	intron (NM_001163754, intron 2 of 34)	ORR1B2|LTR|ERVL-MaLR	-11586	NR_034044	100217449	Mm.429560	NR_034044	ENSMUSG00000077571	Snora36b	MBI-87	small nucleolar RNA, H/ACA box 36B	snoRNA	0.005000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6815	chr7	35348028	35348228	+	1.02518	NA	intron (NM_027897, intron 1 of 14)	intron (NM_027897, intron 1 of 14)	13891	NM_027897	52428	Mm.286600	NM_027897	ENSMUSG00000030494	Rhpn2	1300002E07Rik|AA536890|C85860|D7Ertd784e	rhophilin, Rho GTPase binding protein 2	protein-coding	0.020000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7017	chr7	109644518	109644718	+	1.02518	NA	Intergenic	Intergenic	-27471	NM_001001326	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3442	chr17	23661546	23661746	+	1.02518	NA	intron (NM_153784, intron 1 of 9)	intron (NM_153784, intron 1 of 9)	1140	NM_153784	212733	Mm.59997	NM_153784	ENSMUSG00000043782	Bicdl2	BICDR-2|Ccdc64b	BICD family like cargo adaptor 2	protein-coding	0.025000	0.562189			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1263	chr11	43398385	43398585	+	1.02518	NA	Intergenic	RLTR11A|LTR|ERVK	-24024	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6129	chr5	104442963	104443163	+	1.02518	NA	Intergenic	RLTR13D6|LTR|ERVK	6871	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding	0.005000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4725	chr2	150173274	150173474	+	1.02518	NA	Intergenic	RLTR22_Mur|LTR|ERVK	-8381	NM_001145863	100271882		NM_001145863	ENSMUSG00000079009	Gm14139	-	predicted gene 14139	protein-coding	0.000000	0.318408			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7573	chr9	28212346	28212546	+	1.02518	NA	Intergenic	Intergenic	-191882	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4232	chr2	29055102	29055302	+	1.02518	NA	promoter-TSS (NM_001166705)	promoter-TSS (NM_001166705)	-136	NM_001166705	329375	Mm.425079	NM_001085514	ENSMUSG00000079502	Cfap77	1700101E01Rik|Gm823	cilia and flagella associated protein 77	protein-coding	0.065000	0.616915			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2744	chr14	122427774	122427974	+	1.02518	NA	intron (NR_033326, intron 1 of 3)	intron (NR_033326, intron 1 of 3)	23241	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3333	chr16	78411358	78411558	+	1.02518	NA	Intergenic	RMER17C|LTR|ERVK	-34277	NM_001297747	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7540	chr9	16014242	16014442	+	1.02518	NA	intron (NM_001080814, intron 7 of 25)	intron (NM_001080814, intron 7 of 25)	-139786	NM_145712	244701	Mm.222631	NM_145712	ENSMUSG00000050901	Mtnr1b	Mel-1B-R|Mel1b|Mt2	melatonin receptor 1B	protein-coding	0.000000	0.452736			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2369	chr14	15881421	15881621	+	1.02518	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	361810	NM_001359883	71147	Mm.197960	NM_027695	ENSMUSG00000021786	Oxsm	4933425A18Rik|C80494	3-oxoacyl-ACP synthase, mitochondrial	protein-coding	0.000000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4606	chr2	129741295	129741495	+	1.02518	NA	Intergenic	L1ME1|LINE|L1	-41457	NM_018863	18610	Mm.6239	NM_018863	ENSMUSG00000027400	Pdyn	Dyn	prodynorphin	protein-coding	0.000000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3590	chr17	74976343	74976543	+	1.02485	NA	Intergenic	Intergenic	-29086	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6712	chr6	126803240	126803440	+	1.02485	NA	Intergenic	Intergenic	45804	NM_025358	66108	Mm.29939	NM_025358	ENSMUSG00000000399	Ndufa9	1010001N11Rik	NADH:ubiquinone oxidoreductase subunit A9	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-608	chr4	14968396	14968596	+	1.02307	NA	intron (NM_178617, intron 9 of 12)	intron (NM_178617, intron 9 of 12)	37855	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	-	predicted gene 11837	protein-coding	0.000000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4365	chr2	66178398	66178598	+	1.02303	NA	Intergenic	Intergenic	-53705	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1237	chr11	35961171	35961371	+	1.02303	NA	intron (NM_170779, intron 1 of 22)	intron (NM_170779, intron 1 of 22)	19256	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra	WW, C2 and coiled-coil domain containing 1	protein-coding	0.010000	0.482587			-13(CCTTTTTTATTGAGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4774	chr2	164907115	164907315	+	1.02303	NA	intron (NM_199027, intron 6 of 27)	intron (NM_199027, intron 6 of 27)	4535	NM_199027	329559	Mm.330776	NM_199027	ENSMUSG00000039834	Zfp335	1810045J01Rik|NIF-1|Nif1|Znf335	zinc finger protein 335	protein-coding	0.030000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2898	chr15	44806729	44806929	+	1.02303	NA	TTS (NR_040309)	TTS (NR_040309)	-18766	NM_001032727	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding	0.000000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1247	chr11	38067825	38068025	+	1.02303	NA	Intergenic	Intergenic	408936	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6150	chr5	110898216	110898416	+	1.02303	NA	intron (NM_001267622, intron 2 of 22)	intron (NM_001267622, intron 2 of 22)	18513	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4008	chr19	12762906	12763106	+	1.02303	NA	TTS (NR_024093)	TTS (NR_024093)	2626	NM_170786	12803	Mm.290924	NM_053007	ENSMUSG00000079415	Cntf	AI429687	ciliary neurotrophic factor	protein-coding	0.000000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-903	chr10	82762738	82762938	+	1.02303	NA	intron (NM_010914, intron 1 of 7)	intron (NM_010914, intron 1 of 7)	1303	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding	0.005000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-152	chr11	65356474	65356674	+	1.02303	NA	Intergenic	Intergenic	-68741	NR_040280	327946	Mm.383301	NR_040280	ENSMUSG00000085162	Gm12295	A730013G04	predicted gene 12295	ncRNA	0.015000	0.368159			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-902	chrX	85636279	85636479	+	1.02303	NA	Intergenic	Intergenic	62357	NM_025729	66724	Mm.119646	NM_025729	ENSMUSG00000035476	Tab3	4921526G09Rik|Map3k7ip3|mKIAA4135	TGF-beta activated kinase 1/MAP3K7 binding protein 3	protein-coding	0.000000	0.288557			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-496	chr2	77889654	77889854	+	1.02293	NA	intron (NM_001362664, intron 19 of 19)	intron (NM_001362664, intron 19 of 19)	56602	NM_001362658	80744	Mm.288151	NM_030560	ENSMUSG00000027014	Cwc22	AA684037|AI173004|AL022752|B230213M24|mKIAA1604	CWC22 spliceosome-associated protein	protein-coding	0.000000	0.348259			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-795	chr7	79719154	79719354	+	1.02251	NA	Intergenic	Intergenic	-5068	NM_001291222	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6922	chr7	79719231	79719431	+	1.02251	NA	Intergenic	Intergenic	-5145	NM_001291222	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding	0.005000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-789	chr7	45800588	45800788	+	1.02251	NA	intron (NM_001005511, intron 14 of 15)	intron (NM_001005511, intron 14 of 15)	13628	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding	0.030000	0.597015			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7209	chr8	37570628	37570828	+	1.02199	NA	intron (NM_145841, intron 4 of 7)	intron (NM_145841, intron 4 of 7)	-546490	NR_126063	414128	Mm.450976	NR_126063	ENSMUSG00000110242	G630064G18Rik	-	RIKEN cDNA G630064G18 gene	ncRNA	0.015000	0.412935	-48(AATGAATTTTTTATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1169	chr11	16240601	16240801	+	1.02199	NA	Intergenic	RLTR13B1|LTR|ERVK	-17041	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0.010000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-39	chr1	136674817	136675017	+	1.02199	NA	Intergenic	Intergenic	-8479	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA	0.025000	0.452736			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-260	chr13	90358906	90359106	+	1.02199	NA	Intergenic	Intergenic	269339	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0.010000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-227	chr13	12423070	12423270	+	1.02199	NA	intron (NM_144835, intron 28 of 44)	RMER1B|Other|Other	27795	NM_144835	217995	Mm.171186	NM_144835	ENSMUSG00000050244	Heatr1	AA517551|B130016L12Rik|BC019693	HEAT repeat containing 1	protein-coding	0.010000	0.472637			31(TCTGTGTCATGGAGAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-250	chr13	70793181	70793381	+	1.02171	NA	intron (NM_172053, intron 6 of 22)	intron (NM_172053, intron 6 of 22)	48530	NM_172053	271127	Mm.115970	NM_172053	ENSMUSG00000049538	Adamts16	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7087	chr7	130166435	130166635	+	1.02171	NA	intron (NM_201601, intron 15 of 15)	intron (NM_201601, intron 15 of 15)	100273	NM_001347638	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding	0.015000	0.383085			13(TATTTGTTTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8137	chrX	160136113	160136313	+	1.02149	NA	intron (NM_008810, intron 1 of 10)	intron (NM_008810, intron 1 of 10)	2217	NM_008810	18597	Mm.34775	NM_008810	ENSMUSG00000031299	Pdha1	Pdha-1	pyruvate dehydrogenase E1 alpha 1	protein-coding	0.020000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-170	chr11	111397847	111398047	+	1.02146	NA	Intergenic	RLTR11A2|LTR|ERVK	331783	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding	0.000000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-325	chr14	120604286	120604486	+	1.02130	NA	Intergenic	Intergenic	125925	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2731	chr14	120604290	120604490	+	1.02130	NA	Intergenic	Intergenic	125929	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5223	chr3	137642785	137642985	+	1.02129	NA	Intergenic	Intergenic	19213	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5222	chr3	137642548	137642748	+	1.02129	NA	Intergenic	Intergenic	18976	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding	0.000000	0.328358			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7777	chr9	82761091	82761291	+	1.02129	NA	Intergenic	RMER20B|LTR|ERVK	-68615	NM_001168240	65099	Mm.41415	NM_022986	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding	0.005000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6999	chr7	101541235	101541435	+	1.02129	NA	Intergenic	Intergenic	14467	NM_007490	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a	ARTC2|Art2a-ps|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a	protein-coding	0.040000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5024	chr3	76420302	76420502	+	1.02129	NA	intron (NM_178673, intron 5 of 15)	intron (NM_178673, intron 5 of 15)	344819	NM_001253719	213262	Mm.379337	NM_178673	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4355	chr2	65143486	65143686	+	1.02129	NA	intron (NM_177025, intron 2 of 13)	RLTR25B|LTR|ERVK	95205	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1503	chr11	121143531	121143731	+	1.02129	NA	Intergenic	Intergenic	-2512	NM_028602	73679	Mm.390423	NM_028602	ENSMUSG00000039329	Tex19.1	2410081M02Rik|Tex19|Tex19a|mTex19.1	testis expressed gene 19.1	protein-coding	0.015000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-328	chr1	119986649	119986849	+	1.02129	NA	intron (NM_001115074, intron 3 of 23)	intron (NM_001115074, intron 3 of 23)	10483	NM_001115074	226356	Mm.297290	NM_001115074	ENSMUSG00000036962	Cfap221	Gm101|Pcdp1	cilia and flagella associated protein 221	protein-coding	0.015000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3033	chr15	93472199	93472399	+	1.02129	NA	intron (NM_175363, intron 8 of 8)	Lx8|LINE|L1	47221	NM_001364846	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1898	chr12	116660201	116660401	+	1.02129	NA	intron (NM_011215, intron 2 of 22)	intron (NM_011215, intron 2 of 22)	174581	NM_011215	19276	Mm.206054	NM_011215	ENSMUSG00000056553	Ptprn2	4930425H11Rik|IA2beta|PTP-NP|Phol|mKIAA0387|phogrin	protein tyrosine phosphatase, receptor type, N polypeptide 2	protein-coding	0.020000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7123	chr7	141569925	141570125	+	1.02129	NA	intron (NM_007459, intron 1 of 21)	intron (NM_007459, intron 1 of 21)	7845	NM_001357068	11772	Mm.253090	NM_007459	ENSMUSG00000002957	Ap2a2	2410074K14Rik|AF006990|AW146353|Adtab|C78001|L25	adaptor-related protein complex 2, alpha 2 subunit	protein-coding	0.015000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-429	chr1	143672130	143672330	+	1.02129	NA	intron (NM_145991, intron 7 of 16)	intron (NM_145991, intron 7 of 16)	30663	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6845	chr7	50088709	50088909	+	1.02129	NA	intron (NM_001037906, intron 3 of 19)	intron (NM_001037906, intron 3 of 19)	113459	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding	0.000000	0.393035			-35(ACATTGTTTAGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6942	chr7	84579582	84579782	+	1.02129	NA	Intergenic	Intergenic	26260	NM_010176	14085	Mm.3798	NM_010176	ENSMUSG00000030630	Fah	swst	fumarylacetoacetate hydrolase	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3573	chr17	69277358	69277558	+	1.02129	NA	promoter-TSS (NR_045428)	promoter-TSS (NR_045428)	-252	NR_045428	69750	Mm.439063	NR_045428	ENSMUSG00000100572	2410021H03Rik	-	RIKEN cDNA 2410021H03 gene	ncRNA	0.020000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3264	chr16	59677873	59678073	+	1.02129	NA	intron (NM_007938, intron 15 of 17)	intron (NM_007938, intron 15 of 17)	-38564	NM_001347244	56297	Mm.392505	NM_019665	ENSMUSG00000022722	Arl6	1110018H24Rik|2210411E14Rik|BBS3	ADP-ribosylation factor-like 6	protein-coding	0.000000	0.303483			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-400	chr1	137919837	137920037	+	1.02129	NA	Intergenic	L2a|LINE|L2	-46518	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA	0.010000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1378	chr11	82183424	82183624	+	1.02129	NA	Intergenic	Intergenic	-3712	NM_011329	20290	Mm.1283	NM_011329	ENSMUSG00000020702	Ccl1	BF534335|I-309|P500|Scya1|Tca-3|Tca3	chemokine (C-C motif) ligand 1	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8073	chrX	128828928	128829128	+	1.02129	NA	Intergenic	Intergenic	-222496	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1146	chr11	6685163	6685363	+	1.02129	NA	Intergenic	PB1D10|SINE|Alu	-25027	NR_028586	100041311	Mm.388018	NR_028586	ENSMUSG00000086373	Gm11978	-	predicted gene 11978	pseudo	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7941	chrX	23839417	23839617	+	1.02129	NA	Intergenic	RLTR22_Mus|LTR|ERVK	-53246	NM_001034864	236749	Mm.296422	NM_001034864	ENSMUSG00000068113	Gm4907	EG236749	predicted gene 4907	protein-coding	0.010000	0.328358		-19(AATGAATATGTATA,+,0.00),-19(AATGAATATGTATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2089	chr13	58282058	58282258	+	1.02129	NA	Intergenic	Intergenic	-7970	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-987	chr10	104298833	104299033	+	1.02129	NA	Intergenic	Intergenic	11664	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA	0.000000	0.303483			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-740	chr6	44899990	44900190	+	1.02004	NA	Intergenic	Intergenic	-159971	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.000000	0.303483			-72(ATTTCCAAAAGAAAAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-543	chr2	165664587	165664787	+	1.02004	NA	intron (NM_010165, intron 1 of 15)	intron (NM_010165, intron 1 of 15)	9389	NM_010165	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.000000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6678	chr6	115647815	115648015	+	1.01991	NA	intron (NM_001356333, intron 1 of 17)	intron (NM_001356333, intron 1 of 17)	27973	NM_001356334	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|cRaf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding	0.015000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5530	chr4	70414529	70414729	+	1.01948	NA	Intergenic	L2b|LINE|L2	-4194	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding	0.000000	0.358209			-60(ATTAGCATGATAATAA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-574	chr3	119142851	119143051	+	1.01948	NA	intron (NM_170778, intron 16 of 22)	intron (NM_170778, intron 16 of 22)	580771	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DHPDHase|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-787	chr7	37514755	37514955	+	1.01948	NA	intron (NM_172385, intron 4 of 5)	intron (NM_172385, intron 4 of 5)	254897	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-756	chr10	29703248	29703448	+	1.01948	NA	Intergenic	Intergenic	-167481	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding	0.000000	0.328358			34(AATTATTTATGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1104	chr10	123038501	123038701	+	1.01948	NA	exon (NM_153395, exon 8 of 34)	exon (NM_153395, exon 8 of 34)	37904	NM_001163024	67074	Mm.169924	NM_153395	ENSMUSG00000034602	Mon2	2610528O22Rik|AW495628|Sf21|mKIAA1040	MON2 homolog, regulator of endosome to Golgi trafficking	protein-coding	0.030000	0.412935			57(ATTTGCAAAGGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6468	chr6	58735861	58736061	+	1.01948	NA	Intergenic	Intergenic	-95504	NM_001361966	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4476	chr2	102122141	102122341	+	1.01948	NA	intron (NM_178886, intron 1 of 5)	intron (NM_178886, intron 1 of 5)	64219	NM_001290784	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.000000	0.457711			13(GAATTTTCTTGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6821	chr7	37514767	37514967	+	1.01948	NA	intron (NM_172385, intron 4 of 5)	intron (NM_172385, intron 4 of 5)	254885	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding	0.010000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-107	chr10	110773477	110773677	+	1.01948	NA	intron (NM_178609, intron 7 of 12)	intron (NM_178609, intron 7 of 12)	28138	NM_001358560	52679	Mm.11747	NM_178609	ENSMUSG00000020185	E2f7	A630014C11Rik|D10Ertd739e|E2F-7	E2F transcription factor 7	protein-coding	0.030000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-98	chr10	72350071	72350271	+	1.01948	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-304675	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-658	chr4	153567504	153567704	+	1.01948	NA	Intergenic	Intergenic	-84774	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5802	chr4	153567522	153567722	+	1.01948	NA	Intergenic	Intergenic	-84792	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding	0.005000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4490	chr2	105719658	105719858	+	1.01948	NA	intron (NM_023876, intron 9 of 9)	intron (NM_023876, intron 9 of 9)	37295	NM_001310146	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding	0.000000	0.358209			44(TTTTAAATGAAAATGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-348	chr15	71975892	71976092	+	1.01903	NA	intron (NM_027174, intron 6 of 63)	intron (NM_027174, intron 6 of 63)	58235	NM_027174	69700	Mm.322500	NM_027174	ENSMUSG00000079022	Col22a1	2310067L16Rik|C80743	collagen, type XXII, alpha 1	protein-coding	0.000000	0.402985			-39(ATTTGCAGCACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2990	chr15	71975933	71976133	+	1.01903	NA	intron (NM_027174, intron 6 of 63)	intron (NM_027174, intron 6 of 63)	58194	NM_027174	69700	Mm.322500	NM_027174	ENSMUSG00000079022	Col22a1	2310067L16Rik|C80743	collagen, type XXII, alpha 1	protein-coding	0.000000	0.348259			-80(ATTTGCAGCACAATGC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3096	chr16	15519772	15519972	+	1.01874	NA	Intergenic	MERVL_2A-int|LTR|ERVL	74646	NM_023585	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding	0.000000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6715	chr6	128993252	128993452	+	1.01874	NA	intron (NR_015455, intron 1 of 2)	intron (NR_015455, intron 1 of 2)	391	NR_015455	408064	Mm.172429	NR_015455		BC064078	-	cDNA sequence BC064078	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2095	chr13	59768659	59768859	+	1.01874	NA	intron (NM_026921, intron 1 of 3)	intron (NM_026921, intron 1 of 3)	1030	NM_026921	69046	Mm.7884	NM_026921	ENSMUSG00000044792	Isca1	1810010A06Rik|Hbld2	iron-sulfur cluster assembly 1	protein-coding	0.035000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6589	chr6	93668023	93668223	+	1.01874	NA	Intergenic	RMER6D|LTR|ERVK	244840	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.000000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-583	chr3	132982072	132982272	+	1.01874	NA	3' UTR (NM_026231, exon 12 of 12)	3' UTR (NM_026231, exon 12 of 12)	-31881	NM_033525	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2387	chr14	19975690	19975890	+	1.01874	NA	intron (NM_001285908, intron 1 of 3)	intron (NM_001285908, intron 1 of 3)	903	NM_001285911	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding	0.005000	0.303483	26(TTTTAATAATTCATG,+,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3394	chr16	95173492	95173692	+	1.01874	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-83966	NM_001271694	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding	0.000000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7208	chr8	37570422	37570622	+	1.01868	NA	intron (NM_145841, intron 4 of 7)	intron (NM_145841, intron 4 of 7)	-546284	NR_126063	414128	Mm.450976	NR_126063	ENSMUSG00000110242	G630064G18Rik	-	RIKEN cDNA G630064G18 gene	ncRNA	0.005000	0.407960			53(TATTTGCAATTCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-698	chr10	12383906	12384106	+	1.01868	NA	3' UTR (NM_011682, exon 74 of 74)	3' UTR (NM_011682, exon 74 of 74)	477729	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding	0.015000	0.398010			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-821	chr8	37570247	37570447	+	1.01868	NA	intron (NM_145841, intron 4 of 7)	Lx8|LINE|L1	-546109	NR_126063	414128	Mm.450976	NR_126063	ENSMUSG00000110242	G630064G18Rik	-	RIKEN cDNA G630064G18 gene	ncRNA	0.005000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-641	chr4	100910730	100910930	+	1.01868	NA	intron (NM_198037, intron 3 of 26)	intron (NM_198037, intron 3 of 26)	134151	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding	0.025000	0.432836			-8(TCTTTTTCTTTCTAAG,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-572	chr3	118299253	118299453	+	1.01868	NA	Intergenic	Intergenic	-134504	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA	0.000000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-847	chr10	60027736	60027936	+	1.01766	NA	intron (NM_001199187, intron 5 of 10)	intron (NM_001199187, intron 5 of 10)	24509	NM_001199187	69090	Mm.155839	NM_026937	ENSMUSG00000044475	Ascc1	1810015P09Rik|AI550520|ASC1p50|CGI-18	activating signal cointegrator 1 complex subunit 1	protein-coding	0.000000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4390	chr2	72881686	72881886	+	1.01766	NA	Intergenic	Intergenic	-68069	NR_102349	76218	Mm.75260	NR_102348	ENSMUSG00000085427	6430710C18Rik	5033406J01Rik	RIKEN cDNA 6430710C18 gene	ncRNA	0.005000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-281	chr14	28467748	28467948	+	1.01766	NA	intron (NM_001347497, intron 19 of 19)	intron (NM_001347497, intron 19 of 19)	-37625	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding	0.010000	0.437811			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-596	chr3	149567124	149567324	+	1.01766	NA	Intergenic	Intergenic	292487	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7685	chr9	63131948	63132148	+	1.01760	NA	Intergenic	Intergenic	14932	NM_172446	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding	0.020000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7971	chrX	57260751	57260951	+	1.01760	NA	intron (NM_001358573, intron 8 of 20)	intron (NM_001358573, intron 8 of 20)	48708	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding	0.005000	0.442786		15(TATGCAAATTCAGG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4143	chr19	59981658	59981858	+	1.01760	NA	Intergenic	Intergenic	-38104	NM_001164367	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-596	chr1	182589259	182589459	+	1.01760	NA	intron (NM_130890, intron 2 of 20)	intron (NM_130890, intron 2 of 20)	24352	NM_001145806	170725	Mm.189201	NM_130890	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding	0.020000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-547	chr1	173101769	173101969	+	1.01760	NA	Intergenic	Intergenic	35465	NM_146764	258759	Mm.389211	NM_146764	ENSMUSG00000062527	Olfr1408	MOR267-4	olfactory receptor 1408	protein-coding	0.000000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6125	chr5	103367190	103367390	+	1.01760	NA	Intergenic	Intergenic	20692	NR_152117	75519	Mm.416851	NR_152117	ENSMUSG00000105426	1700021F02Rik	Gm42618	RIKEN cDNA 1700021F02 gene	ncRNA	0.015000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7898	chr9	116786221	116786421	+	1.01760	NA	intron (NM_001172123, intron 6 of 14)	intron (NM_001172123, intron 6 of 14)	466162	NM_178660	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding	0.015000	0.477612			35(GCTCTGTCATTCTGAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7049	chr7	120893925	120894125	+	1.01760	NA	intron (NM_001267711, intron 15 of 17)	intron (NM_001267711, intron 15 of 17)	-23719	NM_025298	26939	Mm.193632	NM_025298	ENSMUSG00000030880	Polr3e	RPC5|Sin	polymerase (RNA) III (DNA directed) polypeptide E	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5128	chr3	113988536	113988736	+	1.01760	NA	Intergenic	Intergenic	-41904	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding	0.005000	0.323383			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-889	chr10	73725819	73726019	+	1.01760	NA	Intergenic	Intergenic	-95948	NM_001142747	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding	0.015000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8046	chrX	103389928	103390128	+	1.01760	NA	3' UTR (NM_009767, exon 6 of 6)	3' UTR (NM_009767, exon 6 of 6)	-24439	NM_009440	22127	Mm.358644	NM_009440	ENSMUSG00000031329	Tsx	AV207184	testis specific X-linked gene	protein-coding	0.000000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7155	chr8	12151806	12152006	+	1.01760	NA	Intergenic	Intergenic	-233865	NR_027975	434280	Mm.447484	NM_001013812	ENSMUSG00000047935	Sox1ot	EG434280|Gm5607	Sox1 overlapping transcript	ncRNA	0.020000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5888	chr5	30713405	30713605	+	1.01760	NA	intron (NM_023047, intron 1 of 12)	intron (NM_023047, intron 1 of 12)	1941	NM_001356949	65254	Mm.27732	NM_023047	ENSMUSG00000029168	Dpysl5	CRAM|CRMP-5|Crmp5	dihydropyrimidinase-like 5	protein-coding	0.055000	0.592040			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4889	chr3	29171838	29172038	+	1.01760	NA	intron (NR_151638, intron 4 of 13)	intron (NR_151638, intron 4 of 13)	89407	NM_001357198	75740	Mm.330948	NM_029412	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding	0.010000	0.393035			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-112	chr10	116052396	116052596	+	1.01760	NA	intron (NM_011217, intron 2 of 13)	Lx8|LINE|L1	34133	NM_011217	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1980	chr13	21306064	21306264	+	1.01760	NA	Intergenic	Intergenic	-6039	NM_145451	75512	Mm.46195	NM_145451	ENSMUSG00000004341	Gpx6	1700020G18Rik|Ry2d1|olfactory	glutathione peroxidase 6	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-134	chr1	44998469	44998669	+	1.01760	NA	Intergenic	RMER16-int|LTR|ERVK	-253620	NR_040602	75066	Mm.416932	NR_040602	ENSMUSG00000101701	4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	ncRNA	0.000000	0.412935			-60(GTTTGCAAGACAAAAG,-,0.00),23(GTATTCTCCTGCAAAA,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7974	chrX	59129438	59129638	+	1.01760	NA	intron (NM_001356335, intron 2 of 4)	intron (NM_001356335, intron 2 of 4)	4898	NM_010200	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding	0.000000	0.253731	-90(AATGCATAATTTATA,+,0.00),-90(AATGCATAATTTATA,-,0.00),30(TATACATAAAGCATG,+,0.00),30(TATACATAAAGCATG,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-57	chr1	182589270	182589470	+	1.01760	NA	intron (NM_130890, intron 2 of 20)	MLT1A0|LTR|ERVL-MaLR	24363	NM_001145806	170725	Mm.189201	NM_130890	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding	0.020000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-621	chr4	59850164	59850364	+	1.01760	NA	intron (NM_172468, intron 1 of 8)	intron (NM_172468, intron 1 of 8)	44614	NM_172468	209131	Mm.259705	NM_172468	ENSMUSG00000028385	Snx30	4732481H14Rik|C030041J06Rik	sorting nexin family member 30	protein-coding	0.015000	0.512438			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4960	chr3	57555677	57555877	+	1.01760	NA	intron (NM_133784, intron 2 of 6)	intron (NM_133784, intron 2 of 6)	20099	NM_133784	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding	0.010000	0.537313			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3018	chr15	90603772	90603972	+	1.01760	NA	intron (NM_025815, intron 5 of 19)	intron (NM_025815, intron 5 of 19)	75516	NM_001033851	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4618	chr2	132474762	132474962	+	1.01760	NA	Intergenic	Intergenic	-15866	NR_028286	70371	Mm.394667	NR_028286	ENSMUSG00000086379	1700026D11Rik	-	RIKEN cDNA 1700026D11 gene	ncRNA	0.030000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3411	chr17	5862387	5862587	+	1.01760	NA	intron (NM_025664, intron 1 of 17)	intron (NM_025664, intron 1 of 17)	21163	NM_025664	66616	Mm.89515	NM_025664	ENSMUSG00000002365	Snx9	2700073N08Rik|SDP1|SH3PX1	sorting nexin 9	protein-coding	0.020000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2559	chr14	76578387	76578587	+	1.01760	NA	Intergenic	MIRc|SINE|MIR	-21571	NM_001360046	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding	0.005000	0.283582			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5092	chr3	102717834	102718034	+	1.01760	NA	Intergenic	Intergenic	-16836	NM_027533	70747	Mm.27469	NM_027533	ENSMUSG00000027858	Tspan2	6330415F13Rik|B230119D02Rik|tspan-2	tetraspanin 2	protein-coding	0.000000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1294	chr11	55757841	55758041	+	1.01760	NA	Intergenic	Intergenic	-149743	NM_001290821	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding	0.000000	0.318408			7(CATTTATCATTCTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2558	chr14	76578114	76578314	+	1.01760	NA	Intergenic	Intergenic	-21298	NM_001360046	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding	0.010000	0.402985			83(CATTTGGTGTGCAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4150	chr2	3912679	3912879	+	1.01760	NA	Intergenic	RLTR13B3|LTR|ERVK	-104904	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|mKIAA1294	FERM domain containing 4A	protein-coding	0.010000	0.383085	30(ATTGCATAATTCATG,+,0.00),30(ATTGCATAATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-876	chr10	69838224	69838424	+	1.01760	NA	intron (NM_146005, intron 7 of 42)	intron (NM_146005, intron 7 of 42)	-87208	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding	0.010000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-149	chr11	55757890	55758090	+	1.01760	NA	Intergenic	Intergenic	-149792	NM_001290821	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding	0.000000	0.318408			-42(CATTTATCATTCTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-898	chrX	57260709	57260909	+	1.01760	NA	intron (NM_001358573, intron 8 of 20)	intron (NM_001358573, intron 8 of 20)	48666	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding	0.000000	0.447761		57(TATGCAAATTCAGG,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7697	chr9	65496381	65496581	+	1.01760	NA	intron (NM_001370871, intron 14 of 14)	ORR1A2|LTR|ERVL-MaLR	23738	NM_001370871	330963	Mm.379561	NM_001370871	ENSMUSG00000066510	Ankdd1a	A730067D02|A730067D02Rik|EG330963|Gm1473	ankyrin repeat and death domain containing 1A	protein-coding	0.000000	0.422886			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-729	chr6	18240556	18240756	+	1.01724	NA	intron (NM_021050, intron 11 of 26)	intron (NM_021050, intron 11 of 26)	69969	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding	0.000000	0.293532			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-129	chr10	126992159	126992359	+	1.01662	NA	intron (NM_001113470, intron 2 of 7)	intron (NM_001113470, intron 2 of 7)	-3271	NR_029803	723962		NR_029803	ENSMUSG00000065430	Mir26a-2	Mirn26a-2|mir-26a-2	microRNA 26a-2	ncRNA	0.000000	0.358209		81(CCTTCATATTCATG,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7199	chr8	34815412	34815612	+	1.01608	NA	intron (NM_176933, intron 1 of 3)	intron (NM_176933, intron 1 of 3)	7902	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding	0.020000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7570	chr9	27616732	27616932	+	1.01608	NA	Intergenic	Intergenic	219620	NM_001305058	75469	Mm.45824	NM_029299	ENSMUSG00000031991	Spata19	1700001L23Rik|AV047838|spergen-1	spermatogenesis associated 19	protein-coding	0.010000	0.427861			-75(CCTTTGTGAAGCAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4751	chr2	159069215	159069415	+	1.01608	NA	Intergenic	Intergenic	274508	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding	0.005000	0.562189			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-614	chr4	34643225	34643425	+	1.01608	NA	intron (NR_151507, intron 8 of 19)	intron (NR_151507, intron 8 of 19)	28368	NR_151507	109093	Mm.22363	NM_181406	ENSMUSG00000028292	Rars2	1500002I10Rik|PRO1992|Rarsl	arginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.010000	0.383085			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-616	chr4	41114505	41114705	+	1.01608	NA	3' UTR (NM_139236, exon 26 of 26)	3' UTR (NM_139236, exon 26 of 26)	9734	NM_139236	230082	Mm.285797	NM_139236	ENSMUSG00000028430	Nol6	AA410091|Nrap	nucleolar protein family 6 (RNA-associated)	protein-coding	0.010000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-8054	chrX	105764166	105764366	+	1.01608	NA	promoter-TSS (NM_030614)	promoter-TSS (NM_030614)	-211	NM_030614	80903	Mm.154768	NM_030614	ENSMUSG00000031230	Fgf16	-	fibroblast growth factor 16	protein-coding	0.040000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3790	chr18	35848546	35848746	+	1.01608	NA	intron (NM_001357458, intron 1 of 2)	intron (NM_001357458, intron 1 of 2)	-6041	NM_001357459	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding	0.015000	0.562189			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-642	chr4	102627515	102627715	+	1.01575	NA	Intergenic	Intergenic	37772	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding	0.010000	0.457711			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5646	chr4	100910641	100910841	+	1.01575	NA	intron (NM_198037, intron 3 of 26)	intron (NM_198037, intron 3 of 26)	134062	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding	0.020000	0.432836			-24(ATTTGCCTGGCAAATC,-,0.00),81(TCTTTTTCTTTCTAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2651	chr14	99885428	99885628	+	1.01575	NA	intron (NM_010636, intron 6 of 6)	intron (NM_010636, intron 6 of 6)	264268	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2354	chr14	11376753	11376953	+	1.01561	NA	Intergenic	Intergenic	94376	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA	0.010000	0.417910			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-506	chr2	102087501	102087701	+	1.01561	NA	intron (NM_178886, intron 2 of 5)	RMER19B|LTR|ERVK	98859	NM_001290784	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.010000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7028	chr7	113347477	113347677	+	1.01561	NA	intron (NM_133700, intron 4 of 10)	intron (NM_133700, intron 4 of 10)	21762	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding	0.005000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6645	chr6	106455543	106455743	+	1.01561	NA	intron (NM_001109749, intron 8 of 25)	intron (NM_001109749, intron 8 of 25)	293394	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding	0.005000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5640	chr4	99641934	99642134	+	1.01561	NA	Intergenic	Intergenic	-14265	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding	0.000000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2751	chr15	3272778	3272978	+	1.01561	NA	intron (NM_009155, intron 1 of 4)	intron (NM_009155, intron 1 of 4)	1901	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding	0.015000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1518	chr12	4417666	4417866	+	1.01561	NA	intron (NM_010881, intron 1 of 22)	L1MA6|LINE|L1	59416	NM_010881	17977	Mm.301039	NM_010881	ENSMUSG00000020647	Ncoa1	KAT13A|NCoA-1|NRC-1|SRC-1|SRC-a|SRC1|bHLHe74|mNRC-1	nuclear receptor coactivator 1	protein-coding	0.005000	0.393035			24(ATCAAAAAGACAAAAG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-475	chr2	38621612	38621812	+	1.01561	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	22194	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding	0.020000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-360	chr1	127575507	127575707	+	1.01452	NA	intron (NM_028135, intron 2 of 7)	intron (NM_028135, intron 2 of 7)	102414	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|A-cre|Act-Cre|SV31|Tg(ACTB-cre)2Mrt|actin-cre|cre<actin>	transmembrane protein 163	protein-coding	0.015000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3923	chr18	69500804	69501004	+	1.01410	NA	intron (NM_001361127, intron 5 of 19)	intron (NM_001361127, intron 5 of 19)	154744	NM_001361128	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding	0.030000	0.487562			-75(ATTTACATAGTAAAAC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2364	chr14	13524022	13524222	+	1.01410	NA	intron (NM_028052, intron 3 of 5)	intron (NM_028052, intron 3 of 5)	70164	NM_001163032	72003	Mm.317515	NM_028052	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding	0.005000	0.368159		13(GTTGAATATGTATA,+,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-483	chr1	157258070	157258270	+	1.01410	NA	intron (NM_177644, intron 3 of 17)	intron (NM_177644, intron 3 of 17)	-149490	NM_001305063	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding	0.000000	0.363184	84(AATCAATTATTCATA,+,0.00),84(AATCAATTATTCATA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3032	chr15	93288524	93288724	+	1.01410	NA	intron (NM_024189, intron 2 of 3)	MER5A|DNA|hAT-Charlie	-13445	NM_001357006	223827	Mm.22819	NM_001033275	ENSMUSG00000036197	Gxylt1	Glt8d3|Gm1228|Gm87	glucoside xylosyltransferase 1	protein-coding	0.005000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-792	chr10	42107574	42107774	+	1.01410	NA	Intergenic	Intergenic	-89292	NM_001034858	213402	Mm.211320	NM_001034858	ENSMUSG00000071324	Armc2	2610018I05Rik	armadillo repeat containing 2	protein-coding	0.015000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3354	chr16	85155347	85155547	+	1.01410	NA	intron (NM_007471, intron 1 of 15)	intron (NM_007471, intron 1 of 15)	18260	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding	0.005000	0.348259			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7235	chr8	47232384	47232584	+	1.01410	NA	intron (NM_175162, intron 1 of 4)	MTE2a|LTR|ERVL-MaLR	56918	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding	0.000000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6290	chr6	6604196	6604396	+	1.01410	NA	Intergenic	Intergenic	-25638	NM_009169	20422	Mm.2469	NM_009169	ENSMUSG00000042541	Sem1	DSS1|Shfdg1|Shfg|Shfm1	SEM1, 26S proteasome complex subunit	protein-coding	0.005000	0.383085			73(ATTAGAAGAACAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4578	chr2	124505974	124506174	+	1.01410	NA	intron (NM_001290997, intron 5 of 20)	intron (NM_001290997, intron 5 of 20)	-104222	NM_199238	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6135	chr5	106825538	106825738	+	1.01410	NA	Intergenic	Intergenic	100252	NM_001252516	330149	Mm.121664	NM_177873	ENSMUSG00000043410	Hfm1	A330009G12Rik|Gm1046|Mer3|Sec63d1	HFM1, ATP-dependent DNA helicase homolog	protein-coding	0.050000	0.597015			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5282	chr3	149498601	149498801	+	1.01410	NA	Intergenic	Intergenic	223964	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA	0.005000	0.343284			-44(GAATTCTCATGCATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2384	chr14	19861310	19861510	+	1.01410	NA	Intergenic	BGLII|LTR|ERVK	22485	NR_105025	52512	Mm.483998	NR_105025	ENSMUSG00000114350	D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA	0.010000	0.383085			-91(CCTTTATTTTACAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2812	chr15	18908137	18908337	+	1.01410	NA	intron (NM_001316758, intron 2 of 11)	intron (NM_001316758, intron 2 of 11)	87908	NM_009865	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0.010000	0.358209			48(ATTTGAAACAGAGTAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-258	chr1	89136522	89136722	+	1.01410	NA	intron (NM_133816, intron 2 of 5)	intron (NM_133816, intron 2 of 5)	66207	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding	0.005000	0.527363			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-910	chr10	86033909	86034109	+	1.01410	NA	intron (NM_001310745, intron 5 of 8)	intron (NM_001310745, intron 5 of 8)	11855	NM_001310745	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding	0.000000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4643	chr2	135439565	135439765	+	1.01283	NA	intron (NM_019677, intron 32 of 32)	intron (NM_019677, intron 32 of 32)	143555	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA	0.015000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4897	chr3	31131314	31131514	+	1.01283	NA	Intergenic	Intergenic	-18506	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding	0.010000	0.452736			-24(TCTTTCTCCTTCAAAC,+,0.00),20(GTTTGAATGAGAATGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7223	chr8	41387153	41387353	+	1.01283	NA	Intergenic	Intergenic	-12556	NM_019734	11886	Mm.22547	NM_019734	ENSMUSG00000031591	Asah1	2310081N20Rik|AC|Asah	N-acylsphingosine amidohydrolase 1	protein-coding	0.000000	0.407960			-82(CTTCTCTGATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2695	chr14	112121601	112121801	+	1.01283	NA	Intergenic	Intergenic	446586	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding	0.005000	0.363184			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4982	chr3	65358941	65359141	+	1.01260	NA	intron (NM_010597, intron 11 of 13)	intron (NM_010597, intron 11 of 13)	-9612	NR_040390	319798	Mm.445698	NR_040390		A730090N16Rik	-	RIKEN cDNA A730090N16 gene	ncRNA	0.000000	0.402985			82(ATTAGAATCACAAATT,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-92	chr10	58949831	58950031	+	1.01260	NA	intron (NM_172788, intron 1 of 9)	intron (NM_172788, intron 1 of 9)	136572	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6037	chr5	76333992	76334192	+	1.01260	NA	intron (NM_019515, intron 9 of 9)	intron (NM_019515, intron 9 of 9)	2854	NR_152115	74621	Mm.444687	NR_152115		4930432L08Rik	-	RIKEN cDNA 4930432L08 gene	ncRNA	0.000000	0.472637			-19(ATGTGAAAAAGAAAGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2366	chr14	14063018	14063218	+	1.01255	NA	intron (NM_139227, intron 4 of 11)	intron (NM_139227, intron 4 of 11)	50627	NM_139227	246103	Mm.133625	NM_139227	ENSMUSG00000021738	Atxn7	A430107N12Rik|AI627028|Sca7|ataxin-7	ataxin 7	protein-coding	0.035000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4204	chr2	20734308	20734508	+	1.01255	NA	intron (NM_001081006, intron 6 of 21)	intron (NM_001081006, intron 6 of 21)	214895	NM_001369134	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-704	chr5	117177998	117178198	+	1.01189	NA	intron (NM_001081308, intron 1 of 19)	L1M2|LINE|L1	44510	NM_001081308	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding	0.035000	0.517413			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-471	chr2	24260615	24260815	+	1.01189	NA	Intergenic	BGLII|LTR|ERVK	-16239	NM_001146087	54450	Mm.29261	NM_019451	ENSMUSG00000026983	Il1f5	AI413231|Fil1delta|IL-36Ra|IL36RN|Il-1h3|Il1hy1	interleukin 1 family, member 5 (delta)	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4636	chr2	135067517	135067717	+	1.01077	NA	intron (NM_001145830, intron 3 of 31)	RLTR26_Mus|LTR|ERVK	147999	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA	0.000000	0.567164			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2269	chr13	106569755	106569955	+	1.01077	NA	Intergenic	Intergenic	367103	NM_001360897	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding	0.005000	0.323383			13(TTATTTGCATGAAAAT,+,0.00),15(ATTTGCATGAAAATGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6144	chr5	108077169	108077369	+	1.01077	NA	promoter-TSS (NM_001253878)	promoter-TSS (NM_001253878)	-896	NM_001253878	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3030	chr15	92867328	92867528	+	1.01077	NA	Intergenic	Intergenic	270319	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5503	chr4	62653713	62653913	+	1.01077	NA	intron (NM_134257, intron 10 of 15)	MIR|SINE|MIR	-20161	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2138	chr13	72594828	72595028	+	1.01077	NA	Intergenic	Intergenic	33636	NR_030701	328287	Mm.235072	NR_030701		Gm20554	D430050G20	predicted gene, 20554	ncRNA	0.010000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5712	chr4	118838098	118838298	+	1.01077	NA	Intergenic	Intergenic	-7760	NM_207157	258265	Mm.482029	NM_207157	ENSMUSG00000110947	Olfr1333	GA_x5J8B7TQTH0-2-774|MOR259-11|MOR259-6	olfactory receptor 1333	protein-coding	0.005000	0.348259			40(TAATTTTCTTTTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5467	chr4	53474099	53474299	+	1.01077	NA	intron (NM_133891, intron 1 of 15)	intron (NM_133891, intron 1 of 15)	33786	NM_133891	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding	0.005000	0.402985			26(TCTTTGTCTTTAATAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3629	chr17	82048534	82048734	+	1.01077	NA	Intergenic	RMER19B|LTR|ERVK	-310247	NM_011406	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding	0.005000	0.398010			-83(CCTTTTTCTTTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6390	chr6	34292932	34293132	+	1.01077	NA	Intergenic	Intergenic	24411	NR_037965	626009	Mm.451	NR_028277		Gm6644	Akr1b3p|EG626009	Akr1b3 pseudogene	pseudo	0.025000	0.532338			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-492	chr2	68575561	68575761	+	1.01077	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-6752	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding	0.005000	0.268657			-35(CTATTTTTATTTAAAT,+,0.00),-3(ATATTATTATGTTAAT,+,0.00),6(TGTTAATCATGAAAAT,+,0.00),62(ATATACAAGACTAAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-451	chr1	150893856	150894056	+	1.01077	NA	intron (NM_001024720, intron 1 of 106)	intron (NM_001024720, intron 1 of 106)	99479	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding	0.010000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4375	chr2	68575646	68575846	+	1.01077	NA	Intergenic	Intergenic	-6667	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding	0.010000	0.253731			-88(ATATTATTATGTTAAT,+,0.00),-79(TGTTAATCATGAAAAT,+,0.00),-23(ATATACAAGACTAAGG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-584	chr3	132984228	132984428	+	1.01077	NA	intron (NM_001356309, intron 11 of 11)	intron (NM_001356309, intron 11 of 11)	-34037	NM_033525	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding	0.010000	0.497512			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3537	chr17	56439919	56440119	+	1.01077	NA	intron (NM_001252455, intron 6 of 27)	intron (NM_001252455, intron 6 of 27)	-21110	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA	0.020000	0.457711			-69(GCATTGTCATGGAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5137	chr3	116985225	116985425	+	1.01077	NA	TTS (NR_040596)	TTS (NR_040596)	-16373	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding	0.000000	0.427861			44(ATTTACATGGCAAAGC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-680	chr5	66385768	66385968	+	1.01077	NA	intron (NM_001201413, intron 9 of 16)	MLT1H|LTR|ERVL-MaLR	-48203	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding	0.005000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7139	chr8	8609111	8609311	+	1.01077	NA	Intergenic	Intergenic	52031	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0.010000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-458	chr1	152573268	152573468	+	1.01077	NA	intron (NM_001346118, intron 4 of 18)	intron (NM_001346118, intron 4 of 18)	51849	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding	0.005000	0.383085			-34(GTTTTGTTATGTTAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4587	chr2	125500410	125500610	+	1.01077	NA	intron (NM_007993, intron 2 of 65)	intron (NM_007993, intron 2 of 65)	5928	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding	0.020000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3459	chr17	29451120	29451320	+	1.01077	NA	Intergenic	Intergenic	-39565	NM_008842	18712	Mm.328931	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding	0.025000	0.577114			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4685	chr2	142148394	142148594	+	1.01019	NA	intron (NM_001013802, intron 8 of 18)	MIRb|SINE|MIR	752970	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0.000000	0.368159			-95(ATTTGAATGACAAGGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-97	chr10	68536951	68537151	+	1.01017	NA	intron (NM_028491, intron 1 of 7)	L1M5|LINE|L1	4824	NM_028491	73287	Mm.141830	NM_028491	ENSMUSG00000019945	Cabcoco1	1700040L02Rik	ciliary associated calcium binding coiled-coil 1	protein-coding	0.025000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2989	chr15	71975689	71975889	+	1.01010	NA	intron (NM_027174, intron 6 of 63)	intron (NM_027174, intron 6 of 63)	58438	NM_027174	69700	Mm.322500	NM_027174	ENSMUSG00000079022	Col22a1	2310067L16Rik|C80743	collagen, type XXII, alpha 1	protein-coding	0.005000	0.442786			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5131	chr3	114999424	114999624	+	1.00973	NA	intron (NM_001286750, intron 1 of 5)	L1M2|LINE|L1	-81441	NM_153157	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding	0.005000	0.313433			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-28	chr1	98025680	98025880	+	1.00973	NA	intron (NM_001357127, intron 1 of 25)	intron (NM_001357127, intron 1 of 25)	22013	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA	0.010000	0.378109			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5254	chr3	146612447	146612647	+	1.00973	NA	exon (NM_009474, exon 4 of 8)	exon (NM_009474, exon 4 of 8)	3051	NM_019957	56629	Mm.25853	NM_019957	ENSMUSG00000028185	Dnase2b	AI526873|Dlad|DnaseIIb	deoxyribonuclease II beta	protein-coding	0.035000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-628	chr1	188998848	188999048	+	1.00973	NA	intron (NM_001359576, intron 4 of 17)	intron (NM_001359576, intron 4 of 17)	8892	NM_001359577	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding	0.005000	0.417910			-72(TTTTGAAAAACAAATT,-,0.00),-10(CTTTAAATGACAAAAG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3449	chr17	27240464	27240664	+	1.00973	NA	intron (NR_131118, intron 1 of 2)	PB1D10|SINE|Alu	7502	NR_131118	319720	Mm.394996	NR_131118	ENSMUSG00000117916	9630028I04Rik	-	RIKEN cDNA 9630028I04 gene	ncRNA	0.020000	0.542289			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-484	chr2	59272149	59272349	+	1.00973	NA	intron (NM_001362991, intron 3 of 20)	intron (NM_001362991, intron 3 of 20)	110380	NM_001362996	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding	0.025000	0.477612			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4941	chr3	51516712	51516912	+	1.00973	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	32846	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding	0.005000	0.313433			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5488	chr4	57193082	57193282	+	1.00973	NA	3' UTR (NM_011207, exon 26 of 26)	3' UTR (NM_011207, exon 26 of 26)	21111	NR_040669	329851	Mm.392470	NR_040669	ENSMUSG00000085967	Gm12530	D730003B17	predicted gene 12530	ncRNA	0.000000	0.338308			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-483	chr2	57303409	57303609	+	1.00970	NA	intron (NM_001145820, intron 3 of 16)	intron (NM_001145820, intron 3 of 16)	65127	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1151	chr11	8147175	8147375	+	1.00970	NA	Intergenic	Intergenic	517260	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding	0.015000	0.497512			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-521	chr2	124731453	124731653	+	1.00970	NA	Intergenic	L1ME2|LINE|L1	77972	NM_199239	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding	0.020000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-607	chr4	14968235	14968435	+	1.00933	NA	intron (NM_178617, intron 9 of 12)	intron (NM_178617, intron 9 of 12)	37694	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	-	predicted gene 11837	protein-coding	0.000000	0.353234			57(ATTTAAAAGACAACTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-785	chr10	39452075	39452275	+	1.00933	NA	intron (NM_001122892, intron 2 of 12)	intron (NM_001122892, intron 2 of 12)	82376	NM_001122892	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding	0.010000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-121	chr10	124630748	124630948	+	1.00933	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	161774	NR_028310	75030	Mm.159403	NR_028310	ENSMUSG00000112364	4930503E24Rik	-	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo	0.005000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5358	chr4	14968258	14968458	+	1.00933	NA	intron (NM_178617, intron 9 of 12)	intron (NM_178617, intron 9 of 12)	37717	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	-	predicted gene 11837	protein-coding	0.000000	0.343284			34(ATTTAAAAGACAACTC,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2206	chr13	92896644	92896844	+	1.00760	NA	Intergenic	RLTR13D2|LTR|ERVK	51976	NM_001162945	382793	Mm.296770	NM_001162945	ENSMUSG00000021704	Mtx3	4930470O13Rik|AA409304|AI853833|AU067765|EG624619|Gm1194|Gm6514	metaxin 3	protein-coding	0.005000	0.393035	-14(CATGAATAATGCAAT,+,0.00),-14(CATGAATAATGCAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7650	chr9	50746049	50746249	+	1.00760	NA	intron (NM_025865, intron 1 of 3)	MIRb|SINE|MIR	378	NM_025865	66952	Mm.273375	NM_025865	ENSMUSG00000032062	2310030G06Rik	2610024D04Rik|AV017521	RIKEN cDNA 2310030G06 gene	protein-coding	0.030000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3895	chr18	62708277	62708477	+	1.00760	NA	intron (NM_001168423, intron 1 of 4)	Lx7|LINE|L1	33010	NM_001168423	100038417	Mm.387557	NM_001168423	ENSMUSG00000073551	Spink13	Gm10534|Spink5l3	serine peptidase inhibitor, Kazal type 13	protein-coding	0.010000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6143	chr5	107601861	107602061	+	1.00760	NA	intron (NM_001289569, intron 3 of 12)	intron (NM_001289569, intron 3 of 12)	4000	NM_001359917	231571	Mm.482420	NM_144911	ENSMUSG00000033773	Rpap2	AW060207	RNA polymerase II associated protein 2	protein-coding	0.005000	0.398010			-88(ATTTAAAATAGAATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3525	chr17	52668050	52668250	+	1.00760	NA	intron (NM_001031811, intron 1 of 15)	intron (NM_001031811, intron 1 of 15)	65441	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding	0.000000	0.378109			-7(AGATTTTGATTTAAAT,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-459	chr1	152573439	152573639	+	1.00760	NA	intron (NM_001346118, intron 4 of 18)	intron (NM_001346118, intron 4 of 18)	51678	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding	0.000000	0.398010			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3708	chr18	11810812	11811012	+	1.00760	NA	Intergenic	Intergenic	-28362	NM_001146287	63955	Mm.40717	NM_022021	ENSMUSG00000040957	Cables1	Cables|ik3-1	CDK5 and Abl enzyme substrate 1	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4895	chr3	30506974	30507174	+	1.00760	NA	intron (NM_001361034, intron 1 of 16)	intron (NM_001361034, intron 1 of 16)	2601	NM_021442	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0.050000	0.512438			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-527	chr2	134252762	134252962	+	1.00760	NA	Intergenic	Intergenic	301490	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	hydroxyacid oxidase 1, liver	protein-coding	0.010000	0.432836			28(CTTAGCATAACAGAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7537	chr9	15535224	15535424	+	1.00760	NA	intron (NM_133214, intron 2 of 2)	MIRc|SINE|MIR	29829	NM_133214	170748	Mm.86572	NM_133214	ENSMUSG00000058173	Smco4	Fn5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.005000	0.447761	9(AATGAATAATGCACA,+,0.00),9(AATGAATAATGCACA,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7531	chr9	14568618	14568818	+	1.00760	NA	intron (NM_001081395, intron 6 of 12)	ORR1D2|LTR|ERVL-MaLR	46282	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding	0.010000	0.422886			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1506	chr11	121777767	121777967	+	1.00760	NA	Intergenic	Intergenic	-52351	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding	0.005000	0.437811	28(ATTCCATTATTCATG,+,0.00),28(ATTCCATTATTCATG,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-174	chr11	121777771	121777971	+	1.00760	NA	Intergenic	Intergenic	-52347	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding	0.005000	0.427861	24(ATTCCATTATTCATG,+,0.00),24(ATTCCATTATTCATG,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4634	chr2	134252747	134252947	+	1.00760	NA	Intergenic	Intergenic	301505	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	hydroxyacid oxidase 1, liver	protein-coding	0.010000	0.432836			43(CTTAGCATAACAGAGG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-446	chr1	149919346	149919546	+	1.00760	NA	intron (NM_001305632, intron 2 of 16)	intron (NM_001305632, intron 2 of 16)	2993	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding	0.010000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3020	chr15	91007412	91007612	+	1.00760	NA	intron (NM_001109041, intron 1 of 35)	MER5B|DNA|hAT-Charlie	42439	NM_001109041	16564	Mm.41379	NM_016705	ENSMUSG00000022629	Kif21a	-	kinesin family member 21A	protein-coding	0.020000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-956	chr10	95862754	95862954	+	1.00760	NA	Intergenic	Intergenic	-77809	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7514	chr9	9169596	9169796	+	1.00760	NA	intron (NM_027823, intron 2 of 22)	intron (NM_027823, intron 2 of 22)	-66592	NR_045754	100579151	Mm.412450	NR_045754	ENSMUSG00000085253	Gm16833	-	predicted gene, 16833	ncRNA	0.010000	0.338308			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7635	chr9	45626195	45626395	+	1.00760	NA	intron (NM_001081270, intron 3 of 32)	intron (NM_001081270, intron 3 of 32)	-195063	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	ncRNA	0.005000	0.522388			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1487	chr11	115409666	115409866	+	1.00691	NA	intron (NR_154991, intron 2 of 4)	intron (NR_154991, intron 2 of 4)	6014	NM_001361463	68572	Mm.271062	NM_026729	ENSMUSG00000018858	Mrpl58	1110001A02Rik|1110002E03Rik|Ict1|MRP-L58	mitochondrial ribosomal protein L58	protein-coding	0.020000	0.507463			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7402	chr8	99416393	99416593	+	1.00691	NA	promoter-TSS (NM_007667)	promoter-TSS (NM_007667)	-22	NR_133570	12564	Mm.441131	NM_007667	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0.055000	0.621891			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1858	chr12	102658828	102659028	+	1.00691	NA	intron (NM_172584, intron 2 of 9)	intron (NM_172584, intron 2 of 9)	26092	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA	0.030000	0.507463		-77(AATAAATATACATA,-,0.00),-71(TATACATATTTATG,+,0.00),-71(TATACATATTTATG,-,0.00)	
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-356	chr15	101221681	101221881	+	1.00691	NA	non-coding (NR_045328, exon 3 of 3)	non-coding (NR_045328, exon 3 of 3)	534	NR_045996	105968	Mm.120798	NR_045996	ENSMUSG00000115944	AU021063	-	expressed sequence AU021063	ncRNA	0.025000	0.552239			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-815	chr7	130166369	130166569	+	1.00691	NA	intron (NM_201601, intron 15 of 15)	intron (NM_201601, intron 15 of 15)	100339	NM_001347638	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding	0.015000	0.412935			79(TATTTGTTTTTTAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-507	chr2	102138342	102138542	+	1.00685	NA	intron (NM_178886, intron 1 of 5)	intron (NM_178886, intron 1 of 5)	48018	NM_001290784	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1131	chr10	127000520	127000720	+	1.00685	NA	promoter-TSS (NM_009635)	promoter-TSS (NM_009635)	-89	NM_009635	11567	Mm.10739	NM_009635	ENSMUSG00000025432	Avil	Advil|DOC6	advillin	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4477	chr2	102138336	102138536	+	1.00685	NA	intron (NM_178886, intron 1 of 5)	intron (NM_178886, intron 1 of 5)	48024	NM_001290784	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.005000	0.437811			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3155	chr16	32456125	32456325	+	1.00674	NA	intron (NM_001163160, intron 3 of 8)	ORR1A2|LTR|ERVL-MaLR	24995	NM_001163160	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding	0.000000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-532	chr2	138326377	138326577	+	1.00674	NA	Intergenic	Intergenic	47984	NM_145534	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding	0.000000	0.432836			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1810	chr12	90975933	90976133	+	1.00674	NA	Intergenic	Intergenic	-69815	NR_045858	71349	Mm.442093	NR_045858	ENSMUSG00000085004	5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA	0.015000	0.457711			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-320	chr14	114002124	114002324	+	1.00674	NA	Intergenic	Intergenic	-829741	NR_045661	75822	Mm.410813	NR_045661	ENSMUSG00000115320	4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	ncRNA	0.000000	0.328358			-92(TCTTTTACATGCAAAC,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1170	chr11	16240713	16240913	+	1.00674	NA	Intergenic	RLTR13B1|LTR|ERVK	-16929	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0.010000	0.432836	71(CATGAATAATGTAAT,+,0.00),71(CATGAATAATGTAAT,-,0.00)		
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3305	chr16	70474847	70475047	+	1.00674	NA	intron (NM_028803, intron 7 of 15)	intron (NM_028803, intron 7 of 15)	-141478	NR_040474	52645	Mm.188475	NR_040474	ENSMUSG00000116792	D16Ertd519e	-	DNA segment, Chr 16, ERATO Doi 519, expressed	ncRNA	0.005000	0.333333			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-756	chr6	82957307	82957507	+	1.00674	NA	intron (NM_033079, intron 2 of 9)	intron (NM_033079, intron 2 of 9)	10485	NM_033079	110958	Mm.100652	NM_033079	ENSMUSG00000030041	M1ap	D6Mm5e	meiosis 1 associated protein	protein-coding	0.030000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-366	chr16	32456120	32456320	+	1.00674	NA	intron (NM_001163160, intron 3 of 8)	ORR1A2|LTR|ERVL-MaLR	24990	NM_001163160	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding	0.000000	0.507463			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-703	chr5	115078801	115079001	+	1.00674	NA	intron (NM_029012, intron 3 of 10)	intron (NM_029012, intron 3 of 10)	29061	NM_001271591	100502825	Mm.361657	NM_001271590		Rpl37rt	EyeLinc4|Gm13826|Rpl37	ribosomal protein L37, retrotransposed	protein-coding	0.000000	0.343284			7(TTTTTCTTAGGTTAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-453	chr18	85403691	85403891	+	1.00674	NA	Intergenic	Intergenic	451675	NM_001367965	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding	0.005000	0.422886			8(ATTTACAAGGGAATTG,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-184	chr12	34048581	34048781	+	1.00674	NA	3' UTR (NM_001271386, exon 28 of 28)	3' UTR (NM_001271386, exon 28 of 28)	91010	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding	0.000000	0.412935		-25(TATACATATACATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2193	chr13	90358989	90359189	+	1.00674	NA	Intergenic	Intergenic	269422	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0.010000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-190	chr12	64849068	64849268	+	1.00674	NA	Intergenic	Intergenic	-68743	NM_001025605	217648	Mm.341586	NM_001025605	ENSMUSG00000047227	Gm527	-	predicted gene 527	protein-coding	0.015000	0.368159			-42(ATTTCAATAATAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2685	chr14	105860328	105860528	+	1.00674	NA	Intergenic	Intergenic	36391	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty RTK signaling antagonist 2	protein-coding	0.015000	0.402985			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5819	chr5	8316756	8316956	+	1.00674	NA	intron (NM_001007220, intron 3 of 28)	intron (NM_001007220, intron 3 of 28)	51304	NM_001098225	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding	0.005000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2822	chr15	23416174	23416374	+	1.00539	NA	intron (NM_001081299, intron 8 of 11)	RLTR18B|LTR|ERVK	379811	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l|Tg(GFAP-APOE_i4)1Hol	cadherin 18	protein-coding	0.015000	0.432836			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-907	chrX	129645456	129645656	+	1.00497	NA	Intergenic	Intergenic	-104186	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding	0.000000	0.323383			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-80	chr10	9603422	9603622	+	1.00497	NA	Intergenic	Intergenic	71686	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding	0.010000	0.383085			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4663	chr2	138325931	138326131	+	1.00457	NA	Intergenic	Intergenic	47538	NM_145534	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding	0.005000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7387	chr8	95784895	95785095	+	1.00457	NA	intron (NM_001205226, intron 2 of 48)	intron (NM_001205226, intron 2 of 48)	-21835	NR_015574	319960	Mm.386996	NR_015574	ENSMUSG00000074136	4930513N10Rik	-	RIKEN cDNA 4930513N10 gene	ncRNA	0.000000	0.288557			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1208	chr11	26252245	26252445	+	1.00457	NA	Intergenic	Intergenic	-41769	NR_027973	70626	Mm.379180	NM_027486		5730522E02Rik	-	RIKEN cDNA 5730522E02 gene	ncRNA	0.000000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-606	chr4	11893361	11893561	+	1.00457	NA	Intergenic	Intergenic	72252	NM_001098231	381511	Mm.331489	NM_001033453	ENSMUSG00000049225	Pdp1	Gm1024|Ppm2c	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.005000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7981	chrX	68682533	68682733	+	1.00457	NA	intron (NM_001290424, intron 1 of 16)	intron (NM_001290424, intron 1 of 16)	4092	NM_008031	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation 1	protein-coding	0.000000	0.323383			-62(ATTTACATGTTAAAGA,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-651	chr4	124048558	124048758	+	1.00457	NA	Intergenic	Intergenic	131225	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding	0.020000	0.527363			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-622	chr4	62607275	62607475	+	1.00457	NA	intron (NM_019492, intron 6 of 19)	intron (NM_019492, intron 6 of 19)	-12297	NM_001081650	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding	0.020000	0.447761			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2359	chr14	11716906	11717106	+	1.00457	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	163453	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding	0.020000	0.358209		75(CATGCATTTGCATA,+,0.00),75(CATGCATTTGCATA,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2553	chr14	75982626	75982826	+	1.00457	NA	intron (NM_026816, intron 4 of 7)	intron (NM_026816, intron 4 of 7)	27723	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding	0.005000	0.298507			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5725	chr4	124406763	124406963	+	1.00457	NA	Intergenic	Intergenic	79096	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	ncRNA	0.005000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-652	chr4	124406776	124406976	+	1.00457	NA	Intergenic	Intergenic	79083	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	ncRNA	0.005000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5312	chr3	157348530	157348730	+	1.00457	NA	Intergenic	Intergenic	185460	NR_152231	381498	Mm.402095	NR_152231	ENSMUSG00000105834	4930592C13Rik	Gm1657|Gm43159	RIKEN cDNA 4930592C13 gene	ncRNA	0.000000	0.333333			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2428	chr14	31934655	31934855	+	1.00457	NA	Intergenic	Intergenic	-94348	NM_030166	78754	Mm.40681	NM_030166	ENSMUSG00000021903	Galnt15	4631401E18Rik|Galntl2|mpp-GalNAc-T15	polypeptide N-acetylgalactosaminyltransferase 15	protein-coding	0.000000	0.388060			33(ATTTGAATGTCTAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5359	chr4	15064595	15064795	+	1.00457	NA	intron (NM_178617, intron 4 of 12)	intron (NM_178617, intron 4 of 12)	84436	NM_178617	69352	Mm.389031	NM_178617	ENSMUSG00000040536	Necab1	1700003H21Rik|Efcbp1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding	0.000000	0.273632			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-589	chr3	142443417	142443617	+	1.00457	NA	Intergenic	Intergenic	-47821	NM_019809	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding	0.020000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-94	chr10	60027704	60027904	+	1.00443	NA	intron (NM_001199187, intron 5 of 10)	intron (NM_001199187, intron 5 of 10)	24477	NM_001199187	69090	Mm.155839	NM_026937	ENSMUSG00000044475	Ascc1	1810015P09Rik|AI550520|ASC1p50|CGI-18	activating signal cointegrator 1 complex subunit 1	protein-coding	0.000000	0.467662			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7323	chr8	77310968	77311168	+	1.00443	NA	intron (NM_001363418, intron 18 of 21)	intron (NM_001363418, intron 18 of 21)	141021	NM_001363420	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PS-GAP|PSGAP|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding	0.010000	0.333333			-51(TTTAACATCAGAAAAG,-,0.00),-35(ATTAACATAAAAATTC,-,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-737	chr6	35288461	35288661	+	1.00421	NA	intron (NM_172892, intron 3 of 15)	intron (NM_172892, intron 3 of 15)	19565	NM_172892	243755	Mm.23666	NM_172892	ENSMUSG00000029843	Slc13a4	9630060C05Rik|SUT-1|SUT1	solute carrier family 13 (sodium/sulfate symporters), member 4	protein-coding	0.005000	0.492537			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-498	chr1	161148171	161148371	+	1.00421	NA	intron (NM_001368766, intron 2 of 7)	MLT1F2|LTR|ERVL-MaLR	5559	NM_028664	73844	Mm.38830	NM_028664	ENSMUSG00000044835	Ankrd45	4933409K03Rik	ankyrin repeat domain 45	protein-coding	0.005000	0.502488			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-775	chr6	126803176	126803376	+	1.00421	NA	Intergenic	Intergenic	45868	NM_025358	66108	Mm.29939	NM_025358	ENSMUSG00000000399	Ndufa9	1010001N11Rik	NADH:ubiquinone oxidoreductase subunit A9	protein-coding	0.020000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-76	chr10	4653143	4653343	+	1.00421	NA	intron (NM_007956, intron 1 of 8)	intron (NM_007956, intron 1 of 8)	41254	NR_126357	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding	0.005000	0.333333	18(CATGAAAAATGCATG,+,0.00),18(CATGAAAAATGCATG,-,0.00)		
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-375	chr16	57736453	57736653	+	1.00421	NA	intron (NM_007739, intron 1 of 3)	intron (NM_007739, intron 1 of 3)	18184	NM_007739	12837	Mm.130388	NM_007739	ENSMUSG00000068196	Col8a1	Col8a-1	collagen, type VIII, alpha 1	protein-coding	0.000000	0.343284			8(ATTTGCTTAAAAAATA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6026	chr5	73419410	73419610	+	1.00388	NA	intron (NM_181323, intron 7 of 15)	L2a|LINE|L2	13432	NM_181323	231293	Mm.280211	NM_181323	ENSMUSG00000029154	Cwh43	C130090K23Rik|imds-60	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.030000	0.542289			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-34	chr1	129710271	129710471	+	1.00388	NA	intron (NM_172485, intron 7 of 27)	intron (NM_172485, intron 7 of 27)	437067	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding	0.000000	0.447761			-93(ATCAGCATAACTATAT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1317	chr11	63109233	63109433	+	1.00388	NA	Intergenic	Intergenic	-19649	NM_001302257	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|TRE002|Tr|trembler	peripheral myelin protein 22	protein-coding	0.000000	0.398010			78(ATTTGAATATGAAATG,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5369	chr4	19699886	19700086	+	1.00388	NA	intron (NM_177327, intron 1 of 24)	intron (NM_177327, intron 1 of 24)	9018	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.005000	0.412935			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-665	chr5	27313427	27313627	+	1.00388	NA	intron (NM_001136060, intron 1 of 25)	intron (NM_001136060, intron 1 of 25)	51592	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0.000000	0.447761			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-19	chr1	69178612	69178812	+	1.00388	NA	Intergenic	Intergenic	-70653	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding	0.005000	0.402985			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-228	chr13	13831314	13831514	+	1.00388	NA	Intergenic	Intergenic	47107	NM_010317	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding	0.000000	0.502488			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5878	chr5	27313507	27313707	+	1.00388	NA	intron (NM_001136060, intron 1 of 25)	intron (NM_001136060, intron 1 of 25)	51672	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0.005000	0.487562			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6338	chr6	18240559	18240759	+	1.00249	NA	intron (NM_021050, intron 11 of 26)	intron (NM_021050, intron 11 of 26)	69972	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding	0.000000	0.293532			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1951	chr13	12423483	12423683	+	1.00209	NA	intron (NM_144835, intron 28 of 44)	intron (NM_144835, intron 28 of 44)	28208	NM_144835	217995	Mm.171186	NM_144835	ENSMUSG00000050244	Heatr1	AA517551|B130016L12Rik|BC019693	HEAT repeat containing 1	protein-coding	0.000000	0.343284			10(ATTTGAAAGAGAAAAA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5956	chr5	53250624	53250824	+	1.00166	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-16382	NM_001145433	66278	Mm.27900	NM_001145433	ENSMUSG00000061461	Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding	0.010000	0.407960			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-298	chr14	75982589	75982789	+	1.00166	NA	intron (NM_026816, intron 4 of 7)	intron (NM_026816, intron 4 of 7)	27686	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding	0.000000	0.293532			-67(ATTAAAATGAAAAGGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7439	chr8	108302428	108302628	+	1.00166	NA	Intergenic	Intergenic	282149	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA	0.025000	0.552239			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2256	chr13	102842422	102842622	+	1.00166	NA	intron (NM_175171, intron 5 of 28)	intron (NM_175171, intron 5 of 28)	82267	NR_130318	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7196	chr8	34372534	34372734	+	1.00166	NA	Intergenic	Intergenic	-205922	NR_105820	102465211		NR_105820	ENSMUSG00000098785	Mir6395	Gm27561|mmu-mir-6395	microRNA 6395	ncRNA	0.010000	0.482587			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1697	chr12	65110704	65110904	+	1.00166	NA	intron (NM_001364447, intron 14 of 22)	ORR1D1-int|LTR|ERVL-MaLR	35201	NM_178912	104806	Mm.374847	NM_178912	ENSMUSG00000055884	Fancm	AI427100|C730036B14Rik|D12Ertd364e	Fanconi anemia, complementation group M	protein-coding	0.015000	0.517413			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4185	chr2	16423373	16423573	+	1.00166	NA	intron (NM_026162, intron 1 of 13)	B3|SINE|B2	67169	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0.010000	0.407960			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6363	chr6	25543987	25544187	+	1.00166	NA	Intergenic	Intergenic	145893	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding	0.000000	0.353234			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-5721	chr4	123404102	123404302	+	1.00166	NA	3' UTR (NM_001167918, exon 1 of 1)	3' UTR (NM_001167918, exon 1 of 1)	7709	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1364	chr11	76425835	76426035	+	1.00166	NA	intron (NM_198894, intron 16 of 22)	Charlie2b|DNA|hAT-Charlie	11370	NM_001363379	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding	0.010000	0.412935			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6907	chr7	74013758	74013958	+	1.00166	NA	promoter-TSS (NM_009181)	promoter-TSS (NM_009181)	-176	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding	0.065000	0.656716			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3134	chr16	27113128	27113328	+	1.00166	NA	Intergenic	Intergenic	-121576	NM_001013761	239789	Mm.326909	NM_001013761	ENSMUSG00000068428	Gmnc	Gemc1|Gm1778|Gm606	geminin coiled-coil domain containing	protein-coding	0.000000	0.338308			16(ATTTGAAAGAAAAAGA,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6556	chr6	82956845	82957045	+	1.00166	NA	intron (NM_033079, intron 2 of 9)	intron (NM_033079, intron 2 of 9)	10023	NM_033079	110958	Mm.100652	NM_033079	ENSMUSG00000030041	M1ap	D6Mm5e	meiosis 1 associated protein	protein-coding	0.005000	0.427861			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4977	chr3	63844927	63845127	+	1.00166	NA	intron (NM_001370984, intron 3 of 23)	intron (NM_001370984, intron 3 of 23)	6258	NM_001177733	269437	Mm.316391	NM_183191	ENSMUSG00000036834	Plch1	BC042549|PLC-eta-1|PLCeta1|Plcl3	phospholipase C, eta 1	protein-coding	0.010000	0.467662			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-539	chr2	159093389	159093589	+	1.00166	NA	Intergenic	MT2A|LTR|ERVL	298682	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding	0.015000	0.388060			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-7774	chr9	81712911	81713111	+	1.00166	NA	Intergenic	L1MA5|LINE|L1	-79179	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	5-HT-1B	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding	0.010000	0.343284			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-245	chr1	86263917	86264117	+	1.00166	NA	intron (NM_030184, intron 23 of 24)	intron (NM_030184, intron 23 of 24)	-39204	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding	0.005000	0.542289			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6476	chr6	59602281	59602481	+	1.00166	NA	Intergenic	MYSERV16_I-int|LTR|ERVK	-176075	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0.000000	0.338308			36(GTAAGCATGACAATGT,-,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4752	chr2	159093412	159093612	+	1.00166	NA	Intergenic	MT2A|LTR|ERVL	298705	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding	0.015000	0.393035			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-264	chr1	91490453	91490653	+	1.00166	NA	Intergenic	Intergenic	-4115	NM_028718	74019	Mm.318430	NM_028718	ENSMUSG00000034292	Traf3ip1	3930402D05Rik|AU041749|MIP-T3	TRAF3 interacting protein 1	protein-coding	0.005000	0.472637			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-295	chr1	104652554	104652754	+	1.00166	NA	Intergenic	Intergenic	-115866	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.005000	0.417910			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-3929	chr18	70628708	70628908	+	1.00160	NA	Intergenic	L2a|LINE|L2	60516	NM_001311071	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding	0.025000	0.462687			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2386	chr14	19975537	19975737	+	1.00160	NA	intron (NM_001285908, intron 1 of 3)	intron (NM_001285908, intron 1 of 3)	1056	NM_001285911	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding	0.010000	0.378109			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-696	chr5	102727242	102727442	+	1.00160	NA	intron (NM_029270, intron 3 of 9)	intron (NM_029270, intron 3 of 9)	-41468	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding	0.015000	0.427861			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-631	chr4	82311615	82311815	+	1.00160	NA	intron (NM_001286131, intron 8 of 9)	intron (NM_001286131, intron 8 of 9)	194064	NM_001286131	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding	0.005000	0.393035			-87(ACTTTGCTATTTAAAG,+,0.00)
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-622	chr1	187939361	187939561	+	1.00112	NA	intron (NM_001357534, intron 2 of 7)	intron (NM_001357534, intron 2 of 7)	-58366	NM_001357536	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding	0.030000	0.482587			48(CACTTGTAATGGAAAT,+,0.00)
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-272	chr13	117235530	117235730	+	1.00112	NA	intron (NM_010330, intron 2 of 8)	intron (NM_010330, intron 2 of 8)	15057	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding	0.020000	0.557214			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-1058	chr10	115509843	115510043	+	1.00112	NA	intron (NM_010195, intron 2 of 17)	intron (NM_010195, intron 2 of 17)	-60043	NM_029982	77798	Mm.446685	NM_029982	ENSMUSG00000092210	A930009A15Rik	-	RIKEN cDNA A930009A15 gene	protein-coding	0.005000	0.373134			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4812	chr2	180087077	180087277	+	1.00112	NA	Intergenic	Intergenic	16584	NM_028422	52856	Mm.219658	NM_028422	ENSMUSG00000039069	Mtg2	1810011P19Rik|2900056P18Rik|D2Bwg0647e|Gtpbp5	mitochondrial ribosome associated GTPase 2	protein-coding	0.015000	0.572139			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-4262	chr2	38621840	38622040	+	1.00112	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	21966	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding	0.005000	0.472637			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-770	chr6	108965739	108965939	+	1.00112	NA	Intergenic	Intergenic	137198	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding	0.010000	0.462687			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-625	chr4	63971653	63971853	+	1.00112	NA	intron (NM_001369214, intron 13 of 20)	intron (NM_001369214, intron 13 of 20)	75183	NM_001369212	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding	0.005000	0.368159			
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-2323	chr13	117235524	117235724	+	1.00112	NA	intron (NM_010330, intron 2 of 8)	intron (NM_010330, intron 2 of 8)	15051	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding	0.020000	0.547264			
OSKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-681	chr5	66853809	66854009	+	1.00092	NA	intron (NM_001001980, intron 1 of 25)	intron (NM_001001980, intron 1 of 25)	-3560	NM_001368863	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding	0.005000	0.328358		-74(TGTGAATATTCATT,+,0.00),-74(TGTGAATATTCATT,-,0.00)	
ESKM-D3-R2_trimmed_macs2_callpeak_summits.bed_rmchrM_unique-6309	chr6	13294785	13294985	+	1.00092	NA	Intergenic	Intergenic	-69920	NM_001013757	232585	Mm.389082	NM_001013757	ENSMUSG00000079679	Vwde	Gm467	von Willebrand factor D and EGF domains	protein-coding	0.010000	0.462687