PeakID (cmd=annotatePeaks.pl KO_blchirp.bed mm10 -cpu 120)	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
Merged-chr17-38579227-1	chr17	38579149	38579306	+	1	NA	Intergenic	Intergenic	25035	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr1-171541373-1	chr1	171541206	171541540	+	1	NA	Intergenic	BGLII_B|LTR|ERVK	-6079	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
Merged-chr19-44836073-1	chr19	44835937	44836210	+	1	NA	promoter-TSS (NR_045315)	promoter-TSS (NR_045315)	-135	NR_045315	73322	Mm.250457	NR_045315	ENSMUSG00000092369	1700039E22Rik	-	RIKEN cDNA 1700039E22 gene	ncRNA
Merged-chr1-165408520-1	chr1	165408420	165408621	+	1	NA	intron (NM_028759, intron 6 of 18)	L1Md_Gf|LINE|L1	51943	NM_028759	74106	Mm.227605	NM_028759	ENSMUSG00000026571	Dcaf6	1200006M05Rik|Iqwd1|PC326	DDB1 and CUL4 associated factor 6	protein-coding
Merged-chr5-93807874-1	chr5	93807639	93808109	+	1	NA	Intergenic	L1Md_T|LINE|L1	-136411	NM_001164284	381654	Mm.326591	NM_001164284	ENSMUSG00000070686	C87414	-	expressed sequence C87414	protein-coding
Merged-chr11-16730685-1	chr11	16730562	16730808	+	1	NA	Intergenic	L1Md_T|LINE|L1	-21518	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
Merged-chr1-154935360-1	chr1	154935260	154935460	+	1	NA	Intergenic	L1Md_A|LINE|L1	147904	NR_151545	671336	Mm.393476	NR_151545	ENSMUSG00000096950	Gm9530	-	predicted gene 9530	ncRNA
Merged-chr17-69324855-1	chr17	69324743	69324968	+	1	NA	Intergenic	L1Md_T|LINE|L1	-47649	NR_045428	69750	Mm.439063	NR_045428	ENSMUSG00000100572	2410021H03Rik	-	RIKEN cDNA 2410021H03 gene	ncRNA
Merged-chr4-113952221-1	chr4	113952078	113952364	+	1	NA	intron (NM_001167878, intron 2 of 57)	L1_Mus2|LINE|L1	47282	NM_001167876	242627	Mm.484115	NM_001167876	ENSMUSG00000078598	Skint5	Skint-5	selection and upkeep of intraepithelial T cells 5	protein-coding
Merged-chr1-44486048-1	chr1	44485969	44486128	+	1	NA	Intergenic	L1Md_T|LINE|L1	-65623	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
Merged-chr11-64304001-1	chr11	64303860	64304142	+	1	NA	Intergenic	L1Md_T|LINE|L1	-131331	NM_178870	15478	Mm.340214	NM_178870	ENSMUSG00000047759	Hs3st3a1	3Ost3a|Hs3st3a	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	protein-coding
Merged-chr17-66449194-1	chr17	66449083	66449305	+	1	NA	exon (NM_001114098, exon 1 of 15)	exon (NM_001114098, exon 1 of 15)	556	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
Merged-chr15-18665556-1	chr15	18665411	18665701	+	1	NA	Intergenic	L1Md_T|LINE|L1	-153391	NM_001316758	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
Merged-chr5-89206651-1	chr5	89206554	89206748	+	1	NA	intron (NM_001359211, intron 19 of 26)	MMETn-int|LTR|ERVK	178685	NM_001359213	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
Merged-chr11-64302303-1	chr11	64302207	64302399	+	1	NA	Intergenic	L1Md_T|LINE|L1	-133029	NM_178870	15478	Mm.340214	NM_178870	ENSMUSG00000047759	Hs3st3a1	3Ost3a|Hs3st3a	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	protein-coding
Merged-chr10-66075871-1	chr10	66075757	66075985	+	1	NA	Intergenic	L1Md_T|LINE|L1	48193	NR_038039	69433	Mm.23366	NR_038039	ENSMUSG00000100000	1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	ncRNA
Merged-chr4-62495485-1	chr4	62495371	62495599	+	1	NA	intron (NM_138653, intron 5 of 6)	intron (NM_138653, intron 5 of 6)	6715	NM_024257	72748	Mm.41506	NM_024257	ENSMUSG00000038422	Hdhd3	2810435D12Rik	haloacid dehalogenase-like hydrolase domain containing 3	protein-coding
Merged-chr11-92597124-1	chr11	92596990	92597259	+	1	NA	Intergenic	L1Md_A|LINE|L1	-501242	NM_001361707	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
Merged-chr11-120660118-1	chr11	120659876	120660360	+	1	NA	exon (NM_175263, exon 2 of 12)	exon (NM_175263, exon 2 of 12)	719	NM_175263	77583	Mm.32839	NM_175263	ENSMUSG00000042988	Notum	5730593N15Rik	notum palmitoleoyl-protein carboxylesterase	protein-coding
Merged-chr17-72450606-1	chr17	72450525	72450688	+	1	NA	intron (NM_007439, intron 1 of 28)	IAPEz-int|LTR|ERVK	153701	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding
Merged-chr16-33757512-1	chr16	33757379	33757645	+	1	NA	intron (NM_175256, intron 12 of 14)	(TG)n|Simple_repeat|Simple_repeat	-36525	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
Merged-chr1-20250666-1	chr1	20250483	20250850	+	1	NA	intron (NM_153179, intron 52 of 66)	L1Md_T|LINE|L1	-105788	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA
Merged-chr1-171518457-1	chr1	171518379	171518536	+	1	NA	intron (NM_010584, intron 7 of 7)	intron (NM_010584, intron 7 of 7)	14979	NM_019484	56009	Mm.389208	NM_019484	ENSMUSG00000060244	Alyref2	C130042O11Rik|REF2|Refbp2	Aly/REF export factor 2	protein-coding
Merged-chr11-15782932-1	chr11	15782775	15783089	+	1	NA	Intergenic	L1Md_T|LINE|L1	-474792	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding
Merged-chr7-12288112-1	chr7	12288011	12288213	+	1	NA	Intergenic	L1Md_T|LINE|L1	-16693	NM_134234	171268	Mm.377220	NM_134234	ENSMUSG00000058132	Vmn1r82	V1rg12	vomeronasal 1 receptor 82	protein-coding
Merged-chr8-120188145-1	chr8	120188054	120188237	+	1	NA	Intergenic	Intergenic	-10676	NM_001033980	436062	Mm.334852	NM_001033980	ENSMUSG00000042269	Fam92b	1700120B06Rik	family with sequence similarity 92, member B	protein-coding
Merged-chr1-107629965-1	chr1	107629741	107630189	+	1	NA	Intergenic	L1Md_T|LINE|L1	39959	NM_001159748	20725	Mm.83909	NM_011459	ENSMUSG00000026315	Serpinb8	CAP-2|CAP2|NK10|Spi8|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 8	protein-coding
Merged-chr19-4045266-1	chr19	4045131	4045402	+	1	NA	Intergenic	RLTR6_Mm|LTR|ERV1	-3045	NM_181796	14869	Mm.441542	NM_181796	ENSMUSG00000038155	Gstp2	GSTpiA|Gst-3|Gst3	glutathione S-transferase, pi 2	protein-coding
Merged-chr10-17144847-1	chr10	17144764	17144930	+	1	NA	Intergenic	L1Md_T|LINE|L1	-49065	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA
Merged-chr15-89155316-1	chr15	89155223	89155409	+	1	NA	TTS (NM_138749)	TTS (NM_138749)	-5710	NM_011161	19094	Mm.91969	NM_011161	ENSMUSG00000053137	Mapk11	P38b|Prkm11|Sapk2|Sapk2b|p38-2|p38beta|p38beta2	mitogen-activated protein kinase 11	protein-coding
Merged-chr10-13895972-1	chr10	13895822	13896122	+	1	NA	Intergenic	L1Md_T|LINE|L1	24692	NR_152745	102634635		NR_152745	ENSMUSG00000112172	Gm32172	-	predicted gene, 32172	ncRNA
Merged-chr11-13382893-1	chr11	13382808	13382979	+	1	NA	Intergenic	L1Md_T|LINE|L1	796148	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
Merged-chr19-29686364-1	chr19	29686231	29686498	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-11577	NM_029993	77836	Mm.138437	NM_029993	ENSMUSG00000024806	Mlana	A930034P04Rik|Mart1	melan-A	protein-coding
Merged-chr16-26269570-1	chr16	26269488	26269653	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	102269	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding
Merged-chr13-66364848-1	chr13	66364722	66364974	+	1	NA	Intergenic	RLTR1A2_MM|LTR|ERV1	76270	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-80576992-1	chr10	80576835	80577149	+	1	NA	exon (NM_078477, exon 1 of 2)	exon (NM_078477, exon 1 of 2)	304	NM_078477	118445	Mm.41513	NM_078477	ENSMUSG00000035397	Klf16	AI843742|BTEB4|DRRF	Kruppel-like factor 16	protein-coding
Merged-chr1-165531230-1	chr1	165531058	165531402	+	1	NA	intron (NM_173029, intron 13 of 33)	L1Md_T|LINE|L1	46047	NM_001357427	271639	Mm.66952	NM_173029	ENSMUSG00000026567	Adcy10	4930431D04Rik|4931412F17|Sacy|sAC	adenylate cyclase 10	protein-coding
Merged-chr10-22336318-1	chr10	22336231	22336405	+	1	NA	intron (NM_009018, intron 6 of 6)	Lx8|LINE|L1	-25576	NM_020030	56554	Mm.458004	NM_020030	ENSMUSG00000078452	Raet1d	RAE-1delta	retinoic acid early transcript delta	protein-coding
Merged-chr1-146448952-1	chr1	146448740	146449165	+	1	NA	Intergenic	L1Md_A|LINE|L1	-46677	NM_001357571	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr17-34765565-1	chr17	34765199	34765931	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-21668	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
Merged-chr11-26432359-1	chr11	26432163	26432555	+	1	NA	intron (NM_001277273, intron 6 of 13)	L1Md_T|LINE|L1	45275	NR_102382	67030	Mm.18875	NM_025923	ENSMUSG00000004018	Fancl	2010322C19Rik|AW554273|B230118H11Rik|Phf9|Pog|gcd	Fanconi anemia, complementation group L	protein-coding
Merged-chr7-85100479-1	chr7	85100399	85100560	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	55423	NM_001102579	620672	Mm.469836	NM_001102579	ENSMUSG00000095664	Vmn2r67	EG620672	vomeronasal 2, receptor 67	protein-coding
Merged-chr10-101570113-1	chr10	101570027	101570199	+	1	NA	Intergenic	L1Md_A|LINE|L1	-111374	NM_001205098	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
Merged-chr9-108601231-1	chr9	108601124	108601339	+	1	NA	Intergenic	ORR1A3-int|LTR|ERVL-MaLR	-3619	NM_001357465	74443	Mm.226534	NM_028944	ENSMUSG00000006675	P4htm	4933406E20Rik|AI853847|BB128974|HIF-PH4|HPH-4|P4H-TM|Ph-4	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	protein-coding
Merged-chr11-17582151-1	chr11	17581868	17582435	+	1	NA	Intergenic	L1Md_A|LINE|L1	324463	NM_001330649	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
Merged-chr19-57619510-1	chr19	57619395	57619626	+	1	NA	intron (NM_181415, intron 1 of 28)	L1MA7|LINE|L1	8476	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
Merged-chr1-40915487-1	chr1	40915381	40915594	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	109886	NM_001081198	381339	Mm.334678	NM_001081198	ENSMUSG00000079588	Tmem182	2310079P10Rik|AI414494	transmembrane protein 182	protein-coding
Merged-chr8-56943219-1	chr8	56943063	56943376	+	1	NA	Intergenic	L1Md_T|LINE|L1	377640	NR_110474	102636514	Mm.229304	NR_110474	ENSMUSG00000100510	AV026068	Uph	expressed sequence AV026068	ncRNA
Merged-chr10-28709928-1	chr10	28709806	28710050	+	1	NA	intron (NR_131208, intron 1 of 3)	L1Md_T|LINE|L1	41568	NM_001305663	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
Merged-chr10-42379216-1	chr10	42379117	42379316	+	1	NA	intron (NM_001359297, intron 6 of 11)	L1Md_A|LINE|L1	99349	NM_001359297	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Afg1l	CG8520|Lace1	AFG1 like ATPase	protein-coding
Merged-chr8-105947119-1	chr8	105947039	105947200	+	1	NA	exon (NM_001253804, exon 16 of 24)	exon (NM_001253804, exon 16 of 24)	-3717	NM_008490	16816	Mm.1593	NM_008490	ENSMUSG00000035237	Lcat	AI046659|D8Wsu61e	lecithin cholesterol acyltransferase	protein-coding
Merged-chr12-42562050-1	chr12	42561896	42562204	+	1	NA	Intergenic	L1Md_T|LINE|L1	472167	NR_148724	102636207		NR_148724		Gm33340	Gm40882	predicted gene, 33340	ncRNA
Merged-chrX-3226683-1	chrX	3226564	3226803	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	149763	NM_001270667	100861966	Mm.443264	NM_001270667	ENSMUSG00000100249	Btbd35f23	Gm21950|Mgclh	BTB domain containing 35, family member 23	protein-coding
Merged-chr8-7037228-1	chr8	7037123	7037334	+	1	NA	Intergenic	L1Md_F2|LINE|L1	1623545	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr17-36134630-1	chr17	36134549	36134712	+	1	NA	Intergenic	RMER21A|LTR|ERV1	-5205	NM_001177467	630294	Mm.484916	NM_001177467	ENSMUSG00000092243	Gm7030	EG630294|H2-t9	predicted gene 7030	protein-coding
Merged-chr10-72460158-1	chr10	72460062	72460254	+	1	NA	Intergenic	L1Md_A|LINE|L1	-194688	NM_025635	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
Merged-chr5-123544103-1	chr5	123544025	123544182	+	1	NA	intron (NM_001359513, intron 8 of 11)	ETnERV3-int|LTR|ERVK	-19939	NM_023232	66593	Mm.46716	NM_023232	ENSMUSG00000029433	Diablo	0610041G12Rik|1700006L01Rik|AU040403|Smac	diablo, IAP-binding mitochondrial protein	protein-coding
Merged-chr12-116007965-1	chr12	116007668	116008263	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-39759	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
Merged-chr11-119275737-1	chr11	119275639	119275835	+	1	NA	intron (NM_008064, intron 8 of 19)	PB1D10|SINE|Alu	7774	NM_001159324	14387	Mm.4793	NM_008064	ENSMUSG00000025579	Gaa	E430018M07Rik	glucosidase, alpha, acid	protein-coding
Merged-chr10-121943880-1	chr10	121943798	121943962	+	1	NA	intron (NM_001081037, intron 1 of 21)	L1Md_T|LINE|L1	103435	NM_001081037	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding
Merged-chr17-17047515-1	chr17	17047433	17047597	+	1	NA	Intergenic	Lx6|LINE|L1	-16588	NM_001163919	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr1-173977744-1	chr1	173977639	173977850	+	1	NA	intron (NM_008327, intron 1 of 6)	intron (NM_008327, intron 1 of 6)	5100	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
Merged-chr5-89204684-1	chr5	89204156	89205212	+	1	NA	intron (NM_001359211, intron 19 of 26)	ETnERV-int|LTR|ERVK	176718	NM_001359213	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
Merged-chr10-46916255-1	chr10	46916090	46916420	+	1	NA	Intergenic	L1Md_T|LINE|L1	671506	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr11-116500140-1	chr11	116500048	116500233	+	1	NA	Intergenic	Intergenic	-9794	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding
Merged-chr10-47799932-1	chr10	47799851	47800013	+	1	NA	Intergenic	L1Md_T|LINE|L1	1555183	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr16-8502806-1	chr16	8502664	8502949	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	-10623	NM_172961	268860	Mm.259315	NM_172961	ENSMUSG00000057880	Abat	9630038C02Rik|AI255750|Gabaat|Gabat|Gm9851|I54|Laibat|X61497	4-aminobutyrate aminotransferase	protein-coding
Merged-chr17-17222225-1	chr17	17222114	17222336	+	1	NA	Intergenic	Lx3_Mus|LINE|L1	-12678	NM_001362181	102640673		NM_001362181		LOC102640673	-	zinc finger protein 431-like	protein-coding
Merged-chrX-42573256-1	chrX	42573071	42573441	+	1	NA	intron (NM_011855, intron 26 of 32)	L1Md_T|LINE|L1	67934	NM_001313691	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
Merged-chrX-107455672-1	chrX	107455576	107455769	+	1	NA	Intergenic	Lx|LINE|L1	-52312	NM_008409	16431	Mm.193	NM_008409	ENSMUSG00000031239	Itm2a	AW108051|Bricd2a|E25|Itm2	integral membrane protein 2A	protein-coding
Merged-chr13-68079389-1	chr13	68079154	68079624	+	1	NA	Intergenic	Intergenic	152431	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr5-107576548-1	chr5	107576463	107576633	+	1	NA	intron (NM_001161739, intron 4 of 16)	L1Md_F2|LINE|L1	-20825	NM_001163462	231571	Mm.482420	NM_144911	ENSMUSG00000033773	Rpap2	AW060207	RNA polymerase II associated protein 2	protein-coding
Merged-chr13-66497229-1	chr13	66497141	66497317	+	1	NA	Intergenic	Intergenic	-56111	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr3-24239623-1	chr3	24239442	24239805	+	1	NA	intron (NM_001326288, intron 5 of 13)	L1Md_T|LINE|L1	544383	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
Merged-chr1-126793821-1	chr1	126793724	126793918	+	1	NA	intron (NM_176957, intron 1 of 12)	L1Md_T|LINE|L1	36811	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
Merged-chrX-14571378-1	chrX	14571257	14571499	+	1	NA	Intergenic	L1Md_T|LINE|L1	360230	NM_001034100	385328	Mm.275681	NM_001034100	ENSMUSG00000078346	H2al1n	EG385328|Gm5382	H2A histone family member L1N	protein-coding
Merged-chr19-34107511-1	chr19	34107359	34107663	+	1	NA	intron (NM_023903, intron 2 of 9)	L1Md_A|LINE|L1	6568	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
Merged-chr1-140763027-1	chr1	140762873	140763181	+	1	NA	Intergenic	L1Md_T|LINE|L1	-106625	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr6-96596430-1	chr6	96596227	96596634	+	1	NA	intron (NM_182808, intron 3 of 4)	L1Md_T|LINE|L1	-430225	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
Merged-chr11-21444791-1	chr11	21444653	21444929	+	1	NA	Intergenic	L1Md_F2|LINE|L1	66389	NR_028259	237694	Mm.72926	NM_172792	ENSMUSG00000078962	4932414J04Rik	-	RIKEN cDNA 4932414J04 gene	ncRNA
Merged-chr8-20997032-1	chr8	20996845	20997219	+	1	NA	Intergenic	RLTR51B_Mm|LTR|ERVK?	-28513	NM_183253	66298	Mm.482941	NM_183253	ENSMUSG00000074447	Defa21	2010016B13Rik|Defcr21	defensin, alpha, 21	protein-coding
Merged-chr10-50678667-1	chr10	50678575	50678759	+	1	NA	intron (NM_198007, intron 13 of 41)	L1Md_T|LINE|L1	85998	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
Merged-chr12-44491755-1	chr12	44491600	44491910	+	1	NA	intron (NM_001146031, intron 3 of 27)	L1Md_T|LINE|L1	162870	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
Merged-chr19-4215152-1	chr19	4215044	4215261	+	1	NA	intron (NM_001310039, intron 1 of 2)	CpG	763	NM_001310039	56708	Mm.347919	NM_019952	ENSMUSG00000040663	Clcf1	BSF-3|Bsf3|CLC|NNT-1	cardiotrophin-like cytokine factor 1	protein-coding
Merged-chr1-69193493-1	chr1	69193390	69193596	+	1	NA	Intergenic	L1Md_A|LINE|L1	-85434	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
Merged-chr19-48980347-1	chr19	48980118	48980577	+	1	NA	Intergenic	L1Md_T|LINE|L1	774322	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
Merged-chr10-87067232-1	chr10	87067131	87067333	+	1	NA	intron (NM_029685, intron 1 of 5)	L1Md_T|LINE|L1	9186	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
Merged-chr17-45622406-1	chr17	45622313	45622500	+	1	NA	Intergenic	B3|SINE|B2	-20304	NM_001177469	653016	Mm.45676	NM_001177468	ENSMUSG00000079471	Mymx	EG653016|Esgp|Gm7325|minion|myomerger	myomixer, myoblast fusion factor	protein-coding
Merged-chr13-68444571-1	chr13	68444450	68444692	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-87746	NR_152173	666272	Mm.309128	NR_152173	ENSMUSG00000113050	Gm8016	EG666272	predicted gene 8016	ncRNA
Merged-chr8-24472332-1	chr8	24472238	24472426	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	12654	NR_035483								
Merged-chr5-34573773-1	chr5	34573672	34573874	+	1	NA	promoter-TSS (NR_106111)	promoter-TSS (NR_106111)	109	NM_001331087	11518	Mm.289106	NM_013457	ENSMUSG00000029106	Add1	AI256389	adducin 1 (alpha)	protein-coding
Merged-chr13-66458853-1	chr13	66458753	66458954	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-17735	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr12-14672130-1	chr12	14671992	14672268	+	1	NA	Intergenic	L1Md_T|LINE|L1	378259	NR_045960	73972	Mm.107680	NR_045960	ENSMUSG00000113644	4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA
Merged-chr10-12999917-1	chr10	12999792	13000043	+	1	NA	Intergenic	L1Md_T|LINE|L1	-8533	NM_175102	66125	Mm.29743	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	splicing factor 3b, subunit 5	protein-coding
Merged-chr11-52554629-1	chr11	52554488	52554771	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	158201	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
Merged-chr8-7272611-1	chr8	7272529	7272694	+	1	NA	Intergenic	Intergenic	1388162	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr1-114736059-1	chr1	114735962	114736156	+	1	NA	Intergenic	L1Md_A|LINE|L1	-949078	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr10-112427480-1	chr10	112427394	112427566	+	1	NA	intron (NM_001359753, intron 2 of 4)	L1Md_T|LINE|L1	156207	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
Merged-chr15-97889076-1	chr15	97888998	97889155	+	1	NA	intron (NM_009504, intron 1 of 9)	intron (NM_009504, intron 1 of 9)	19220	NM_009504	22337	Mm.245084	NM_009504	ENSMUSG00000022479	Vdr	Nr1i1	vitamin D (1,25-dihydroxyvitamin D3) receptor	protein-coding
Merged-chr14-51594182-1	chr14	51594023	51594342	+	1	NA	intron (NM_001013816, intron 1 of 4)	RLTR14-int|LTR|ERV1	41392	NM_001013816	434459	Mm.359230	NM_001013816	ENSMUSG00000079244	Gm5622	EG434459	predicted gene 5622	protein-coding
Merged-chr1-68629902-1	chr1	68629814	68629991	+	1	NA	intron (NM_010154, intron 2 of 26)	L1Md_T|LINE|L1	478157	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
Merged-chr10-45842683-1	chr10	45842539	45842827	+	1	NA	intron (NR_040624, intron 2 of 2)	L1Md_T|LINE|L1	34979	NR_040624	320363	Mm.123343	NR_040624	ENSMUSG00000110874	D030045P18Rik	-	RIKEN cDNA D030045P18 gene	ncRNA
Merged-chr19-46503960-1	chr19	46503838	46504082	+	1	NA	intron (NM_053100, intron 1 of 5)	intron (NM_053100, intron 1 of 5)	2312	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
Merged-chr15-55906473-1	chr15	55906395	55906551	+	1	NA	exon (NM_016667, exon 1 of 7)	exon (NM_016667, exon 1 of 7)	476	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
Merged-chr12-115295598-1	chr12	115295506	115295690	+	1	NA	Intergenic	Intergenic	400196	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr11-91445971-1	chr11	91445870	91446073	+	1	NA	Intergenic	L1Md_A|LINE|L1	131584	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding
Merged-chr1-44965173-1	chr1	44964913	44965433	+	1	NA	Intergenic	L1Md_T|LINE|L1	-220224	NR_040602	75066	Mm.416932	NR_040602	ENSMUSG00000101701	4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	ncRNA
Merged-chr11-114660962-1	chr11	114660878	114661046	+	1	NA	Intergenic	RLTR10-int|LTR|ERVK	-7581	NM_001048057	67671	Mm.238817	NM_023372	ENSMUSG00000057322	Rpl38	0610025G13Rik|Rbt|Ts|Tss	ribosomal protein L38	protein-coding
Merged-chr1-99186934-1	chr1	99186714	99187154	+	1	NA	Intergenic	L1Md_A|LINE|L1	-585831	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
Merged-chr14-35532568-1	chr14	35532403	35532733	+	1	NA	intron (NM_008166, intron 13 of 15)	L1Md_A|LINE|L1	279410	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding
Merged-chr1-46566060-1	chr1	46565954	46566166	+	1	NA	intron (NM_001310335, intron 19 of 64)	L1Md_A|LINE|L1	140542	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
Merged-chr8-49574292-1	chr8	49573949	49574636	+	1	NA	Intergenic	L1Md_T|LINE|L1	-793820	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
Merged-chr11-71383239-1	chr11	71383076	71383403	+	1	NA	Intergenic	L1Md_A|LINE|L1	-98007	NR_027858	627984	Mm.390378	NM_001039234	ENSMUSG00000092528	Nlrp1c-ps	Nalp1c|Nlrp1c	NLR family, pyrin domain containing 1C, pseudogene	pseudo
Merged-chr1-130492274-1	chr1	130492104	130492445	+	1	NA	Intergenic	L1Md_T|LINE|L1	-29530	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
Merged-chr15-72378254-1	chr15	72378116	72378393	+	1	NA	Intergenic	L1_Mm|LINE|L1	168025	NM_001033876	223604	Mm.386856	NM_001033876	ENSMUSG00000036760	Kcnk9	Task3	potassium channel, subfamily K, member 9	protein-coding
Merged-chr19-33286581-1	chr19	33286463	33286699	+	1	NA	intron (NM_001146342, intron 2 of 4)	L1Md_T|LINE|L1	105714	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
Merged-chr1-163161282-1	chr1	163161072	163161493	+	1	NA	Intergenic	L1Md_A|LINE|L1	-75612	NM_030071	78258	Mm.78368	NM_030071	ENSMUSG00000071890	Mroh9	4921528O07Rik|Armc11	maestro heat-like repeat family member 9	protein-coding
Merged-chr1-81503195-1	chr1	81503063	81503328	+	1	NA	Intergenic	L1Md_T|LINE|L1	425788	NM_001356397	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
Merged-chr10-64822085-1	chr10	64821979	64822191	+	1	NA	intron (NM_001164376, intron 13 of 17)	L1Md_T|LINE|L1	298282	NR_152621	102632700		NR_152621	ENSMUSG00000100528	Gm28881	-	predicted gene 28881	ncRNA
Merged-chr8-70779799-1	chr8	70779691	70779907	+	1	NA	exon (NM_199308, exon 26 of 26)	exon (NM_199308, exon 26 of 26)	2937	NR_029440	72093	Mm.271208	NR_029440		2010320M18Rik	-	RIKEN cDNA 2010320M18 gene	ncRNA
Merged-chr3-155150510-1	chr3	155150349	155150671	+	1	NA	intron (NM_028938, intron 5 of 7)	L1Md_T|LINE|L1	57076	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
Merged-chr15-4284707-1	chr15	4284623	4284791	+	1	NA	Intergenic	L1Md_A|LINE|L1	-90784	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	phosphatidylinositol-specific phospholipase C, X domain containing 3	protein-coding
Merged-chr8-70650370-1	chr8	70650262	70650479	+	1	NA	3' UTR (NM_023217, exon 5 of 5)	3' UTR (NM_023217, exon 5 of 5)	9368	NM_023217	66522	Mm.154906	NM_023217	ENSMUSG00000056204	Pgpep1	2810003H13Rik|Gm19458|PAP-I|PGP|PGP-I|PGPI|Pcp	pyroglutamyl-peptidase I	protein-coding
Merged-chr1-171562516-1	chr1	171562373	171562660	+	1	NA	intron (NM_018729, intron 1 of 8)	intron (NM_018729, intron 1 of 8)	3323	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
Merged-chr19-38819222-1	chr19	38819137	38819307	+	1	NA	promoter-TSS (NM_021315)	promoter-TSS (NM_021315)	15	NM_021315	57753	Mm.86482	NM_021315	ENSMUSG00000024999	Noc3l	AF233884|Fad24	NOC3 like DNA replication regulator	protein-coding
Merged-chr1-20706714-1	chr1	20706592	20706837	+	1	NA	Intergenic	L1Md_A|LINE|L1	23945	NR_029902	723817		NR_029902	ENSMUSG00000065480	Mir133b	Mirn133b|mir-133b	microRNA 133b	ncRNA
Merged-chr13-66731798-1	chr13	66731708	66731889	+	1	NA	Intergenic	L1_Mus4|LINE|L1	173552	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr10-43259933-1	chr10	43259848	43260018	+	1	NA	intron (NM_027772, intron 1 of 7)	L1Md_A|LINE|L1	38447	NM_027772	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding
Merged-chr14-56202134-1	chr14	56202050	56202219	+	1	NA	Intergenic	L1Md_T|LINE|L1	9273	NM_010374	14943	Mm.457976	NM_010374	ENSMUSG00000015441	Gzmf	CCP4|Ctla-7|Ctla7|MCSP-3	granzyme F	protein-coding
Merged-chr12-115187763-1	chr12	115187675	115187851	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	508031	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr17-34592629-1	chr17	34592551	34592707	+	1	NA	TTS (NM_134116)	TTS (NM_134116)	158	NM_017463	18515	Mm.390957	NM_017463	ENSMUSG00000034673	Pbx2	AU043397|G17	pre B cell leukemia homeobox 2	protein-coding
Merged-chr8-116978847-1	chr8	116978662	116979032	+	1	NA	promoter-TSS (NM_001357254)	promoter-TSS (NM_001357254)	112	NM_001357255	69528	Mm.272846	NM_027103	ENSMUSG00000031847	1700030J22Rik	-	RIKEN cDNA 1700030J22 gene	protein-coding
Merged-chr11-10533309-1	chr11	10533210	10533409	+	1	NA	Intergenic	L1Md_A|LINE|L1	-580707	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
Merged-chr19-18622152-1	chr19	18622069	18622235	+	1	NA	intron (NM_017375, intron 1 of 9)	Lx3A|LINE|L1	9661	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding
Merged-chr18-48980800-1	chr18	48980703	48980897	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-542489	NR_033785	67321	Mm.245802	NR_033785	ENSMUSG00000100297	1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	ncRNA
Merged-chr19-5980144-1	chr19	5980051	5980238	+	1	NA	intron (NM_198650, intron 6 of 9)	B4|SINE|B4	5999	NM_198650	381203	Mm.329638	NM_198650	ENSMUSG00000037451	Slc22a20	Gm963|OAT1-L|mOAT6	solute carrier family 22 (organic anion transporter), member 20	protein-coding
Merged-chr15-38253443-1	chr15	38253342	38253545	+	1	NA	Intergenic	B4A|SINE|B4	34240	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding
Merged-chr1-173259170-1	chr1	173259056	173259285	+	1	NA	Intergenic	L1Md_A|LINE|L1	-10977	NM_146651	258645	Mm.377611	NM_146651	ENSMUSG00000049605	Olfr418	MOR267-12P|MOR267-8|Olfr1403|Olfr418-ps1	olfactory receptor 418	protein-coding
Merged-chr1-62672662-1	chr1	62672430	62672895	+	1	NA	Intergenic	L1Md_T|LINE|L1	-30655	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
Merged-chr12-113661309-1	chr12	113661212	113661407	+	1	NA	Intergenic	Intergenic	117401	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr17-23902693-1	chr17	23902540	23902847	+	1	NA	Intergenic	Intergenic	3971	NM_001039238	630537	Mm.436677	NM_001039238	ENSMUSG00000096278	Dcpp2	Dcpp-2|EG630537|SPT-2	demilune cell and parotid protein 2	protein-coding
Merged-chr10-99663817-1	chr10	99663662	99663972	+	1	NA	Intergenic	L1Md_T|LINE|L1	-21897	NR_038018	100417125	Mm.391428	NR_038018	ENSMUSG00000112503	Gm18409	-	mediator of cell motility 1 pseudogene	pseudo
Merged-chr5-145675605-1	chr5	145675502	145675708	+	1	NA	Intergenic	IAP1-MM_I-int|LTR|ERVK	44531	NM_017396	53973	Mm.379071	NM_017396	ENSMUSG00000075551	Cyp3a41a	Cyp3a41	cytochrome P450, family 3, subfamily a, polypeptide 41A	protein-coding
Merged-chr12-18643288-1	chr12	18643195	18643382	+	1	NA	Intergenic	Lx4B|LINE|L1	128778	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
Merged-chr15-76821483-1	chr15	76821373	76821593	+	1	NA	Intergenic	L2|LINE|L2	-3313	NM_001168288	223666	Mm.322931	NM_198420	ENSMUSG00000033697	Arhgap39	9530053N22|AI843066|D15Wsu169e|Kiaa1688|Porf-2	Rho GTPase activating protein 39	protein-coding
Merged-chr1-68627911-1	chr1	68627797	68628025	+	1	NA	intron (NM_010154, intron 2 of 26)	L1Md_T|LINE|L1	480148	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
Merged-chr16-9245682-1	chr16	9245566	9245799	+	1	NA	Intergenic	Intergenic	415582	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
Merged-chr17-83256477-1	chr17	83256389	83256566	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	41194	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	protein kinase domain containing, cytoplasmic	protein-coding
Merged-chr11-73472835-1	chr11	73472739	73472931	+	1	NA	Intergenic	L1Md_T|LINE|L1	13987	NM_147022	259024	Mm.390415	NM_147022	ENSMUSG00000072708	Olfr381	MOR135-4	olfactory receptor 381	protein-coding
Merged-chr4-88788056-1	chr4	88787920	88788193	+	1	NA	promoter-TSS (NM_001098840)	promoter-TSS (NM_001098840)	79	NM_001098840	545650	Mm.473677	NM_001098840	ENSMUSG00000100234	Gm13277	-	predicted gene 13277	protein-coding
Merged-chr3-8449517-1	chr3	8449422	8449613	+	1	NA	Intergenic	L1Md_T|LINE|L1	13581	NR_033512	620966	Mm.301719	NR_033512		Gm6194	1700003N22Rik|EG620966	transmembrane protein 189 pseudogene	pseudo
Merged-chr16-56838440-1	chr16	56838345	56838536	+	1	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	-42582	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
Merged-chr15-75921926-1	chr15	75921842	75922010	+	1	NA	promoter-TSS (NM_025412)	promoter-TSS (NM_025412)	-366	NM_025412	66194	Mm.250599	NM_025412	ENSMUSG00000022571	Pycrl	1110058B13Rik|2700073G24Rik|Pycr3	pyrroline-5-carboxylate reductase-like	protein-coding
Merged-chr15-101246523-1	chr15	101246426	101246620	+	1	NA	Intergenic	CpG	-20323	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|NUR77-1|NUR77-2|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
Merged-chr1-10386117-1	chr1	10386014	10386220	+	1	NA	intron (NM_001289497, intron 7 of 9)	L1Md_T|LINE|L1	-153447	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
Merged-chr2-9514617-1	chr2	9514526	9514709	+	1	NA	Intergenic	L1Md_A|LINE|L1	325102	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
Merged-chr1-7979640-1	chr1	7979550	7979730	+	1	NA	Intergenic	L1Md_A|LINE|L1	890720	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
Merged-chr8-79100655-1	chr8	79100492	79100818	+	1	NA	intron (NM_001294279, intron 5 of 14)	Lx|LINE|L1	72218	NM_001294279	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
Merged-chr10-63668017-1	chr10	63667922	63668112	+	1	NA	intron (NM_001164376, intron 5 of 17)	L1Md_A|LINE|L1	-153038	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
Merged-chr15-46155801-1	chr15	46155713	46155889	+	1	NA	Intergenic	L1Md_A|LINE|L1	-168784	NR_045509	71120	Mm.158571	NR_045509	ENSMUSG00000099751	1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	ncRNA
Merged-chr12-36339372-1	chr12	36339205	36339540	+	1	NA	Intergenic	L1Md_T|LINE|L1	25203	NM_025312	66042	Mm.43375	NM_025312	ENSMUSG00000036169	Sostdc1	0610006G05Rik|Sostl|USAG-1|Wise|ectodin	sclerostin domain containing 1	protein-coding
Merged-chr7-10014524-1	chr7	10014401	10014647	+	1	NA	Intergenic	MMERVK10C-int|LTR|ERVK	-22385	NM_001105156	625605	Mm.484763	NM_001105156	ENSMUSG00000096180	Vmn2r49	-	vomeronasal 2, receptor 49	protein-coding
Merged-chr10-96670863-1	chr10	96670779	96670947	+	1	NA	Intergenic	L1Md_T|LINE|L1	53862	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
Merged-chr10-64821136-1	chr10	64820927	64821345	+	1	NA	intron (NM_001164376, intron 13 of 17)	L1Md_T|LINE|L1	299231	NR_152621	102632700		NR_152621	ENSMUSG00000100528	Gm28881	-	predicted gene 28881	ncRNA
Merged-chr17-35274728-1	chr17	35274643	35274814	+	1	NA	Intergenic	Intergenic	11605	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
Merged-chr5-108881553-1	chr5	108881450	108881657	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-29043	NM_001104621	435864	Mm.387745	NM_001104621	ENSMUSG00000091624	Vmn2r9	EG435864	vomeronasal 2, receptor 9	protein-coding
Merged-chr1-174709002-1	chr1	174708902	174709103	+	1	NA	intron (NM_019445, intron 13 of 17)	L1Md_A|LINE|L1	207177	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding
Merged-chr1-83514423-1	chr1	83514335	83514512	+	1	NA	Intergenic	L1Md_T|LINE|L1	-106223	NM_001356547	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding
Merged-chr12-59501294-1	chr12	59501209	59501379	+	1	NA	Intergenic	L1Md_T|LINE|L1	-281811	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding
Merged-chr16-27737609-1	chr16	27737504	27737714	+	1	NA	Intergenic	L1Md_A|LINE|L1	-112321	NR_033475	100038623	Mm.387135	NR_033475		Gm10823	-	predicted gene 10823	ncRNA
Merged-chr1-16164960-1	chr1	16164825	16165095	+	1	NA	Intergenic	L1Md_T|LINE|L1	59078	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding
Merged-chr10-45689289-1	chr10	45689202	45689376	+	1	NA	intron (NM_172473, intron 20 of 23)	L1Md_A|LINE|L1	111460	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
Merged-chr15-97078415-1	chr15	97078335	97078496	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-22459	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
Merged-chr13-6673290-1	chr13	6673171	6673409	+	1	NA	Intergenic	L1Md_T|LINE|L1	-24519	NM_001291071	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
Merged-chr10-28968571-1	chr10	28968423	28968720	+	1	NA	Intergenic	Intergenic	17735	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
Merged-chr17-35255846-1	chr17	35255750	35255943	+	1	NA	Intergenic	Intergenic	4557	NR_106169	102465886		NR_106169	ENSMUSG00000098269	Mir8094	Gm27513|mmu-mir-8094	microRNA 8094	ncRNA
Merged-chr10-23634447-1	chr10	23634185	23634709	+	1	NA	Intergenic	L1Md_T|LINE|L1	151004	NR_037680	100529074	Mm.371846	NR_037680	ENSMUSG00000070063	Snora33	ACA33|MBI-42	small nucleolar RNA, H/ACA box 33	snoRNA
Merged-chr11-16191250-1	chr11	16191132	16191369	+	1	NA	Intergenic	L1Md_T|LINE|L1	-66474	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding
Merged-chr1-163279220-1	chr1	163279073	163279367	+	1	NA	intron (NM_001025570, intron 1 of 2)	L1Md_T|LINE|L1	34430	NM_175686	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
Merged-chr1-61671048-1	chr1	61670913	61671183	+	1	NA	intron (NM_001081050, intron 1 of 22)	L1Md_A|LINE|L1	32224	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
Merged-chr8-7277153-1	chr8	7277070	7277237	+	1	NA	Intergenic	Intergenic	1383620	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr10-22174475-1	chr10	22174327	22174623	+	1	NA	intron (NM_001359808, intron 5 of 8)	intron (NM_001359808, intron 5 of 8)	573	NM_009018	19370	Mm.439724	NM_009018		Raet1c	RAE-1gamma	retinoic acid early transcript gamma	protein-coding
Merged-chr1-18541535-1	chr1	18541320	18541751	+	1	NA	Intergenic	L1Md_T|LINE|L1	-276397	NM_001040027	77673	Mm.99530	NM_183124	ENSMUSG00000067773	Defb41	9230102D03Rik|BD-17|Bd-41|Defb16|Defb17|Gm15386	defensin beta 41	protein-coding
Merged-chr19-21013246-1	chr19	21013135	21013358	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-59044	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding
Merged-chr3-24191543-1	chr3	24191404	24191683	+	1	NA	intron (NM_001326288, intron 6 of 13)	L1Md_A|LINE|L1	592463	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
Merged-chr8-20988744-1	chr8	20988636	20988852	+	1	NA	Intergenic	Intergenic	-36801	NM_183253	66298	Mm.482941	NM_183253	ENSMUSG00000074447	Defa21	2010016B13Rik|Defcr21	defensin, alpha, 21	protein-coding
Merged-chr13-66653538-1	chr13	66653401	66653676	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-212420	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr17-38589163-1	chr17	38588870	38589457	+	1	NA	Intergenic	Lx5|LINE|L1	34971	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr13-62081646-1	chr13	62081561	62081732	+	1	NA	Intergenic	Lx2A1|LINE|L1	-48244	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr13-68060165-1	chr13	68060013	68060318	+	1	NA	Intergenic	Intergenic	171655	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chrX-124215493-1	chrX	124215305	124215682	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-79583	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
Merged-chr7-10016359-1	chr7	10016120	10016599	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-24220	NM_001105156	625605	Mm.484763	NM_001105156	ENSMUSG00000096180	Vmn2r49	-	vomeronasal 2, receptor 49	protein-coding
Merged-chrX-66476385-1	chrX	66476268	66476502	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-172933	NM_001161431	245450	Mm.336081	NM_198863	ENSMUSG00000036790	Slitrk2	A930040J07	SLIT and NTRK-like family, member 2	protein-coding
Merged-chr1-130035052-1	chr1	130034962	130035142	+	1	NA	intron (NM_172485, intron 15 of 27)	L1Md_A|LINE|L1	-387772	NR_151525	102640368		NR_151525	ENSMUSG00000087691	Gm15674	-	predicted gene 15674	ncRNA
Merged-chr17-56476547-1	chr17	56476459	56476635	+	1	NA	promoter-TSS (NM_011218)	promoter-TSS (NM_011218)	-67	NM_001252455	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
Merged-chr19-31937505-1	chr19	31937319	31937691	+	1	NA	intron (NM_001081074, intron 9 of 11)	L1Md_T|LINE|L1	68744	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
Merged-chr1-20577588-1	chr1	20577428	20577749	+	1	NA	intron (NM_153179, intron 11 of 66)	L1Md_A|LINE|L1	40469	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
Merged-chr15-83350360-1	chr15	83350229	83350492	+	1	NA	promoter-TSS (NM_025445)	promoter-TSS (NM_025445)	-113	NM_001357756	66251	Mm.258910	NM_025445	ENSMUSG00000054277	Arfgap3	0610009H19Rik|1810004P07Rik|1810035F16Rik|9130416J18Rik|Arfgap1	ADP-ribosylation factor GTPase activating protein 3	protein-coding
Merged-chr6-84764503-1	chr6	84764376	84764631	+	1	NA	intron (NM_177077, intron 19 of 21)	L1Md_Gf|LINE|L1	-170595	NM_001177713	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
Merged-chr12-115605198-1	chr12	115604981	115605415	+	1	NA	Intergenic	Intergenic	90596	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr12-58123650-1	chr12	58123450	58123850	+	1	NA	Intergenic	L1Md_A|LINE|L1	-88154	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
Merged-chr1-145416219-1	chr1	145416127	145416312	+	1	NA	Intergenic	L1Md_T|LINE|L1	-640792	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
Merged-chr8-15218132-1	chr8	15218050	15218215	+	1	NA	Intergenic	Intergenic	160479	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
Merged-chr11-117323861-1	chr11	117323768	117323955	+	1	NA	intron (NM_001113486, intron 3 of 11)	B4A|SINE|B4	-7854	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
Merged-chr1-55478912-1	chr1	55478815	55479009	+	1	NA	intron (NM_001114663, intron 1 of 5)	L1Md_T|LINE|L1	72966	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
Merged-chr5-115158610-1	chr5	115158510	115158710	+	1	NA	promoter-TSS (NM_175403)	promoter-TSS (NM_175403)	-434	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
Merged-chr1-54391850-1	chr1	54391547	54392154	+	1	NA	Intergenic	L1Md_T|LINE|L1	47176	NM_001033194	98488	Mm.25856	NM_001033194	ENSMUSG00000041303	Gtf3c3	TF3C-gamma|TFIIIC102	general transcription factor IIIC, polypeptide 3	protein-coding
Merged-chr10-106082305-1	chr10	106082202	106082408	+	1	NA	Intergenic	L1Md_A|LINE|L1	240826	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding
Merged-chr19-27132607-1	chr19	27132497	27132717	+	1	NA	Intergenic	L1Md_T|LINE|L1	-83877	NM_001347441	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
Merged-chr10-47801755-1	chr10	47801603	47801907	+	1	NA	Intergenic	L1Md_T|LINE|L1	1557006	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr12-115613943-1	chr12	115613848	115614039	+	1	NA	Intergenic	Lx7|LINE|L1	81851	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr5-3987966-1	chr5	3987885	3988048	+	1	NA	intron (NM_194462, intron 14 of 47)	L1Md_T|LINE|L1	59780	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
Merged-chr7-41230505-1	chr7	41230327	41230684	+	1	NA	Intergenic	Intergenic	-53822	NM_001033782	434172	Mm.247214	NM_001033782	ENSMUSG00000072259	Gm5592	EG434172	predicted gene 5592	protein-coding
Merged-chr17-23903969-1	chr17	23903878	23904061	+	1	NA	Intergenic	Intergenic	5247	NM_001039238	630537	Mm.436677	NM_001039238	ENSMUSG00000096278	Dcpp2	Dcpp-2|EG630537|SPT-2	demilune cell and parotid protein 2	protein-coding
Merged-chr11-99885311-1	chr11	99885222	99885401	+	1	NA	Intergenic	L1Md_A|LINE|L1	6124	NM_001101613	670533	Mm.459090	NM_001101613	ENSMUSG00000059845	Gm11567	-	predicted gene 11567	protein-coding
Merged-chr14-58326427-1	chr14	58326275	58326579	+	1	NA	Intergenic	L1Md_T|LINE|L1	253741	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
Merged-chr11-40968803-1	chr11	40968703	40968903	+	1	NA	Intergenic	L1Md_T|LINE|L1	-213517	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
Merged-chr11-120237142-1	chr11	120236934	120237350	+	1	NA	exon (NM_001347621, exon 2 of 28)	exon (NM_001347621, exon 2 of 28)	4195	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
Merged-chrX-144052489-1	chrX	144052358	144052620	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-101206	NM_001354493	319764	Mm.208482	NM_001354493	ENSMUSG00000085139	A730046J19Rik	SERTM2	RIKEN cDNA A730046J19 gene	protein-coding
Merged-chr17-38522005-1	chr17	38521818	38522192	+	1	NA	Intergenic	Intergenic	-32187	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr10-118328434-1	chr10	118328329	118328539	+	1	NA	Intergenic	MusHAL1|LINE|L1	-33396	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
Merged-chr10-58963988-1	chr10	58963881	58964096	+	1	NA	intron (NM_172788, intron 1 of 9)	L1Md_T|LINE|L1	150629	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
Merged-chr15-4669338-1	chr15	4669260	4669416	+	1	NA	Intergenic	L1Md_T|LINE|L1	-57872	NM_016704	12274	Mm.20247	NM_016704	ENSMUSG00000022181	C6	AW111623	complement component 6	protein-coding
Merged-chrX-123043908-1	chrX	123043796	123044020	+	1	NA	Intergenic	Intergenic	-59615	NM_001310652	73061	Mm.292979	NM_028426	ENSMUSG00000079450	Cldn34c1	3110007F17Rik	claudin 34C1	protein-coding
Merged-chr1-97422308-1	chr1	97422159	97422457	+	1	NA	Intergenic	L1Md_T|LINE|L1	239368	NM_001355072	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
Merged-chr10-56580415-1	chr10	56580315	56580516	+	1	NA	Intergenic	L1Md_T|LINE|L1	148434	NR_152769	102640560	Mm.417249	NR_152768		Gm36595	-	predicted gene, 36595	ncRNA
Merged-chr17-69325250-1	chr17	69325144	69325357	+	1	NA	Intergenic	L1Md_T|LINE|L1	-48044	NR_045428	69750	Mm.439063	NR_045428	ENSMUSG00000100572	2410021H03Rik	-	RIKEN cDNA 2410021H03 gene	ncRNA
Merged-chr10-104894756-1	chr10	104894629	104894883	+	1	NA	Intergenic	L1Md_T|LINE|L1	607487	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA
Merged-chr1-173847749-1	chr1	173847367	173848132	+	1	NA	Intergenic	Lx|LINE|L1	32438	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
Merged-chr13-66623211-1	chr13	66622957	66623465	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-182093	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr11-64303250-1	chr11	64303132	64303368	+	1	NA	Intergenic	L1Md_T|LINE|L1	-132082	NM_178870	15478	Mm.340214	NM_178870	ENSMUSG00000047759	Hs3st3a1	3Ost3a|Hs3st3a	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	protein-coding
Merged-chr1-171517296-1	chr1	171517174	171517419	+	1	NA	TTS (NM_010584)	TTS (NM_010584)	13818	NM_019484	56009	Mm.389208	NM_019484	ENSMUSG00000060244	Alyref2	C130042O11Rik|REF2|Refbp2	Aly/REF export factor 2	protein-coding
Merged-chr12-113718087-1	chr12	113717948	113718226	+	1	NA	Intergenic	Intergenic	174179	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr1-20281173-1	chr1	20281094	20281252	+	1	NA	intron (NM_153179, intron 51 of 66)	L1Md_T|LINE|L1	-75281	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA
Merged-chr13-64835028-1	chr13	64834946	64835111	+	1	NA	intron (NM_001081129, intron 3 of 23)	LTRIS_Mm|LTR|ERV1	68860	NM_001081129	238680	Mm.390590	NM_001081129	ENSMUSG00000033063	Cntnap3	-	contactin associated protein-like 3	protein-coding
Merged-chr1-84455551-1	chr1	84455372	84455730	+	1	NA	intron (NM_152915, intron 7 of 12)	L1Md_A|LINE|L1	-170906	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4|P-CLI1	phosphotyrosine interaction domain containing 1	protein-coding
Merged-chr8-72084360-1	chr8	72084256	72084465	+	1	NA	Intergenic	ID_B1|SINE|B4	-15402	NM_146539	258532	Mm.377557	NM_146539	ENSMUSG00000061561	Olfr373	MOR282-2	olfactory receptor 373	protein-coding
Merged-chr1-20280272-1	chr1	20280061	20280484	+	1	NA	intron (NM_153179, intron 51 of 66)	L1Md_T|LINE|L1	-76182	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA
Merged-chrX-3231795-1	chrX	3231646	3231945	+	1	NA	Intergenic	Intergenic	154875	NM_001270667	100861966	Mm.443264	NM_001270667	ENSMUSG00000100249	Btbd35f23	Gm21950|Mgclh	BTB domain containing 35, family member 23	protein-coding
Merged-chr10-80764935-1	chr10	80764820	80765050	+	1	NA	intron (NM_199322, intron 2 of 27)	intron (NM_199322, intron 2 of 27)	9732	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
Merged-chr8-84326654-1	chr8	84326556	84326753	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-56252	NM_026350	67736	Mm.30095	NM_026350	ENSMUSG00000004994	Ccdc130	4930527D15Rik|C77430	coiled-coil domain containing 130	protein-coding
Merged-chr19-4110808-1	chr19	4110726	4110891	+	1	NA	intron (NM_008851, intron 15 of 22)	intron (NM_008851, intron 15 of 22)	10186	NM_008851	18739	Mm.1860	NM_008851	ENSMUSG00000024851	Pitpnm1	DRES9|Mpt-1|Nir-2|PITPnm 1|Pitpnm|R75447|Rd9|RdgB|RdgB1	phosphatidylinositol transfer protein, membrane-associated 1	protein-coding
Merged-chr19-22098301-1	chr19	22098166	22098436	+	1	NA	Intergenic	L1Md_T|LINE|L1	-40816	NM_001035242	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
Merged-chr7-27015540-1	chr7	27015421	27015659	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-13550	NM_133657	13085	Mm.20770	NM_133657	ENSMUSG00000060407	Cyp2a12	-	cytochrome P450, family 2, subfamily a, polypeptide 12	protein-coding
Merged-chr12-116542566-1	chr12	116542474	116542659	+	1	NA	intron (NM_011215, intron 1 of 22)	L1Md_A|LINE|L1	56846	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
Merged-chr1-145104426-1	chr1	145104254	145104599	+	1	NA	Intergenic	L1Md_T|LINE|L1	-328999	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
Merged-chr1-147672177-1	chr1	147672091	147672263	+	1	NA	Intergenic	L1Md_T|LINE|L1	1174490	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chrX-123498205-1	chrX	123498126	123498284	+	1	NA	Intergenic	Intergenic	-284902	NR_152852	100302634	Mm.417665	NR_152852	ENSMUSG00000095005	Astx6	Gm14949	amplified spermatogenic transcripts X encoded 6	ncRNA
Merged-chr8-120101735-1	chr8	120101635	120101836	+	1	NA	promoter-TSS (NM_133967)	promoter-TSS (NM_133967)	-263	NM_133967	102193	Mm.240076	NM_133967	ENSMUSG00000031823	Zdhhc7	AL024087|Gramp2	zinc finger, DHHC domain containing 7	protein-coding
Merged-chr8-84753076-1	chr8	84752998	84753154	+	1	NA	intron (NM_001081982, intron 2 of 9)	intron (NM_001081982, intron 2 of 9)	21293	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
Merged-chr10-101572262-1	chr10	101571748	101572777	+	1	NA	Intergenic	L1Md_A|LINE|L1	-109225	NM_001205098	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
Merged-chr9-70166299-1	chr9	70166212	70166387	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-24742	NM_029784	76886	Mm.44355	NM_029784	ENSMUSG00000032224	Fam81a	6430514L14Rik	family with sequence similarity 81, member A	protein-coding
Merged-chr2-172509504-1	chr2	172509404	172509604	+	1	NA	Intergenic	Intergenic	36950	NM_029608	76426	Mm.46148	NM_029608	ENSMUSG00000027505	Fam209	1700029J11Rik	family with sequence similarity 209	protein-coding
Merged-chr17-46346384-1	chr17	46346265	46346503	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	-18361	NM_001347396	224814	Mm.76543	NM_145140	ENSMUSG00000032842	Abcc10	Mrp7|mFLJ00002	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	protein-coding
Merged-chr1-33016607-1	chr1	33016527	33016688	+	1	NA	Intergenic	L1Md_T|LINE|L1	-469314	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
Merged-chr11-28463386-1	chr11	28463297	28463476	+	1	NA	intron (NM_181577, intron 2 of 4)	L1Md_T|LINE|L1	120938	NM_181577	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
Merged-chr10-13000432-1	chr10	13000296	13000568	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-8018	NM_175102	66125	Mm.29743	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	splicing factor 3b, subunit 5	protein-coding
Merged-chr4-115670725-1	chr4	115670619	115670831	+	1	NA	Intergenic	L1Md_T|LINE|L1	-23020	NM_007823	13120	Mm.1840	NM_007823	ENSMUSG00000028713	Cyp4b1	-	cytochrome P450, family 4, subfamily b, polypeptide 1	protein-coding
Merged-chr2-86560121-1	chr2	86560035	86560208	+	1	NA	Intergenic	L1Md_A|LINE|L1	-1983	NM_146409	258404	Mm.271334	NM_146409	ENSMUSG00000110912	Olfr1080	MOR192-1	olfactory receptor 1080	protein-coding
Merged-chr10-47803466-1	chr10	47803387	47803545	+	1	NA	Intergenic	L1Md_T|LINE|L1	1558717	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr4-29815722-1	chr4	29815644	29815800	+	1	NA	Intergenic	L1Md_F2|LINE|L1	747643	NR_151693	102634169		NR_151693		Gm11917	-	predicted gene 11917	ncRNA
Merged-chr17-9810530-1	chr17	9810420	9810641	+	1	NA	Intergenic	L1Md_A|LINE|L1	-34664	NR_045433	71092	Mm.243827	NR_045433		4930452A19Rik	4933424P20Rik	RIKEN cDNA 4930452A19 gene	ncRNA
Merged-chr5-19977866-1	chr5	19977705	19978028	+	1	NA	intron (NM_015823, intron 1 of 21)	IAPEz-int|LTR|ERVK	70348	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
Merged-chr19-7441611-1	chr19	7441524	7441699	+	1	NA	intron (NM_053076, intron 1 of 6)	intron (NM_053076, intron 1 of 6)	19038	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
Merged-chr13-113564538-1	chr13	113564390	113564686	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	54026	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
Merged-chr15-75909384-1	chr15	75909099	75909669	+	1	NA	promoter-TSS (NM_001285430)	promoter-TSS (NM_001285430)	-40	NM_029663	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	EF-1-delta	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding
Merged-chr8-15011726-1	chr8	15011564	15011888	+	1	NA	intron (NM_029116, intron 1 of 1)	CpG	701	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
Merged-chr8-95332151-1	chr8	95331941	95332361	+	1	NA	promoter-TSS (NM_024467)	promoter-TSS (NM_024467)	-133	NM_133954	101985	Mm.29069	NM_133954	ENSMUSG00000031792	Usb1	AA960436	U6 snRNA biogenesis 1	protein-coding
Merged-chr1-147596802-1	chr1	147596579	147597026	+	1	NA	Intergenic	L1Md_F2|LINE|L1	1099115	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr3-136511771-1	chr3	136511691	136511851	+	1	NA	Intergenic	L1Md_A|LINE|L1	-62422	NR_040592	70055	Mm.261063	NR_040592	ENSMUSG00000099508	1700030L20Rik	-	RIKEN cDNA 1700030L20 gene	ncRNA
Merged-chr15-38530617-1	chr15	38530535	38530700	+	1	NA	Intergenic	Intergenic	-11351	NR_125913	54375	Mm.250214	NM_018745	ENSMUSG00000037458	Azin1	1700085L02Rik|AZI|Oazi|Oazin	antizyme inhibitor 1	protein-coding
Merged-chr12-28245016-1	chr12	28244923	28245110	+	1	NA	Intergenic	L1Md_T|LINE|L1	303321	NM_001177964	68511	Mm.310284	NM_001177964	ENSMUSG00000020633	Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding
Merged-chr1-143866906-1	chr1	143866749	143867063	+	1	NA	Intergenic	L1Md_T|LINE|L1	89628	NM_001159866	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding
Merged-chr13-66417037-1	chr13	66416939	66417136	+	1	NA	Intergenic	Intergenic	24081	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-79399162-1	chr10	79399070	79399255	+	1	NA	Intergenic	L1Md_A|LINE|L1	42571	NM_001101572	624845	Mm.469866	NM_001101572	ENSMUSG00000091468	Vmn2r82	EG624845	vomeronasal 2, receptor 82	protein-coding
Merged-chr1-178008439-1	chr1	178008355	178008523	+	1	NA	intron (NM_001034899, intron 2 of 7)	L1Md_T|LINE|L1	17004	NM_001034899	545391	Mm.442974	NM_001034899	ENSMUSG00000091476	Gm16432	EG545391|EG666250	predicted gene 16432	protein-coding
Merged-chr8-107294337-1	chr8	107294246	107294428	+	1	NA	intron (NM_001286260, intron 1 of 12)	CpG	867	NM_133957	54446	Mm.390057	NM_018823	ENSMUSG00000003847	Nfat5	AI225870|B130038B15Rik|CAG-8|CAG80|NFATL1|OREBP|TonEBP|mKIAA0827|nfatz	nuclear factor of activated T cells 5	protein-coding
Merged-chr1-112553757-1	chr1	112553609	112553906	+	1	NA	Intergenic	L1Md_A|LINE|L1	-688839	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
Merged-chr4-88785243-1	chr4	88785155	88785332	+	1	NA	5' UTR (NM_001085532, exon 1 of 1)	5' UTR (NM_001085532, exon 1 of 1)	189	NM_001085532	545649	Mm.474424	NM_001085532	ENSMUSG00000099545	Gm13276	-	predicted gene 13276	protein-coding
Merged-chr17-46338701-1	chr17	46338614	46338788	+	1	NA	Intergenic	RLTR17B_Mm|LTR|ERVK	-10678	NM_001347396	224814	Mm.76543	NM_145140	ENSMUSG00000032842	Abcc10	Mrp7|mFLJ00002	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	protein-coding
Merged-chr13-68035367-1	chr13	68035287	68035447	+	1	NA	Intergenic	Intergenic	172041	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr1-33115798-1	chr1	33115527	33116070	+	1	NA	Intergenic	L1_Mm|LINE|L1	553996	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
Merged-chr10-87363257-1	chr10	87363178	87363337	+	1	NA	Intergenic	L1Md_T|LINE|L1	130403	NM_008553	17172	Mm.136217	NM_008553	ENSMUSG00000020052	Ascl1	AI225900|ASH1|Mash1|bHLHa46	achaete-scute family bHLH transcription factor 1	protein-coding
Merged-chr10-37039256-1	chr10	37039121	37039392	+	1	NA	Intergenic	L1Md_A|LINE|L1	64712	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
Merged-chr5-36796423-1	chr5	36796297	36796549	+	1	NA	exon (NM_026242, exon 1 of 2)	exon (NM_026242, exon 1 of 2)	331	NM_026242	67568	Mm.332336	NM_026242	ENSMUSG00000055302	Mrfap1	9130413I22Rik|AL022827|Pam14	Morf4 family associated protein 1	protein-coding
Merged-chr17-74528181-1	chr17	74528100	74528262	+	1	NA	promoter-TSS (NM_007566)	promoter-TSS (NM_007566)	-114	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
Merged-chr15-84147976-1	chr15	84147763	84148190	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-19840	NM_054088	116939	Mm.390817	NM_054088	ENSMUSG00000041653	Pnpla3	Adpn	patatin-like phospholipase domain containing 3	protein-coding
Merged-chr13-66719533-1	chr13	66719424	66719642	+	1	NA	Intergenic	L1_Mur3|LINE|L1	185817	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr1-165410295-1	chr1	165410064	165410526	+	1	NA	intron (NM_028759, intron 6 of 18)	L1Md_Gf|LINE|L1	50168	NM_028759	74106	Mm.227605	NM_028759	ENSMUSG00000026571	Dcaf6	1200006M05Rik|Iqwd1|PC326	DDB1 and CUL4 associated factor 6	protein-coding
Merged-chr1-81503786-1	chr1	81503526	81504047	+	1	NA	Intergenic	L1Md_T|LINE|L1	426379	NM_001356397	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
Merged-chr12-14017406-1	chr12	14017290	14017522	+	1	NA	Intergenic	L1Md_T|LINE|L1	134632	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	family with sequence similarity 84, member A	protein-coding
Merged-chr11-64299527-1	chr11	64299388	64299666	+	1	NA	Intergenic	L1Md_T|LINE|L1	-135805	NM_178870	15478	Mm.340214	NM_178870	ENSMUSG00000047759	Hs3st3a1	3Ost3a|Hs3st3a	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	protein-coding
Merged-chr19-45105349-1	chr19	45105243	45105456	+	1	NA	Intergenic	Intergenic	29262	NM_001362397	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
Merged-chr12-42335275-1	chr12	42335105	42335446	+	1	NA	Intergenic	L1Md_T|LINE|L1	698942	NR_148724	102636207		NR_148724		Gm33340	Gm40882	predicted gene, 33340	ncRNA
Merged-chr1-186106717-1	chr1	186106589	186106845	+	1	NA	intron (NM_146106, intron 2 of 4)	L1Md_T|LINE|L1	10593	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding
Merged-chr13-33536811-1	chr13	33536709	33536913	+	1	NA	Intergenic	L1Md_T|LINE|L1	32058	NR_131140	619715	Mm.390575	NR_131140	ENSMUSG00000112963	Gm6093	EG619715	predicted gene 6093	ncRNA
Merged-chr1-147674028-1	chr1	147673778	147674278	+	1	NA	Intergenic	L1Md_T|LINE|L1	1176341	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr17-24137010-1	chr17	24136873	24137148	+	1	NA	intron (NM_001286662, intron 1 of 13)	B3|SINE|B2	4584	NM_011062	18607	Mm.10504	NM_011062	ENSMUSG00000024122	Pdpk1	Pdk1	3-phosphoinositide dependent protein kinase 1	protein-coding
Merged-chr8-70283449-1	chr8	70283343	70283556	+	1	NA	intron (NM_001146153, intron 1 of 9)	CpG	450	NM_001146153	26558	Mm.388127	NM_011984	ENSMUSG00000003573	Homer3	AW146114	homer scaffolding protein 3	protein-coding
Merged-chr11-27687211-1	chr11	27687033	27687389	+	1	NA	Intergenic	L1Md_A|LINE|L1	897113	NM_181577	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
Merged-chr10-14711203-1	chr10	14711015	14711392	+	1	NA	intron (NR_045824, intron 1 of 5)	L1Md_T|LINE|L1	5594	NR_045824	69412	Mm.259735	NR_045824	ENSMUSG00000019865	1700016L04Rik	-	RIKEN cDNA 1700016L04 gene	ncRNA
Merged-chr11-56847674-1	chr11	56847592	56847757	+	1	NA	Intergenic	L1Md_T|LINE|L1	-163944	NM_008165	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
Merged-chr19-5953646-1	chr19	5953526	5953766	+	1	NA	intron (NM_001164057, intron 6 of 17)	intron (NM_001164057, intron 6 of 17)	10560	NM_008893	18969	Mm.209931	NM_008893	ENSMUSG00000024833	Pola2	AI573378	polymerase (DNA directed), alpha 2	protein-coding
Merged-chr1-70687988-1	chr1	70687771	70688206	+	1	NA	intron (NM_025728, intron 7 of 7)	L1Md_T|LINE|L1	-37727	NM_001310658	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding
Merged-chr15-83086106-1	chr15	83085984	83086229	+	1	NA	Intergenic	Intergenic	-14099	NM_023475	68607	Mm.30056	NM_023475	ENSMUSG00000058586	Serhl	0610008B10Rik|1110019M09Rik|AU019786	serine hydrolase-like	protein-coding
Merged-chr3-131110345-1	chr3	131110258	131110433	+	1	NA	promoter-TSS (NM_010703)	promoter-TSS (NM_010703)	48	NM_010703	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
Merged-chr10-126702505-1	chr10	126702398	126702613	+	1	NA	Intergenic	L1Md_T|LINE|L1	7886	NR_105841	102465224		NR_105841	ENSMUSG00000098756	Mir378d	Gm27650|mmu-mir-378d	microRNA 378d	ncRNA
Merged-chr1-175012934-1	chr1	175012769	175013100	+	1	NA	Intergenic	L1Md_A|LINE|L1	-91115	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
Merged-chr9-79904015-1	chr9	79903925	79904106	+	1	NA	intron (NM_001357352, intron 1 of 5)	L1Md_A|LINE|L1	58066	NM_001357353	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
Merged-chr17-21265724-1	chr17	21265573	21265875	+	1	NA	Intergenic	Lx|LINE|L1	5297	NM_134199	171233	Mm.222636	NM_134199	ENSMUSG00000050102	Vmn1r235	V1rf2	vomeronasal 1 receptor 235	protein-coding
Merged-chr7-12403431-1	chr7	12403336	12403526	+	1	NA	Intergenic	RLTR43C|LTR|ERVK	19060	NM_001033820	619331	Mm.361832	NM_001033820	ENSMUSG00000034071	Zfp551	9630004E07Rik|Znf551	zinc fingr protein 551	protein-coding
Merged-chr8-84969586-1	chr8	84969488	84969685	+	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	-36	NM_001317385	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
Merged-chr3-41189716-1	chr3	41189635	41189797	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-106670	NM_027558	70804	Mm.40321	NM_027558	ENSMUSG00000049940	Pgrmc2	4631434O19Rik|5730409G06Rik|DG6|PMBP	progesterone receptor membrane component 2	protein-coding
Merged-chr13-51986345-1	chr13	51986242	51986449	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-110396	NR_045061	74050	Mm.84860	NR_045061	ENSMUSG00000113211	4921525O09Rik	-	RIKEN cDNA 4921525O09 gene	ncRNA
Merged-chr11-117892645-1	chr11	117892560	117892730	+	1	NA	Intergenic	ID_B1|SINE|B4	-19119	NM_027919	71776	Mm.3200	NM_027919	ENSMUSG00000017713	Tha1	1300017K07Rik|GLY1	threonine aldolase 1	protein-coding
Merged-chr8-70691854-1	chr8	70691775	70691933	+	1	NA	Intergenic	Intergenic	-5885	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
Merged-chr6-52335463-1	chr6	52335337	52335589	+	1	NA	Intergenic	ORR1A0-int|LTR|ERVL-MaLR	-20631	NR_038163	70593	Mm.158412	NR_038163	ENSMUSG00000086126	Evx1os	5730457N03Rik|Evx1as	even skipped homeotic gene 1, opposite strand	ncRNA
Merged-chr15-28025016-1	chr15	28024932	28025101	+	1	NA	intron (NM_001081302, intron 1 of 56)	CpG	832	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
Merged-chr3-106082450-1	chr3	106082317	106082583	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-30932	NM_023186	81600	Mm.46418	NM_023186	ENSMUSG00000062778	Chia1	2200003E03Rik|AMCase|Chia|YNL	chitinase, acidic 1	protein-coding
Merged-chr10-33574515-1	chr10	33574397	33574634	+	1	NA	intron (NM_001359139, intron 2 of 4)	L1Md_A|LINE|L1	-49731	NR_152723	102632938	Mm.417656	NR_152723	ENSMUSG00000090087	Gm15939	-	predicted gene 15939	ncRNA
Merged-chr15-82142775-1	chr15	82142691	82142859	+	1	NA	TTS (NM_172428)	TTS (NM_172428)	-4494	NM_033218	20788	Mm.38016	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
Merged-chr3-36705093-1	chr3	36705008	36705179	+	1	NA	Intergenic	L1Md_A|LINE|L1	-14926	NM_019510	22065	Mm.74363	NM_019510	ENSMUSG00000027716	Trpc3	Mwk|Trcp3|Trp3|Trrp3	transient receptor potential cation channel, subfamily C, member 3	protein-coding
Merged-chr8-105171419-1	chr8	105171334	105171504	+	1	NA	intron (NM_001161456, intron 2 of 4)	CpG-14413	745	NM_022309	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
Merged-chr17-87750217-1	chr17	87750119	87750315	+	1	NA	intron (NM_199251, intron 1 of 1)	IAPEz-int|LTR|ERVK	47777	NM_199251	210741	Mm.312046	NM_199251	ENSMUSG00000050138	Kcnk12	mntk1	potassium channel, subfamily K, member 12	protein-coding
Merged-chr10-112152639-1	chr10	112152558	112152720	+	1	NA	Intergenic	L1Md_T|LINE|L1	-10982	NM_001310675	353025	Mm.194428	NM_178278	ENSMUSG00000035694	Caps2	D630005B03Rik	calcyphosphine 2	protein-coding
Merged-chr2-35256523-1	chr2	35256423	35256624	+	1	NA	intron (NM_001206368, intron 1 of 16)	CpG	164	NM_001206367	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
Merged-chr10-29763174-1	chr10	29762968	29763381	+	1	NA	Intergenic	L1Md_T|LINE|L1	-227307	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding
Merged-chr4-88774882-1	chr4	88774645	88775120	+	1	NA	TTS (NM_001243155)	TTS (NM_001243155)	888	NM_001161609	545654	Mm.478784	NM_001161609	ENSMUSG00000095101	Gm13285	limitin	predicted gene 13285	protein-coding
Merged-chr17-70324392-1	chr17	70324287	70324498	+	1	NA	intron (NM_001347411, intron 3 of 14)	L1Md_T|LINE|L1	-100400	NM_027712	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
Merged-chr19-5511182-1	chr19	5511037	5511327	+	1	NA	promoter-TSS (NM_001024560)	promoter-TSS (NM_001024560)	-665	NM_001024560	225861	Mm.20071	NM_001024560	ENSMUSG00000056185	Snx32	B930037P14Rik|Snx6b	sorting nexin 32	protein-coding
Merged-chr16-8830678-1	chr16	8830577	8830779	+	1	NA	exon (NM_001081400, exon 1 of 4)	exon (NM_001081400, exon 1 of 4)	578	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
Merged-chr12-7114822-1	chr12	7114710	7114934	+	1	NA	Intergenic	L1Md_A|LINE|L1	265508	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
Merged-chr1-171529876-1	chr1	171529778	171529975	+	1	NA	intron (NM_010584, intron 6 of 7)	intron (NM_010584, intron 6 of 7)	5418	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
Merged-chr10-93055401-1	chr10	93055277	93055526	+	1	NA	intron (NM_001347060, intron 5 of 67)	L1Md_A|LINE|L1	26195	NM_001347060	380654	Mm.34980	NM_001347060	ENSMUSG00000020014	Cfap54	4930485B16Rik|Gm872	cilia and flagella associated protein 54	protein-coding
Merged-chr15-102693110-1	chr15	102693022	102693198	+	1	NA	Intergenic	CpG	-21244	NR_030460	751542		NR_030460	ENSMUSG00000076009	Mir688	Mirn688|mmu-mir-688	microRNA 688	ncRNA
Merged-chr15-33659753-1	chr15	33659652	33659855	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-6317	NR_045070	75880	Mm.396109	NR_045070	ENSMUSG00000115779	4930592A05Rik	-	RIKEN cDNA 4930592A05 gene	ncRNA
Merged-chr15-77778236-1	chr15	77778145	77778327	+	1	NA	intron (NM_022410, intron 18 of 40)	intron (NM_022410, intron 18 of 40)	-21226	NM_001357895	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
Merged-chr1-159023206-1	chr1	159023058	159023354	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-65768	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
Merged-chr17-36241219-1	chr17	36241119	36241320	+	1	NA	Intergenic	Intergenic	16627	NM_026308	67676	Mm.27131	NM_026308	ENSMUSG00000024446	Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding
Merged-chr10-46384903-1	chr10	46384794	46385013	+	1	NA	Intergenic	L1Md_T|LINE|L1	140154	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr4-40595695-1	chr4	40595592	40595798	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	-70147	NR_040644	71293	Mm.399556	NR_040644	ENSMUSG00000086355	4933428C19Rik	-	RIKEN cDNA 4933428C19 gene	ncRNA
Merged-chr19-3891325-1	chr19	3891193	3891458	+	1	NA	intron (NM_001271496, intron 9 of 11)	intron (NM_001271496, intron 9 of 11)	13905	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
Merged-chr6-114764081-1	chr6	114763983	114764179	+	1	NA	intron (NM_001253718, intron 18 of 19)	L1Md_A|LINE|L1	120984	NM_028835	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
Merged-chr8-7047830-1	chr8	7047667	7047994	+	1	NA	Intergenic	Intergenic	1612943	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr10-57626757-1	chr10	57626572	57626943	+	1	NA	Intergenic	L1Md_T|LINE|L1	-5224	NM_008863	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
Merged-chr5-3335116-1	chr5	3335021	3335211	+	1	NA	Intergenic	Intergenic	-8777	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
Merged-chr15-76199193-1	chr15	76199075	76199312	+	1	NA	promoter-TSS (NM_201393)	promoter-TSS (NM_201393)	213	NM_201392	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
Merged-chr10-14712397-1	chr10	14712179	14712616	+	1	NA	intron (NR_045824, intron 1 of 5)	L1Md_T|LINE|L1	5817	NM_029722	76743	Mm.136985	NM_029722	ENSMUSG00000019867	Gje1	AEY12|Cx23|D230044M03Rik|Gjf1|Gsfaey12	gap junction protein, epsilon 1	protein-coding
Merged-chr17-38550003-1	chr17	38549837	38550170	+	1	NA	Intergenic	Lx5|LINE|L1	-4189	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr1-84375570-1	chr1	84375259	84375881	+	1	NA	intron (NM_152915, intron 12 of 12)	L1Md_T|LINE|L1	-90925	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4|P-CLI1	phosphotyrosine interaction domain containing 1	protein-coding
Merged-chr19-38870229-1	chr19	38870144	38870314	+	1	NA	intron (NM_145952, intron 2 of 12)	RLTR13G|LTR|ERVK	33650	NM_145952	209478	Mm.391153	NM_145952	ENSMUSG00000048720	Tbc1d12	BC033574	TBC1D12: TBC1 domain family, member 12	protein-coding
Merged-chr5-69503993-1	chr5	69503910	69504077	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	38654	NM_023784	75581	Mm.154776	NM_023784	ENSMUSG00000029158	Yipf7	2310016N21Rik|Yip1b	Yip1 domain family, member 7	protein-coding
Merged-chr16-86981556-1	chr16	86981418	86981694	+	1	NA	Intergenic	L1Md_A|LINE|L1	146883	NR_153792	102635567	Mm.233725	NR_153792		Gm32865	-	predicted gene, 32865	ncRNA
Merged-chr4-80961374-1	chr4	80961285	80961464	+	1	NA	Intergenic	L1Md_T|LINE|L1	50688	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
Merged-chr17-25777335-1	chr17	25777209	25777462	+	1	NA	exon (NM_026238, exon 4 of 11)	exon (NM_026238, exon 4 of 11)	-3473	NR_105932	102466776		NR_105932	ENSMUSG00000098329	Mir6966	Gm27272|mmu-mir-6966	microRNA 6966	ncRNA
Merged-chr5-60652038-1	chr5	60651808	60652269	+	1	NA	Intergenic	L1Md_T|LINE|L1	-666036	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
Merged-chrX-100865168-1	chrX	100865021	100865316	+	1	NA	intron (NM_031384, intron 25 of 29)	L1Md_T|LINE|L1	87897	NM_001177780	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs large MAGUK scaffold protein 3	protein-coding
Merged-chr4-21581151-1	chr4	21581033	21581269	+	1	NA	Intergenic	L1Md_T|LINE|L1	104812	NM_001080771	230025	Mm.208541	NM_001080771	ENSMUSG00000040478	Prdm13	-	PR domain containing 13	protein-coding
Merged-chr7-10002695-1	chr7	10002530	10002860	+	1	NA	Intergenic	Intergenic	-10556	NM_001105156	625605	Mm.484763	NM_001105156	ENSMUSG00000096180	Vmn2r49	-	vomeronasal 2, receptor 49	protein-coding
Merged-chr11-46762840-1	chr11	46762699	46762981	+	1	NA	intron (NM_001166631, intron 4 of 7)	L1Md_T|LINE|L1	11672	NM_134248	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
Merged-chr1-143865064-1	chr1	143864979	143865150	+	1	NA	Intergenic	L1Md_T|LINE|L1	87786	NM_001159866	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding
Merged-chr10-22340670-1	chr10	22340590	22340751	+	1	NA	intron (NM_009018, intron 6 of 6)	ETnERV-int|LTR|ERVK	-21224	NM_020030	56554	Mm.458004	NM_020030	ENSMUSG00000078452	Raet1d	RAE-1delta	retinoic acid early transcript delta	protein-coding
Merged-chr11-121156758-1	chr11	121156669	121156848	+	1	NA	Intergenic	CpG	-3513	NM_145440	217369	Mm.20122	NM_145440	ENSMUSG00000039321	Uts2r	Gpr14|UR-2-R|UTR|UTR2	urotensin 2 receptor	protein-coding
Merged-chr1-112169027-1	chr1	112168864	112169191	+	1	NA	Intergenic	L1Md_A|LINE|L1	-304109	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
Merged-chr15-102306272-1	chr15	102306191	102306354	+	1	NA	exon (NM_001014976, exon 11 of 31)	exon (NM_001014976, exon 11 of 31)	9979	NM_001356312	105988	Mm.288324	NM_001014976	ENSMUSG00000058290	Espl1	AL024103|AU045071|Cerp|ESP1|PRCE|SSE	extra spindle pole bodies 1, separase	protein-coding
Merged-chr15-81983898-1	chr15	81983811	81983985	+	1	NA	Intergenic	RLTR1A2_MM|LTR|ERV1	3358	NM_025503	66346	Mm.54292	NM_025503	ENSMUSG00000061633	1700029P11Rik	-	RIKEN cDNA 1700029P11 gene	protein-coding
Merged-chr10-91689562-1	chr10	91689475	91689649	+	1	NA	Intergenic	L1Md_T|LINE|L1	-199267	NR_152729	102633867	Mm.351514	NR_152729	ENSMUSG00000111657	Gm31592	-	predicted gene, 31592	ncRNA
Merged-chr12-14670667-1	chr12	14670519	14670816	+	1	NA	Intergenic	L1Md_T|LINE|L1	379722	NR_045960	73972	Mm.107680	NR_045960	ENSMUSG00000113644	4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA
Merged-chr1-144810098-1	chr1	144809832	144810364	+	1	NA	Intergenic	L1Md_A|LINE|L1	-34671	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
Merged-chr11-121316330-1	chr11	121316141	121316519	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	38117	NM_025793	66840	Mm.103986	NM_025793	ENSMUSG00000025173	Wdr45b	0610008N23Rik|AA408735|D16Bwg0193e|WIPI-3|Wdr45l	WD repeat domain 45B	protein-coding
Merged-chr10-41309796-1	chr10	41309600	41309993	+	1	NA	Intergenic	L1Md_T|LINE|L1	-6555	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
Merged-chr1-52400334-1	chr1	52400180	52400488	+	1	NA	Intergenic	L1Md_T|LINE|L1	100114	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
Merged-chr1-31696147-1	chr1	31696058	31696237	+	1	NA	Intergenic	L1Md_T|LINE|L1	431300	NR_015347	226957	Mm.25966	NR_015347		Gm4850	EG226957	THO complex 4 pseudogene	pseudo
Merged-chr8-7043316-1	chr8	7043198	7043434	+	1	NA	Intergenic	L1Md_F2|LINE|L1	1617457	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr12-62177324-1	chr12	62177219	62177430	+	1	NA	Intergenic	L1Md_T|LINE|L1	-510463	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
Merged-chr13-62187072-1	chr13	62186914	62187230	+	1	NA	Intergenic	Lx3A|LINE|L1	57182	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr15-36634397-1	chr15	36634299	36634496	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-25424	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
Merged-chr1-154343447-1	chr1	154343338	154343556	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-86541	NR_040629	78112	Mm.401935	NR_040629	ENSMUSG00000099933	4930452N14Rik	-	RIKEN cDNA 4930452N14 gene	ncRNA
Merged-chr12-17961227-1	chr12	17961096	17961358	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	270418	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVL-3|NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
Merged-chr4-150855067-1	chr4	150854945	150855189	+	1	NA	promoter-TSS (NR_040649)	promoter-TSS (NR_040649)	-3	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
Merged-chr8-70375432-1	chr8	70375341	70375524	+	1	NA	intron (NM_016685, intron 4 of 18)	intron (NM_016685, intron 4 of 18)	1884	NM_016685	12845	Mm.45071	NM_016685	ENSMUSG00000031849	Comp	TSP5	cartilage oligomeric matrix protein	protein-coding
Merged-chr15-78408885-1	chr15	78408797	78408973	+	1	NA	intron (NM_138670, intron 1 of 2)	intron (NM_138670, intron 1 of 2)	1781	NM_138670	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
Merged-chr15-8253882-1	chr15	8253794	8253971	+	1	NA	intron (NM_001162906, intron 45 of 52)	L1Md_F2|LINE|L1	84776	NM_001162906	73692	Mm.164436	NM_001162906	ENSMUSG00000039801	2410089E03Rik	4732468D17Rik|Hug|Jbts17|b2b012Clo	RIKEN cDNA 2410089E03 gene	protein-coding
Merged-chr1-105837007-1	chr1	105836870	105837145	+	1	NA	intron (NM_009399, intron 9 of 9)	L1Md_T|LINE|L1	56284	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
Merged-chr13-68428259-1	chr13	68428106	68428412	+	1	NA	Intergenic	ERVB4_2-I_MM-int|LTR|ERVK	-71434	NR_152173	666272	Mm.309128	NR_152173	ENSMUSG00000113050	Gm8016	EG666272	predicted gene 8016	ncRNA
Merged-chr1-48420969-1	chr1	48420799	48421140	+	1	NA	Intergenic	L1Md_A|LINE|L1	-823647	NR_151585	442837	Mm.337149	NM_001002792	ENSMUSG00000051616	C230029F24Rik	-	RIKEN cDNA C230029F24 gene	ncRNA
Merged-chr11-121512840-1	chr11	121512749	121512931	+	1	NA	exon (NM_178763, exon 2 of 3)	exon (NM_178763, exon 2 of 3)	6502	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
Merged-chr15-49171699-1	chr15	49171507	49171891	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-379710	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding
Merged-chr13-62079802-1	chr13	62079654	62079951	+	1	NA	Intergenic	Lx2A1|LINE|L1	-50088	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr8-70699528-1	chr8	70699450	70699607	+	1	NA	exon (NM_010592, exon 1 of 1)	exon (NM_010592, exon 1 of 1)	1789	NM_010592	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
Merged-chrX-67017558-1	chrX	67017415	67017701	+	1	NA	Intergenic	L1Md_T|LINE|L1	-178433	NR_030149	723888		NR_030149	ENSMUSG00000070071	Mir465	Mirn465|mir-465a|mmu-mir-465	microRNA 465	ncRNA
Merged-chr4-14633216-1	chr4	14633073	14633360	+	1	NA	Intergenic	L1Md_T|LINE|L1	-11438	NM_145947	208890	Mm.483839	NM_145947	ENSMUSG00000040569	Slc26a7	-	solute carrier family 26, member 7	protein-coding
Merged-chr1-30611754-1	chr1	30611630	30611879	+	1	NA	Intergenic	L1Md_T|LINE|L1	251502	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik	PHD finger protein 3	protein-coding
Merged-chr11-7618282-1	chr11	7618071	7618494	+	1	NA	Intergenic	L1Md_A|LINE|L1	-404359	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
Merged-chr10-87633469-1	chr10	87633380	87633559	+	1	NA	Intergenic	L1Md_T|LINE|L1	111674	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
Merged-chr15-58002928-1	chr15	58002813	58003044	+	1	NA	intron (NM_173862, intron 3 of 3)	intron (NM_173862, intron 3 of 3)	17025	NM_173862	239463	Mm.221241	NM_173862	ENSMUSG00000051225	Fam83a	-	family with sequence similarity 83, member A	protein-coding
Merged-chr13-106309777-1	chr13	106309634	106309920	+	1	NA	Intergenic	L1Md_T|LINE|L1	627181	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
Merged-chr1-13550216-1	chr1	13550108	13550325	+	1	NA	Intergenic	L1Md_T|LINE|L1	39694	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding
Merged-chr12-50980159-1	chr12	50980051	50980267	+	1	NA	Intergenic	ETnERV-int|LTR|ERVK	-24997	NR_126468	75494	Mm.416848	NR_126468	ENSMUSG00000111986	1700008C04Rik	-	RIKEN cDNA 1700008C04 gene	ncRNA
Merged-chr8-27110578-1	chr8	27110491	27110665	+	1	NA	exon (NM_054044, exon 6 of 19)	exon (NM_054044, exon 6 of 19)	18054	NM_025686	66653	Mm.334467	NM_025686	ENSMUSG00000031487	Brf2	2700059M06Rik|5730512K07Rik|AU018504|AU022602|BRFU|TFIIIB50	BRF2, RNA polymerase III transcription initiation factor 50kDa subunit	protein-coding
Merged-chr12-113625532-1	chr12	113625449	113625615	+	1	NA	Intergenic	Intergenic	81624	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr1-177932521-1	chr1	177932353	177932690	+	1	NA	Intergenic	L1Md_T|LINE|L1	-58877	NR_155538	545391	Mm.442974	NM_001034899	ENSMUSG00000091476	Gm16432	EG545391|EG666250	predicted gene 16432	protein-coding
Merged-chr10-43811382-1	chr10	43811289	43811475	+	1	NA	Intergenic	L1Md_A|LINE|L1	-14525	NR_131055	71018	Mm.410796	NR_131055	ENSMUSG00000111342	4933404K13Rik	-	RIKEN cDNA 4933404K13 gene	ncRNA
Merged-chr1-61673938-1	chr1	61673806	61674071	+	1	NA	intron (NM_001081050, intron 1 of 22)	L1Md_A|LINE|L1	35114	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
Merged-chr17-27269481-1	chr17	27269363	27269599	+	1	NA	Intergenic	IAPLTR2_Mm|LTR|ERVK	-21415	NR_131118	319720	Mm.394996	NR_131118		9630028I04Rik	-	RIKEN cDNA 9630028I04 gene	ncRNA
Merged-chr1-147593125-1	chr1	147593003	147593248	+	1	NA	Intergenic	L1Md_F2|LINE|L1	1095438	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr17-23329639-1	chr17	23329551	23329727	+	1	NA	Intergenic	Lx5|LINE|L1	-14338	NM_001104579	638102	Mm.469849	NM_001104579	ENSMUSG00000091076	Vmn2r115	EG638102|V2Rp4	vomeronasal 2, receptor 115	protein-coding
Merged-chr1-144092452-1	chr1	144092326	144092578	+	1	NA	Intergenic	L1Md_T|LINE|L1	84920	NM_153171	246709	Mm.38271	NM_153171	ENSMUSG00000051079	Rgs13	-	regulator of G-protein signaling 13	protein-coding
Merged-chr10-103750297-1	chr10	103750160	103750434	+	1	NA	Intergenic	L1Md_T|LINE|L1	382489	NM_001252330	103098	Mm.458408	NM_175328	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	solute carrier family 6 (neurotransmitter transporter), member 15	protein-coding
Merged-chr4-20289340-1	chr4	20289255	20289425	+	1	NA	intron (NM_172987, intron 3 of 4)	L1Md_A|LINE|L1	247288	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
Merged-chr11-24810804-1	chr11	24810657	24810951	+	1	NA	Intergenic	L1Md_T|LINE|L1	-80082	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	-	predicted gene 10466	ncRNA
Merged-chr10-30218870-1	chr10	30218770	30218970	+	1	NA	Intergenic	L1Md_T|LINE|L1	-18330	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding
Merged-chr1-27760840-1	chr1	27760696	27760985	+	1	NA	Intergenic	L1Md_T|LINE|L1	-123206	NR_151583	433281	Mm.329306	NR_151583	ENSMUSG00000101514	Gm5524	AI875557|EG433281	predicted gene 5524	ncRNA
Merged-chr11-56179555-1	chr11	56179452	56179658	+	1	NA	Intergenic	L1Md_A|LINE|L1	-138568	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding
Merged-chr4-29620283-1	chr4	29620192	29620374	+	1	NA	Intergenic	L1Md_T|LINE|L1	552204	NR_151693	102634169		NR_151693		Gm11917	-	predicted gene 11917	ncRNA
Merged-chr3-93280369-1	chr3	93280206	93280533	+	1	NA	Intergenic	Intergenic	-39380	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
Merged-chr1-146450244-1	chr1	146450143	146450345	+	1	NA	Intergenic	L1Md_A|LINE|L1	-45385	NM_001357571	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr15-77557216-1	chr15	77557111	77557321	+	1	NA	Intergenic	RMER10A|LTR|ERVL	4676	NR_040310	76409	Mm.183491	NR_040310	ENSMUSG00000101113	1700025B11Rik	-	RIKEN cDNA 1700025B11 gene	ncRNA
Merged-chr5-79738057-1	chr5	79737930	79738184	+	1	NA	Intergenic	L1Md_A|LINE|L1	-1282514	NM_001347371	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
Merged-chr13-113721380-1	chr13	113721276	113721485	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	-57704	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding
Merged-chr6-42452332-1	chr6	42452244	42452420	+	1	NA	Intergenic	L1Md_T|LINE|L1	8685	NM_146444	258436	Mm.377501	NM_146444	ENSMUSG00000068574	Olfr458	MOR211-8P|MOR221-4|MOR257-4|Olfr301	olfactory receptor 458	protein-coding
Merged-chr1-173975101-1	chr1	173975009	173975193	+	1	NA	exon (NM_011940, exon 3 of 7)	exon (NM_011940, exon 3 of 7)	7743	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
Merged-chr15-76012796-1	chr15	76012682	76012910	+	1	NA	intron (NM_134087, intron 1 of 4)	intron (NM_134087, intron 1 of 4)	1540	NM_134087	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
Merged-chrX-40834059-1	chrX	40833951	40834168	+	1	NA	Intergenic	L1Md_T|LINE|L1	-566795	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
Merged-chr8-84767773-1	chr8	84767610	84767936	+	1	NA	intron (NM_001081982, intron 2 of 9)	intron (NM_001081982, intron 2 of 9)	6596	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
Merged-chr1-18084910-1	chr1	18084748	18085073	+	1	NA	Intergenic	L1Md_A|LINE|L1	60992	NM_001347048	78081	Mm.319913	NM_030033	ENSMUSG00000025774	Crisp4	9230112K08Rik	cysteine-rich secretory protein 4	protein-coding
Merged-chr15-58747809-1	chr15	58747727	58747892	+	1	NA	Intergenic	RLTR28|LTR|ERVL	75618	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
Merged-chr17-17036306-1	chr17	17036109	17036503	+	1	NA	Intergenic	Lx2B2|LINE|L1	-27797	NM_001163919	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr10-112868514-1	chr10	112868429	112868599	+	1	NA	Intergenic	L1Md_T|LINE|L1	30762	NR_152199	100042639	Mm.403280	NR_152199		Gm3942	-	predicted gene 3942	ncRNA
Merged-chr1-20491863-1	chr1	20491734	20491992	+	1	NA	intron (NM_153179, intron 35 of 66)	L1Md_A|LINE|L1	126194	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
Merged-chr5-42188680-1	chr5	42188580	42188780	+	1	NA	intron (NR_131130, intron 1 of 2)	L1Md_T|LINE|L1	120720	NR_131130	433882	Mm.319353	NR_131130	ENSMUSG00000067285	Gm16223	EG433882	predicted gene 16223	ncRNA
Merged-chr1-171556160-1	chr1	171555936	171556384	+	1	NA	Intergenic	Intergenic	-3033	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
Merged-chr1-29607746-1	chr1	29607588	29607904	+	1	NA	Intergenic	L1Md_T|LINE|L1	186258	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
Merged-chr11-120951848-1	chr11	120951746	120951951	+	1	NA	intron (NM_001038654, intron 1 of 4)	intron (NM_001038654, intron 1 of 4)	2781	NM_001038653	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
Merged-chr15-44611199-1	chr15	44611104	44611294	+	1	NA	Intergenic	ORR1A0-int|LTR|ERVL-MaLR	-8028	NM_001357690	55960	Mm.287896	NM_019480	ENSMUSG00000022339	Ebag9	AI835379|Rcas1	estrogen receptor-binding fragment-associated gene 9	protein-coding
Merged-chr12-115822072-1	chr12	115821991	115822153	+	1	NA	Intergenic	MLTR25C|LTR|ERVK	-126278	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr1-176550663-1	chr1	176550455	176550872	+	1	NA	Intergenic	L1Md_T|LINE|L1	-23394	NR_151528	102640488	Mm.415515	NR_151528	ENSMUSG00000104021	Gm36536	-	predicted gene, 36536	ncRNA
Merged-chr12-5741631-1	chr12	5741514	5741749	+	1	NA	Intergenic	L1Md_T|LINE|L1	365129	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
Merged-chr8-119971831-1	chr8	119971712	119971951	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-20607	NM_030209	78892	Mm.264680	NM_030209	ENSMUSG00000031825	Crispld2	1810049K24Rik|Lcrisp2|Lgl1|coffeecrisp	cysteine-rich secretory protein LCCL domain containing 2	protein-coding
Merged-chr11-15781893-1	chr11	15781735	15782052	+	1	NA	Intergenic	L1Md_T|LINE|L1	-475831	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding
Merged-chr13-109372614-1	chr13	109372479	109372750	+	1	NA	intron (NM_011056, intron 3 of 16)	L1Md_T|LINE|L1	47870	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
Merged-chr1-27758719-1	chr1	27758633	27758806	+	1	NA	Intergenic	L1Md_T|LINE|L1	-125327	NR_151583	433281	Mm.329306	NR_151583	ENSMUSG00000101514	Gm5524	AI875557|EG433281	predicted gene 5524	ncRNA
Merged-chr1-94391017-1	chr1	94390938	94391096	+	1	NA	Intergenic	L1Md_A|LINE|L1	-338464	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
Merged-chr1-103150185-1	chr1	103150050	103150320	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1618335	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr11-10451801-1	chr11	10451712	10451891	+	1	NA	Intergenic	L1Md_A|LINE|L1	-662215	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
Merged-chr3-32163132-1	chr3	32162950	32163314	+	1	NA	intron (NM_028231, intron 3 of 5)	L1Md_A|LINE|L1	-202357	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
Merged-chr13-68080277-1	chr13	68080175	68080380	+	1	NA	Intergenic	L1MA10|LINE|L1	151543	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chrX-3083906-1	chrX	3083743	3084070	+	1	NA	Intergenic	L1_Mus3|LINE|L1	6986	NM_001270667	100861966	Mm.443264	NM_001270667	ENSMUSG00000100249	Btbd35f23	Gm21950|Mgclh	BTB domain containing 35, family member 23	protein-coding
Merged-chr5-145609571-1	chr5	145609451	145609692	+	1	NA	Intergenic	ERVB4_2-I_MM-int|LTR|ERVK	-24841	NM_001105159	100041375	Mm.489591	NM_001105159	ENSMUSG00000075552	Cyp3a41b	-	cytochrome P450, family 3, subfamily a, polypeptide 41B	protein-coding
Merged-chr10-16696057-1	chr10	16695881	16696234	+	1	NA	Intergenic	L1Md_T|LINE|L1	399725	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA
Merged-chr10-81582765-1	chr10	81582628	81582902	+	1	NA	exon (NM_001252401, exon 11 of 20)	exon (NM_001252401, exon 11 of 20)	7478	NM_001252401	21886	Mm.38608	NM_019725	ENSMUSG00000034771	Tle2	Grg2|mKIAA4188	transducin-like enhancer of split 2	protein-coding
Merged-chr11-117298978-1	chr11	117298888	117299068	+	1	NA	intron (NM_001113486, intron 3 of 11)	intron (NM_001113486, intron 3 of 11)	32732	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
Merged-chr8-82594177-1	chr8	82594049	82594305	+	1	NA	Intergenic	L1Md_A|LINE|L1	179949	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding
Merged-chr15-77665897-1	chr15	77665801	77665994	+	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-22611	NM_001143686	328563	Mm.17957	NM_001143686	ENSMUSG00000091694	Apol11b	A330102K04Rik	apolipoprotein L 11b	protein-coding
Merged-chr13-111731967-1	chr13	111731889	111732046	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	45789	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
Merged-chr1-143511916-1	chr1	143511795	143512037	+	1	NA	Intergenic	L1Md_T|LINE|L1	-128781	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
Merged-chr13-66625133-1	chr13	66625042	66625224	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-184015	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr15-102362840-1	chr15	102362715	102362966	+	1	NA	intron (NM_001348205, intron 1 of 1)	intron (NM_001348205, intron 1 of 1)	3493	NM_130458	170574	Mm.263284	NM_130458	ENSMUSG00000060284	Sp7	6430578P22Rik|C22|Osx	Sp7 transcription factor 7	protein-coding
Merged-chr15-65951502-1	chr15	65951323	65951682	+	1	NA	intron (NM_001145096, intron 6 of 16)	L1Md_F3|LINE|L1	25302	NM_001145096	654498	Mm.364550	NM_001145096	ENSMUSG00000072511	Hhla1	F930104E18Rik	HERV-H LTR-associating 1	protein-coding
Merged-chr5-114892444-1	chr5	114892270	114892618	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-4490	NM_001359181	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
Merged-chr12-35865880-1	chr12	35865775	35865986	+	1	NA	Intergenic	L1Md_A|LINE|L1	-59741	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding
Merged-chr17-23898763-1	chr17	23898665	23898861	+	1	NA	promoter-TSS (NM_001039238)	promoter-TSS (NM_001039238)	41	NM_001039238	630537	Mm.436677	NM_001039238	ENSMUSG00000096278	Dcpp2	Dcpp-2|EG630537|SPT-2	demilune cell and parotid protein 2	protein-coding
Merged-chr1-61674460-1	chr1	61674318	61674603	+	1	NA	intron (NM_001081050, intron 1 of 22)	L1Md_A|LINE|L1	35636	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
Merged-chr1-171554410-1	chr1	171554259	171554562	+	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-4783	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
Merged-chrX-67143744-1	chrX	67143602	67143887	+	1	NA	Intergenic	Lx2|LINE|L1	-304619	NR_030149	723888		NR_030149	ENSMUSG00000070071	Mir465	Mirn465|mir-465a|mmu-mir-465	microRNA 465	ncRNA
Merged-chr1-98370296-1	chr1	98369991	98370601	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-50828	NM_001164233	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
Merged-chr19-45293582-1	chr19	45293503	45293661	+	1	NA	Intergenic	Intergenic	-58346	NM_010691	16814	Mm.116815	NM_010691	ENSMUSG00000025216	Lbx1	Lbx1h	ladybird homeobox 1	protein-coding
Merged-chr16-10886754-1	chr16	10886623	10886885	+	1	NA	Intergenic	Intergenic	28043	NR_131135	545180	Mm.373756	NR_131135	ENSMUSG00000095369	Gm21859	-	predicted gene, 21859	ncRNA
Merged-chr1-173951390-1	chr1	173951174	173951606	+	1	NA	Intergenic	MLTR31F_MM|LTR|ERVK	-8718	NM_001302650	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Ifi203a|Ifi203b|Mndal	interferon activated gene 203	protein-coding
Merged-chr5-26102604-1	chr5	26102434	26102775	+	1	NA	exon (NM_207657, exon 3 of 5)	exon (NM_207657, exon 3 of 5)	2710	NM_207657	381622	Mm.226878	NM_207657	ENSMUSG00000051940	5031410I06Rik	-	RIKEN cDNA 5031410I06 gene	protein-coding
Merged-chr10-23485998-1	chr10	23485755	23486242	+	1	NA	Intergenic	L1Md_A|LINE|L1	-136055	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
Merged-chr1-140110555-1	chr1	140110408	140110702	+	1	NA	intron (NM_009888, intron 12 of 21)	L1Md_T|LINE|L1	72856	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding
Merged-chr1-76465061-1	chr1	76464948	76465174	+	1	NA	Intergenic	L1Md_T|LINE|L1	-24072	NR_038012	620079	Mm.378379	NR_038012	ENSMUSG00000100553	Gm17751	-	predicted gene, 17751	ncRNA
Merged-chr1-18473845-1	chr1	18473700	18473991	+	1	NA	Intergenic	L1Md_T|LINE|L1	-208707	NM_001040027	77673	Mm.99530	NM_183124	ENSMUSG00000067773	Defb41	9230102D03Rik|BD-17|Bd-41|Defb16|Defb17|Gm15386	defensin beta 41	protein-coding
Merged-chr5-145659460-1	chr5	145659372	145659548	+	1	NA	Intergenic	RLTR13D6|LTR|ERVK	60676	NM_017396	53973	Mm.379071	NM_017396	ENSMUSG00000075551	Cyp3a41a	Cyp3a41	cytochrome P450, family 3, subfamily a, polypeptide 41A	protein-coding
Merged-chr11-56183170-1	chr11	56183017	56183324	+	1	NA	Intergenic	L1Md_A|LINE|L1	-142183	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding
Merged-chr10-122394996-1	chr10	122394911	122395082	+	1	NA	Intergenic	L1Md_T|LINE|L1	-53503	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding
Merged-chr11-38016134-1	chr11	38015967	38016301	+	1	NA	Intergenic	L1Md_T|LINE|L1	357145	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA
Merged-chr1-118125229-1	chr1	118125080	118125378	+	1	NA	Intergenic	L1Md_T|LINE|L1	185499	NR_153836	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding
Merged-chr10-129274051-1	chr10	129273967	129274136	+	1	NA	Intergenic	L1Md_T|LINE|L1	-4730	NM_146544	258537	Mm.271447	NM_146544	ENSMUSG00000062914	Olfr777	MOR114-9	olfactory receptor 777	protein-coding
Merged-chr1-24498042-1	chr1	24497953	24498132	+	1	NA	intron (NM_007733, intron 11 of 50)	L1Md_A|LINE|L1	89395	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
Merged-chr4-25852938-1	chr4	25852853	25853024	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-52935	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
Merged-chr8-52304822-1	chr8	52304729	52304915	+	1	NA	Intergenic	L1Md_T|LINE|L1	-51789	NR_151738	330767	Mm.246790	NR_151738	ENSMUSG00000110013	1190028D05Rik	-	RIKEN cDNA 1190028D05 gene	ncRNA
Merged-chr13-62180811-1	chr13	62180654	62180968	+	1	NA	Intergenic	Intergenic	50921	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr1-146609164-1	chr1	146608991	146609337	+	1	NA	intron (NM_001357572, intron 3 of 8)	L1Md_T|LINE|L1	111477	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr15-97563671-1	chr15	97563585	97563758	+	1	NA	Intergenic	RMER17A|LTR|ERVK	142151	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
Merged-chr1-18538810-1	chr1	18538648	18538972	+	1	NA	Intergenic	L1Md_T|LINE|L1	-273672	NM_001040027	77673	Mm.99530	NM_183124	ENSMUSG00000067773	Defb41	9230102D03Rik|BD-17|Bd-41|Defb16|Defb17|Gm15386	defensin beta 41	protein-coding
Merged-chr1-140714048-1	chr1	140713958	140714138	+	1	NA	Intergenic	L1Md_A|LINE|L1	-57646	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr5-88166695-1	chr5	88166601	88166789	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	80139	NM_001252681	20600	Mm.1397	NM_021289	ENSMUSG00000029281	Smr2	MSG2|Vcs2	submaxillary gland androgen regulated protein 2	protein-coding
Merged-chr1-131682754-1	chr1	131682632	131682877	+	1	NA	Intergenic	L1Md_T|LINE|L1	-5941	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
Merged-chr4-78513369-1	chr4	78513290	78513449	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-80678	NR_131142	623726		NR_131142		A430085M09Rik	EG623726	RIKEN cDNA A430085M09 gene	ncRNA
Merged-chr11-115541233-1	chr11	115541136	115541330	+	1	NA	Intergenic	B1_Mm|SINE|Alu	-5003	NM_133354	170930	Mm.29923	NM_133354	ENSMUSG00000020738	Sumo2	SUMO-2|Smt3A|Smt3b|Smt3h2	small ubiquitin-like modifier 2	protein-coding
Merged-chr1-9245588-1	chr1	9245507	9245669	+	1	NA	intron (NM_027671, intron 1 of 20)	L1Md_T|LINE|L1	54289	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
Merged-chr1-112841901-1	chr1	112841815	112841988	+	1	NA	Intergenic	L1Md_T|LINE|L1	-976983	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
Merged-chr10-44910679-1	chr10	44910577	44910782	+	1	NA	Intergenic	L1Md_A|LINE|L1	-156535	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
Merged-chr15-89140265-1	chr15	89140168	89140362	+	1	NA	intron (NM_013871, intron 1 of 11)	CpG-5233	438	NM_013871	29857	Mm.38343	NM_013871	ENSMUSG00000022610	Mapk12	AW123708|Erk6|P38gamma|Prkm12|Sapk3	mitogen-activated protein kinase 12	protein-coding
Merged-chrX-3267745-1	chrX	3267667	3267824	+	1	NA	Intergenic	L1Md_F2|LINE|L1	175945	NM_001099643	100042254		NM_001099643	ENSMUSG00000078213	Btbd35f4	Gm3750	BTB domain containing 35, family member 4	protein-coding
Merged-chr1-114225048-1	chr1	114224899	114225198	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1460089	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr12-115067082-1	chr12	115066934	115067231	+	1	NA	Intergenic	Lx7|LINE|L1	-553388	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
Merged-chr10-78353376-1	chr10	78353262	78353490	+	1	NA	Intergenic	Intergenic	-1676	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
Merged-chr11-116602541-1	chr11	116602451	116602631	+	1	NA	intron (NM_001167680, intron 9 of 18)	intron (NM_001167680, intron 9 of 18)	8854	NM_009591	11298	Mm.42233	NM_009591	ENSMUSG00000020804	Aanat	AA-NAT|Nat-2|Nat4|Snat	arylalkylamine N-acetyltransferase	protein-coding
Merged-chr12-68959399-1	chr12	68959305	68959494	+	1	NA	Intergenic	L1Md_T|LINE|L1	199787	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
Merged-chr1-47081515-1	chr1	47081404	47081626	+	1	NA	Intergenic	L1Md_T|LINE|L1	-155739	NM_001356417	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|Zip10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
Merged-chr10-51225481-1	chr10	51225369	51225594	+	1	NA	Intergenic	L1Md_A|LINE|L1	-255131	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000112023	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
Merged-chr12-114819802-1	chr12	114819715	114819889	+	1	NA	Intergenic	Intergenic	-306108	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
Merged-chr15-81859227-1	chr15	81859145	81859309	+	1	NA	promoter-TSS (NM_020507)	promoter-TSS (NM_020507)	-901	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	transducer of ERBB2, 2	protein-coding
Merged-chr11-42782020-1	chr11	42781914	42782127	+	1	NA	Intergenic	L1Md_T|LINE|L1	360670	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
Merged-chr10-91142473-1	chr10	91142387	91142559	+	1	NA	Intergenic	B2_Mm1a|SINE|B2	-18510	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
Merged-chr1-71086027-1	chr1	71085841	71086214	+	1	NA	intron (NM_007525, intron 3 of 10)	L1Md_A|LINE|L1	16945	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	-	BRCA1 associated RING domain 1	protein-coding
Merged-chr12-28193369-1	chr12	28193269	28193470	+	1	NA	Intergenic	L1Md_A|LINE|L1	354968	NM_001177964	68511	Mm.310284	NM_001177964	ENSMUSG00000020633	Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding
Merged-chr1-101304672-1	chr1	101304585	101304760	+	1	NA	Intergenic	L1Md_T|LINE|L1	148904	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
Merged-chr8-4687638-1	chr8	4687472	4687805	+	1	NA	Intergenic	MMERVK10C-int|LTR|ERVK	74468	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
Merged-chr1-137150824-1	chr1	137150735	137150914	+	1	NA	Intergenic	L1Md_A|LINE|L1	-190376	NM_030676	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
Merged-chr17-33919875-1	chr17	33919774	33919976	+	1	NA	TTS (NM_020625)	TTS (NM_020625)	397	NM_001025313	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
Merged-chr13-66693365-1	chr13	66693168	66693563	+	1	NA	Intergenic	L1_Mus3|LINE|L1	211985	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr17-10952118-1	chr17	10952038	10952198	+	1	NA	intron (NM_001317726, intron 1 of 6)	L1Md_T|LINE|L1	111759	NM_001317726	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
Merged-chr1-107922518-1	chr1	107922330	107922706	+	1	NA	intron (NR_102306, intron 1 of 3)	L1Md_T|LINE|L1	5259	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr8-120537712-1	chr8	120537405	120538020	+	1	NA	promoter-TSS (NR_106159)	promoter-TSS (NR_106159)	14	NR_151732	74227	Mm.334856	NR_151732	ENSMUSG00000102737	1700016A09Rik	-	RIKEN cDNA 1700016A09 gene	ncRNA
Merged-chr13-62117757-1	chr13	62117645	62117869	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-12133	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr1-137343625-1	chr1	137343478	137343772	+	1	NA	Intergenic	L1Md_T|LINE|L1	-383177	NM_030676	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
Merged-chr11-23839339-1	chr11	23839144	23839535	+	1	NA	Intergenic	L1Md_T|LINE|L1	55931	NM_172555	216578	Mm.470599	NM_172555	ENSMUSG00000020273	Papolg	9630006B20Rik	poly(A) polymerase gamma	protein-coding
Merged-chrX-98179233-1	chrX	98179110	98179357	+	1	NA	intron (NM_013476, intron 1 of 7)	L1Md_T|LINE|L1	30476	NM_013476	11835	Mm.39005	NM_013476	ENSMUSG00000046532	Ar	AW320017|Tfm	androgen receptor	protein-coding
Merged-chr1-163774502-1	chr1	163774418	163774586	+	1	NA	Intergenic	L1Md_T|LINE|L1	-5081	NM_010629	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
Merged-chr13-66594719-1	chr13	66594549	66594890	+	1	NA	Intergenic	MurSatRep1|Unknown|Unknown	-153601	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr1-163566268-1	chr1	163566169	163566367	+	1	NA	Intergenic	L1Md_F2|LINE|L1	158964	NM_001143956	240879	Mm.484621	NM_001143956	ENSMUSG00000040113	Mettl11b	Gm207|NTM1B	methyltransferase like 11B	protein-coding
Merged-chr17-35284314-1	chr17	35284234	35284394	+	1	NA	Intergenic	BGLII_B|LTR|ERVK	21191	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
Merged-chr15-89156770-1	chr15	89156649	89156891	+	1	NA	intron (NM_001159521, intron 36 of 37)	intron (NM_001159521, intron 36 of 37)	6138	NR_106066	102465672		NR_106066	ENSMUSG00000106328	Mir7118	mmu-mir-7118	microRNA 7118	ncRNA
Merged-chr5-145644174-1	chr5	145643981	145644367	+	1	NA	Intergenic	B3A|SINE|B2	-59444	NM_001105159	100041375	Mm.489591	NM_001105159	ENSMUSG00000075552	Cyp3a41b	-	cytochrome P450, family 3, subfamily a, polypeptide 41B	protein-coding
Merged-chr2-22005051-1	chr2	22004962	22005141	+	1	NA	Intergenic	L1Md_A|LINE|L1	-222452	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding
Merged-chr5-26119890-1	chr5	26119766	26120014	+	1	NA	intron (NM_001134299, intron 2 of 4)	intron (NM_001134299, intron 2 of 4)	1535	NM_001134299	434689	Mm.484129	NM_001134299	ENSMUSG00000067698	Gm10220	-	predicted gene 10220	protein-coding
Merged-chr10-119283570-1	chr10	119283491	119283649	+	1	NA	Intergenic	L1Md_T|LINE|L1	-36664	NR_126086	74905	Mm.399357	NR_126085	ENSMUSG00000112155	4930477N07Rik	-	RIKEN cDNA 4930477N07 gene	ncRNA
Merged-chr1-84456594-1	chr1	84456432	84456757	+	1	NA	intron (NM_152915, intron 7 of 12)	L1Md_A|LINE|L1	-171949	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4|P-CLI1	phosphotyrosine interaction domain containing 1	protein-coding
Merged-chr12-115832623-1	chr12	115832508	115832738	+	1	NA	Intergenic	Lx3_Mus|LINE|L1	-136829	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr11-42784404-1	chr11	42784318	42784490	+	1	NA	Intergenic	L1Md_T|LINE|L1	363054	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
Merged-chr1-5351650-1	chr1	5351484	5351816	+	1	NA	Intergenic	L1Md_T|LINE|L1	-236843	NM_001318735	18387	Mm.7977	NM_011011	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	opioid receptor, kappa 1	protein-coding
Merged-chr8-120596630-1	chr8	120596534	120596726	+	1	NA	Intergenic	L1MC3|LINE|L1	-7555	NM_178856	272551	Mm.275910	NM_178856	ENSMUSG00000031821	Gins2	2210013I18Rik|4833427B12Rik|AI323585|Pfs2	GINS complex subunit 2 (Psf2 homolog)	protein-coding
Merged-chr11-11614625-1	chr11	11614394	11614857	+	1	NA	intron (NM_001305143, intron 2 of 3)	L1Md_A|LINE|L1	13213	NM_001305143	102631730	Mm.159430	NM_001305143	ENSMUSG00000062511	4930512M02Rik	-	RIKEN cDNA 4930512M02 gene	protein-coding
Merged-chr11-55666232-1	chr11	55666039	55666425	+	1	NA	Intergenic	L1Md_A|LINE|L1	-58034	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
Merged-chrX-3224257-1	chrX	3224041	3224473	+	1	NA	Intergenic	L1_Mur2|LINE|L1	147337	NM_001270667	100861966	Mm.443264	NM_001270667	ENSMUSG00000100249	Btbd35f23	Gm21950|Mgclh	BTB domain containing 35, family member 23	protein-coding
Merged-chr2-114894546-1	chr2	114894454	114894638	+	1	NA	Intergenic	L1Md_A|LINE|L1	-239582	NM_001356439	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Dph6	5730421E18Rik|Atpbd4	diphthamine biosynthesis 6	protein-coding
Merged-chr1-165446656-1	chr1	165446565	165446748	+	1	NA	intron (NM_028759, intron 1 of 18)	L1Md_T|LINE|L1	13807	NM_028759	74106	Mm.227605	NM_028759	ENSMUSG00000026571	Dcaf6	1200006M05Rik|Iqwd1|PC326	DDB1 and CUL4 associated factor 6	protein-coding
Merged-chr11-38905866-1	chr11	38905776	38905957	+	1	NA	Intergenic	L1Md_A|LINE|L1	-385821	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	-	predicted gene 12130	ncRNA
Merged-chr15-43022234-1	chr15	43022134	43022335	+	1	NA	3' UTR (NM_172815, exon 6 of 6)	3' UTR (NM_172815, exon 6 of 6)	148584	NM_001357956	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
Merged-chr8-19956889-1	chr8	19956795	19956984	+	1	NA	intron (NM_001270553, intron 6 of 9)	intron (NM_001270553, intron 6 of 9)	227313	NM_001039553	626415	Mm.425517	NM_001039553	ENSMUSG00000096265	4930467E23Rik	TSAP	RIKEN cDNA 4930467E23 gene	protein-coding
Merged-chr8-70527774-1	chr8	70527567	70527981	+	1	NA	promoter-TSS (NM_001199631)	promoter-TSS (NM_001199631)	31	NM_001111066	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|FKBPR38|Fkbp38|mFKBP38	FK506 binding protein 8	protein-coding
Merged-chr11-39701646-1	chr11	39701336	39701957	+	1	NA	Intergenic	L1Md_A|LINE|L1	-311421	NR_126439	75315	Mm.461295	NR_126439		4930553C11Rik	-	RIKEN cDNA 4930553C11 gene	ncRNA
Merged-chr1-20421567-1	chr1	20421452	20421682	+	1	NA	intron (NM_153179, intron 36 of 66)	L1Md_T|LINE|L1	65113	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA
Merged-chr17-27280135-1	chr17	27280057	27280213	+	1	NA	Intergenic	MMERVK9E_I-int|LTR|ERVK	-32069	NR_131118	319720	Mm.394996	NR_131118		9630028I04Rik	-	RIKEN cDNA 9630028I04 gene	ncRNA
Merged-chr1-138242094-1	chr1	138241945	138242244	+	1	NA	Intergenic	L1Md_T|LINE|L1	-31644	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding
Merged-chr3-134557298-1	chr3	134557216	134557380	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-133663	NR_040600	75208	Mm.84580	NR_040600	ENSMUSG00000105765	4930539C22Rik	-	RIKEN cDNA 4930539C22 gene	ncRNA
Merged-chr10-17323320-1	chr10	17323202	17323438	+	1	NA	Intergenic	MMERGLN-int|LTR|ERV1	-227538	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA
Merged-chr1-142495041-1	chr1	142494891	142495191	+	1	NA	Intergenic	L1Md_A|LINE|L1	-1145656	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
Merged-chr17-23806967-1	chr17	23806826	23807109	+	1	NA	intron (NM_175229, intron 1 of 13)	CpG	3780	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
Merged-chr1-25525734-1	chr1	25525634	25525834	+	1	NA	intron (NM_175642, intron 7 of 30)	L1Md_T|LINE|L1	-247780	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
Merged-chr15-79039596-1	chr15	79039437	79039755	+	1	NA	intron (NM_001161712, intron 8 of 8)	intron (NM_001161712, intron 8 of 8)	-2289	NM_015738	14429	Mm.390805	NM_015738	ENSMUSG00000114755	Galr3	Galnr3	galanin receptor 3	protein-coding
Merged-chr12-119518354-1	chr12	119518204	119518505	+	1	NA	Intergenic	L1Md_T|LINE|L1	74944	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding
Merged-chr15-58822968-1	chr15	58822849	58823087	+	1	NA	exon (NM_175212, exon 1 of 7)	exon (NM_175212, exon 1 of 7)	459	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
Merged-chr17-35249981-1	chr17	35249839	35250123	+	1	NA	intron (NM_019693, intron 6 of 10)	intron (NM_019693, intron 6 of 10)	-1308	NR_106169	102465886		NR_106169	ENSMUSG00000098269	Mir8094	Gm27513|mmu-mir-8094	microRNA 8094	ncRNA
Merged-chr10-35353178-1	chr10	35353036	35353321	+	1	NA	Intergenic	L1Md_A|LINE|L1	869778	NM_001358769	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
Merged-chr10-63774205-1	chr10	63774025	63774385	+	1	NA	intron (NM_001164376, intron 5 of 17)	L1Md_A|LINE|L1	-46850	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
Merged-chr6-66655246-1	chr6	66655044	66655448	+	1	NA	Intergenic	L1Md_A|LINE|L1	-17494	NM_001166719	546901	Mm.480276	NM_001166719	ENSMUSG00000091012	Vmn1r34	EG546901|Gm5991	vomeronasal 1 receptor 34	protein-coding
Merged-chr19-6906519-1	chr19	6906410	6906629	+	1	NA	TTS (NM_001358444)	TTS (NM_001358444)	-3179	NM_001166370	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
Merged-chr10-22862158-1	chr10	22862020	22862296	+	1	NA	Intergenic	L1Md_T|LINE|L1	-42030	NM_011545	21412	Mm.16497	NM_011545	ENSMUSG00000045680	Tcf21	Pod-1|Pod1|bHLHa23|capsulin|epc|epicardin	transcription factor 21	protein-coding
Merged-chr1-34604534-1	chr1	34604413	34604656	+	1	NA	Intergenic	RLTR10-int|LTR|ERVK	24841	NM_213727	211383	Mm.330696	NM_213727	ENSMUSG00000045174	Amer3	9430069J07Rik|Fam123c	APC membrane recruitment 3	protein-coding
Merged-chr11-40415806-1	chr11	40415694	40415918	+	1	NA	Intergenic	L1Md_T|LINE|L1	276876	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
Merged-chr1-14479625-1	chr1	14479511	14479739	+	1	NA	Intergenic	L1Md_T|LINE|L1	-169426	NM_001252192	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
Merged-chr6-4177833-1	chr6	4177741	4177925	+	1	NA	Intergenic	MMERVK10C-int|LTR|ERVK	-90903	NM_009748	12068	Mm.286457	NM_009748	ENSMUSG00000032757	Bet1	AW555236|Bet-1	Bet1 golgi vesicular membrane trafficking protein	protein-coding
Merged-chr1-157883622-1	chr1	157883466	157883779	+	1	NA	Intergenic	L1Md_A|LINE|L1	357452	NM_001159986	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding
Merged-chr8-117381066-1	chr8	117380959	117381173	+	1	NA	intron (NM_028941, intron 2 of 20)	intron (NM_028941, intron 2 of 20)	31896	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
Merged-chr1-158149837-1	chr1	158149697	158149978	+	1	NA	Intergenic	L1_Mm|LINE|L1	206423	NM_207583	240843	Mm.329579	NM_207583	ENSMUSG00000004031	Brinp2	6430517E21Rik|BB361039|Fam5b|mKIAA1747	bone morphogenic protein/retinoic acid inducible neural-specific 2	protein-coding
Merged-chr10-55578379-1	chr10	55578247	55578511	+	1	NA	Intergenic	L1Md_T|LINE|L1	-528538	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	MSL3 like 2	protein-coding
Merged-chr5-102197026-1	chr5	102196842	102197210	+	1	NA	Intergenic	L1Md_T|LINE|L1	-127105	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
Merged-chr10-13897591-1	chr10	13897334	13897849	+	1	NA	Intergenic	L1Md_T|LINE|L1	26311	NR_152745	102634635		NR_152745	ENSMUSG00000112172	Gm32172	-	predicted gene, 32172	ncRNA
Merged-chr5-69119550-1	chr5	69119410	69119691	+	1	NA	intron (NM_175519, intron 1 of 1)	L1Md_A|LINE|L1	222159	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding
Merged-chr4-12133972-1	chr4	12133862	12134083	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-6145	NM_028226	72397	Mm.430709	NM_028226	ENSMUSG00000046667	Rbm12b1	3000004N20Rik|Rbm12b|Rbm12ba	RNA binding motif protein 12 B1	protein-coding
Merged-chr13-5488396-1	chr13	5488304	5488489	+	1	NA	Intergenic	L1Md_T|LINE|L1	369696	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
Merged-chrX-145115324-1	chrX	145115246	145115402	+	1	NA	intron (NM_001033795, intron 4 of 6)	L1Md_A|LINE|L1	75980	NR_037309	100499526		NR_037309	ENSMUSG00000092917	Mir3472	mmu-mir-3472	microRNA 3472	ncRNA
Merged-chr3-146499710-1	chr3	146499626	146499794	+	1	NA	promoter-TSS (NM_027617)	promoter-TSS (NM_027617)	43	NM_001316756	70951	Mm.383235	NM_027617	ENSMUSG00000028188	Spata1	4921536I21Rik|AV266943|SP-2	spermatogenesis associated 1	protein-coding
Merged-chr15-81585981-1	chr15	81585736	81586227	+	1	NA	promoter-TSS (NM_177821)	promoter-TSS (NM_177821)	-233	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
Merged-chr13-96359829-1	chr13	96359643	96360015	+	1	NA	Intergenic	L1Md_A|LINE|L1	-28465	NM_026173	67463	Mm.86472	NM_026173	ENSMUSG00000021671	Poc5	1200014M14Rik|AV144706	POC5 centriolar protein	protein-coding
Merged-chr13-66678378-1	chr13	66678056	66678700	+	1	NA	Intergenic	Intergenic	226972	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr2-20387989-1	chr2	20387862	20388116	+	1	NA	intron (NM_001081006, intron 2 of 21)	MMERGLN-int|LTR|ERV1	98076	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
Merged-chr1-84266019-1	chr1	84265694	84266345	+	1	NA	intron (NM_001003948, intron 1 of 2)	L1Md_A|LINE|L1	18626	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4|P-CLI1	phosphotyrosine interaction domain containing 1	protein-coding
Merged-chr1-36955339-1	chr1	36955210	36955469	+	1	NA	Intergenic	L1Md_T|LINE|L1	-15812	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
Merged-chr4-101923407-1	chr4	101923321	101923494	+	1	NA	Intergenic	L1Md_T|LINE|L1	-17000	NM_001085516	332923	Mm.473672	NM_001085516	ENSMUSG00000070890	Gm12794	-	predicted gene 12794	protein-coding
Merged-chr1-67280454-1	chr1	67280286	67280622	+	1	NA	Intergenic	L1Md_A|LINE|L1	157427	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
Merged-chr13-66673944-1	chr13	66673597	66674292	+	1	NA	Intergenic	Intergenic	231406	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr18-20620938-1	chr18	20620845	20621031	+	1	NA	intron (NR_155534, intron 1 of 2)	L1M3e|LINE|L1	-44312	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
Merged-chr6-136328415-1	chr6	136328131	136328700	+	1	NA	intron (NM_001142734, intron 1 of 1)	Lx2|LINE|L1	876	NM_001142734	668137	Mm.417085	NM_001142734	ENSMUSG00000094973	Gm8994	B020013A22Rik|EG668137	predicted gene 8994	protein-coding
Merged-chr1-55466606-1	chr1	55466512	55466700	+	1	NA	intron (NM_001114663, intron 1 of 5)	L1Md_A|LINE|L1	60660	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
Merged-chr1-114765756-1	chr1	114765620	114765892	+	1	NA	Intergenic	L1Md_T|LINE|L1	-919381	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr12-115566408-1	chr12	115566265	115566552	+	1	NA	Intergenic	Lx7|LINE|L1	129386	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr12-113777941-1	chr12	113777619	113778263	+	1	NA	Intergenic	MLTR31A_MM|LTR|ERVK	234033	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr10-92476225-1	chr10	92476061	92476389	+	1	NA	Intergenic	L1Md_A|LINE|L1	-100852	NR_046027	627800	Mm.391417	NR_046027	ENSMUSG00000098040	Gm20757	-	predicted gene, 20757	ncRNA
Merged-chr1-62673678-1	chr1	62673537	62673819	+	1	NA	Intergenic	L1Md_T|LINE|L1	-29639	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
Merged-chr11-56207771-1	chr11	56207632	56207910	+	1	NA	Intergenic	L1Md_T|LINE|L1	-166784	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding
Merged-chr11-10223670-1	chr11	10223540	10223800	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-890346	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
Merged-chr12-4801926-1	chr12	4801791	4802061	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-15682	NM_025323	66055	Mm.102627	NM_025323	ENSMUSG00000037361	Sf3b6	0610009D07Rik|6030419K15Rik|AV001342|Sf3b14	splicing factor 3B, subunit 6	protein-coding
Merged-chr17-37560462-1	chr17	37560383	37560542	+	1	NA	Intergenic	L1Md_F3|LINE|L1	8989	NM_001013575	258096	Mm.159619	NM_001013575	ENSMUSG00000051611	Olfr112	4930580F03Rik|MOR218-4	olfactory receptor 112	protein-coding
Merged-chr15-102995632-1	chr15	102995549	102995715	+	1	NA	Intergenic	Intergenic	5093	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
Merged-chr10-103209017-1	chr10	103208889	103209145	+	1	NA	intron (NM_001163559, intron 8 of 25)	L1Md_T|LINE|L1	27305	NM_001163559	74978	Mm.483817	NM_029134	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding
Merged-chr12-26040395-1	chr12	26040301	26040490	+	1	NA	Intergenic	L1Md_A|LINE|L1	170110	NR_131149	629481	Mm.390460	NR_131149	ENSMUSG00000113550	Gm29687	-	predicted gene, 29687	ncRNA
Merged-chr3-142619517-1	chr3	142619361	142619673	+	1	NA	TTS (NM_010259)	TTS (NM_010259)	-1146	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
Merged-chr19-29693686-1	chr19	29693605	29693768	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-4255	NM_029993	77836	Mm.138437	NM_029993	ENSMUSG00000024806	Mlana	A930034P04Rik|Mart1	melan-A	protein-coding
Merged-chr1-173952446-1	chr1	173952330	173952563	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-9774	NM_001302650	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Ifi203a|Ifi203b|Mndal	interferon activated gene 203	protein-coding
Merged-chr8-10511113-1	chr8	10511032	10511195	+	1	NA	intron (NM_001319151, intron 27 of 34)	B4|SINE|B4	357202	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
Merged-chr1-69234972-1	chr1	69234839	69235106	+	1	NA	Intergenic	L1Md_T|LINE|L1	-126913	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
Merged-chr1-162973292-1	chr1	162973214	162973371	+	1	NA	intron (NM_008030, intron 2 of 8)	ETnERV3-int|LTR|ERVK	11236	NM_008030	14262	Mm.2900	NM_008030	ENSMUSG00000026691	Fmo3	AW111792	flavin containing monooxygenase 3	protein-coding
Merged-chr10-45693966-1	chr10	45693853	45694079	+	1	NA	intron (NM_172473, intron 20 of 23)	L1Md_A|LINE|L1	-113738	NR_040624	320363	Mm.123343	NR_040624	ENSMUSG00000110874	D030045P18Rik	-	RIKEN cDNA D030045P18 gene	ncRNA
Merged-chr1-173805151-1	chr1	173805025	173805277	+	1	NA	Intergenic	Lx2|LINE|L1	-38232	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
Merged-chr4-25834924-1	chr4	25834831	25835018	+	1	NA	Intergenic	L1Md_A|LINE|L1	-34921	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
Merged-chr19-10551930-1	chr19	10551824	10552036	+	1	NA	exon (NM_026798, exon 4 of 5)	exon (NM_026798, exon 4 of 5)	3833	NM_001277860	68642	Mm.31236	NM_026798	ENSMUSG00000024667	Tmem216	1110017C22Rik|2810441K11Rik|4921533J23Rik|A930021F15Rik|AI482550	transmembrane protein 216	protein-coding
Merged-chr4-54696776-1	chr4	54696645	54696907	+	1	NA	Intergenic	L1Md_A|LINE|L1	-251169	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
Merged-chr12-113684040-1	chr12	113683961	113684120	+	1	NA	Intergenic	Lx4B|LINE|L1	140132	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr10-66584099-1	chr10	66583987	66584212	+	1	NA	Intergenic	L1Md_T|LINE|L1	336285	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
Merged-chr1-18449623-1	chr1	18449410	18449837	+	1	NA	Intergenic	L1Md_T|LINE|L1	-184485	NM_001040027	77673	Mm.99530	NM_183124	ENSMUSG00000067773	Defb41	9230102D03Rik|BD-17|Bd-41|Defb16|Defb17|Gm15386	defensin beta 41	protein-coding
Merged-chrX-112216723-1	chrX	112216619	112216828	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-22326	NM_001177389	71030	Mm.158538	NM_001177389	ENSMUSG00000079460	4933403O08Rik	-	RIKEN cDNA 4933403O08 gene	protein-coding
Merged-chr8-84945503-1	chr8	84945384	84945622	+	1	NA	Intergenic	Intergenic	-1488	NM_001357326	234542	Mm.461701	NM_144929	ENSMUSG00000048617	Rtbdn	A330096I21Rik|BC022744|Rtbnd	retbindin	protein-coding
Merged-chr1-70212542-1	chr1	70212456	70212628	+	1	NA	intron (NM_025728, intron 2 of 7)	L1Md_T|LINE|L1	260927	NM_025728	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
Merged-chr13-66732999-1	chr13	66732917	66733082	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	172351	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr1-140045558-1	chr1	140045388	140045728	+	1	NA	Intergenic	L1Md_T|LINE|L1	137853	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding
Merged-chr1-78952337-1	chr1	78952254	78952421	+	1	NA	intron (NR_151519, intron 2 of 3)	L1Md_A|LINE|L1	135426	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	potassium voltage-gated channel, Isk-related subfamily, gene 4	protein-coding
Merged-chr2-109836392-1	chr2	109836240	109836545	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-54486	NM_011699	22343	Mm.235300	NM_011699	ENSMUSG00000027162	Lin7c	9130007B12Rik|AI303698|AU019331|AW125731|D2Ertd520e|LIN-7-C|LIN-7C|MALS-3|Veli3	lin-7 homolog C (C. elegans)	protein-coding
Merged-chr5-31048241-1	chr5	31048156	31048326	+	1	NA	promoter-TSS (NM_177870)	promoter-TSS (NM_177870)	-162	NM_177870	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
Merged-chr10-22860335-1	chr10	22860257	22860413	+	1	NA	Intergenic	L1Md_T|LINE|L1	-40207	NM_011545	21412	Mm.16497	NM_011545	ENSMUSG00000045680	Tcf21	Pod-1|Pod1|bHLHa23|capsulin|epc|epicardin	transcription factor 21	protein-coding
Merged-chr11-54384623-1	chr11	54384413	54384833	+	1	NA	intron (NM_029105, intron 4 of 13)	L1Md_T|LINE|L1	13971	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
Merged-chr1-114875448-1	chr1	114875348	114875549	+	1	NA	Intergenic	L1Md_T|LINE|L1	-809689	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr10-126762342-1	chr10	126762253	126762432	+	1	NA	Intergenic	L1_Mm|LINE|L1	31368	NR_131015	75813	Mm.159583	NR_131015	ENSMUSG00000112832	4930484H19Rik	-	RIKEN cDNA 4930484H19 gene	ncRNA
Merged-chr15-97829070-1	chr15	97828968	97829173	+	1	NA	intron (NM_001204276, intron 1 of 25)	intron (NM_001204276, intron 1 of 25)	2697	NM_019572	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
Merged-chr17-85486748-1	chr17	85486628	85486869	+	1	NA	Intergenic	CpG	131648	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
Merged-chr1-137341440-1	chr1	137341261	137341619	+	1	NA	Intergenic	L1Md_T|LINE|L1	-380992	NM_030676	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
Merged-chr19-5052860-1	chr19	5052674	5053047	+	1	NA	intron (NM_145495, intron 6 of 9)	intron (NM_145495, intron 6 of 9)	2052	NM_145495	225870	Mm.271922	NM_145495	ENSMUSG00000024883	Rin1	-	Ras and Rab interactor 1	protein-coding
Merged-chr7-7515986-1	chr7	7515872	7516101	+	1	NA	Intergenic	L1Md_F|LINE|L1	-36013	NM_001105063	22311	Mm.482571	NM_001105063	ENSMUSG00000096743	Vmn2r32	V2r5	vomeronasal 2, receptor 32	protein-coding
Merged-chrX-82267294-1	chrX	82267186	82267402	+	1	NA	Intergenic	L1Md_A|LINE|L1	-681576	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
Merged-chr8-35588400-1	chr8	35588312	35588489	+	1	NA	exon (NM_001081279, exon 1 of 3)	exon (NM_001081279, exon 1 of 3)	602	NM_001081279	52065	Mm.103246	NM_001081279	ENSMUSG00000070056	Mfhas1	2310066G09Rik|D8Ertd91e	malignant fibrous histiocytoma amplified sequence 1	protein-coding
Merged-chr1-106295624-1	chr1	106295541	106295708	+	1	NA	intron (NM_133821, intron 3 of 16)	L1Md_A|LINE|L1	123755	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
Merged-chr1-190351653-1	chr1	190351555	190351752	+	1	NA	Intergenic	L1Md_A|LINE|L1	-51995	NR_151624	433390	Mm.331295	NR_151624	ENSMUSG00000103644	Gm29678	-	predicted gene, 29678	ncRNA
Merged-chr5-88166013-1	chr5	88165712	88166315	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	79457	NM_001252681	20600	Mm.1397	NM_021289	ENSMUSG00000029281	Smr2	MSG2|Vcs2	submaxillary gland androgen regulated protein 2	protein-coding
Merged-chr13-66415974-1	chr13	66415608	66416340	+	1	NA	Intergenic	Intergenic	25144	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr19-5741936-1	chr19	5741823	5742050	+	1	NA	5' UTR (NM_008520, exon 2 of 28)	5' UTR (NM_008520, exon 2 of 28)	1032	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
Merged-chr1-71534359-1	chr1	71534192	71534526	+	1	NA	Intergenic	L1Md_T|LINE|L1	-22797	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
Merged-chr15-102235141-1	chr15	102235050	102235233	+	1	NA	3' UTR (NM_011244, exon 10 of 10)	3' UTR (NM_011244, exon 10 of 10)	-3206	NM_013566	16421	Mm.58	NM_013566	ENSMUSG00000001281	Itgb7	Ly69	integrin beta 7	protein-coding
Merged-chr7-7464156-1	chr7	7464076	7464236	+	1	NA	exon (NM_001105063, exon 6 of 6)	exon (NM_001105063, exon 6 of 6)	15817	NM_001105063	22311	Mm.482571	NM_001105063	ENSMUSG00000096743	Vmn2r32	V2r5	vomeronasal 2, receptor 32	protein-coding
Merged-chr1-162068542-1	chr1	162068406	162068678	+	1	NA	intron (NM_172646, intron 16 of 19)	L1Md_T|LINE|L1	63573	NR_040562	72753	Mm.452125	NR_040562	ENSMUSG00000090260	2810442N19Rik	-	RIKEN cDNA 2810442N19 gene	ncRNA
Merged-chr1-130033029-1	chr1	130032929	130033129	+	1	NA	intron (NM_172485, intron 15 of 27)	L1Md_A|LINE|L1	-389795	NR_151525	102640368		NR_151525	ENSMUSG00000087691	Gm15674	-	predicted gene 15674	ncRNA
Merged-chr17-36166127-1	chr17	36166033	36166221	+	1	NA	intron (NM_001081032, intron 3 of 7)	intron (NM_001081032, intron 3 of 7)	2410	NM_001081032	667977	Mm.441651	NM_001081032	ENSMUSG00000073402	Gm8909	EG667977|H2-Tw5l|H2-gs17	predicted gene 8909	protein-coding
Merged-chr15-55079646-1	chr15	55079509	55079783	+	1	NA	intron (NM_183089, intron 8 of 8)	A-rich|Low_complexity|Low_complexity	-7494	NM_001081288	319944	Mm.380957	NM_001081288	ENSMUSG00000037343	Taf2	150kDa|4732460C16Rik|AI425886|CIF150|TAF2B|TAFII-150|TAFII150	TATA-box binding protein associated factor 2	protein-coding
Merged-chr10-4833856-1	chr10	4833690	4834022	+	1	NA	intron (NM_001302531, intron 4 of 8)	L1Md_A|LINE|L1	123698	NM_001302531	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
Merged-chr4-71623957-1	chr4	71623833	71624082	+	1	NA	Intergenic	L1Md_T|LINE|L1	576936	NM_001285532	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
Merged-chr4-15913294-1	chr4	15913138	15913451	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	29697	NR_105826	102466644		NR_105826	ENSMUSG00000098929	Mir6400	Gm27425|mmu-mir-6400	microRNA 6400	ncRNA
Merged-chr1-116857915-1	chr1	116857821	116858009	+	1	NA	Intergenic	L1Md_T|LINE|L1	1172778	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr5-145612095-1	chr5	145612008	145612183	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-27365	NM_001105159	100041375	Mm.489591	NM_001105159	ENSMUSG00000075552	Cyp3a41b	-	cytochrome P450, family 3, subfamily a, polypeptide 41B	protein-coding
Merged-chr12-29051877-1	chr12	29051788	29051966	+	1	NA	Intergenic	L1Md_T|LINE|L1	-90052	NR_154987	102633526	Mm.134217	NR_154987		Gm31333	-	predicted gene, 31333	ncRNA
Merged-chr13-62436410-1	chr13	62436212	62436609	+	1	NA	Intergenic	Intergenic	30402	NM_178875	71508	Mm.442497	NM_178875	ENSMUSG00000113450	Zfp935	8430426H19Rik|Es113	zinc finger protein 935	protein-coding
Merged-chr15-34506738-1	chr15	34506651	34506826	+	1	NA	intron (NM_152894, intron 5 of 16)	intron (NM_152894, intron 5 of 16)	11427	NM_152894	67724	Mm.248779	NM_026340	ENSMUSG00000022325	Pop1	4932434G09Rik	processing of precursor 1, ribonuclease P/MRP family, (S. cerevisiae)	protein-coding
Merged-chr13-67994259-1	chr13	67994087	67994431	+	1	NA	Intergenic	MT2B|LTR|ERVL	130933	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr12-59503877-1	chr12	59503762	59503992	+	1	NA	Intergenic	L1Md_T|LINE|L1	-284394	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding
Merged-chr13-60393290-1	chr13	60393181	60393399	+	1	NA	Intergenic	L1Md_T|LINE|L1	187819	NR_036449	100503759	Mm.38101	NM_177810	ENSMUSG00000050765	Gm5084	A030007L22|EG328264	predicted gene 5084	ncRNA
Merged-chr11-13820298-1	chr11	13820175	13820421	+	1	NA	Intergenic	L1Md_A|LINE|L1	358743	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
Merged-chr5-3344464-1	chr5	3344297	3344632	+	1	NA	exon (NM_009873, exon 2 of 8)	exon (NM_009873, exon 2 of 8)	571	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
Merged-chr1-44284426-1	chr1	44284219	44284634	+	1	NA	Intergenic	L1Md_A|LINE|L1	-65495	NM_207281	403183	Mm.336176	NM_207281	ENSMUSG00000046828	Mettl21e	4832428D23Rik|Gm991	methyltransferase like 21E	protein-coding
Merged-chr12-37191833-1	chr12	37191649	37192017	+	1	NA	Intergenic	L1Md_T|LINE|L1	-49806	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
Merged-chr11-55670384-1	chr11	55670204	55670565	+	1	NA	Intergenic	L1Md_A|LINE|L1	-62186	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
Merged-chr10-86235802-1	chr10	86235703	86235902	+	1	NA	intron (NM_013722, intron 6 of 13)	L1Md_T|LINE|L1	-64610	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
Merged-chr17-78369318-1	chr17	78369238	78369399	+	1	NA	3' UTR (NM_001285949, exon 8 of 8)	3' UTR (NM_001285949, exon 8 of 8)	48834	NM_001285940	225020	Mm.236835	NM_199448	ENSMUSG00000056121	Fez2	9030616F16|D17Ertd315e	fasciculation and elongation protein zeta 2 (zygin II)	protein-coding
Merged-chr15-75753832-1	chr15	75753746	75753919	+	1	NA	TTS (NM_172121)	TTS (NM_172121)	-5910	NM_194350	378435	Mm.309589	NM_194350	ENSMUSG00000047591	Mafa	RIPE3b1	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein A (avian)	protein-coding
Merged-chr11-15169968-1	chr11	15169879	15170057	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	570728	NM_001164166	432536	Mm.33646	NM_001164166	ENSMUSG00000084135	Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding
Merged-chr8-72057032-1	chr8	72056928	72057137	+	1	NA	promoter-TSS (NM_207555)	promoter-TSS (NM_207555)	-628	NM_207555	404315	Mm.377936	NM_207555	ENSMUSG00000069998	Olfr372	MOR282-1	olfactory receptor 372	protein-coding
Merged-chr4-88805553-1	chr4	88805311	88805796	+	1	NA	promoter-TSS (NM_001243167)	promoter-TSS (NM_001243167)	22	NM_001243167	668208	Mm.487241	NM_001243167	ENSMUSG00000070908	Gm13288	-	predicted gene 13288	protein-coding
Merged-chr8-71562798-1	chr8	71562691	71562905	+	1	NA	exon (NM_145598, exon 2 of 2)	exon (NM_145598, exon 2 of 2)	3851	NM_145598	234404	Mm.213208	NM_145598	ENSMUSG00000034829	Nxnl1	A930031O08Rik|RdCVF|Txnl6	nucleoredoxin-like 1	protein-coding
Merged-chr4-88780732-1	chr4	88780616	88780848	+	1	NA	TTS (NM_001161609).3	TTS (NM_001161609).3	882	NM_001161608	545648	Mm.368246	NM_001161608	ENSMUSG00000096591	Gm13272	-	predicted gene 13272	protein-coding
Merged-chr13-46582098-1	chr13	46582008	46582188	+	1	NA	intron (NM_026056, intron 4 of 12)	L1Md_A|LINE|L1	80195	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	CAP, adenylate cyclase-associated protein, 2 (yeast)	protein-coding
Merged-chr17-90682575-1	chr17	90682435	90682715	+	1	NA	intron (NM_001346957, intron 6 of 18)	L1Md_A|LINE|L1	110901	NR_136930	102634634		NR_136930		Gm20491	-	enolase 1, alpha non-neuron pseudogene	pseudo
Merged-chr1-33047565-1	chr1	33047479	33047651	+	1	NA	Intergenic	L1Md_A|LINE|L1	-500272	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
Merged-chr12-43727301-1	chr12	43727167	43727435	+	1	NA	Intergenic	L1Md_T|LINE|L1	482767	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
Merged-chr15-102058971-1	chr15	102058834	102059108	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-14802	NM_145625	75705	Mm.290022	NM_145625	ENSMUSG00000058655	Eif4b	2310046H11Rik|AL024095|C85189|Eif4a2	eukaryotic translation initiation factor 4B	protein-coding
Merged-chr12-49055829-1	chr12	49055651	49056007	+	1	NA	Intergenic	L1Md_T|LINE|L1	-327054	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
Merged-chr5-88167783-1	chr5	88167681	88167885	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	81227	NM_001252681	20600	Mm.1397	NM_021289	ENSMUSG00000029281	Smr2	MSG2|Vcs2	submaxillary gland androgen regulated protein 2	protein-coding
Merged-chr17-35135112-1	chr17	35135028	35135197	+	1	NA	promoter-TSS (NM_001252468)	promoter-TSS (NM_001252468)	-66	NM_057171	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
Merged-chr15-74607984-1	chr15	74607851	74608117	+	1	NA	intron (NM_001177437, intron 24 of 26)	intron (NM_001177437, intron 24 of 26)	28334	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
Merged-chr8-63674615-1	chr8	63674499	63674731	+	1	NA	Intergenic	L1Md_A|LINE|L1	277555	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgo2b	EG244495|Gm4975|Sgol2b	shugoshin 2B	protein-coding
Merged-chr1-47210668-1	chr1	47210582	47210755	+	1	NA	Intergenic	L1Md_T|LINE|L1	256457	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
Merged-chr19-38871607-1	chr19	38871493	38871721	+	1	NA	intron (NM_145952, intron 2 of 12)	MMETn-int|LTR|ERVK	35028	NM_145952	209478	Mm.391153	NM_145952	ENSMUSG00000048720	Tbc1d12	BC033574	TBC1D12: TBC1 domain family, member 12	protein-coding
Merged-chr11-18627146-1	chr11	18627059	18627233	+	1	NA	Intergenic	L1Md_A|LINE|L1	391823	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
Merged-chr7-59583328-1	chr7	59583186	59583470	+	1	NA	intron (NR_146211, intron 91 of 171)	intron (NR_146211, intron 91 of 171)	92751	NR_033778	64244		NR_033778	ENSMUSG00000096475	Snord116l1	Pwcr1l1	small nucleolar RNA, C/D box 116-like 1	snoRNA
Merged-chr10-102891723-1	chr10	102891600	102891847	+	1	NA	Intergenic	L1Md_T|LINE|L1	137054	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
Merged-chr1-70211659-1	chr1	70211499	70211820	+	1	NA	intron (NM_025728, intron 2 of 7)	L1Md_T|LINE|L1	260044	NM_025728	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
Merged-chr12-113773333-1	chr12	113773223	113773444	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	229425	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr1-15023854-1	chr1	15023649	15024059	+	1	NA	Intergenic	L1Md_A|LINE|L1	-104992	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding
Merged-chr11-15302360-1	chr11	15302221	15302500	+	1	NA	Intergenic	L1Md_A|LINE|L1	703120	NM_001164166	432536	Mm.33646	NM_001164166	ENSMUSG00000084135	Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding
Merged-chr13-36009003-1	chr13	36008898	36009108	+	1	NA	intron (NM_201358, intron 2 of 2)	L1Md_A|LINE|L1	41097	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	protein phosphatase 1, regulatory (inhibitor) subunit 3G	protein-coding
Merged-chr1-187064213-1	chr1	187063989	187064438	+	1	NA	intron (NM_028848, intron 9 of 9)	L1Md_T|LINE|L1	60152	NR_151534	105244050		NR_151534		Gm15509	-	predicted gene 15509	ncRNA
Merged-chr11-38251142-1	chr11	38251053	38251231	+	1	NA	Intergenic	L1Md_T|LINE|L1	268903	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	-	predicted gene 12130	ncRNA
Merged-chr6-129809743-1	chr6	129809656	129809831	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-25473	NM_001014997	232415	Mm.290598	NM_001014997	ENSMUSG00000071158	Gm156	Klrh1	predicted gene 156	protein-coding
Merged-chr4-88806789-1	chr4	88806598	88806980	+	1	NA	TTS (NM_001161609).10	TTS (NM_001161609).10	603	NM_001161609	545654	Mm.478784	NM_001161609	ENSMUSG00000095101	Gm13285	limitin	predicted gene 13285	protein-coding
Merged-chr10-81400063-1	chr10	81399980	81400147	+	1	NA	3' UTR (NM_008688, exon 10 of 10)	3' UTR (NM_008688, exon 10 of 10)	6999	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
Merged-chr1-68129776-1	chr1	68129604	68129948	+	1	NA	intron (NM_010154, intron 20 of 26)	L1Md_T|LINE|L1	978283	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
Merged-chr7-143860667-1	chr7	143860560	143860774	+	1	NA	Intergenic	MMERVK10C-int|LTR|ERVK	37500	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
Merged-chr15-66891497-1	chr15	66891397	66891598	+	1	NA	5' UTR (NM_018865, exon 1 of 5)	5' UTR (NM_018865, exon 1 of 5)	104	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
Merged-chr1-144067142-1	chr1	144067015	144067270	+	1	NA	Intergenic	L1Md_A|LINE|L1	-62993	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
Merged-chr4-17309577-1	chr4	17309406	17309748	+	1	NA	Intergenic	L1Md_T|LINE|L1	-543316	NR_135158	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
Merged-chr4-44474362-1	chr4	44474226	44474498	+	1	NA	Intergenic	L1Md_F3|LINE|L1	133206	NR_039580	100628590		NR_039580	ENSMUSG00000092761	Mir5120	mmu-mir-5120|mu-mir-5120	microRNA 5120	ncRNA
Merged-chr11-73613913-1	chr11	73613817	73614010	+	1	NA	Intergenic	L1Md_A|LINE|L1	11331	NM_207224	193053	Mm.377230	NM_207224	ENSMUSG00000060335	Olfr384	GA_x5J8B7U2A8F-1-327|GA_x6K02T2P1NL-3773152-3774090|MOR135-5|Olfr384-ps1|Olfr386	olfactory receptor 384	protein-coding
Merged-chr1-31698011-1	chr1	31697882	31698141	+	1	NA	Intergenic	L1Md_T|LINE|L1	433164	NR_015347	226957	Mm.25966	NR_015347		Gm4850	EG226957	THO complex 4 pseudogene	pseudo
Merged-chr17-37561537-1	chr17	37561434	37561641	+	1	NA	Intergenic	Intergenic	7914	NM_001013575	258096	Mm.159619	NM_001013575	ENSMUSG00000051611	Olfr112	4930580F03Rik|MOR218-4	olfactory receptor 112	protein-coding
Merged-chr17-36207679-1	chr17	36207533	36207826	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-17528	NM_008208	15043	Mm.426002	NM_008208	ENSMUSG00000054128	H2-T3	H-2T3|H2-Tw3|MumuTL|TL	histocompatibility 2, T region locus 3	protein-coding
Merged-chr10-114536784-1	chr10	114536656	114536912	+	1	NA	intron (NM_146241, intron 6 of 18)	L1Md_T|LINE|L1	264586	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
Merged-chr10-23635434-1	chr10	23635220	23635649	+	1	NA	Intergenic	L1Md_T|LINE|L1	150017	NR_037680	100529074	Mm.371846	NR_037680	ENSMUSG00000070063	Snora33	ACA33|MBI-42	small nucleolar RNA, H/ACA box 33	snoRNA
Merged-chr10-17463512-1	chr10	17463351	17463673	+	1	NA	Intergenic	L1Md_A|LINE|L1	-259716	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
Merged-chr1-62105044-1	chr1	62104750	62105339	+	1	NA	intron (NM_001081050, intron 4 of 22)	L1Md_T|LINE|L1	31065	NR_151537	105243940		NR_151537		Pard3bos2	Gm12747	par-3 family cell polarity regulator beta, opposite strand 2	ncRNA
Merged-chr14-34708654-1	chr14	34708454	34708854	+	1	NA	intron (NM_001004436, intron 4 of 18)	L1Md_T|LINE|L1	34726	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
Merged-chr1-99346347-1	chr1	99346264	99346430	+	1	NA	Intergenic	L1Md_A|LINE|L1	-426418	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
Merged-chr2-15023967-1	chr2	15023844	15024091	+	1	NA	intron (NM_001165941, intron 8 of 11)	L1Md_T|LINE|L1	25345	NM_001355685	74455	Mm.478923	NM_028950	ENSMUSG00000026707	Nsun6	4933403D21Rik|4933414E04Rik|NOPD1	NOL1/NOP2/Sun domain family member 6	protein-coding
Merged-chr1-94723939-1	chr1	94723805	94724074	+	1	NA	Intergenic	L1Md_T|LINE|L1	-73503	NR_040473	74689	Mm.399187	NR_040473	ENSMUSG00000100518	4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	ncRNA
Merged-chr17-46111090-1	chr17	46110945	46111236	+	1	NA	promoter-TSS (NM_026768)	promoter-TSS (NM_026768)	86	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
Merged-chr13-68028681-1	chr13	68028539	68028823	+	1	NA	Intergenic	LTRIS_Mus|LTR|ERV1	165355	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr1-28186965-1	chr1	28186782	28187148	+	1	NA	Intergenic	L1Md_T|LINE|L1	302919	NR_151583	433281	Mm.329306	NR_151583	ENSMUSG00000101514	Gm5524	AI875557|EG433281	predicted gene 5524	ncRNA
Merged-chr1-84267197-1	chr1	84267042	84267353	+	1	NA	intron (NM_001003948, intron 1 of 2)	L1Md_A|LINE|L1	17448	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4|P-CLI1	phosphotyrosine interaction domain containing 1	protein-coding
Merged-chr8-88021002-1	chr8	88020921	88021084	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-61407	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
Merged-chr11-8154246-1	chr11	8153988	8154504	+	1	NA	Intergenic	L1Md_T|LINE|L1	510289	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
Merged-chr1-34603760-1	chr1	34603588	34603933	+	1	NA	Intergenic	RLTR10-int|LTR|ERVK	24067	NM_213727	211383	Mm.330696	NM_213727	ENSMUSG00000045174	Amer3	9430069J07Rik|Fam123c	APC membrane recruitment 3	protein-coding
Merged-chr8-70332248-1	chr8	70332164	70332333	+	1	NA	TTS (NM_001163282)	TTS (NM_001163282)	2483	NM_008107	14559	Mm.258280	NM_008107	ENSMUSG00000087408	Gdf1	AI385651|Gdf-1	growth differentiation factor 1	protein-coding
Merged-chr1-33013941-1	chr1	33013837	33014046	+	1	NA	Intergenic	L1Md_T|LINE|L1	-466648	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
Merged-chr14-123069797-1	chr14	123069691	123069904	+	1	NA	Intergenic	L1Md_A|LINE|L1	-86514	NR_153663	70551	Mm.271988	NM_028651	ENSMUSG00000041594	Tmtc4	4930403J22Rik|5730419O14Rik	transmembrane and tetratricopeptide repeat containing 4	protein-coding
Merged-chr12-50248734-1	chr12	50248562	50248906	+	1	NA	Intergenic	L1Md_A|LINE|L1	400489	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding
Merged-chr1-116535107-1	chr1	116535012	116535203	+	1	NA	intron (NM_001077425, intron 21 of 23)	L1Md_A|LINE|L1	849970	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr5-95498694-1	chr5	95498501	95498887	+	1	NA	Intergenic	L1Md_A|LINE|L1	-12048	NM_001167793	100041354	Mm.422721	NM_001122678	ENSMUSG00000079423	Gm3286	-	predicted gene 3286	protein-coding
Merged-chr4-45398941-1	chr4	45398858	45399024	+	1	NA	3' UTR (NM_001009949, exon 3 of 3)	3' UTR (NM_001009949, exon 3 of 3)	9825	NM_001009949	230125	Mm.260210	NM_001009949	ENSMUSG00000045973	Slc25a51	9130208E07Rik|D130005A03Rik|Gm138|Mcart1	solute carrier family 25, member 51	protein-coding
Merged-chr8-72320362-1	chr8	72320215	72320510	+	1	NA	intron (NM_008452, intron 2 of 2)	intron (NM_008452, intron 2 of 2)	1300	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
Merged-chr19-51892001-1	chr19	51891902	51892101	+	1	NA	Intergenic	Intergenic	-372296	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding
Merged-chr11-36345493-1	chr11	36345349	36345637	+	1	NA	intron (NM_011856, intron 3 of 28)	L1Md_T|LINE|L1	-365404	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
Merged-chr17-23887984-1	chr17	23887870	23888098	+	1	NA	Intergenic	RMER6A|LTR|ERVK	7108	NM_019910	13184	Mm.371556	NM_019910	ENSMUSG00000096445	Dcpp1	BC005655|C86550|Dcpp|Dcpp-1|p20	demilune cell and parotid protein 1	protein-coding
Merged-chrX-124227898-1	chrX	124227734	124228062	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-91988	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
Merged-chr1-89222407-1	chr1	89222122	89222692	+	1	NA	Intergenic	L1Md_A|LINE|L1	151992	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
Merged-chr15-77986150-1	chr15	77986070	77986231	+	1	NA	Intergenic	ID_B1|SINE|B4	-15326	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
Merged-chr17-46756255-1	chr17	46756161	46756350	+	1	NA	exon (NM_011195, exon 4 of 4)	exon (NM_011195, exon 4 of 4)	-4041	NM_001305989	72029	Mm.240325	NM_028065	ENSMUSG00000023973	Cnpy3	1600025D17Rik|2410050O22Rik|AI413153|CAG4A|ERDA5|PRAT4A|Tnrc5	canopy FGF signaling regulator 3	protein-coding
Merged-chr16-8034659-1	chr16	8034576	8034742	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	390477	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Tmem114	4930511J11Rik|Cldn26	transmembrane protein 114	protein-coding
Merged-chr8-72044874-1	chr8	72044714	72045035	+	1	NA	Intergenic	Intergenic	-12786	NM_207555	404315	Mm.377936	NM_207555	ENSMUSG00000069998	Olfr372	MOR282-1	olfactory receptor 372	protein-coding
Merged-chr13-106532519-1	chr13	106532349	106532689	+	1	NA	Intergenic	L1Md_A|LINE|L1	404439	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
Merged-chr17-33185192-1	chr17	33185108	33185277	+	1	NA	Intergenic	L1_Mus1|LINE|L1	8776	NM_010998	100038859	Mm.246543	NM_010998	ENSMUSG00000094891	Olfr55	IF6|MOR267-17|MOR267-20	olfactory receptor 55	protein-coding
Merged-chr12-24474832-1	chr12	24474741	24474923	+	1	NA	Intergenic	L1Md_T|LINE|L1	-23749	NR_028341	21340	Mm.39082	NM_020614	ENSMUSG00000059669	Taf1b	4930408G01Rik|A230108M10Rik|TAFI68|Tafi86|p63	TATA-box binding protein associated factor, RNA polymerase I, B	protein-coding
Merged-chr7-7521456-1	chr7	7521289	7521624	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-41483	NM_001105063	22311	Mm.482571	NM_001105063	ENSMUSG00000096743	Vmn2r32	V2r5	vomeronasal 2, receptor 32	protein-coding
Merged-chr1-6636752-1	chr1	6636658	6636847	+	1	NA	intron (NM_001244693, intron 2 of 22)	L1Md_A|LINE|L1	-93299	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
Merged-chr1-86004345-1	chr1	86004215	86004476	+	1	NA	Intergenic	L1Md_T|LINE|L1	-17597	NM_028647	70060	Mm.196313	NM_027029	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding
Merged-chr11-27385813-1	chr11	27385709	27385918	+	1	NA	Intergenic	L1Md_T|LINE|L1	600705	NR_002890	654472	Mm.347777	NR_002890		Gm12070	-	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
Merged-chr1-28288522-1	chr1	28288421	28288623	+	1	NA	Intergenic	L1Md_T|LINE|L1	404476	NR_151583	433281	Mm.329306	NR_151583	ENSMUSG00000101514	Gm5524	AI875557|EG433281	predicted gene 5524	ncRNA
Merged-chr19-4005183-1	chr19	4005104	4005262	+	1	NA	intron (NM_021791, intron 7 of 10)	intron (NM_021791, intron 7 of 10)	1798	NM_021791	60425	Mm.266972	NM_021791	ENSMUSG00000024871	Doc2g	D830013O18Rik	double C2, gamma	protein-coding
Merged-chr8-84638806-1	chr8	84638708	84638905	+	1	NA	exon (NM_007578, exon 46 of 47)	exon (NM_007578, exon 46 of 47)	24046	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
Merged-chr6-140869456-1	chr6	140869356	140869556	+	1	NA	Intergenic	L1Md_T|LINE|L1	242571	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
Merged-chr8-105847816-1	chr8	105847678	105847954	+	1	NA	intron (NM_177150, intron 7 of 12)	MT2B1|LTR|ERVL	4192	NM_177150	320394	Mm.334775	NM_177150	ENSMUSG00000036672	Cenpt	G630055P03Rik	centromere protein T	protein-coding
Merged-chr12-95581847-1	chr12	95581724	95581970	+	1	NA	Intergenic	L1Md_T|LINE|L1	-110379	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
Merged-chr15-61027921-1	chr15	61027731	61028111	+	1	NA	Intergenic	L1Md_A|LINE|L1	-106651	NM_001081067	117586	Mm.291499	NM_001081067	ENSMUSG00000022347	A1bg	C44	alpha-1-B glycoprotein	protein-coding
Merged-chr12-115613457-1	chr12	115613322	115613593	+	1	NA	Intergenic	Intergenic	82337	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chrX-16590793-1	chrX	16590678	16590908	+	1	NA	Intergenic	L1Md_A|LINE|L1	-28905	NM_173740	17161	Mm.21108	NM_173740	ENSMUSG00000025037	Maoa	1110061B18Rik|AA407771	monoamine oxidase A	protein-coding
Merged-chr12-41089277-1	chr12	41089141	41089413	+	1	NA	intron (NM_053122, intron 3 of 6)	L1Md_T|LINE|L1	65187	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2|Tg(HLA-A/H2-D)2Enge	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
Merged-chr17-17045776-1	chr17	17045456	17046097	+	1	NA	Intergenic	Lx6|LINE|L1	-18327	NM_001163919	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr17-22542236-1	chr17	22542153	22542319	+	1	NA	Intergenic	L1_Mus3|LINE|L1	31037	NM_001104573	210876	Mm.390947	NM_001104573	ENSMUSG00000095093	Vmn2r111	EG210876|V2rp2	vomeronasal 2, receptor 111	protein-coding
Merged-chr13-78948985-1	chr13	78948901	78949069	+	1	NA	Intergenic	L1Md_T|LINE|L1	-750112	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
Merged-chr10-47442485-1	chr10	47442360	47442611	+	1	NA	Intergenic	Intergenic	1197736	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr10-46587079-1	chr10	46586901	46587257	+	1	NA	Intergenic	L1Md_A|LINE|L1	342330	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr6-29059430-1	chr6	29059264	29059596	+	1	NA	promoter-TSS (NM_008493)	promoter-TSS (NM_008493)	-791	NM_008493	16846	Mm.277072	NM_008493	ENSMUSG00000059201	Lep	ob|obese	leptin	protein-coding
Merged-chr1-28292081-1	chr1	28291911	28292252	+	1	NA	Intergenic	L1Md_T|LINE|L1	408035	NR_151583	433281	Mm.329306	NR_151583	ENSMUSG00000101514	Gm5524	AI875557|EG433281	predicted gene 5524	ncRNA
Merged-chr12-68440314-1	chr12	68440208	68440421	+	1	NA	Intergenic	L1Md_T|LINE|L1	718872	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
Merged-chr1-44903969-1	chr1	44903833	44904105	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-159020	NR_040602	75066	Mm.416932	NR_040602	ENSMUSG00000101701	4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	ncRNA
Merged-chr12-95613739-1	chr12	95613559	95613919	+	1	NA	Intergenic	L1Md_A|LINE|L1	-78487	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
Merged-chr15-61570610-1	chr15	61570516	61570704	+	1	NA	Intergenic	L1Md_A|LINE|L1	203841	NR_040350	432956	Mm.404918	NR_040350	ENSMUSG00000116031	D030024E09Rik	-	RIKEN cDNA D030024E09 gene	ncRNA
Merged-chr13-66726155-1	chr13	66725884	66726427	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	179195	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr1-19402519-1	chr1	19402399	19402640	+	1	NA	Intergenic	L1Md_T|LINE|L1	190465	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
Merged-chr11-120261611-1	chr11	120261515	120261708	+	1	NA	intron (NM_198423, intron 3 of 27)	intron (NM_198423, intron 3 of 27)	28664	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
Merged-chr1-122089641-1	chr1	122089554	122089728	+	1	NA	Intergenic	L1Md_T|LINE|L1	-115504	NR_151524	102638832	Mm.112794	NR_151524	ENSMUSG00000099960	Gm28590	-	predicted gene 28590	ncRNA
Merged-chr17-17018203-1	chr17	17018099	17018308	+	1	NA	Intergenic	RLTR44C|LTR|ERVK	-45900	NM_001163919	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr1-105571973-1	chr1	105571866	105572081	+	1	NA	intron (NM_013784, intron 22 of 30)	L1Md_T|LINE|L1	91703	NM_013784	27392	Mm.268911	NM_013784	ENSMUSG00000056536	Pign	Gm20308|PIG-N	phosphatidylinositol glycan anchor biosynthesis, class N	protein-coding
Merged-chr10-112870265-1	chr10	112870178	112870353	+	1	NA	Intergenic	L1Md_T|LINE|L1	32513	NR_152199	100042639	Mm.403280	NR_152199		Gm3942	-	predicted gene 3942	ncRNA
Merged-chr1-107823835-1	chr1	107823743	107823928	+	1	NA	Intergenic	L1Md_T|LINE|L1	-93424	NR_102307	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr13-66442852-1	chr13	66442734	66442971	+	1	NA	Intergenic	Intergenic	-1734	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr17-16123228-1	chr17	16123132	16123324	+	1	NA	Intergenic	L1Md_T|LINE|L1	-296642	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
Merged-chr1-88029325-1	chr1	88029231	88029420	+	1	NA	Intergenic	L1Md_A|LINE|L1	-20774	NM_001198573	227334	Mm.80484	NM_001033291	ENSMUSG00000005501	Usp40	B230215L03Rik|C730029K03	ubiquitin specific peptidase 40	protein-coding
Merged-chr12-42745432-1	chr12	42745320	42745545	+	1	NA	Intergenic	L1Md_T|LINE|L1	288785	NR_148724	102636207		NR_148724		Gm33340	Gm40882	predicted gene, 33340	ncRNA
Merged-chr8-16794030-1	chr8	16793901	16794160	+	1	NA	intron (NM_053171, intron 3 of 69)	IAPEz-int|LTR|ERVK	-625192	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
Merged-chr10-22330660-1	chr10	22330545	22330775	+	1	NA	intron (NM_009018, intron 6 of 6)	L1_Mus1|LINE|L1	23940	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
Merged-chr4-115533765-1	chr4	115533687	115533843	+	1	NA	TTS (NM_010011)	TTS (NM_010011)	15478	NM_010011	13117	Mm.10742	NM_010011	ENSMUSG00000066072	Cyp4a10	AI647584|Cyp4a|D4Rp1|Msp-3|RP1	cytochrome P450, family 4, subfamily a, polypeptide 10	protein-coding
Merged-chr8-60983074-1	chr8	60982931	60983217	+	1	NA	5' UTR (NM_007711, exon 1 of 12)	5' UTR (NM_007711, exon 1 of 12)	237	NM_173873	12725	Mm.25263	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel, voltage-sensitive 3	protein-coding
Merged-chr18-4223289-1	chr18	4223137	4223441	+	1	NA	Intergenic	L1Md_F2|LINE|L1	57457	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
Merged-chr1-151327219-1	chr1	151327137	151327301	+	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	-17267	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
Merged-chr5-144059290-1	chr5	144059211	144059369	+	1	NA	Intergenic	RLTR10|LTR|ERVK	-8681	NM_033039	18261	Mm.270533	NM_033039	ENSMUSG00000029618	Ocm	-	oncomodulin	protein-coding
Merged-chr13-66298929-1	chr13	66298728	66299130	+	1	NA	Intergenic	B4|SINE|B4	142189	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-115037207-1	chr10	115037092	115037323	+	1	NA	Intergenic	L1Md_T|LINE|L1	147815	NM_173391	216343	Mm.31597	NM_173391	ENSMUSG00000006764	Tph2	AU043594|Ntph	tryptophan hydroxylase 2	protein-coding
Merged-chr1-80987715-1	chr1	80987514	80987917	+	1	NA	Intergenic	L1Md_T|LINE|L1	-89235	NM_001356399	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
Merged-chr19-9975227-1	chr19	9975116	9975339	+	1	NA	Intergenic	Intergenic	-5373	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
Merged-chr11-24878931-1	chr11	24878707	24879156	+	1	NA	Intergenic	L1Md_T|LINE|L1	-148209	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	-	predicted gene 10466	ncRNA
Merged-chr1-140516860-1	chr1	140516692	140517028	+	1	NA	intron (NM_001081027, intron 17 of 27)	L1Md_T|LINE|L1	139542	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr19-5848208-1	chr19	5848125	5848292	+	1	NA	Intergenic	Intergenic	-2728	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
Merged-chr1-32668439-1	chr1	32668246	32668633	+	1	NA	Intergenic	L1Md_T|LINE|L1	-121146	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
Merged-chr7-7484108-1	chr7	7483942	7484275	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-4135	NM_001105063	22311	Mm.482571	NM_001105063	ENSMUSG00000096743	Vmn2r32	V2r5	vomeronasal 2, receptor 32	protein-coding
Merged-chr5-103318063-1	chr5	103317953	103318174	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-19034	NR_040699	74624	Mm.389662	NR_040699	ENSMUSG00000104956	4930429D17Rik	-	RIKEN cDNA 4930429D17 gene	ncRNA
Merged-chr17-17057392-1	chr17	17057177	17057608	+	1	NA	Intergenic	Intergenic	-6711	NM_001163919	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr15-39989119-1	chr15	39988987	39989252	+	1	NA	Intergenic	L1Md_T|LINE|L1	26470	NR_045719	105976	Mm.394885	NR_045719		AU022793	-	expressed sequence AU022793	ncRNA
Merged-chr15-77666511-1	chr15	77666421	77666602	+	1	NA	Intergenic	Intergenic	-23225	NM_001143686	328563	Mm.17957	NM_001143686	ENSMUSG00000091694	Apol11b	A330102K04Rik	apolipoprotein L 11b	protein-coding
Merged-chr1-7329753-1	chr1	7329671	7329835	+	1	NA	Intergenic	L1Md_T|LINE|L1	240833	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
Merged-chr10-55577622-1	chr10	55577519	55577726	+	1	NA	Intergenic	L1Md_T|LINE|L1	-529295	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	MSL3 like 2	protein-coding
Merged-chr8-72085497-1	chr8	72085409	72085585	+	1	NA	Intergenic	Intergenic	-14265	NM_146539	258532	Mm.377557	NM_146539	ENSMUSG00000061561	Olfr373	MOR282-2	olfactory receptor 373	protein-coding
Merged-chr17-36185525-1	chr17	36185415	36185635	+	1	NA	TTS (NM_008208)	TTS (NM_008208)	4626	NM_008208	15043	Mm.426002	NM_008208	ENSMUSG00000054128	H2-T3	H-2T3|H2-Tw3|MumuTL|TL	histocompatibility 2, T region locus 3	protein-coding
Merged-chr10-70884453-1	chr10	70884292	70884615	+	1	NA	Intergenic	L1Md_T|LINE|L1	-228490	NR_045292	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
Merged-chr10-27255642-1	chr10	27255555	27255730	+	1	NA	intron (NM_008481, intron 14 of 63)	L1Md_T|LINE|L1	-134224	NR_131034	75855	Mm.402080	NR_131034	ENSMUSG00000101636	4930579H20Rik	-	RIKEN cDNA 4930579H20 gene	ncRNA
Merged-chr1-20579374-1	chr1	20579296	20579452	+	1	NA	intron (NM_153179, intron 11 of 66)	L1Md_A|LINE|L1	38683	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
Merged-chr11-42984334-1	chr11	42984233	42984435	+	1	NA	Intergenic	L1Md_A|LINE|L1	-165543	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
Merged-chr15-100423030-1	chr15	100422929	100423132	+	1	NA	promoter-TSS (NM_001356952)	promoter-TSS (NM_001356952)	25	NM_001356952	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
Merged-chr1-70982735-1	chr1	70982618	70982852	+	1	NA	Intergenic	L1Md_A|LINE|L1	120237	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	-	BRCA1 associated RING domain 1	protein-coding
Merged-chr13-66308787-1	chr13	66308597	66308977	+	1	NA	Intergenic	MMSAT4|Satellite|Satellite	132331	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr17-33164183-1	chr17	33164044	33164323	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-12233	NM_010998	100038859	Mm.246543	NM_010998	ENSMUSG00000094891	Olfr55	IF6|MOR267-17|MOR267-20	olfactory receptor 55	protein-coding
Merged-chr1-126665115-1	chr1	126665013	126665217	+	1	NA	intron (NM_176957, intron 2 of 12)	L1Md_T|LINE|L1	165517	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
Merged-chr1-4557346-1	chr1	4557227	4557466	+	1	NA	Intergenic	IAPLTR2_Mm|LTR|ERVK	-59992	NM_001289467	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
Merged-chr10-22365806-1	chr10	22365709	22365903	+	1	NA	intron (NM_020030, intron 3 of 6)	MTA_Mm|LTR|ERVL-MaLR	3912	NM_020030	56554	Mm.458004	NM_020030	ENSMUSG00000078452	Raet1d	RAE-1delta	retinoic acid early transcript delta	protein-coding
Merged-chr13-66797811-1	chr13	66797643	66797979	+	1	NA	Intergenic	Lx4B|LINE|L1	107539	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr10-56035738-1	chr10	56035533	56035944	+	1	NA	intron (NM_001033385, intron 31 of 32)	L1Md_T|LINE|L1	-71179	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	MSL3 like 2	protein-coding
Merged-chr18-22989617-1	chr18	22989451	22989784	+	1	NA	intron (NM_001361224, intron 1 of 10)	L1Md_T|LINE|L1	49046	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
Merged-chr15-75748542-1	chr15	75748439	75748646	+	1	NA	promoter-TSS (NM_194350)	promoter-TSS (NM_194350)	-620	NM_194350	378435	Mm.309589	NM_194350	ENSMUSG00000047591	Mafa	RIPE3b1	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein A (avian)	protein-coding
Merged-chrX-154505888-1	chrX	154505732	154506044	+	1	NA	Intergenic	L1Md_F2|LINE|L1	23886	NM_029199	75185	Mm.159452	NM_029199	ENSMUSG00000025051	Samt4	4930542N07Rik	spermatogenesis associated multipass transmembrane protein 4	protein-coding
Merged-chr5-57500979-1	chr5	57500867	57501092	+	1	NA	Intergenic	L1Md_A|LINE|L1	216940	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
Merged-chr17-35897059-1	chr17	35896976	35897143	+	1	NA	TTS (NM_001142744)	TTS (NM_001142744)	319	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
Merged-chr1-83823970-1	chr1	83823717	83824224	+	1	NA	Intergenic	L1Md_T|LINE|L1	394991	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
Merged-chr17-21148032-1	chr17	21147948	21148117	+	1	NA	Intergenic	Intergenic	56824	NR_137274	328766	Mm.50947	NR_137274	ENSMUSG00000102080	Gm5092	4933430A09	predicted gene 5092	ncRNA
Merged-chr1-11617366-1	chr1	11617218	11617514	+	1	NA	intron (NM_001160369, intron 7 of 13)	L1Md_T|LINE|L1	203261	NM_001160369	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
Merged-chrX-82215804-1	chrX	82215674	82215934	+	1	NA	Intergenic	L1Md_A|LINE|L1	-733066	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
Merged-chr17-14015746-1	chr17	14015638	14015855	+	1	NA	Intergenic	L1Md_A|LINE|L1	67373	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
Merged-chr1-170689302-1	chr1	170689126	170689479	+	1	NA	Intergenic	L1Md_T|LINE|L1	44770	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
Merged-chr10-33826268-1	chr10	33826190	33826347	+	1	NA	Intergenic	L1Md_T|LINE|L1	-31454	NM_020565	57430	Mm.6590	NM_020565	ENSMUSG00000069668	Sult3a1	ST3A1|Sult-x2|Sultx2	sulfotransferase family 3A, member 1	protein-coding
Merged-chr12-18946961-1	chr12	18946828	18947095	+	1	NA	Intergenic	Intergenic	432451	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
Merged-chr16-70273176-1	chr16	70272992	70273360	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-40773	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
Merged-chr15-55410723-1	chr15	55410558	55410888	+	1	NA	intron (NM_181277, intron 18 of 47)	intron (NM_181277, intron 18 of 47)	102973	NM_181277	12818	Mm.297859	NM_181277	ENSMUSG00000022371	Col14a1	5730412L22Rik|AW108078	collagen, type XIV, alpha 1	protein-coding
Merged-chr15-102134946-1	chr15	102134792	102135101	+	1	NA	intron (NM_001033277, intron 1 of 10)	B1_Mur3|SINE|Alu	1269	NM_001033277	223918	Mm.385009	NM_001033277	ENSMUSG00000036966	Spryd3	BC008150	SPRY domain containing 3	protein-coding
Merged-chr16-9101731-1	chr16	9101628	9101835	+	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	271631	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
Merged-chr17-27411223-1	chr17	27411081	27411366	+	1	NA	Intergenic	Intergenic	53126	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
Merged-chr7-8359616-1	chr7	8359442	8359791	+	1	NA	Intergenic	Intergenic	23622	NM_001105074	434113	Mm.469891	NM_001105074	ENSMUSG00000094098	Vmn2r44	EG434113	vomeronasal 2, receptor 44	protein-coding
Merged-chr12-113716306-1	chr12	113716173	113716440	+	1	NA	Intergenic	Intergenic	172398	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr11-98796246-1	chr11	98796043	98796449	+	1	NA	exon (NM_001361932, exon 1 of 3)	exon (NM_001361932, exon 1 of 3)	730	NM_001361931	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male specific lethal 1	protein-coding
Merged-chr8-19959346-1	chr8	19959267	19959425	+	1	NA	intron (NM_001270553, intron 6 of 9)	RMER15-int|LTR|ERVL	229770	NM_001039553	626415	Mm.425517	NM_001039553	ENSMUSG00000096265	4930467E23Rik	TSAP	RIKEN cDNA 4930467E23 gene	protein-coding
Merged-chr1-35410667-1	chr1	35410557	35410778	+	1	NA	Intergenic	L1Md_A|LINE|L1	560678	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
Merged-chr17-17032209-1	chr17	17032114	17032304	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-31894	NM_001163919	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr1-137981926-1	chr1	137981833	137982020	+	1	NA	Intergenic	L1Md_A|LINE|L1	15287	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
Merged-chr8-88272924-1	chr8	88272806	88273043	+	1	NA	intron (NM_007406, intron 1 of 27)	intron (NM_007406, intron 1 of 27)	521	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
Merged-chr19-58861065-1	chr19	58860950	58861181	+	1	NA	promoter-TSS (NM_175199)	promoter-TSS (NM_175199)	-81	NM_175199	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
Merged-chr11-49346903-1	chr11	49346787	49347019	+	1	NA	Intergenic	L1Md_A|LINE|L1	6369	NM_147065	259068	Mm.377819	NM_147065	ENSMUSG00000045421	Olfr1390	MOR256-2	olfactory receptor 1390	protein-coding
Merged-chr12-115802975-1	chr12	115802879	115803071	+	1	NA	Intergenic	Intergenic	-107181	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr1-171713887-1	chr1	171713799	171713975	+	1	NA	Intergenic	Intergenic	31895	NM_001360767	12506	Mm.1738	NM_007649	ENSMUSG00000015355	Cd48	AI449234|AW610730|BCM1|BLAST|BLAST-1|BLAST1|Bcm-1|MEM-102|SLAMF2|Sgp-60	CD48 antigen	protein-coding
Merged-chr5-145645093-1	chr5	145644918	145645268	+	1	NA	Intergenic	Intergenic	-60363	NM_001105159	100041375	Mm.489591	NM_001105159	ENSMUSG00000075552	Cyp3a41b	-	cytochrome P450, family 3, subfamily a, polypeptide 41B	protein-coding
Merged-chr1-187065799-1	chr1	187065712	187065887	+	1	NA	intron (NM_028848, intron 9 of 9)	L1Md_T|LINE|L1	58566	NR_151534	105244050		NR_151534		Gm15509	-	predicted gene 15509	ncRNA
Merged-chr4-111572695-1	chr4	111572564	111572827	+	1	NA	intron (NM_001284190, intron 9 of 12)	IAPEz-int|LTR|ERVK	-147315	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
Merged-chr12-30825856-1	chr12	30825765	30825947	+	1	NA	Intergenic	L1Md_A|LINE|L1	-58468	NM_001159743	100294583	Mm.399726	NM_001159743	ENSMUSG00000054204	Alkal2	6230419C23Rik|Fam150b	ALK and LTK ligand 2	protein-coding
Merged-chr15-76048727-1	chr15	76048623	76048831	+	1	NA	exon (NM_134089, exon 32 of 38)	exon (NM_134089, exon 32 of 38)	16161	NR_105917	102466772		NR_105917	ENSMUSG00000098451	Mir6952	Gm27948|mmu-mir-6952	microRNA 6952	ncRNA
Merged-chr16-32751976-1	chr16	32751881	32752071	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	16090	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
Merged-chr12-115621613-1	chr12	115621535	115621691	+	1	NA	Intergenic	Intergenic	74181	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr11-45371924-1	chr11	45371740	45372108	+	1	NA	Intergenic	L1Md_T|LINE|L1	-254996	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA
Merged-chr1-23666860-1	chr1	23666777	23666944	+	1	NA	Intergenic	L1Md_A|LINE|L1	92273	NR_151529	105243890	Mm.383635	NR_151529		Gm28822	-	predicted gene 28822	ncRNA
Merged-chr19-10067194-1	chr19	10067023	10067366	+	1	NA	intron (NM_019699, intron 7 of 11)	intron (NM_019699, intron 7 of 11)	25646	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
Merged-chr1-130203303-1	chr1	130203160	130203446	+	1	NA	intron (NM_172485, intron 26 of 27)	L1Md_A|LINE|L1	-219521	NR_151525	102640368		NR_151525	ENSMUSG00000087691	Gm15674	-	predicted gene 15674	ncRNA
Merged-chr6-78400597-1	chr6	78400510	78400684	+	1	NA	Intergenic	L1Md_T|LINE|L1	-4558	NM_009043	19693	Mm.46360	NM_009043	ENSMUSG00000023140	Reg2	PSP|PTP|REG-2	regenerating islet-derived 2	protein-coding
Merged-chr2-150551094-1	chr2	150550984	150551205	+	1	NA	Intergenic	ETnERV3-int|LTR|ERVK	-19321	NM_009977	13011	Mm.12965	NM_009977	ENSMUSG00000068129	Cst7	Cmap	cystatin F (leukocystatin)	protein-coding
Merged-chr5-10486620-1	chr5	10486527	10486713	+	1	NA	Intergenic	RLTR13A2|LTR|ERVK	-378409	NR_003596	623849	Mm.335888	NR_003596	ENSMUSG00000091422	Gm6455	EG623849	predicted gene 6455	pseudo
Merged-chr6-116746758-1	chr6	116746664	116746853	+	1	NA	Intergenic	L1Md_A|LINE|L1	-30000	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
Merged-chr17-16999788-1	chr17	16999655	16999921	+	1	NA	Intergenic	L1Md_A|LINE|L1	-64315	NM_001163919	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr17-17020779-1	chr17	17020682	17020876	+	1	NA	Intergenic	Lx6|LINE|L1	-43324	NM_001163919	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr1-173924003-1	chr1	173923831	173924175	+	1	NA	exon (NM_001302651, exon 7 of 8)	exon (NM_001302651, exon 7 of 8)	-10957	NM_001033450	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
Merged-chr10-103870318-1	chr10	103870133	103870504	+	1	NA	Intergenic	L1Md_T|LINE|L1	-272669	NM_001270644	637578	Mm.441727	NM_001270644	ENSMUSG00000095022	Gm20765	-	predicted gene, 20765	protein-coding
Merged-chr11-115454354-1	chr11	115454252	115454456	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-6294	NR_039549	100628623		NR_039549	ENSMUSG00000093096	Mir3968	mmu-mir-3968|mu-mir-3968	microRNA 3968	ncRNA
Merged-chr12-50690736-1	chr12	50690630	50690842	+	1	NA	Intergenic	L1Md_T|LINE|L1	-41513	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding
Merged-chr1-31075894-1	chr1	31075805	31075983	+	1	NA	intron (NR_136907, intron 1 of 3)	L1Md_T|LINE|L1	20560	NR_136907	102634473	Mm.484482	NR_136907	ENSMUSG00000100371	Gm29669	-	predicted gene 29669	ncRNA
Merged-chr13-66424418-1	chr13	66424327	66424510	+	1	NA	intron (NM_183119, intron 3 of 4)	L1_Mur3|LINE|L1	16700	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-81328439-1	chr10	81328248	81328630	+	1	NA	promoter-TSS (NM_009325)	promoter-TSS (NM_009325)	171	NM_001358512	21390	Mm.4545	NM_009325	ENSMUSG00000034881	Tbxa2r	TP|TXA2-R	thromboxane A2 receptor	protein-coding
Merged-chr15-99426423-1	chr15	99426297	99426549	+	1	NA	exon (NM_001001884, exon 8 of 13)	exon (NM_001001884, exon 8 of 13)	31325	NM_001001884	380969	Mm.22915	NM_001001884	ENSMUSG00000023009	Nckap5l	C230021P08Rik|Cep169	NCK-associated protein 5-like	protein-coding
Merged-chr10-30216263-1	chr10	30216124	30216403	+	1	NA	Intergenic	L1Md_T|LINE|L1	-15723	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding
Merged-chr11-40958884-1	chr11	40958765	40959003	+	1	NA	Intergenic	L1Md_T|LINE|L1	-203598	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
Merged-chr8-7278682-1	chr8	7278449	7278915	+	1	NA	Intergenic	Intergenic	1382091	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr1-54028095-1	chr1	54027978	54028213	+	1	NA	intron (NM_001001883, intron 2 of 28)	L1Md_T|LINE|L1	166939	NM_172655	329152	Mm.132150	NM_172655	ENSMUSG00000042807	Hecw2	A730039N16Rik|D030049F17Rik|Gm971|Nedl2|mKIAA1301	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	protein-coding
Merged-chr12-27402375-1	chr12	27402262	27402488	+	1	NA	Intergenic	L1Md_T|LINE|L1	-59657	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
Merged-chr1-15261221-1	chr1	15261040	15261402	+	1	NA	Intergenic	L1Md_T|LINE|L1	-51231	NM_001098528	98741	Mm.156081	NM_001033195	ENSMUSG00000092083	Kcnb2	9630047L19Rik|BB130875|Kv2.2	potassium voltage gated channel, Shab-related subfamily, member 2	protein-coding
Merged-chr1-150852632-1	chr1	150852493	150852771	+	1	NA	intron (NM_001024720, intron 4 of 106)	L1Md_T|LINE|L1	140803	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding
Merged-chr1-94069272-1	chr1	94069103	94069442	+	1	NA	Intergenic	L1Md_T|LINE|L1	-16719	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
Merged-chr10-25938728-1	chr10	25938649	25938808	+	1	NA	Intergenic	L1Md_T|LINE|L1	-101291	NR_045349	73803	Mm.258921	NR_045349	ENSMUSG00000112444	4930401C15Rik	-	RIKEN cDNA 4930401C15 gene	ncRNA
Merged-chr11-54388099-1	chr11	54387936	54388262	+	1	NA	intron (NM_029105, intron 4 of 13)	L1Md_T|LINE|L1	17447	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
Merged-chr12-9632027-1	chr12	9631931	9632123	+	1	NA	Intergenic	L1Md_T|LINE|L1	57585	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related transcription factor 1	protein-coding
Merged-chr1-24500861-1	chr1	24500649	24501073	+	1	NA	intron (NM_007733, intron 11 of 50)	L1Md_A|LINE|L1	86576	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
Merged-chr1-146605433-1	chr1	146605186	146605680	+	1	NA	intron (NM_001357572, intron 3 of 8)	L1Md_T|LINE|L1	107746	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr19-4163232-1	chr19	4163132	4163333	+	1	NA	exon (NM_021485, exon 1 of 15)	exon (NM_021485, exon 1 of 15)	151	NR_153659	58988	Mm.271937	NM_021485	ENSMUSG00000024830	Rps6kb2	S6K-beta-2|S6K2	ribosomal protein S6 kinase, polypeptide 2	protein-coding
Merged-chrX-124120671-1	chrX	124120542	124120800	+	1	NA	Intergenic	L1_Mus3|LINE|L1	15239	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
Merged-chr15-25875971-1	chr15	25875851	25876092	+	1	NA	intron (NM_001034851, intron 1 of 8)	intron (NM_001034851, intron 1 of 8)	32673	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Retreg1	1810015C04Rik|AU015349|Fam134b|Retreg1d	reticulophagy regulator 1	protein-coding
Merged-chr13-29072245-1	chr13	29072092	29072399	+	1	NA	Intergenic	L1Md_T|LINE|L1	55990	NR_045073	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
Merged-chr1-48265795-1	chr1	48265636	48265955	+	1	NA	Intergenic	L1Md_T|LINE|L1	-798670	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
Merged-chr9-61176713-1	chr9	61176635	61176792	+	1	NA	Intergenic	Intergenic	38198	NR_045705	619328	Mm.325722	NR_045705	ENSMUSG00000110998	I730028E13Rik	-	RIKEN cDNA I730028E13 gene	ncRNA
Merged-chr5-52678238-1	chr5	52678154	52678323	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-8537	NM_172490	211006	Mm.244719	NM_172490	ENSMUSG00000029173	Sepsecs	AA986712|D5Ertd135e|SLA|SecS	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	protein-coding
Merged-chr10-65384441-1	chr10	65384326	65384557	+	1	NA	Intergenic	L1Md_T|LINE|L1	-264074	NR_152621	102632700		NR_152621	ENSMUSG00000100528	Gm28881	-	predicted gene 28881	ncRNA
Merged-chr1-171542461-1	chr1	171542261	171542662	+	1	NA	Intergenic	MYSERV16_I-int|LTR|ERVK	-7167	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
Merged-chr1-125137728-1	chr1	125137616	125137840	+	1	NA	Intergenic	L1Md_T|LINE|L1	297999	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
Merged-chr1-92413478-1	chr1	92413340	92413616	+	1	NA	Intergenic	L1Md_A|LINE|L1	51064	NR_105865	102465542		NR_105865	ENSMUSG00000098288	Mir6900	Gm27708|mmu-mir-6900	microRNA 6900	ncRNA
Merged-chr13-69172423-1	chr13	69172254	69172592	+	1	NA	Intergenic	L1Md_T|LINE|L1	-172882	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
Merged-chr10-16825863-1	chr10	16825691	16826036	+	1	NA	Intergenic	L1Md_T|LINE|L1	269919	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA
Merged-chr2-8189668-1	chr2	8189539	8189798	+	1	NA	Intergenic	L1Md_T|LINE|L1	-793470	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
Merged-chr15-77649778-1	chr15	77649695	77649862	+	1	NA	Intergenic	Intergenic	-6492	NM_001143686	328563	Mm.17957	NM_001143686	ENSMUSG00000091694	Apol11b	A330102K04Rik	apolipoprotein L 11b	protein-coding
Merged-chr1-46586825-1	chr1	46586630	46587021	+	1	NA	intron (NM_001310335, intron 19 of 64)	L1Md_T|LINE|L1	161307	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
Merged-chr3-104511580-1	chr3	104511486	104511674	+	1	NA	exon (NM_001310698, exon 1 of 18)	exon (NM_001310698, exon 1 of 18)	338	NM_001025067	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938|LIG-2	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding
Merged-chr3-122970980-1	chr3	122970855	122971105	+	1	NA	intron (NM_133857, intron 1 of 15)	MLTR31F_MM|LTR|ERVK	13467	NM_133857	99526	Mm.491248	NM_133857	ENSMUSG00000039701	Usp53	AA939927|Phxr3|Sp6|mKIAA1350|mbo	ubiquitin specific peptidase 53	protein-coding
Merged-chr13-60925307-1	chr13	60925201	60925413	+	1	NA	Intergenic	L1Md_F2|LINE|L1	11259	NM_001145799	13024	Mm.482089	NM_007796	ENSMUSG00000044258	Ctla2a	Ctla-2a	cytotoxic T lymphocyte-associated protein 2 alpha	protein-coding
Merged-chr15-101400342-1	chr15	101400257	101400428	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-12061	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
Merged-chr10-119286550-1	chr10	119286326	119286774	+	1	NA	Intergenic	L1Md_T|LINE|L1	-33684	NR_126086	74905	Mm.399357	NR_126085	ENSMUSG00000112155	4930477N07Rik	-	RIKEN cDNA 4930477N07 gene	ncRNA
Merged-chr11-38018623-1	chr11	38018350	38018896	+	1	NA	Intergenic	L1Md_T|LINE|L1	359634	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA
Merged-chr19-7265943-1	chr19	7265839	7266047	+	1	NA	Intergenic	Intergenic	-1451	NM_054048	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
Merged-chr17-35265905-1	chr17	35265694	35266116	+	1	NA	exon (NM_010380, exon 4 of 8)	exon (NM_010380, exon 4 of 8)	2782	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
Merged-chr11-120666845-1	chr11	120666764	120666927	+	1	NA	Intergenic	Intergenic	-6008	NM_175263	77583	Mm.32839	NM_175263	ENSMUSG00000042988	Notum	5730593N15Rik	notum palmitoleoyl-protein carboxylesterase	protein-coding
Merged-chr10-23506226-1	chr10	23506121	23506331	+	1	NA	Intergenic	L1Md_T|LINE|L1	-156283	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
Merged-chr8-19945875-1	chr8	19945590	19946161	+	1	NA	intron (NM_001270553, intron 6 of 9)	L1_Mus2|LINE|L1	216299	NM_001039553	626415	Mm.425517	NM_001039553	ENSMUSG00000096265	4930467E23Rik	TSAP	RIKEN cDNA 4930467E23 gene	protein-coding
Merged-chr19-47919026-1	chr19	47918940	47919112	+	1	NA	intron (NM_001001738, intron 1 of 1)	CpG	273	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
Merged-chr10-42378228-1	chr10	42378053	42378403	+	1	NA	intron (NM_001359297, intron 6 of 11)	L1Md_A|LINE|L1	100337	NM_001359297	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Afg1l	CG8520|Lace1	AFG1 like ATPase	protein-coding
Merged-chr10-124709234-1	chr10	124709144	124709324	+	1	NA	Intergenic	L1Md_T|LINE|L1	240160	NR_028310	75030	Mm.159403	NR_028310	ENSMUSG00000112364	4930503E24Rik	-	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo
Merged-chr11-116654178-1	chr11	116654034	116654323	+	1	NA	5' UTR (NM_030206, exon 1 of 4)	5' UTR (NM_030206, exon 1 of 4)	135	NM_030206	114886	Mm.34598	NM_030206	ENSMUSG00000020810	Cygb	3110001K20Rik|HGb|Staap	cytoglobin	protein-coding
Merged-chr10-19984325-1	chr10	19984226	19984424	+	1	NA	intron (NM_008580, intron 1 of 29)	L1Md_T|LINE|L1	49799	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
Merged-chr14-51594746-1	chr14	51594607	51594886	+	1	NA	intron (NM_001013816, intron 1 of 4)	RLTR14-int|LTR|ERV1	41956	NM_001013816	434459	Mm.359230	NM_001013816	ENSMUSG00000079244	Gm5622	EG434459	predicted gene 5622	protein-coding
Merged-chr10-81310587-1	chr10	81310505	81310670	+	1	NA	intron (NM_001293647, intron 7 of 17)	intron (NM_001293647, intron 7 of 17)	-10516	NM_027381	70312	Mm.87628	NM_027381	ENSMUSG00000034889	Cactin	2510012J08Rik	cactin, spliceosome C complex subunit	protein-coding
Merged-chr8-4238974-1	chr8	4238849	4239099	+	1	NA	exon (NM_001164172, exon 1 of 12)	exon (NM_001164172, exon 1 of 12)	234	NM_011944	26400	Mm.3906	NM_011944	ENSMUSG00000002948	Map2k7	5930412N11Rik|JNKK 2|Jnkk2|MAPKK 7|MEK 7|Mapkk7|Mek7|Mkk7|Prkmk7|sek2	mitogen-activated protein kinase kinase 7	protein-coding
Merged-chr11-58675786-1	chr11	58675662	58675910	+	1	NA	Intergenic	L1Md_A|LINE|L1	-8089	NM_207230	216783	Mm.377240	NM_207230	ENSMUSG00000107711	Olfr320	GA_x6K02T2NKPP-730312-729392|MOR285-4|MOR285-5|Olfr321-ps1	olfactory receptor 320	protein-coding
Merged-chr4-105740565-1	chr4	105740439	105740692	+	1	NA	Intergenic	L1Md_T|LINE|L1	-500648	NR_151521	105244641	Mm.404914	NR_151521		Gm12724	-	predicted gene 12724	ncRNA
Merged-chr8-71155589-1	chr8	71155415	71155764	+	1	NA	intron (NM_001324526, intron 6 of 10)	L1Md_F|LINE|L1	15220	NM_001324526	665858	Mm.411658	NM_001324526		Gm7827	EG665858	predicted gene 7827	protein-coding
Merged-chr5-72074286-1	chr5	72074116	72074456	+	1	NA	intron (NM_008069, intron 5 of 8)	IAPEz-int|LTR|ERVK	93903	NM_001356613	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding
Merged-chr17-94344253-1	chr17	94344166	94344340	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	405766	NM_001357138	76781	Mm.139146	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding
Merged-chr10-122241520-1	chr10	122241436	122241604	+	1	NA	Intergenic	L1Md_T|LINE|L1	121823	NR_027637	100043513	Mm.429141	NR_027637	ENSMUSG00000111952	Gm4489	Gm241	predicted gene 4489	ncRNA
Merged-chr12-61701306-1	chr12	61701219	61701393	+	1	NA	intron (NM_001310586, intron 2 of 5)	L1Md_T|LINE|L1	178139	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
Merged-chr12-104206913-1	chr12	104206761	104207065	+	1	NA	Intergenic	L1Md_T|LINE|L1	-7541	NM_009251	20715	Mm.312628	NM_009251		Serpina3g	2A2|AI119734|Spi2-1|Spi2/eb.1|Spi2A|spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3G	protein-coding
Merged-chr10-80168174-1	chr10	80168014	80168334	+	1	NA	intron (NR_152857, intron 1 of 7)	CpG	335	NM_007705	12696	Mm.17898	NM_007705	ENSMUSG00000045193	Cirbp	Cirp|R74941	cold inducible RNA binding protein	protein-coding
Merged-chr1-167200188-1	chr1	167200092	167200285	+	1	NA	Intergenic	L1Md_T|LINE|L1	84939	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
Merged-chr15-82203116-1	chr15	82202992	82203240	+	1	NA	intron (NM_033218, intron 17 of 18)	intron (NM_033218, intron 17 of 18)	4994	NR_029804	723897		NR_029804	ENSMUSG00000065465	Mir33	Mirn33|mir-33|mmu-mir-33	microRNA 33	ncRNA
Merged-chr1-108327040-1	chr1	108326942	108327139	+	1	NA	Intergenic	L1Md_T|LINE|L1	409781	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr4-88776116-1	chr4	88775976	88776256	+	1	NA	promoter-TSS (NM_001243155).2	promoter-TSS (NM_001243155).2	-646	NM_001243155	545646	Mm.380019	NM_001243155	ENSMUSG00000094271	Gm13290	-	predicted gene 13290	protein-coding
Merged-chr1-61676448-1	chr1	61676336	61676561	+	1	NA	intron (NM_001081050, intron 1 of 22)	L1Md_A|LINE|L1	37624	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
Merged-chr17-23344333-1	chr17	23344244	23344422	+	1	NA	intron (NM_001104579, intron 1 of 5)	intron (NM_001104579, intron 1 of 5)	356	NM_001104579	638102	Mm.469849	NM_001104579	ENSMUSG00000091076	Vmn2r115	EG638102|V2Rp4	vomeronasal 2, receptor 115	protein-coding
Merged-chr4-88776857-1	chr4	88776776	88776938	+	1	NA	promoter-TSS (NM_001243155).2	promoter-TSS (NM_001243155).2	-65	NM_001161609	545654	Mm.478784	NM_001161609	ENSMUSG00000095101	Gm13285	limitin	predicted gene 13285	protein-coding
Merged-chr7-38193514-1	chr7	38193407	38193622	+	1	NA	intron (NM_001085385, intron 2 of 3)	intron (NM_001085385, intron 2 of 3)	9727	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
Merged-chr3-107760166-1	chr3	107760042	107760291	+	1	NA	5' UTR (NM_001113530, exon 1 of 9)	5' UTR (NM_001113530, exon 1 of 9)	303	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
Merged-chr4-62519991-1	chr4	62519859	62520123	+	1	NA	promoter-TSS (NM_008525)	promoter-TSS (NM_008525)	72	NM_008525	17025	Mm.6988	NM_008525	ENSMUSG00000028393	Alad	ALADH|Lv	aminolevulinate, delta-, dehydratase	protein-coding
Merged-chr11-56206612-1	chr11	56206479	56206745	+	1	NA	Intergenic	L1Md_T|LINE|L1	-165625	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding
Merged-chr17-33187352-1	chr17	33187221	33187483	+	1	NA	Intergenic	L1_Mus3|LINE|L1	10936	NM_010998	100038859	Mm.246543	NM_010998	ENSMUSG00000094891	Olfr55	IF6|MOR267-17|MOR267-20	olfactory receptor 55	protein-coding
Merged-chr4-116276625-1	chr4	116276475	116276775	+	1	NA	intron (NM_001355585, intron 6 of 10)	L1Md_F2|LINE|L1	53878	NM_001355586	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55|p55pik	phosphoinositide-3-kinase regulatory subunit 3	protein-coding
Merged-chr13-50894639-1	chr13	50894551	50894727	+	1	NA	Intergenic	L1Md_T|LINE|L1	-129391	NR_045364	71654	Mm.427318	NR_045364	ENSMUSG00000113652	4930518P08Rik	-	RIKEN cDNA 4930518P08 gene	ncRNA
Merged-chr1-94475971-1	chr1	94475886	94476057	+	1	NA	Intergenic	L1Md_A|LINE|L1	-321471	NR_040473	74689	Mm.399187	NR_040473	ENSMUSG00000100518	4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	ncRNA
Merged-chr1-58329767-1	chr1	58329661	58329873	+	1	NA	intron (NM_001008419, intron 20 of 35)	IAPEz-int|LTR|ERVK	51441	NM_001008419	213043	Mm.414292	NM_001008419	ENSMUSG00000079554	Aox2	Aoh3|Aox3l1	aldehyde oxidase 2	protein-coding
Merged-chr1-158881458-1	chr1	158881224	158881692	+	1	NA	intron (NM_001085376, intron 2 of 21)	L1Md_T|LINE|L1	75980	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
Merged-chr12-113772911-1	chr12	113772816	113773006	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	229003	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr1-71532536-1	chr1	71532431	71532641	+	1	NA	Intergenic	L1Md_T|LINE|L1	-24620	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
Merged-chr1-185159389-1	chr1	185159259	185159520	+	1	NA	Intergenic	L1Md_T|LINE|L1	-44779	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
Merged-chr15-76180476-1	chr15	76180373	76180579	+	1	NA	exon (NM_201391, exon 31 of 32)	exon (NM_201391, exon 31 of 32)	15234	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
Merged-chr1-15258635-1	chr1	15258488	15258782	+	1	NA	Intergenic	L1Md_T|LINE|L1	-53817	NM_001098528	98741	Mm.156081	NM_001033195	ENSMUSG00000092083	Kcnb2	9630047L19Rik|BB130875|Kv2.2	potassium voltage gated channel, Shab-related subfamily, member 2	protein-coding
Merged-chr6-123362519-1	chr6	123362338	123362701	+	1	NA	Intergenic	L1Md_T|LINE|L1	54186	NM_001104632	232358	Mm.469878	NM_001104632	ENSMUSG00000091260	Vmn2r19	EG232358	vomeronasal 2, receptor 19	protein-coding
Merged-chr13-113723680-1	chr13	113723509	113723851	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-60004	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding
Merged-chr19-5424790-1	chr19	5424680	5424901	+	1	NA	promoter-TSS (NM_001256515)	promoter-TSS (NM_001256515)	189	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
Merged-chr8-110805987-1	chr8	110805901	110806073	+	1	NA	promoter-TSS (NM_001135100)	promoter-TSS (NM_001135100)	-63	NM_001135100	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
Merged-chr8-13974378-1	chr8	13974285	13974471	+	1	NA	intron (NM_001361630, intron 2 of 3)	CpG	399	NM_173744	72148	Mm.5727	NM_173744	ENSMUSG00000050052	Tdrp	2610019F03Rik	testis development related protein	protein-coding
Merged-chr13-62175998-1	chr13	62175916	62176081	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	46108	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr2-5318861-1	chr2	5318771	5318951	+	1	NA	intron (NM_001290374, intron 5 of 9)	intron (NM_001290374, intron 5 of 9)	-60529	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
Merged-chr11-40344514-1	chr11	40344397	40344631	+	1	NA	Intergenic	L1Md_A|LINE|L1	348168	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
Merged-chr10-79446485-1	chr10	79446375	79446595	+	1	NA	Intergenic	L1Md_A|LINE|L1	-22473	NM_001104537	625029	Mm.469865	NM_001104537	ENSMUSG00000091381	Vmn2r83	EG625029	vomeronasal 2, receptor 83	protein-coding
Merged-chr1-46449273-1	chr1	46449059	46449487	+	1	NA	intron (NM_001310335, intron 3 of 64)	L1Md_T|LINE|L1	23755	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
Merged-chr1-70546215-1	chr1	70546102	70546329	+	1	NA	intron (NM_025728, intron 7 of 7)	L1Md_A|LINE|L1	-179500	NM_001310658	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding
Merged-chr1-46975241-1	chr1	46975155	46975327	+	1	NA	Intergenic	L1Md_F|LINE|L1	-49465	NM_001356417	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|Zip10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
Merged-chr17-94786776-1	chr17	94786666	94786887	+	1	NA	intron (NR_045963, intron 3 of 4)	L1Md_F3|LINE|L1	36676	NR_024720	77022	Mm.440259	NR_024720	ENSMUSG00000098090	2700099C18Rik	9430041D22Rik	NDC80 homolog, kinetochore complex component pseudogene	pseudo
Merged-chr10-112169760-1	chr10	112169667	112169853	+	1	NA	intron (NM_001310675, intron 2 of 17)	L1Md_T|LINE|L1	4084	NM_178278	353025	Mm.194428	NM_178278	ENSMUSG00000035694	Caps2	D630005B03Rik	calcyphosphine 2	protein-coding
Merged-chr8-21655349-1	chr8	21655259	21655439	+	1	NA	promoter-TSS (NM_001167790)	promoter-TSS (NM_001167790)	-418	NM_001167790	23855	Mm.425519	NM_001167790	ENSMUSG00000060208	Defa17	AU014719|Cryp17|Defcr17	defensin, alpha, 17	protein-coding
Merged-chr13-68016046-1	chr13	68015855	68016237	+	1	NA	Intergenic	Intergenic	152720	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr10-98607314-1	chr10	98607223	98607406	+	1	NA	Intergenic	L1Md_T|LINE|L1	-255447	NR_045179	667438	Mm.414522	NR_045179	ENSMUSG00000112896	Gm8633	EG667438	predicted gene 8633	ncRNA
Merged-chr15-98918143-1	chr15	98918027	98918259	+	1	NA	promoter-TSS (NM_029098)	promoter-TSS (NM_029098)	-45	NM_029098	74775	Mm.385020	NM_029098	ENSMUSG00000022999	Lmbr1l	1110013E13Rik|AA415653|D15Ertd735e|Limr	limb region 1 like	protein-coding
Merged-chr17-17000550-1	chr17	17000456	17000644	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-63553	NM_001163919	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr1-94197251-1	chr1	94197108	94197394	+	1	NA	Intergenic	L1Md_A|LINE|L1	-144698	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
Merged-chr1-124969293-1	chr1	124969212	124969375	+	1	NA	Intergenic	L1Md_T|LINE|L1	466434	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
Merged-chr11-51024367-1	chr11	51024252	51024483	+	1	NA	Intergenic	L1Md_A|LINE|L1	-2637	NM_010997	18354	Mm.222843	NM_010997	ENSMUSG00000059397	Olfr54	F3|MOR126-1	olfactory receptor 54	protein-coding
Merged-chr17-50929410-1	chr17	50929274	50929546	+	1	NA	intron (NM_028162, intron 9 of 21)	L1Md_T|LINE|L1	229968	NM_001285993	72238	Mm.120650	NM_028162	ENSMUSG00000023923	Tbc1d5	1600014N05Rik	TBC1 domain family, member 5	protein-coding
Merged-chr11-56735484-1	chr11	56735340	56735628	+	1	NA	Intergenic	L1Md_T|LINE|L1	-276134	NM_008165	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
Merged-chr13-65349545-1	chr13	65349146	65349945	+	1	NA	Intergenic	Intergenic	70691	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
Merged-chr15-10730707-1	chr15	10730604	10730811	+	1	NA	intron (NR_045063, intron 2 of 6)	B3|SINE|B2	15807	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000096971	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
Merged-chr1-4081579-1	chr1	4081495	4081664	+	1	NA	Intergenic	L1Md_A|LINE|L1	278735	NM_011283	19888	Mm.294263	NM_011283	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding
Merged-chr15-34134049-1	chr15	34133918	34134181	+	1	NA	intron (NM_001357925, intron 7 of 10)	B1_Mus2|SINE|Alu	51330	NM_001357925	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
Merged-chr13-10306223-1	chr13	10306024	10306422	+	1	NA	intron (NM_033269, intron 1 of 4)	L1Md_T|LINE|L1	54580	NM_033269	12671	Mm.342315	NM_033269	ENSMUSG00000046159	Chrm3	Chrm-3|M3|M3R	cholinergic receptor, muscarinic 3, cardiac	protein-coding
Merged-chr1-173926468-1	chr1	173926331	173926606	+	1	NA	intron (NM_001302649, intron 8 of 9)	intron (NM_001302649, intron 8 of 9)	-13422	NM_001033450	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
Merged-chr12-37150143-1	chr12	37149990	37150296	+	1	NA	intron (NM_008584, intron 1 of 2)	L1_Mm|LINE|L1	41603	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
Merged-chr12-105481709-1	chr12	105481603	105481816	+	1	NA	intron (NM_001252508, intron 1 of 1)	L1Md_F2|LINE|L1	27853	NM_001252508	268595	Mm.2388	NM_001252508	ENSMUSG00000094910	D430019H16Rik	AI852661	RIKEN cDNA D430019H16 gene	protein-coding
Merged-chr13-23404523-1	chr13	23404415	23404631	+	1	NA	Intergenic	Lx7|LINE|L1	19343	NM_013924	30946	Mm.292094	NM_013924	ENSMUSG00000036376	Abt1	-	activator of basal transcription 1	protein-coding
Merged-chr10-30222666-1	chr10	30222512	30222821	+	1	NA	Intergenic	L1Md_T|LINE|L1	-22126	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding
Merged-chr1-137983368-1	chr1	137983289	137983447	+	1	NA	Intergenic	L1Md_A|LINE|L1	16729	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
Merged-chr8-120489243-1	chr8	120489154	120489333	+	1	NA	intron (NM_198671, intron 1 of 15)	CpG-14576	377	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
Merged-chr10-70885234-1	chr10	70885062	70885406	+	1	NA	Intergenic	L1Md_T|LINE|L1	-229271	NR_045292	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
Merged-chr12-6776584-1	chr12	6776494	6776674	+	1	NA	Intergenic	L1Md_A|LINE|L1	603746	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
Merged-chr17-38625080-1	chr17	38624995	38625165	+	1	NA	Intergenic	Lx3A|LINE|L1	-14367	NM_001177586	100126768	Mm.471528	NM_001177586	ENSMUSG00000092342	Esp31	Gm20516	exocrine gland secreted peptide 31	protein-coding
Merged-chr1-130034256-1	chr1	130034142	130034370	+	1	NA	intron (NM_172485, intron 15 of 27)	L1Md_A|LINE|L1	-388568	NR_151525	102640368		NR_151525	ENSMUSG00000087691	Gm15674	-	predicted gene 15674	ncRNA
Merged-chr15-75334141-1	chr15	75334028	75334254	+	1	NA	Intergenic	L1Md_A|LINE|L1	65720	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
Merged-chr5-74494208-1	chr5	74494111	74494306	+	1	NA	intron (NM_001114660, intron 2 of 8)	L1Md_F2|LINE|L1	37534	NM_001114660	212986	Mm.134147	NM_178672	ENSMUSG00000062110	Scfd2	E430013M20Rik|STXBP1L1	Sec1 family domain containing 2	protein-coding
Merged-chr13-68352908-1	chr13	68352680	68353137	+	1	NA	TTS (NR_152173)	TTS (NR_152173)	3917	NR_152173	666272	Mm.309128	NR_152173	ENSMUSG00000113050	Gm8016	EG666272	predicted gene 8016	ncRNA
Merged-chr10-121707326-1	chr10	121707212	121707441	+	1	NA	Intergenic	L1Md_A|LINE|L1	-32604	NM_001359720	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding
Merged-chr15-54138253-1	chr15	54138152	54138355	+	1	NA	Intergenic	L1Md_F2|LINE|L1	140231	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)	protein-coding
Merged-chr11-62969492-1	chr11	62969407	62969578	+	1	NA	intron (NM_025496, intron 1 of 1)	L1Md_A|LINE|L1	18299	NM_025496	66338	Mm.46166	NM_025496	ENSMUSG00000042200	Cdrt4	1700019I23Rik	CMT1A duplicated region transcript 4	protein-coding
Merged-chr10-32968632-1	chr10	32968538	32968727	+	1	NA	Intergenic	L1Md_T|LINE|L1	-78717	NM_001025286	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
Merged-chr19-5654901-1	chr19	5654776	5655027	+	1	NA	exon (NM_001164482, exon 8 of 16)	exon (NM_001164482, exon 8 of 16)	8806	NM_011379	20469	Mm.3072	NM_011379	ENSMUSG00000056917	Sipa1	Spa1	signal-induced proliferation associated gene 1	protein-coding
Merged-chr15-33270940-1	chr15	33270806	33271074	+	1	NA	intron (NM_176073, intron 3 of 7)	L1Md_A|LINE|L1	134999	NR_033608	73486	Mm.483393	NM_028551	ENSMUSG00000058101	1700084J12Rik	-	ribosomal protein L7-like 1 pseudogene	pseudo
Merged-chr1-63799528-1	chr1	63799355	63799701	+	1	NA	Intergenic	L1Md_T|LINE|L1	-30261	NM_001256158	74426	Mm.159197	NM_001256158	ENSMUSG00000025961	4933402D24Rik	-	RIKEN cDNA 4933402D24 gene	protein-coding
Merged-chrX-47969346-1	chrX	47969238	47969454	+	1	NA	Intergenic	L1Md_F2|LINE|L1	56890	NM_177215	320634	Mm.210343	NM_177215	ENSMUSG00000001173	Ocrl	9530014D17Rik|BB143339|OCRL1	OCRL, inositol polyphosphate-5-phosphatase	protein-coding
Merged-chr15-97942570-1	chr15	97942482	97942658	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-21659	NM_201359	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
Merged-chr1-101303664-1	chr1	101303514	101303814	+	1	NA	Intergenic	L1Md_T|LINE|L1	147896	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
Merged-chr10-27816554-1	chr10	27816450	27816658	+	1	NA	Intergenic	L1Md_A|LINE|L1	-199612	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	laminin, alpha 2	protein-coding
Merged-chr2-82485869-1	chr2	82485779	82485960	+	1	NA	Intergenic	L1Md_A|LINE|L1	-93667	NR_152125	228116	Mm.246588	NR_152125	ENSMUSG00000087061	A130030D18Rik	Gm558	RIKEN cDNA A130030D18 gene	ncRNA
Merged-chr8-72069916-1	chr8	72069717	72070115	+	1	NA	Intergenic	Lx2A1|LINE|L1	12256	NM_207555	404315	Mm.377936	NM_207555	ENSMUSG00000069998	Olfr372	MOR282-1	olfactory receptor 372	protein-coding
Merged-chr2-17277218-1	chr2	17277080	17277356	+	1	NA	Intergenic	L1Md_T|LINE|L1	-263492	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
Merged-chr10-73441577-1	chr10	73441486	73441669	+	1	NA	Intergenic	L1Md_T|LINE|L1	-354872	NR_040646	327768	Mm.417745	NR_040646	ENSMUSG00000111994	A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
Merged-chr3-65197251-1	chr3	65197099	65197403	+	1	NA	intron (NM_001289450, intron 2 of 14)	L1Md_T|LINE|L1	9148	NM_001289450	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
Merged-chr17-35256554-1	chr17	35256396	35256713	+	1	NA	Intergenic	Intergenic	5265	NR_106169	102465886		NR_106169	ENSMUSG00000098269	Mir8094	Gm27513|mmu-mir-8094	microRNA 8094	ncRNA
Merged-chr8-106442159-1	chr8	106442078	106442241	+	1	NA	Intergenic	Lx8|LINE|L1	26820	NM_011764	22751	Mm.295582	NM_011764	ENSMUSG00000031907	Zfp90	6430515L01Rik|KRAB17|NK10|Zfp64|Zfp83|mKIAA1954	zinc finger protein 90	protein-coding
Merged-chr1-68271723-1	chr1	68271630	68271817	+	1	NA	intron (NM_010154, intron 16 of 26)	L1Md_A|LINE|L1	836336	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
Merged-chr1-146606903-1	chr1	146606777	146607030	+	1	NA	intron (NM_001357572, intron 3 of 8)	L1Md_T|LINE|L1	109216	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr1-55477052-1	chr1	55476846	55477259	+	1	NA	intron (NM_001114663, intron 1 of 5)	L1Md_T|LINE|L1	71106	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
Merged-chr6-64657437-1	chr6	64657288	64657586	+	1	NA	intron (NM_008167, intron 14 of 15)	ETnERV3-int|LTR|ERVK	-71688	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal bHLH transcription factor 1	protein-coding
Merged-chr10-123493887-1	chr10	123493766	123494009	+	1	NA	intron (NR_153334, intron 2 of 6)	L1Md_A|LINE|L1	229811	NR_153334	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|Sam2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
Merged-chr17-38547288-1	chr17	38547137	38547440	+	1	NA	Intergenic	Lx2B2|LINE|L1	-6904	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr1-34604925-1	chr1	34604834	34605016	+	1	NA	Intergenic	RLTR10-int|LTR|ERVK	25232	NM_213727	211383	Mm.330696	NM_213727	ENSMUSG00000045174	Amer3	9430069J07Rik|Fam123c	APC membrane recruitment 3	protein-coding
Merged-chr13-53044166-1	chr13	53044045	53044288	+	1	NA	Intergenic	L1Md_T|LINE|L1	-63127	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
Merged-chr10-48235530-1	chr10	48235339	48235722	+	1	NA	Intergenic	L1Md_T|LINE|L1	1552407	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
Merged-chr1-69233495-1	chr1	69233330	69233660	+	1	NA	Intergenic	L1Md_T|LINE|L1	-125436	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
Merged-chr1-25662894-1	chr1	25662703	25663086	+	1	NA	intron (NM_175642, intron 2 of 30)	L1Md_T|LINE|L1	166813	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
Merged-chr1-66576799-1	chr1	66576650	66576948	+	1	NA	intron (NM_175510, intron 23 of 64)	L1Md_A|LINE|L1	108352	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
Merged-chr12-13424819-1	chr12	13424723	13424916	+	1	NA	intron (NM_027706, intron 35 of 51)	L1Md_T|LINE|L1	155692	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding
Merged-chr15-76522861-1	chr15	76522749	76522973	+	1	NA	promoter-TSS (NM_130893)	promoter-TSS (NM_130893)	-732	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
Merged-chr17-21150698-1	chr17	21150614	21150783	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	59490	NR_137274	328766	Mm.50947	NR_137274	ENSMUSG00000102080	Gm5092	4933430A09	predicted gene 5092	ncRNA
Merged-chr13-77590162-1	chr13	77590057	77590268	+	1	NA	intron (NM_001145676, intron 19 of 19)	L1Md_T|LINE|L1	-118528	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
Merged-chr15-99242310-1	chr15	99242169	99242451	+	1	NA	TTS (NM_016766)	TTS (NM_016766)	-9478	NR_045627	73600	Mm.475134	NR_045627	ENSMUSG00000100599	1700120C14Rik	-	RIKEN cDNA 1700120C14 gene	ncRNA
Merged-chr11-26673370-1	chr11	26673253	26673488	+	1	NA	Intergenic	L1Md_T|LINE|L1	-79450	NM_001252447	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
Merged-chr13-66627404-1	chr13	66627162	66627646	+	1	NA	Intergenic	RLTR45-int|LTR|ERVK	-186286	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr1-80138776-1	chr1	80138627	80138926	+	1	NA	Intergenic	L1Md_T|LINE|L1	75168	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding
Merged-chr11-120833957-1	chr11	120833867	120834048	+	1	NA	intron (NM_027745, intron 18 of 18)	L1M4|LINE|L1	-9410	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
Merged-chr1-114180011-1	chr1	114179773	114180249	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1505126	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr15-77439714-1	chr15	77439409	77440019	+	1	NA	intron (NM_001024848, intron 1 of 4)	LTRIS_Mm|LTR|ERV1	7746	NM_001024848	278679	Mm.440965	NM_001024848	ENSMUSG00000068252	Apol7b	-	apolipoprotein L 7b	protein-coding
Merged-chr13-68006060-1	chr13	68005962	68006158	+	1	NA	Intergenic	L1Md_F3|LINE|L1	142734	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr8-106484392-1	chr8	106484310	106484475	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-26460	NM_001037809	12560	Mm.4658	NM_007665	ENSMUSG00000061048	Cdh3	AI385538|Cadp|Cdhp|P-cadherin|Pcad	cadherin 3	protein-coding
Merged-chr8-71143271-1	chr8	71143149	71143393	+	1	NA	intron (NM_001324526, intron 3 of 10)	intron (NM_001324526, intron 3 of 10)	2902	NM_001324526	665858	Mm.411658	NM_001324526		Gm7827	EG665858	predicted gene 7827	protein-coding
Merged-chr12-69361327-1	chr12	69361193	69361462	+	1	NA	Intergenic	7SLRNA|srpRNA|srpRNA	-4151	NM_025441	66244	Mm.46705	NM_025441	ENSMUSG00000020982	Nemf	1500011I12Rik|4933405E14Rik|Sdccag1	nuclear export mediator factor	protein-coding
Merged-chr19-4856071-1	chr19	4855989	4856153	+	1	NA	exon (NM_019861, exon 3 of 14)	exon (NM_019861, exon 3 of 14)	942	NM_019861	56464	Mm.29561	NM_019861	ENSMUSG00000083282	Ctsf	AI481912	cathepsin F	protein-coding
Merged-chr15-55696807-1	chr15	55696674	55696940	+	1	NA	intron (NM_016667, intron 3 of 6)	(TG)n|Simple_repeat|Simple_repeat	139399	NM_134092	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
Merged-chr1-26259575-1	chr1	26259372	26259778	+	1	NA	Intergenic	L1Md_A|LINE|L1	427885	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding
Merged-chr2-153096026-1	chr2	153095909	153096144	+	1	NA	Intergenic	Intergenic	-12442	NM_010407	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
Merged-chr1-137154375-1	chr1	137154263	137154488	+	1	NA	Intergenic	L1Md_A|LINE|L1	-193927	NM_030676	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
Merged-chr8-70712376-1	chr8	70712262	70712490	+	1	NA	Intergenic	Intergenic	-6167	NM_001195253	100502950	Mm.52981	NM_001195253	ENSMUSG00000095026	Gm3336	100041434|2410018E23Rik	predicted gene 3336	protein-coding
Merged-chr15-76234698-1	chr15	76234592	76234804	+	1	NA	intron (NM_001163576, intron 8 of 9)	intron (NM_001163576, intron 8 of 9)	-3320	NM_001163542	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
Merged-chr5-109902369-1	chr5	109902247	109902491	+	1	NA	Intergenic	RLTR4_MM-int|LTR|ERV1	-31194	NR_040366	100642166		NR_040366	ENSMUSG00000090015	Gm15446	-	predicted gene 15446	ncRNA
Merged-chr5-60757966-1	chr5	60757875	60758058	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-771964	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
Merged-chr12-115638599-1	chr12	115638375	115638823	+	1	NA	Intergenic	RMER13B|LTR|ERVK	57195	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr1-56718697-1	chr1	56718568	56718826	+	1	NA	Intergenic	L1Md_T|LINE|L1	-81246	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
Merged-chr3-106083722-1	chr3	106083622	106083822	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-29660	NM_023186	81600	Mm.46418	NM_023186	ENSMUSG00000062778	Chia1	2200003E03Rik|AMCase|Chia|YNL	chitinase, acidic 1	protein-coding
Merged-chrX-39665826-1	chrX	39665701	39665951	+	1	NA	Intergenic	L1Md_T|LINE|L1	197778	NM_001191032	100504400	Mm.373409	NM_001191032	ENSMUSG00000095240	Cypt14	-	cysteine-rich perinuclear theca 14	protein-coding
Merged-chr10-96508239-1	chr10	96508151	96508327	+	1	NA	Intergenic	L1Md_T|LINE|L1	-108762	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
Merged-chr1-171526791-1	chr1	171526585	171526998	+	1	NA	intron (NM_010584, intron 7 of 7)	RLTR12E|LTR|ERVK	8503	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
Merged-chr10-28045516-1	chr10	28045355	28045678	+	1	NA	Intergenic	L1Md_T|LINE|L1	-29304	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
Merged-chr1-44484837-1	chr1	44484637	44485038	+	1	NA	Intergenic	L1Md_T|LINE|L1	-66834	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
Merged-chr13-22599462-1	chr13	22599356	22599568	+	1	NA	Intergenic	L1Md_A|LINE|L1	-6532	NM_134217	171251	Mm.377206	NM_134217	ENSMUSG00000100296	Vmn1r205	V1rh8	vomeronasal 1 receptor 205	protein-coding
Merged-chr3-25732144-1	chr3	25731992	25732296	+	1	NA	intron (NM_001357095, intron 4 of 6)	intron (NM_001357095, intron 4 of 6)	421842	NM_001357097	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
Merged-chr17-22626689-1	chr17	22626545	22626834	+	1	NA	Intergenic	L1M4|LINE|L1	25541	NM_001104575	628185	Mm.390947	NM_001104575	ENSMUSG00000094921	Vmn2r112	EG628185|V2rp1	vomeronasal 2, receptor 112	protein-coding
Merged-chr11-45374124-1	chr11	45374046	45374202	+	1	NA	Intergenic	L1Md_T|LINE|L1	-257196	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA
Merged-chr17-34119675-1	chr17	34119574	34119777	+	1	NA	non-coding (NR_037970, exon 1 of 13)	non-coding (NR_037970, exon 1 of 13)	225	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
Merged-chr10-98545515-1	chr10	98545393	98545637	+	1	NA	Intergenic	L1Md_T|LINE|L1	-193648	NR_045179	667438	Mm.414522	NR_045179	ENSMUSG00000112896	Gm8633	EG667438	predicted gene 8633	ncRNA
Merged-chr8-7540732-1	chr8	7540624	7540840	+	1	NA	Intergenic	L1Md_F2|LINE|L1	1120041	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr10-25420066-1	chr10	25419977	25420156	+	1	NA	intron (NM_013511, intron 1 of 19)	L1Md_T|LINE|L1	11698	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
Merged-chr5-60985038-1	chr5	60984957	60985120	+	1	NA	Intergenic	L1Md_T|LINE|L1	-823805	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
Merged-chr12-115618509-1	chr12	115618386	115618632	+	1	NA	Intergenic	Intergenic	77285	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr3-3214656-1	chr3	3214577	3214735	+	1	NA	Intergenic	Lx2B|LINE|L1	-293374	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
Merged-chr10-81350449-1	chr10	81350309	81350589	+	1	NA	promoter-TSS (NM_010440)	promoter-TSS (NM_010440)	8	NM_001163166	15353	Mm.38474	NM_010440	ENSMUSG00000020232	Hmg20b	AW610687|BRAF35|Hmgx2|Hmgxb2|Smarce1r	high mobility group 20B	protein-coding
Merged-chr7-7363757-1	chr7	7363664	7363851	+	1	NA	Intergenic	Intergenic	-26264	NM_009490	22306	Mm.458977	NM_009490	ENSMUSG00000070847	Vmn2r30	V2r15	vomeronasal 2, receptor 30	protein-coding
Merged-chr13-66735687-1	chr13	66735520	66735855	+	1	NA	Intergenic	Intergenic	169663	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr12-115589833-1	chr12	115589714	115589952	+	1	NA	Intergenic	Lx7|LINE|L1	105961	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr12-119516100-1	chr12	119515995	119516206	+	1	NA	Intergenic	L1Md_T|LINE|L1	72690	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding
Merged-chr12-42742591-1	chr12	42742442	42742741	+	1	NA	Intergenic	L1Md_T|LINE|L1	291626	NR_148724	102636207		NR_148724		Gm33340	Gm40882	predicted gene, 33340	ncRNA
Merged-chr1-114767686-1	chr1	114767563	114767809	+	1	NA	Intergenic	L1Md_T|LINE|L1	-917451	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr10-109087158-1	chr10	109087039	109087278	+	1	NA	Intergenic	L1Md_T|LINE|L1	-76183	NM_001358504	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
Merged-chr8-70776824-1	chr8	70776746	70776903	+	1	NA	promoter-TSS (NM_008841)	promoter-TSS (NM_008841)	-38	NR_029440	72093	Mm.271208	NR_029440		2010320M18Rik	-	RIKEN cDNA 2010320M18 gene	ncRNA
Merged-chr11-120274818-1	chr11	120274615	120275022	+	1	NA	intron (NM_198423, intron 9 of 27)	intron (NM_198423, intron 9 of 27)	41871	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
Merged-chr1-79827285-1	chr1	79827164	79827407	+	1	NA	intron (NM_009255, intron 1 of 8)	L1Md_A|LINE|L1	31380	NM_009255	20720	Mm.3093	NM_009255	ENSMUSG00000026249	Serpine2	B230326M24Rik|PAI-1|PI-7|PI7|PN-1|Spi4	serine (or cysteine) peptidase inhibitor, clade E, member 2	protein-coding
Merged-chr19-6996264-1	chr19	6996169	6996359	+	1	NA	promoter-TSS (NM_026675)	promoter-TSS (NM_026675)	133	NM_153597	107328	Mm.391161	NM_153597	ENSMUSG00000047656	Trpt1	AU079016|AW045591|Tpt1|Tpt1h	tRNA phosphotransferase 1	protein-coding
Merged-chr10-58764152-1	chr10	58764017	58764287	+	1	NA	Intergenic	L1Md_A|LINE|L1	-49207	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
Merged-chr7-61741083-1	chr7	61741003	61741164	+	1	NA	intron (NR_015533, intron 6 of 8)	intron (NR_015533, intron 6 of 8)	1342	NR_049201	100885840		NR_049201	ENSMUSG00000094173	Mir344h-1	Gm24425|mmu-mir-344h-1	microRNA 344h-1	ncRNA
Merged-chr11-121318400-1	chr11	121318321	121318479	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	36047	NM_025793	66840	Mm.103986	NM_025793	ENSMUSG00000025173	Wdr45b	0610008N23Rik|AA408735|D16Bwg0193e|WIPI-3|Wdr45l	WD repeat domain 45B	protein-coding
Merged-chr12-95252966-1	chr12	95252843	95253089	+	1	NA	Intergenic	L1Md_T|LINE|L1	-439260	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
Merged-chr8-71191280-1	chr8	71191090	71191470	+	1	NA	intron (NR_131056, intron 2 of 4)	L1_Mur2|LINE|L1	15668	NR_131056	330796	Mm.258257	NR_131056		Gm38415	E230016D10	predicted gene, 38415	ncRNA
Merged-chr17-30083665-1	chr17	30083551	30083779	+	1	NA	intron (NM_001356265, intron 2 of 5)	L1M3e|LINE|L1	78626	NM_001356265	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
Merged-chr1-118124506-1	chr1	118124310	118124702	+	1	NA	Intergenic	L1Md_T|LINE|L1	186222	NR_153836	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding
Merged-chr1-48229678-1	chr1	48229558	48229799	+	1	NA	Intergenic	L1Md_T|LINE|L1	-762553	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
Merged-chr17-33191105-1	chr17	33190989	33191222	+	1	NA	Intergenic	Intergenic	-7957	NM_207175	100038860	Mm.377394	NM_207175	ENSMUSG00000093884	Olfr239	MOR267-10	olfactory receptor 239	protein-coding
Merged-chr16-60438906-1	chr16	60438821	60438991	+	1	NA	intron (NM_007938, intron 2 of 17)	L1Md_T|LINE|L1	166625	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
Merged-chr10-115040098-1	chr10	115039878	115040319	+	1	NA	Intergenic	L1Md_T|LINE|L1	144924	NM_173391	216343	Mm.31597	NM_173391	ENSMUSG00000006764	Tph2	AU043594|Ntph	tryptophan hydroxylase 2	protein-coding
Merged-chr11-7922660-1	chr11	7922565	7922755	+	1	NA	Intergenic	L1Md_T|LINE|L1	-708737	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
Merged-chr17-29144884-1	chr17	29144789	29144980	+	1	NA	intron (NM_001002786, intron 4 of 7)	B1_Mm|SINE|Alu	9828	NM_001002786	442827	Mm.440341	NM_001002786	ENSMUSG00000064147	Rab44	9830134C10Rik	RAB44, member RAS oncogene family	protein-coding
Merged-chr5-89315949-1	chr5	89315858	89316040	+	1	NA	Intergenic	L1Md_A|LINE|L1	141949	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	vitamin D binding protein	protein-coding
Merged-chr3-132827486-1	chr3	132827376	132827596	+	1	NA	intron (NM_001163455, intron 25 of 25)	L1Md_T|LINE|L1	51110	NR_102298	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
Merged-chr11-13817657-1	chr11	13817561	13817753	+	1	NA	Intergenic	L1Md_A|LINE|L1	361384	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
Merged-chr13-62508596-1	chr13	62508483	62508709	+	1	NA	Intergenic	RLTR30D2_MM|LTR|ERV1	-41784	NM_001136496	71508	Mm.442497	NM_178875	ENSMUSG00000113450	Zfp935	8430426H19Rik|Es113	zinc finger protein 935	protein-coding
Merged-chr1-158647412-1	chr1	158647321	158647504	+	1	NA	intron (NM_007495, intron 16 of 22)	L1Md_T|LINE|L1	141787	NR_030441	735253		NR_030441	ENSMUSG00000070103	Mir488	Mirn488|mir-488|mmu-mir-488	microRNA 488	ncRNA
Merged-chr10-56032354-1	chr10	56031984	56032725	+	1	NA	intron (NM_001033385, intron 31 of 32)	L1Md_T|LINE|L1	-74563	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	MSL3 like 2	protein-coding
Merged-chr3-96597870-1	chr3	96597647	96598094	+	1	NA	exon (NM_001024851, exon 2 of 2)	exon (NM_001024851, exon 2 of 2)	1234	NM_001024851	545554	Mm.267664	NM_001024851	ENSMUSG00000049097	Ankrd34a	AW060394|Ankrd34	ankyrin repeat domain 34A	protein-coding
Merged-chr1-158334056-1	chr1	158333963	158334149	+	1	NA	intron (NM_207583, intron 1 of 7)	L1Md_T|LINE|L1	22204	NM_207583	240843	Mm.329579	NM_207583	ENSMUSG00000004031	Brinp2	6430517E21Rik|BB361039|Fam5b|mKIAA1747	bone morphogenic protein/retinoic acid inducible neural-specific 2	protein-coding
Merged-chr8-54709517-1	chr8	54709439	54709595	+	1	NA	intron (NM_028220, intron 1 of 30)	RLTR10-int|LTR|ERVK	9161	NM_028220	244484	Mm.95281	NM_028220	ENSMUSG00000039375	Wdr17	3010002I12Rik|B230207L18Rik	WD repeat domain 17	protein-coding
Merged-chr17-38530496-1	chr17	38529860	38531132	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-23696	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr15-102037559-1	chr15	102037416	102037702	+	1	NA	Intergenic	ID4|SINE|ID	9343	NM_010664	16668	Mm.22479	NM_010664	ENSMUSG00000023043	Krt18	CK18|K18|Krt1-18	keratin 18	protein-coding
Merged-chr15-4420360-1	chr15	4420151	4420569	+	1	NA	intron (NM_177355, intron 1 of 2)	L1Md_T|LINE|L1	44869	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	phosphatidylinositol-specific phospholipase C, X domain containing 3	protein-coding
Merged-chr4-50530062-1	chr4	50529892	50530232	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-684293	NM_001033351	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding
Merged-chrX-123075956-1	chrX	123075871	123076042	+	1	NA	Intergenic	Intergenic	-27567	NM_001310652	73061	Mm.292979	NM_028426	ENSMUSG00000079450	Cldn34c1	3110007F17Rik	claudin 34C1	protein-coding
Merged-chr11-46012826-1	chr11	46012703	46012950	+	1	NA	intron (NM_173384, intron 4 of 4)	L1Md_T|LINE|L1	32516	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY (sex determining region Y)-box 30	protein-coding
Merged-chrX-3217689-1	chrX	3217559	3217819	+	1	NA	Intergenic	RLTR6B_Mm|LTR|ERV1	140769	NM_001270667	100861966	Mm.443264	NM_001270667	ENSMUSG00000100249	Btbd35f23	Gm21950|Mgclh	BTB domain containing 35, family member 23	protein-coding
Merged-chr5-3012571-1	chr5	3012469	3012674	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-331322	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
Merged-chr13-62182379-1	chr13	62182195	62182564	+	1	NA	Intergenic	Intergenic	52489	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr1-82549959-1	chr1	82549814	82550105	+	1	NA	intron (NM_007735, intron 4 of 47)	L1Md_A|LINE|L1	36890	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
Merged-chr1-19437104-1	chr1	19437012	19437197	+	1	NA	Intergenic	L1Md_A|LINE|L1	225050	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
Merged-chr10-42053219-1	chr10	42053130	42053309	+	1	NA	Intergenic	Intergenic	-34837	NM_001034858	213402	Mm.211320	NM_001034858	ENSMUSG00000071324	Armc2	2610018I05Rik	armadillo repeat containing 2	protein-coding
Merged-chr17-24580430-1	chr17	24580351	24580510	+	1	NA	exon (NM_013630, exon 23 of 46)	exon (NM_013630, exon 23 of 46)	30480	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystin 1, transient receptor poteintial channel interacting	protein-coding
Merged-chr12-49052280-1	chr12	49052082	49052479	+	1	NA	Intergenic	L1Md_T|LINE|L1	-330603	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
Merged-chr10-43262032-1	chr10	43261927	43262137	+	1	NA	intron (NM_027772, intron 1 of 7)	L1Md_A|LINE|L1	40546	NM_027772	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding
Merged-chr4-12136764-1	chr4	12136606	12136923	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-3353	NM_028226	72397	Mm.430709	NM_028226	ENSMUSG00000046667	Rbm12b1	3000004N20Rik|Rbm12b|Rbm12ba	RNA binding motif protein 12 B1	protein-coding
Merged-chr10-4915143-1	chr10	4914966	4915320	+	1	NA	intron (NM_001302531, intron 5 of 8)	L1Md_T|LINE|L1	153920	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
Merged-chr16-29270774-1	chr16	29270644	29270904	+	1	NA	intron (NM_175650, intron 22 of 29)	L1Md_A|LINE|L1	60666	NR_154594	27281	Mm.103650	NM_013751	ENSMUSG00000022525	Hrasls	2810012B06Rik|A-C1|HRSL1|Hrasrs	HRAS-like suppressor	protein-coding
Merged-chr15-55751095-1	chr15	55751017	55751173	+	1	NA	intron (NM_016667, intron 2 of 6)	Lx3_Mus|LINE|L1	155854	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
Merged-chr1-176552184-1	chr1	176552076	176552293	+	1	NA	Intergenic	L1Md_T|LINE|L1	-24915	NR_151528	102640488	Mm.415515	NR_151528	ENSMUSG00000104021	Gm36536	-	predicted gene, 36536	ncRNA
Merged-chr12-44236218-1	chr12	44236051	44236385	+	1	NA	Intergenic	L1Md_A|LINE|L1	14862	NR_045113	100039062	Mm.490648	NR_045113		Gm2027	-	nuclear assembly factor 1 homolog pseudogene	pseudo
Merged-chr1-145254278-1	chr1	145254173	145254384	+	1	NA	Intergenic	L1Md_T|LINE|L1	-478851	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
Merged-chr13-49746757-1	chr13	49746576	49746939	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	64627	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
Merged-chr12-103621011-1	chr12	103620897	103621125	+	1	NA	intron (NM_144834, intron 4 of 4)	L1Md_T|LINE|L1	10433	NM_001301404	217847	Mm.29094	NM_144834	ENSMUSG00000061947	Serpina10	PZI|ZPI	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	protein-coding
Merged-chr1-124970757-1	chr1	124970646	124970868	+	1	NA	Intergenic	L1Md_T|LINE|L1	464970	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
Merged-chr12-6016107-1	chr12	6015973	6016242	+	1	NA	Intergenic	L1Md_A|LINE|L1	639605	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
Merged-chr10-70883622-1	chr10	70883536	70883709	+	1	NA	Intergenic	L1Md_T|LINE|L1	-227659	NR_045292	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
Merged-chr1-107826373-1	chr1	107826227	107826520	+	1	NA	Intergenic	L1Md_T|LINE|L1	-90886	NR_102307	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr13-62109941-1	chr13	62109795	62110087	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-19949	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr10-129592619-1	chr10	129592533	129592705	+	1	NA	Intergenic	L1Md_T|LINE|L1	15860	NM_146931	258933	Mm.377755	NM_146931	ENSMUSG00000052012	Olfr796	MOR269-1	olfactory receptor 796	protein-coding
Merged-chr12-98925596-1	chr12	98925460	98925732	+	1	NA	intron (NM_029553, intron 1 of 13)	L1Md_T|LINE|L1	4984	NM_198311	76260	Mm.282660	NM_029553	ENSMUSG00000021013	Ttc8	0610012F22Rik|AV001447|BBS8	tetratricopeptide repeat domain 8	protein-coding
Merged-chr17-8810970-1	chr17	8810693	8811247	+	1	NA	intron (NM_011866, intron 1 of 21)	L1M5|LINE|L1	9225	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
Merged-chr15-25984844-1	chr15	25984752	25984937	+	1	NA	exon (NM_144523, exon 1 of 6)	exon (NM_144523, exon 1 of 6)	478	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
Merged-chrX-124217638-1	chrX	124217554	124217723	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-81728	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
Merged-chr15-82209482-1	chr15	82209305	82209659	+	1	NA	intron (NM_001207021, intron 1 of 3)	intron (NM_001207021, intron 1 of 3)	3333	NM_001207021	435145	Mm.41289	NM_001207021	ENSMUSG00000096883	Shisa8	Orf26|ckamp39	shisa family member 8	protein-coding
Merged-chr10-11584346-1	chr10	11584241	11584451	+	1	NA	Intergenic	L1Md_T|LINE|L1	-24878	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
Merged-chr15-77744013-1	chr15	77743909	77744117	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	11260	NM_001357896	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
Merged-chr1-147498218-1	chr1	147498130	147498307	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	1000531	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr15-77660206-1	chr15	77660092	77660321	+	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-16920	NM_001143686	328563	Mm.17957	NM_001143686	ENSMUSG00000091694	Apol11b	A330102K04Rik	apolipoprotein L 11b	protein-coding
Merged-chr1-166917090-1	chr1	166916998	166917183	+	1	NA	Intergenic	L1Md_T|LINE|L1	82640	NR_037988	100503962	Mm.216842	NR_037988	ENSMUSG00000102548	Gm16701	-	predicted gene, 16701	ncRNA
Merged-chr13-85183790-1	chr13	85183588	85183992	+	1	NA	Intergenic	L1Md_T|LINE|L1	-5595	NM_001347587	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
Merged-chr11-63647528-1	chr11	63647447	63647609	+	1	NA	Intergenic	L1Md_T|LINE|L1	274756	NM_018805	54710	Mm.274426	NM_018805	ENSMUSG00000070407	Hs3st3b1	3-OST-3B|3OST3B1|3Ost3b|AU041882|AW536289|Hs3st3b|m3-OST-3B	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	protein-coding
Merged-chr1-5353623-1	chr1	5353359	5353887	+	1	NA	Intergenic	L1Md_T|LINE|L1	-234870	NM_001318735	18387	Mm.7977	NM_011011	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	opioid receptor, kappa 1	protein-coding
Merged-chr14-100385903-1	chr14	100385752	100386054	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-236107	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
Merged-chrX-123263527-1	chrX	123263419	123263635	+	1	NA	Intergenic	Intergenic	-50224	NR_152852	100302634	Mm.417665	NR_152852	ENSMUSG00000095005	Astx6	Gm14949	amplified spermatogenic transcripts X encoded 6	ncRNA
Merged-chr13-8811579-1	chr13	8811451	8811707	+	1	NA	intron (NM_001039388, intron 13 of 13)	L1Md_A|LINE|L1	59465	NM_172445	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
Merged-chr11-71166974-1	chr11	71166893	71167055	+	1	NA	intron (NM_001040696, intron 7 of 14)	L1Md_A|LINE|L1	-22270	NM_001004142	195046	Mm.240227	NM_001004142	ENSMUSG00000069830	Nlrp1a	CARD7|DEFCAP|Gm14|Gm15|NAC|Nalp1|Nalp1a|Nlrp1|PP1044	NLR family, pyrin domain containing 1A	protein-coding
Merged-chr1-125143571-1	chr1	125143423	125143719	+	1	NA	Intergenic	L1Md_T|LINE|L1	292156	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
Merged-chr1-41472582-1	chr1	41472391	41472773	+	1	NA	Intergenic	L1Md_A|LINE|L1	-291330	NR_040475	74897	Mm.243822	NR_040475	ENSMUSG00000104072	4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	ncRNA
Merged-chr15-102110629-1	chr15	102110458	102110801	+	1	NA	intron (NM_001355636, intron 15 of 28)	intron (NM_001355636, intron 15 of 28)	7695	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
Merged-chr13-66270392-1	chr13	66270090	66270695	+	1	NA	Intergenic	Intergenic	156939	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	-	predicted gene 10324	protein-coding
Merged-chr17-23310961-1	chr17	23310847	23311076	+	1	NA	exon (NM_001102584, exon 2 of 6)	exon (NM_001102584, exon 2 of 6)	1352	NM_001102584	666002	Mm.469838	NM_001102584	ENSMUSG00000091945	Vmn2r114	EG666002|V2Rp3	vomeronasal 2, receptor 114	protein-coding
Merged-chr7-121852153-1	chr7	121852060	121852247	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-12885	NM_011325	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
Merged-chr1-145471940-1	chr1	145471827	145472054	+	1	NA	Intergenic	L1Md_T|LINE|L1	-696513	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
Merged-chr1-13896490-1	chr1	13896394	13896587	+	1	NA	Intergenic	L1Md_T|LINE|L1	-109561	NR_004447	433273	Mm.304088	NR_004447	ENSMUSG00000097711	Gm5523	EG433273	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
Merged-chr11-54382902-1	chr11	54382731	54383073	+	1	NA	intron (NM_029105, intron 4 of 13)	L1Md_T|LINE|L1	12250	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
Merged-chr17-48034512-1	chr17	48034402	48034623	+	1	NA	Intergenic	Intergenic	3781	NM_029689	76651	Mm.76918	NM_029689	ENSMUSG00000094928	1700122O11Rik	-	RIKEN cDNA 1700122O11 gene	protein-coding
Merged-chr19-6226842-1	chr19	6226728	6226957	+	1	NA	TTS (NM_198168)	TTS (NM_198168)	441	NM_130453	170458	Mm.379306	NM_130453	ENSMUSG00000024784	Gpha2	GPA2|zsig51	glycoprotein hormone alpha 2	protein-coding
Merged-chrX-23975034-1	chrX	23974880	23975188	+	1	NA	Intergenic	L1Md_A|LINE|L1	82271	NM_001034864	236749	Mm.296422	NM_001034864	ENSMUSG00000068113	Gm4907	EG236749	predicted gene 4907	protein-coding
Merged-chr1-82548973-1	chr1	82548861	82549086	+	1	NA	intron (NM_007735, intron 4 of 47)	L1Md_A|LINE|L1	37876	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
Merged-chr11-119200698-1	chr11	119200620	119200777	+	1	NA	intron (NM_001347625, intron 3 of 11)	intron (NM_001347625, intron 3 of 11)	27801	NM_001347625	207592	Mm.205263	NM_172443	ENSMUSG00000039976	Tbc1d16	B930087K01|BC026530|Tcd1d16	TBC1 domain family, member 16	protein-coding
Merged-chr15-78693316-1	chr15	78693212	78693421	+	1	NA	intron (NM_001358692, intron 1 of 1)	intron (NM_001358692, intron 1 of 1)	24797	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
Merged-chr10-19385628-1	chr10	19385401	19385856	+	1	NA	Intergenic	L1Md_T|LINE|L1	29089	NM_053008	94222	Mm.156946	NM_053008	ENSMUSG00000045591	Olig3	Bhlhb7|bHLHe20|oligo3	oligodendrocyte transcription factor 3	protein-coding
Merged-chr10-88099908-1	chr10	88099690	88100127	+	1	NA	intron (NM_029249, intron 9 of 10)	L1Md_A|LINE|L1	8836	NM_029971	110312	Mm.391436	NM_029971	ENSMUSG00000035383	Pmch	A230109K23Rik	pro-melanin-concentrating hormone	protein-coding
Merged-chr12-37149127-1	chr12	37149005	37149250	+	1	NA	intron (NM_008584, intron 1 of 2)	L1_Mm|LINE|L1	40587	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
Merged-chr15-6008922-1	chr15	6008823	6009021	+	1	NA	Intergenic	L1Md_F2|LINE|L1	35782	NR_155428	105245876	Mm.128197	NR_155428		Gm41259	-	predicted gene, 41259	ncRNA
Merged-chr5-102196234-1	chr5	102196060	102196409	+	1	NA	Intergenic	L1Md_T|LINE|L1	-126313	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
Merged-chr15-75148363-1	chr15	75148231	75148496	+	1	NA	Intergenic	MERVL-int|LTR|ERVL	-6898	NM_001310438	546644		NM_008531	ENSMUSG00000022582	Ly6g	Gr-1|Gr1|Ly-6G	lymphocyte antigen 6 complex, locus G	protein-coding
Merged-chr18-44737069-1	chr18	44736977	44737161	+	1	NA	intron (NM_001085373, intron 2 of 18)	MMETn-int|LTR|ERVK	-74803	NM_001085374	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
Merged-chr2-36442419-1	chr2	36442297	36442542	+	1	NA	Intergenic	L1Md_A|LINE|L1	-10168	NM_146951	258953	Mm.377768	NM_146951	ENSMUSG00000094266	Olfr340	MOR136-1	olfactory receptor 340	protein-coding
Merged-chr10-125277494-1	chr10	125277358	125277631	+	1	NA	intron (NM_001358496, intron 3 of 5)	L1Md_A|LINE|L1	31322	NM_001358915	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|9030411M13Rik|D630004K10Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
Merged-chr7-38199897-1	chr7	38199772	38200022	+	1	NA	Intergenic	Intergenic	16110	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
Merged-chr3-104626567-1	chr3	104626487	104626648	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-12097	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	solute carrier family 16 (monocarboxylic acid transporters), member 1	protein-coding
Merged-chr15-55674706-1	chr15	55674540	55674873	+	1	NA	intron (NM_016667, intron 4 of 6)	L1Md_T|LINE|L1	117298	NM_134092	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
Merged-chr1-126769893-1	chr1	126769766	126770021	+	1	NA	intron (NM_176957, intron 1 of 12)	L1Md_T|LINE|L1	60739	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
Merged-chr7-10001646-1	chr7	10001502	10001791	+	1	NA	Intergenic	L1Md_F|LINE|L1	-9507	NM_001105156	625605	Mm.484763	NM_001105156	ENSMUSG00000096180	Vmn2r49	-	vomeronasal 2, receptor 49	protein-coding
Merged-chr12-101734961-1	chr12	101734775	101735148	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-16438	NM_001082976	74413	Mm.275939	NM_028924	ENSMUSG00000021187	Tc2n	4933406D09Rik|Mtac2d1|Tac2-N	tandem C2 domains, nuclear	protein-coding
Merged-chr1-13732025-1	chr1	13731810	13732241	+	1	NA	Intergenic	L1Md_T|LINE|L1	54904	NR_004447	433273	Mm.304088	NR_004447	ENSMUSG00000097711	Gm5523	EG433273	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
Merged-chr1-22951275-1	chr1	22951104	22951446	+	1	NA	Intergenic	L1Md_A|LINE|L1	52888	NR_151543	665725	Mm.416993	NR_151543		Gm7759	EG665725	predicted gene 7759	ncRNA
Merged-chr13-11259277-1	chr13	11259108	11259447	+	1	NA	Intergenic	L1Md_A|LINE|L1	-262775	NR_027813	664793	Mm.410565	NR_027813	ENSMUSG00000113593	Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
Merged-chr9-5781171-1	chr9	5780995	5781348	+	1	NA	Intergenic	L1Md_A|LINE|L1	-387315	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
Merged-chr10-79816873-1	chr10	79816772	79816974	+	1	NA	exon (NM_023128, exon 8 of 9)	exon (NM_023128, exon 8 of 9)	-4148	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
Merged-chr18-46691380-1	chr18	46691280	46691481	+	1	NA	Intergenic	L1Md_T|LINE|L1	37122	NR_151681	12583	Mm.241056	NM_033037	ENSMUSG00000033022	Cdo1	1300002L19Rik|Cdo|D18Ucla3	cysteine dioxygenase 1, cytosolic	protein-coding
Merged-chr13-23409697-1	chr13	23409458	23409937	+	1	NA	Intergenic	RMER12B|LTR|ERVK	14169	NM_013924	30946	Mm.292094	NM_013924	ENSMUSG00000036376	Abt1	-	activator of basal transcription 1	protein-coding
Merged-chr13-65335718-1	chr13	65335638	65335799	+	1	NA	Intergenic	ORR1A4-int|LTR|ERVL-MaLR	56864	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
Merged-chr1-148385451-1	chr1	148385264	148385639	+	1	NA	Intergenic	L1Md_A|LINE|L1	1536988	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
Merged-chr8-71291546-1	chr8	71291461	71291631	+	1	NA	intron (NM_001142322, intron 2 of 39)	intron (NM_001142322, intron 2 of 39)	18832	NM_015742	17925	Mm.33779	NM_015742	ENSMUSG00000004677	Myo9b	-	myosin IXb	protein-coding
Merged-chr8-72037108-1	chr8	72036976	72037240	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-20552	NM_207555	404315	Mm.377936	NM_207555	ENSMUSG00000069998	Olfr372	MOR282-1	olfactory receptor 372	protein-coding
Merged-chr1-118586880-1	chr1	118586785	118586976	+	1	NA	intron (NM_001359330, intron 36 of 39)	L1Md_A|LINE|L1	-41065	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
Merged-chr12-13994575-1	chr12	13994432	13994719	+	1	NA	Intergenic	L1Md_T|LINE|L1	157463	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	family with sequence similarity 84, member A	protein-coding
Merged-chr15-100165909-1	chr15	100165796	100166023	+	1	NA	intron (NM_172819, intron 7 of 32)	intron (NM_172819, intron 7 of 32)	11513	NM_172819	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
Merged-chr12-115396182-1	chr12	115396096	115396268	+	1	NA	Intergenic	Intergenic	299612	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr11-23836119-1	chr11	23835953	23836285	+	1	NA	Intergenic	L1Md_T|LINE|L1	59151	NM_172555	216578	Mm.470599	NM_172555	ENSMUSG00000020273	Papolg	9630006B20Rik	poly(A) polymerase gamma	protein-coding
Merged-chr17-78984030-1	chr17	78983900	78984160	+	1	NA	intron (NM_001171005, intron 2 of 17)	intron (NM_001171005, intron 2 of 17)	24475	NM_001171005	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding
Merged-chr3-98013440-1	chr3	98013310	98013570	+	1	NA	promoter-TSS (NM_010928)	promoter-TSS (NM_010928)	-98	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
Merged-chr13-68017113-1	chr13	68016996	68017231	+	1	NA	Intergenic	Intergenic	153787	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr1-173948796-1	chr1	173948673	173948920	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-6124	NM_001302650	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Ifi203a|Ifi203b|Mndal	interferon activated gene 203	protein-coding
Merged-chr17-36059890-1	chr17	36059767	36060013	+	1	NA	Intergenic	Intergenic	-1519	NM_001199967	100529082	Mm.484641	NM_001199967	ENSMUSG00000079492	Gm11127	-	predicted gene 11127	protein-coding
Merged-chr1-150275790-1	chr1	150275510	150276071	+	1	NA	Intergenic	Intergenic	-43627	NM_024458	20028	Mm.440883	NM_024458	ENSMUSG00000006007	Pdc	Rpr-1|Rpr1	phosducin	protein-coding
Merged-chr11-121192375-1	chr11	121192285	121192465	+	1	NA	intron (NM_025402, intron 7 of 8)	ORR1A1|LTR|ERVL-MaLR	-12058	NM_001001333	238023	Mm.275130	NM_001001333	ENSMUSG00000039307	Hexdc	BC069960	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	protein-coding
Merged-chr19-4088313-1	chr19	4088181	4088445	+	1	NA	TTS (NM_001160253)	TTS (NM_001160253)	4794	NM_013878	29866	Mm.46268	NM_013878	ENSMUSG00000024857	Cabp2	-	calcium binding protein 2	protein-coding
Merged-chr13-90443756-1	chr13	90443599	90443913	+	1	NA	Intergenic	L1Md_A|LINE|L1	354089	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|Gm10085|Tmem167a	transmembrane protein 167	protein-coding
Merged-chr4-88785898-1	chr4	88785631	88786165	+	1	NA	exon (NM_001085532, exon 1 of 1)	exon (NM_001085532, exon 1 of 1)	844	NM_001085532	545649	Mm.474424	NM_001085532	ENSMUSG00000099545	Gm13276	-	predicted gene 13276	protein-coding
Merged-chr11-120786665-1	chr11	120786562	120786768	+	1	NA	exon (NM_001346709, exon 5 of 13)	exon (NM_001346709, exon 5 of 13)	2150	NM_145370	209318	Mm.30195	NM_145370	ENSMUSG00000025156	Gps1	Cops1|Csn1|R75577|Sgn1	G protein pathway suppressor 1	protein-coding
Merged-chr19-6258315-1	chr19	6258233	6258397	+	1	NA	intron (NM_194348, intron 34 of 39)	intron (NM_194348, intron 34 of 39)	-6328	NR_029830	723957		NR_029830	ENSMUSG00000065582	Mir194-2	Mirn194-2|mir-194-2	microRNA 194-2	ncRNA
Merged-chr17-51719392-1	chr17	51719314	51719470	+	1	NA	Intergenic	L1Md_F2|LINE|L1	92662	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
Merged-chr1-47083890-1	chr1	47083783	47083997	+	1	NA	Intergenic	L1Md_T|LINE|L1	-158114	NM_001356417	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|Zip10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
Merged-chr10-30802819-1	chr10	30802695	30802944	+	1	NA	intron (NM_001358842, intron 1 of 14)	CpG	507	NM_001358841	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
Merged-chr10-8312919-1	chr10	8312783	8313056	+	1	NA	intron (NM_177387, intron 3 of 7)	L1Md_T|LINE|L1	205906	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
Merged-chr15-89288580-1	chr15	89288481	89288679	+	1	NA	3' UTR (NM_001170561, exon 41 of 41)	3' UTR (NM_001170561, exon 41 of 41)	17152	NR_105924	102465981		NR_105924	ENSMUSG00000098442	Mir6959	Gm27807|mmu-mir-6959	microRNA 6959	ncRNA
Merged-chr19-4425961-1	chr19	4425833	4426090	+	1	NA	3' UTR (NM_007485, exon 5 of 5)	3' UTR (NM_007485, exon 5 of 5)	-13362	NR_045990	319314	Mm.393810	NR_045989	ENSMUSG00000087132	A930001C03Rik	-	RIKEN cDNA A930001C03 gene	ncRNA
Merged-chr8-70780235-1	chr8	70780115	70780355	+	1	NA	intron (NM_199308, intron 25 of 25)	intron (NM_199308, intron 25 of 25)	3373	NR_029440	72093	Mm.271208	NR_029440		2010320M18Rik	-	RIKEN cDNA 2010320M18 gene	ncRNA
Merged-chr4-80905552-1	chr4	80905452	80905652	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-5134	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
Merged-chr13-74357116-1	chr13	74356976	74357257	+	1	NA	exon (NM_001168659, exon 3 of 3)	exon (NM_001168659, exon 3 of 3)	6799	NM_001168658	67433	Mm.101586	NM_024201	ENSMUSG00000021578	Ccdc127	0610011N22Rik|5430420E17Rik|A430066A18|AI256405|AW050060|C130002N06	coiled-coil domain containing 127	protein-coding
Merged-chr1-62297422-1	chr1	62297312	62297533	+	1	NA	intron (NM_001081050, intron 16 of 22)	L1Md_T|LINE|L1	-161313	NR_151537	105243940		NR_151537		Pard3bos2	Gm12747	par-3 family cell polarity regulator beta, opposite strand 2	ncRNA
Merged-chr1-41470831-1	chr1	41470730	41470932	+	1	NA	Intergenic	L1Md_A|LINE|L1	-289579	NR_040475	74897	Mm.243822	NR_040475	ENSMUSG00000104072	4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	ncRNA
Merged-chr7-38833105-1	chr7	38833016	38833194	+	1	NA	intron (NR_153826, intron 3 of 6)	ORR1E|LTR|ERVL-MaLR	41444	NR_153826	105247250	Mm.212736	NR_153826	ENSMUSG00000101855	1700010N08Rik	Gm42380	RIKEN cDNA 1700010N08 gene	ncRNA
Merged-chr10-44908063-1	chr10	44907941	44908185	+	1	NA	Intergenic	L1Md_A|LINE|L1	-159151	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
Merged-chr13-62094382-1	chr13	62093934	62094831	+	1	NA	Intergenic	Intergenic	-35508	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr12-32416941-1	chr12	32416786	32417096	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	38152	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
Merged-chr12-91942668-1	chr12	91942490	91942846	+	1	NA	Intergenic	L1Md_T|LINE|L1	-93511	NM_001039089	20338	Mm.250605	NM_011344	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding
Merged-chrX-57604788-1	chrX	57604645	57604931	+	1	NA	Intergenic	L1Md_T|LINE|L1	-101031	NM_001033360	245424	Mm.336070	NM_001033360	ENSMUSG00000036357	Gpr101	GPCR6|Gm365	G protein-coupled receptor 101	protein-coding
Merged-chr1-17387396-1	chr1	17387289	17387504	+	1	NA	Intergenic	L1Md_T|LINE|L1	-214505	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
Merged-chr17-56349460-1	chr17	56349371	56349550	+	1	NA	intron (NM_172132, intron 1 of 22)	intron (NM_172132, intron 1 of 22)	23410	NM_172132	193796	Mm.45047	NM_172132	ENSMUSG00000024201	Kdm4b	4732474L06Rik|Jmjd2b	lysine (K)-specific demethylase 4B	protein-coding
Merged-chr10-51581533-1	chr10	51581431	51581636	+	1	NA	Intergenic	L1Md_T|LINE|L1	8927	NM_029894	77296	Mm.30588	NM_029894	ENSMUSG00000019909	Fam162b	9430073N08Rik	family with sequence similarity 162, member B	protein-coding
Merged-chr11-41881863-1	chr11	41881784	41881942	+	1	NA	Intergenic	L1Md_T|LINE|L1	118851	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
Merged-chr6-140835135-1	chr6	140834998	140835272	+	1	NA	Intergenic	L1Md_A|LINE|L1	208250	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
Merged-chr8-94463409-1	chr8	94463305	94463514	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-9354	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
Merged-chr1-114229141-1	chr1	114229018	114229264	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1455996	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr2-45682799-1	chr2	45682636	45682962	+	1	NA	Intergenic	L1Md_T|LINE|L1	-13806	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
Merged-chr10-37040000-1	chr10	37039920	37040081	+	1	NA	Intergenic	L1Md_A|LINE|L1	65456	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
Merged-chr5-145660617-1	chr5	145660485	145660750	+	1	NA	Intergenic	L1Md_F|LINE|L1	59519	NM_017396	53973	Mm.379071	NM_017396	ENSMUSG00000075551	Cyp3a41a	Cyp3a41	cytochrome P450, family 3, subfamily a, polypeptide 41A	protein-coding
Merged-chr10-104233145-1	chr10	104233020	104233270	+	1	NA	Intergenic	L1Md_T|LINE|L1	39103	NM_001270644	637578	Mm.441727	NM_001270644	ENSMUSG00000095022	Gm20765	-	predicted gene, 20765	protein-coding
Merged-chr1-44905913-1	chr1	44905828	44905998	+	1	NA	Intergenic	L1Md_T|LINE|L1	-160964	NR_040602	75066	Mm.416932	NR_040602	ENSMUSG00000101701	4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	ncRNA
Merged-chr11-16389014-1	chr11	16388934	16389095	+	1	NA	Intergenic	L1Md_T|LINE|L1	119470	NM_001109972	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding
Merged-chrX-123043335-1	chrX	123043192	123043479	+	1	NA	Intergenic	Intergenic	-60188	NM_001310652	73061	Mm.292979	NM_028426	ENSMUSG00000079450	Cldn34c1	3110007F17Rik	claudin 34C1	protein-coding
Merged-chr1-171546114-1	chr1	171546017	171546212	+	1	NA	Intergenic	Intergenic	-10820	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
Merged-chr1-67590100-1	chr1	67590011	67590189	+	1	NA	Intergenic	L1Md_A|LINE|L1	467073	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
Merged-chr10-87991721-1	chr10	87991642	87991801	+	1	NA	Intergenic	L1Md_T|LINE|L1	25050	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
Merged-chr10-102432071-1	chr10	102431754	102432389	+	1	NA	Intergenic	L1Md_T|LINE|L1	57634	NM_026243	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
Merged-chr1-19403388-1	chr1	19403216	19403560	+	1	NA	Intergenic	L1Md_T|LINE|L1	191334	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
Merged-chr1-174310797-1	chr1	174310706	174310889	+	1	NA	Intergenic	L1Md_T|LINE|L1	-19721	NM_025470	66289	Mm.7150	NM_025470	ENSMUSG00000026531	Mptx1	1810030J14Rik|AV054416|Mptx	mucosal pentraxin 1	protein-coding
Merged-chr8-106235908-1	chr8	106235780	106236037	+	1	NA	intron (NM_145404, intron 6 of 17)	RLTR18|LTR|ERVK	24854	NM_145404	214572	Mm.251804	NM_145404	ENSMUSG00000060098	Prmt7	4933402B05Rik|BC006705	protein arginine N-methyltransferase 7	protein-coding
Merged-chr19-5453534-1	chr19	5453446	5453622	+	1	NA	3' UTR (NM_001243307, exon 2 of 2)	3' UTR (NM_001243307, exon 2 of 2)	4029	NM_001243307	240514	Mm.329657	NM_198616	ENSMUSG00000095098	Ccdc85b	AI842788|BB115872	coiled-coil domain containing 85B	protein-coding
Merged-chr1-104221197-1	chr1	104221009	104221386	+	1	NA	Intergenic	Intergenic	-547323	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr1-97419467-1	chr1	97419353	97419581	+	1	NA	Intergenic	L1Md_T|LINE|L1	242209	NM_001355072	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
Merged-chr3-88503063-1	chr3	88502969	88503158	+	1	NA	exon (NM_001111102, exon 1 of 10)	exon (NM_001111102, exon 1 of 10)	289	NM_001002011	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
Merged-chr12-61699910-1	chr12	61699811	61700009	+	1	NA	intron (NM_001310586, intron 2 of 5)	L1Md_T|LINE|L1	176743	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
Merged-chr1-104218046-1	chr1	104217950	104218142	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-550474	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr5-140533676-1	chr5	140533496	140533856	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	28067	NM_021528	59031	Mm.28934	NM_021528	ENSMUSG00000036599	Chst12	AI595374|C4S-2|C4ST2	carbohydrate sulfotransferase 12	protein-coding
Merged-chr3-126389153-1	chr3	126389023	126389284	+	1	NA	intron (NM_173451, intron 1 of 1)	L1Md_F2|LINE|L1	25301	NM_173451	271970	Mm.317021	NM_173451	ENSMUSG00000046561	Arsj	9330196J05Rik|D830047F08	arylsulfatase J	protein-coding
Merged-chrX-91839487-1	chrX	91839317	91839657	+	1	NA	Intergenic	L1Md_T|LINE|L1	-56511	NM_028847	74271	Mm.141337	NM_028847	ENSMUSG00000061392	Mageb5	1700056A17Rik|mMage-b5	melanoma antigen, family B, 5	protein-coding
Merged-chr1-50335151-1	chr1	50335067	50335236	+	1	NA	Intergenic	L1Md_T|LINE|L1	-592372	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
Merged-chr19-6306658-1	chr19	6306574	6306742	+	1	NA	5' UTR (NM_001033342, exon 1 of 37)	5' UTR (NM_001033342, exon 1 of 37)	201	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
Merged-chr4-59095985-1	chr4	59095877	59096094	+	1	NA	Intergenic	L1Md_F3|LINE|L1	60829	NM_025277	14700	Mm.41780	NM_025277	ENSMUSG00000038607	Gng10	AV006524	guanine nucleotide binding protein (G protein), gamma 10	protein-coding
Merged-chr1-125144000-1	chr1	125143912	125144089	+	1	NA	Intergenic	L1Md_T|LINE|L1	291727	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
Merged-chr4-7622799-1	chr4	7622692	7622906	+	1	NA	Intergenic	L1Md_A|LINE|L1	62111	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
Merged-chr15-75947353-1	chr15	75947259	75947448	+	1	NA	exon (NM_030199, exon 2 of 2)	exon (NM_030199, exon 2 of 2)	6401	NM_030199	78834	Mm.273264	NM_030199	ENSMUSG00000050846	Zfp623	2610029D06Rik|AI847036	zinc finger protein 623	protein-coding
Merged-chr6-78395651-1	chr6	78395510	78395793	+	1	NA	Intergenic	L1Md_T|LINE|L1	-9504	NM_009043	19693	Mm.46360	NM_009043	ENSMUSG00000023140	Reg2	PSP|PTP|REG-2	regenerating islet-derived 2	protein-coding
Merged-chr15-84289142-1	chr15	84289059	84289225	+	1	NA	intron (NM_133167, intron 4 of 12)	intron (NM_133167, intron 4 of 12)	-35578	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
Merged-chr8-7042036-1	chr8	7041908	7042164	+	1	NA	Intergenic	L1Md_F2|LINE|L1	1618737	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr12-116612189-1	chr12	116612097	116612282	+	1	NA	intron (NM_011215, intron 2 of 22)	L1Md_A|LINE|L1	126469	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
Merged-chr16-91255355-1	chr16	91255241	91255469	+	1	NA	Intergenic	RLTR13G|LTR|ERVK	-14414	NM_016968	50914	Mm.39300	NM_016968	ENSMUSG00000046160	Olig1	AI836478|AW494459|Bhlhb6|Olg-1|Oligo1|bHLHe21	oligodendrocyte transcription factor 1	protein-coding
Merged-chr12-62535970-1	chr12	62535870	62536070	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-151817	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
Merged-chr1-104218922-1	chr1	104218505	104219340	+	1	NA	Intergenic	Intergenic	-549598	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr8-70353513-1	chr8	70353424	70353603	+	1	NA	promoter-TSS (NM_001122829)	promoter-TSS (NM_001122829)	-234	NM_001122829	19704	Mm.258280	NM_030680	ENSMUSG00000058301	Upf1	B430202H16Rik|NORF1|PNORF-1|Rent1|Upflp	UPF1 regulator of nonsense transcripts homolog (yeast)	protein-coding
Merged-chr1-22060177-1	chr1	22060034	22060321	+	1	NA	Intergenic	L1Md_A|LINE|L1	-97527	NM_001310477	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding
Merged-chr9-26407323-1	chr9	26407152	26407494	+	1	NA	Intergenic	L1Md_T|LINE|L1	-326485	NM_001310766	76898	Mm.218788	NM_029792	ENSMUSG00000045994	B3gat1	0710007K08Rik|AI846286|GlcAT-P|Glcatp|Hnk1	beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	protein-coding
Merged-chr13-62099839-1	chr13	62099634	62100044	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-30051	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr17-36047956-1	chr17	36047843	36048069	+	1	NA	intron (NM_001034909, intron 1 of 2)	intron (NM_001034909, intron 1 of 2)	4995	NM_001034909	547347	Mm.484641	NM_001034909	ENSMUSG00000073407	Gm6034	EG547347|H2-gs14-2	predicted gene 6034	protein-coding
Merged-chr1-78953838-1	chr1	78953706	78953970	+	1	NA	intron (NR_151519, intron 2 of 3)	L1Md_A|LINE|L1	136927	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	potassium voltage-gated channel, Isk-related subfamily, gene 4	protein-coding
Merged-chr2-153098257-1	chr2	153098074	153098440	+	1	NA	Intergenic	Intergenic	-10211	NM_010407	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
Merged-chr17-27085367-1	chr17	27085240	27085494	+	1	NA	intron (NM_080553, intron 4 of 57)	RLTR17B_Mm|LTR|ERVK	-5878	NR_106142	102465779		NR_106142	ENSMUSG00000098826	Mir7677	Gm27400|mmu-mir-7677	microRNA 7677	ncRNA
Merged-chr10-122108799-1	chr10	122108571	122109027	+	1	NA	Intergenic	L1Md_A|LINE|L1	-10898	NR_027637	100043513	Mm.429141	NR_027637	ENSMUSG00000111952	Gm4489	Gm241	predicted gene 4489	ncRNA
Merged-chr12-69159444-1	chr12	69159314	69159575	+	1	NA	promoter-TSS (NM_009093)	promoter-TSS (NM_009093)	-258	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
Merged-chr13-72386738-1	chr13	72386611	72386865	+	1	NA	Intergenic	L1Md_T|LINE|L1	241826	NR_030701	328287	Mm.235072	NR_030701		Gm20554	D430050G20	predicted gene, 20554	ncRNA
Merged-chr7-11606567-1	chr7	11606478	11606656	+	1	NA	Intergenic	LTRIS_Mm|LTR|ERV1	63952	NM_145843	252905	Mm.377264	NM_145843	ENSMUSG00000095430	Vmn1r72	V1rg1	vomeronasal 1 receptor 72	protein-coding
Merged-chr8-111437947-1	chr8	111437856	111438038	+	1	NA	Intergenic	RSINE1|SINE|B4	-12253	NR_105819								
Merged-chr17-8165331-1	chr17	8165235	8165427	+	1	NA	promoter-TSS (NM_001197046)	promoter-TSS (NM_001197046)	-187	NM_201230	75296	Mm.227250	NM_201230	ENSMUSG00000069135	Fgfr1op	4930553O10Rik|FOP	Fgfr1 oncogene partner	protein-coding
Merged-chr13-29069465-1	chr13	29069303	29069628	+	1	NA	Intergenic	L1Md_T|LINE|L1	53210	NR_045073	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
Merged-chr3-17385185-1	chr3	17385027	17385343	+	1	NA	Intergenic	Intergenic	-404736	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
Merged-chr1-163784073-1	chr1	163783912	163784234	+	1	NA	intron (NM_001305643, intron 2 of 19)	L1Md_T|LINE|L1	4490	NM_001305643	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
Merged-chr1-145798484-1	chr1	145798318	145798651	+	1	NA	Intergenic	L1Md_T|LINE|L1	-697145	NM_001357571	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr5-53777353-1	chr5	53777201	53777505	+	1	NA	Intergenic	L1Md_T|LINE|L1	-32274	NM_144517	67249	Mm.28823	NM_144517	ENSMUSG00000039178	Tbc1d19	2810453K03Rik	TBC1 domain family, member 19	protein-coding
Merged-chr8-21014170-1	chr8	21014091	21014249	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-11375	NM_183253	66298	Mm.482941	NM_183253	ENSMUSG00000074447	Defa21	2010016B13Rik|Defcr21	defensin, alpha, 21	protein-coding
Merged-chr16-17440730-1	chr16	17440586	17440874	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	-11255	NM_007764	12929	Mm.21048	NM_007764	ENSMUSG00000006134	Crkl	1110025F07Rik|AA589403|AI325100|Crkol	v-crk avian sarcoma virus CT10 oncogene homolog-like	protein-coding
Merged-chr3-94109212-1	chr3	94109132	94109292	+	1	NA	Intergenic	RLTR45-int|LTR|ERVK	-36568	NM_207273	399676	Mm.454051	NM_207273	ENSMUSG00000094163	Tdpoz5	-	TD and POZ domain containing 5	protein-coding
Merged-chr10-28709079-1	chr10	28708883	28709275	+	1	NA	intron (NR_131208, intron 1 of 3)	L1Md_T|LINE|L1	40719	NM_001305663	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
Merged-chr10-28528344-1	chr10	28528083	28528606	+	1	NA	intron (NM_001359356, intron 13 of 30)	L1Md_T|LINE|L1	-140016	NR_131208	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
Merged-chr3-7790985-1	chr3	7790834	7791137	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	163902	NR_040587	75476	Mm.491752	NR_040587	ENSMUSG00000100010	1700010I02Rik	-	RIKEN cDNA 1700010I02 gene	ncRNA
Merged-chr12-91937295-1	chr12	91937196	91937395	+	1	NA	Intergenic	L1Md_T|LINE|L1	-88138	NM_001039089	20338	Mm.250605	NM_011344	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding
Merged-chr17-36220428-1	chr17	36220268	36220589	+	1	NA	Intergenic	Intergenic	-30277	NM_008208	15043	Mm.426002	NM_008208	ENSMUSG00000054128	H2-T3	H-2T3|H2-Tw3|MumuTL|TL	histocompatibility 2, T region locus 3	protein-coding
Merged-chr18-19613710-1	chr18	19613609	19613811	+	1	NA	Intergenic	L1Md_A|LINE|L1	388387	NM_001291809	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding
Merged-chr5-145629456-1	chr5	145629320	145629593	+	1	NA	Intergenic	Intergenic	-44726	NM_001105159	100041375	Mm.489591	NM_001105159	ENSMUSG00000075552	Cyp3a41b	-	cytochrome P450, family 3, subfamily a, polypeptide 41B	protein-coding
Merged-chr5-59005224-1	chr5	59005112	59005336	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-552226	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
Merged-chr1-23298157-1	chr1	23298065	23298249	+	1	NA	Intergenic	L1Md_T|LINE|L1	6456	NR_029717	723964		NR_029717	ENSMUSG00000065567	Mir30c-2	Mirn30c-2|mir-30c-2	microRNA 30c-2	ncRNA
Merged-chr1-128851469-1	chr1	128851326	128851612	+	1	NA	Intergenic	L1Md_A|LINE|L1	-259170	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
Merged-chr11-92698340-1	chr11	92698225	92698455	+	1	NA	Intergenic	L1Md_T|LINE|L1	-400026	NM_001361707	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
Merged-chr13-62118579-1	chr13	62118387	62118771	+	1	NA	Intergenic	Lx5|LINE|L1	-11311	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr10-53896846-1	chr10	53896738	53896954	+	1	NA	Intergenic	L1Md_A|LINE|L1	-145937	NM_001081428	75906	Mm.436785	NM_001081428	ENSMUSG00000019856	Fam184a	3110012E06Rik|4930438C08Rik|4930589M24Rik	family with sequence similarity 184, member A	protein-coding
Merged-chr1-107923397-1	chr1	107923253	107923542	+	1	NA	intron (NR_102306, intron 1 of 3)	L1Md_T|LINE|L1	6138	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr17-75426121-1	chr17	75425963	75426279	+	1	NA	Intergenic	L1Md_T|LINE|L1	-9784	NM_001166493	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
Merged-chr1-54958186-1	chr1	54958082	54958290	+	1	NA	Intergenic	L1Md_T|LINE|L1	-31799	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding
Merged-chr8-110920419-1	chr8	110920215	110920623	+	1	NA	intron (NM_009179, intron 1 of 6)	intron (NM_009179, intron 1 of 6)	554	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
Merged-chr5-103128913-1	chr5	103128778	103129049	+	1	NA	intron (NM_001081567, intron 2 of 13)	L1Md_A|LINE|L1	-70521	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
Merged-chr1-176284341-1	chr1	176284205	176284477	+	1	NA	Intergenic	L1Md_A|LINE|L1	-9029	NM_001357844	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
Merged-chr1-117258330-1	chr1	117258193	117258467	+	1	NA	Intergenic	L1Md_T|LINE|L1	1052398	NR_153836	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding
Merged-chr11-99829142-1	chr11	99829064	99829221	+	1	NA	Intergenic	L1Md_T|LINE|L1	8924	NM_001195383	100502865	Mm.476649	NM_001195383	ENSMUSG00000078257	2300003K06Rik	-	RIKEN cDNA 2300003K06 gene	protein-coding
Merged-chr10-23501134-1	chr10	23501056	23501213	+	1	NA	Intergenic	L1Md_T|LINE|L1	-151191	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
Merged-chr15-97705779-1	chr15	97705700	97705859	+	1	NA	promoter-TSS (NM_028003)	promoter-TSS (NM_028003)	43	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
Merged-chr10-80582121-1	chr10	80581914	80582328	+	1	NA	Intergenic	Intergenic	-4825	NM_078477	118445	Mm.41513	NM_078477	ENSMUSG00000035397	Klf16	AI843742|BTEB4|DRRF	Kruppel-like factor 16	protein-coding
Merged-chr8-92822037-1	chr8	92821955	92822119	+	1	NA	Intergenic	Intergenic	-5260	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
Merged-chr1-121038492-1	chr1	121038360	121038625	+	1	NA	Intergenic	L1Md_T|LINE|L1	-48913	NR_110450	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
Merged-chr1-29707024-1	chr1	29706907	29707142	+	1	NA	Intergenic	L1Md_T|LINE|L1	285536	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
Merged-chr19-4105116-1	chr19	4105009	4105224	+	1	NA	non-coding (NR_075078, exon 6 of 24)	non-coding (NR_075078, exon 6 of 24)	4494	NM_008851	18739	Mm.1860	NM_008851	ENSMUSG00000024851	Pitpnm1	DRES9|Mpt-1|Nir-2|PITPnm 1|Pitpnm|R75447|Rd9|RdgB|RdgB1	phosphatidylinositol transfer protein, membrane-associated 1	protein-coding
Merged-chr1-63834692-1	chr1	63834522	63834863	+	1	NA	Intergenic	L1Md_A|LINE|L1	-65425	NM_001256158	74426	Mm.159197	NM_001256158	ENSMUSG00000025961	4933402D24Rik	-	RIKEN cDNA 4933402D24 gene	protein-coding
Merged-chr1-21200175-1	chr1	21199973	21200377	+	1	NA	Intergenic	L1Md_T|LINE|L1	-18400	NM_001290679	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
Merged-chr1-141265501-1	chr1	141265421	141265581	+	1	NA	Intergenic	L1Md_A|LINE|L1	-609099	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr3-100310172-1	chr3	100310089	100310256	+	1	NA	Intergenic	Intergenic	-116233	NR_040543	73806	Mm.396549	NR_040543	ENSMUSG00000086923	4930406D18Rik	-	RIKEN cDNA 4930406D18 gene	ncRNA
Merged-chr16-5049911-1	chr16	5049742	5050080	+	1	NA	promoter-TSS (NM_001356320)	promoter-TSS (NM_001356320)	-1	NM_001079814	74022	Mm.21652	NM_028720	ENSMUSG00000022536	Glyr1	2810419J22Rik|3930401K13Rik|AW545332|Npac	glyoxylate reductase 1 homolog (Arabidopsis)	protein-coding
Merged-chr12-31047521-1	chr12	31047275	31047768	+	1	NA	Intergenic	L1Md_A|LINE|L1	-26447	NM_027828	104943	Mm.248938	NM_027828	ENSMUSG00000036136	Fam110c	9030611O19Rik|AU019489	family with sequence similarity 110, member C	protein-coding
Merged-chr1-32375587-1	chr1	32375430	32375745	+	1	NA	intron (NM_133235, intron 3 of 8)	L1Md_A|LINE|L1	145412	NM_001199956	408192	Mm.485769	NM_001199956		Gm9839	Senp15	predicted gene 9839	protein-coding
Merged-chr2-75748358-1	chr2	75748278	75748438	+	1	NA	Intergenic	Intergenic	-43695	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
Merged-chr8-70598318-1	chr8	70598216	70598421	+	1	NA	intron (NM_133772, intron 14 of 16)	CpG	3837	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
Merged-chr11-21910788-1	chr11	21910654	21910923	+	1	NA	Intergenic	L1Md_T|LINE|L1	90863	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
Merged-chr1-126773673-1	chr1	126773577	126773770	+	1	NA	intron (NM_176957, intron 1 of 12)	L1Md_T|LINE|L1	56959	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
Merged-chr11-116624258-1	chr11	116624143	116624374	+	1	NA	promoter-TSS (NM_001167680)	promoter-TSS (NM_001167680)	-6	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
Merged-chr8-70797808-1	chr8	70797719	70797898	+	1	NA	promoter-TSS (NR_106099)	promoter-TSS (NR_106099)	-327	NR_106099	102466823		NR_106099	ENSMUSG00000099031	Mir7240	Gm27487|mmu-mir-7240	microRNA 7240	ncRNA
Merged-chr19-43826155-1	chr19	43826055	43826255	+	1	NA	intron (NM_013806, intron 24 of 31)	intron (NM_013806, intron 24 of 31)	-12648	NR_033472	100038628	Mm.212585	NR_033472	ENSMUSG00000025194	Gm10768	-	predicted gene 10768	ncRNA
Merged-chrX-165646991-1	chrX	165646816	165647166	+	1	NA	Intergenic	MuRRS-int|LTR|ERV1	-319124	NM_001357099	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	glycine receptor, alpha 2 subunit	protein-coding
Merged-chr19-46031820-1	chr19	46031736	46031905	+	1	NA	TTS (NM_001360336)	TTS (NM_001360336)	5250	NM_001360336	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
Merged-chr15-78926137-1	chr15	78926042	78926232	+	1	NA	promoter-TSS (NM_008495)	promoter-TSS (NM_008495)	-588	NM_008495	16852	Mm.43831	NM_008495	ENSMUSG00000068220	Lgals1	AA410090|Gal-1|Galbp|L-14.5|L14|Lect14|galectin-1	lectin, galactose binding, soluble 1	protein-coding
Merged-chr12-57818599-1	chr12	57818475	57818724	+	1	NA	Intergenic	L1Md_A|LINE|L1	-155688	NR_131112	217601	Mm.488987	NR_131112		BC042761	-	cDNA sequence BC042761	ncRNA
Merged-chr10-27354580-1	chr10	27354392	27354768	+	1	NA	intron (NM_008481, intron 7 of 63)	L1Md_A|LINE|L1	-35286	NR_131034	75855	Mm.402080	NR_131034	ENSMUSG00000101636	4930579H20Rik	-	RIKEN cDNA 4930579H20 gene	ncRNA
Merged-chr8-7149117-1	chr8	7149025	7149210	+	1	NA	Intergenic	L1Md_F3|LINE|L1	1511656	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr17-38557177-1	chr17	38556964	38557391	+	1	NA	intron (NM_001177585, intron 2 of 2)	MTA_Mm-int|LTR|ERVL-MaLR	2985	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr8-84197698-1	chr8	84197560	84197836	+	1	NA	Intergenic	CpG	-10820	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
Merged-chr12-115827029-1	chr12	115826817	115827241	+	1	NA	Intergenic	Intergenic	-131235	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr1-69943291-1	chr1	69943165	69943417	+	1	NA	intron (NM_029160, intron 10 of 16)	L1Md_A|LINE|L1	-8324	NM_025728	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
Merged-chr15-76477638-1	chr15	76477470	76477806	+	1	NA	promoter-TSS (NM_013481)	promoter-TSS (NM_013481)	276	NR_138589	15499	Mm.347444	NM_008296	ENSMUSG00000022556	Hsf1	AA960185|HSTF|HSTF 1|Hsf1alpha|Hsf1beta	heat shock factor 1	protein-coding
Merged-chr15-77633477-1	chr15	77633363	77633591	+	1	NA	TTS (NM_001143686)	TTS (NM_001143686)	9809	NM_001143686	328563	Mm.17957	NM_001143686	ENSMUSG00000091694	Apol11b	A330102K04Rik	apolipoprotein L 11b	protein-coding
Merged-chr4-88779932-1	chr4	88779656	88780208	+	1	NA	promoter-TSS (NM_001161609).3	promoter-TSS (NM_001161609).3	82	NM_001161608	545648	Mm.368246	NM_001161608	ENSMUSG00000096591	Gm13272	-	predicted gene 13272	protein-coding
Merged-chr8-7130578-1	chr8	7130482	7130674	+	1	NA	Intergenic	Intergenic	1530195	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr15-96805485-1	chr15	96805249	96805722	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-105757	NM_001355633	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
Merged-chr10-51995357-1	chr10	51995209	51995506	+	1	NA	Intergenic	L1Md_A|LINE|L1	-27145	NM_153786	215031	Mm.87237	NM_153786	ENSMUSG00000049641	Vgll2	C130057C21Rik|VITO-1|Vito1|vgl-2	vestigial like family member 2	protein-coding
Merged-chr4-62309824-1	chr4	62309700	62309948	+	1	NA	intron (NM_001355385, intron 21 of 27)	MTA_Mm-int|LTR|ERVL-MaLR	18277	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
Merged-chr8-70523203-1	chr8	70523094	70523312	+	1	NA	promoter-TSS (NM_029366)	promoter-TSS (NM_029366)	-23	NM_029366	75620	Mm.482129	NM_029366	ENSMUSG00000055553	Kxd1	0610030B01Rik|2810422J05Rik|C78305	KxDL motif containing 1	protein-coding
Merged-chr10-88096404-1	chr10	88096177	88096632	+	1	NA	intron (NM_029249, intron 9 of 10)	L1Md_A|LINE|L1	5332	NM_029971	110312	Mm.391436	NM_029971	ENSMUSG00000035383	Pmch	A230109K23Rik	pro-melanin-concentrating hormone	protein-coding
Merged-chr11-56228816-1	chr11	56228682	56228950	+	1	NA	Intergenic	L1Md_A|LINE|L1	-187829	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding
Merged-chr10-40991491-1	chr10	40991377	40991606	+	1	NA	Intergenic	L1Md_A|LINE|L1	80799	NM_199058	140741	Mm.290693	NM_199058	ENSMUSG00000046922	Gpr6	AI852874|Gm233	G protein-coupled receptor 6	protein-coding
Merged-chr1-22920700-1	chr1	22920548	22920853	+	1	NA	Intergenic	L1Md_A|LINE|L1	22313	NR_151543	665725	Mm.416993	NR_151543		Gm7759	EG665725	predicted gene 7759	ncRNA
Merged-chrX-105616184-1	chrX	105616057	105616311	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	116412	NM_173436	245566	Mm.250428	NM_173436	ENSMUSG00000090132	Cypt2	Ckt1|Cypt2-ps	cysteine-rich perinuclear theca 2	protein-coding
Merged-chr1-131683410-1	chr1	131683256	131683565	+	1	NA	Intergenic	L1Md_T|LINE|L1	-5285	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
Merged-chr16-61853845-1	chr16	61853733	61853958	+	1	NA	Intergenic	L1Md_T|LINE|L1	932871	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding
Merged-chr1-145474198-1	chr1	145474063	145474333	+	1	NA	Intergenic	L1Md_T|LINE|L1	-698771	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
Merged-chr1-124144017-1	chr1	124143756	124144279	+	1	NA	Intergenic	L1Md_T|LINE|L1	-98458	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
Merged-chr10-80149729-1	chr10	80149638	80149821	+	1	NA	promoter-TSS (NM_001305799)	promoter-TSS (NM_001305799)	47	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
Merged-chr11-41108753-1	chr11	41108642	41108864	+	1	NA	Intergenic	L1Md_T|LINE|L1	-353467	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
Merged-chr13-104769400-1	chr13	104769267	104769533	+	1	NA	intron (NM_001360094, intron 10 of 13)	L1Md_A|LINE|L1	47553	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
Merged-chr12-9680381-1	chr12	9680225	9680537	+	1	NA	Intergenic	L1Md_T|LINE|L1	105939	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related transcription factor 1	protein-coding
Merged-chr12-51174273-1	chr12	51174190	51174356	+	1	NA	Intergenic	L1Md_T|LINE|L1	169117	NR_126468	75494	Mm.416848	NR_126468	ENSMUSG00000111986	1700008C04Rik	-	RIKEN cDNA 1700008C04 gene	ncRNA
Merged-chr17-27557281-1	chr17	27557163	27557400	+	1	NA	intron (NM_001039356, intron 2 of 5)	CpG-6152	628	NM_001166476	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1b	Hmga1-rs1|Hmgi-rs1	high mobility group AT-hook 1B	protein-coding
Merged-chr1-5354596-1	chr1	5354489	5354704	+	1	NA	Intergenic	L1Md_T|LINE|L1	-233897	NM_001318735	18387	Mm.7977	NM_011011	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	opioid receptor, kappa 1	protein-coding
Merged-chrX-46312017-1	chrX	46311877	46312157	+	1	NA	intron (NR_045440, intron 2 of 2)	L1Md_A|LINE|L1	16894	NR_045440	75133	Mm.417818	NR_045440	ENSMUSG00000085157	4930515L19Rik	-	RIKEN cDNA 4930515L19 gene	ncRNA
Merged-chr15-33966482-1	chr15	33966359	33966605	+	1	NA	Intergenic	RMER17D2|LTR|ERVK	-116237	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
Merged-chr5-3013204-1	chr5	3013104	3013305	+	1	NA	Intergenic	Intergenic	-330689	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
Merged-chr19-4212223-1	chr19	4212093	4212354	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-2015	NM_001310038	56708	Mm.347919	NM_019952	ENSMUSG00000040663	Clcf1	BSF-3|Bsf3|CLC|NNT-1	cardiotrophin-like cytokine factor 1	protein-coding
Merged-chr5-145662293-1	chr5	145662109	145662477	+	1	NA	Intergenic	L1Md_F|LINE|L1	57843	NM_017396	53973	Mm.379071	NM_017396	ENSMUSG00000075551	Cyp3a41a	Cyp3a41	cytochrome P450, family 3, subfamily a, polypeptide 41A	protein-coding
Merged-chr8-72039660-1	chr8	72039554	72039767	+	1	NA	Intergenic	Intergenic	-18000	NM_207555	404315	Mm.377936	NM_207555	ENSMUSG00000069998	Olfr372	MOR282-1	olfactory receptor 372	protein-coding
Merged-chr6-96969915-1	chr6	96969755	96970076	+	1	NA	intron (NM_177233, intron 3 of 5)	L1Md_T|LINE|L1	90496	NM_177233	320701	Mm.131700	NM_177233	ENSMUSG00000046500	Fam19a4	C130034I18Rik|Fam19a4 Tafa-4|Tafa-4	family with sequence similarity 19, member A4	protein-coding
Merged-chr1-104267455-1	chr1	104267351	104267560	+	1	NA	Intergenic	L1Md_T|LINE|L1	-501065	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr4-94891444-1	chr4	94891330	94891558	+	1	NA	Intergenic	L1Md_T|LINE|L1	37399	NM_001290623	67753	Mm.25097	NM_027089	ENSMUSG00000028575	Eqtn	1700028B15Rik|4930579C15Rik|Afaf|C81058|Eqtl|Eqts	equatorin, sperm acrosome associated	protein-coding
Merged-chr18-19864428-1	chr18	19864296	19864560	+	1	NA	Intergenic	L1Md_T|LINE|L1	137669	NM_001291809	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding
Merged-chr3-155148960-1	chr3	155148809	155149111	+	1	NA	intron (NM_028938, intron 5 of 7)	L1Md_T|LINE|L1	55526	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
Merged-chr8-71790133-1	chr8	71789925	71790342	+	1	NA	Intergenic	MuRRS4-int|LTR|ERV1	-64452	NR_131256	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
Merged-chr15-79496625-1	chr15	79496538	79496713	+	1	NA	intron (NM_008427, intron 1 of 1)	PB1D9|SINE|Alu	8616	NM_008427	16520	Mm.39759	NM_008427	ENSMUSG00000044216	Kcnj4	IRK3|Kcnf2|MB-IRK3	potassium inwardly-rectifying channel, subfamily J, member 4	protein-coding
Merged-chr1-171540613-1	chr1	171540195	171541032	+	1	NA	Intergenic	Intergenic	-5319	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
Merged-chr10-70222446-1	chr10	70222366	70222526	+	1	NA	Intergenic	B1_Mm|SINE|Alu	17782	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Linc-RAM|Mln	myoregulin	protein-coding
Merged-chr10-47222703-1	chr10	47222514	47222892	+	1	NA	Intergenic	L1Md_A|LINE|L1	977954	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr1-24500122-1	chr1	24499997	24500248	+	1	NA	intron (NM_007733, intron 11 of 50)	L1Md_A|LINE|L1	87315	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
Merged-chr1-150236749-1	chr1	150236581	150236917	+	1	NA	Intergenic	L1Md_T|LINE|L1	-71801	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
Merged-chr11-48327769-1	chr11	48327548	48327990	+	1	NA	Intergenic	L1Md_A|LINE|L1	-472591	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
Merged-chr8-70794495-1	chr8	70794383	70794608	+	1	NA	Intergenic	Intergenic	-2062	NM_199308	546071	Mm.250731	NM_199308	ENSMUSG00000031833	Mast3	BC024265|mKIAA0561	microtubule associated serine/threonine kinase 3	protein-coding
Merged-chr12-23055419-1	chr12	23055324	23055514	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-45176	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
Merged-chr1-76776709-1	chr1	76776623	76776795	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	267149	NR_105761	102465175		NR_105761	ENSMUSG00000098611	Mir6343	Gm27304|mmu-mir-6343	microRNA 6343	ncRNA
Merged-chr12-119515456-1	chr12	119515308	119515605	+	1	NA	Intergenic	L1Md_T|LINE|L1	72046	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding
Merged-chr7-55455175-1	chr7	55455006	55455345	+	1	NA	Intergenic	L1Md_T|LINE|L1	-313009	NM_001310738	233274	Mm.44425	NM_178706	ENSMUSG00000051504	Siglech	6430529G09Rik|Siglec-H	sialic acid binding Ig-like lectin H	protein-coding
Merged-chr1-5552914-1	chr1	5552674	5553155	+	1	NA	Intergenic	L1Md_A|LINE|L1	-35579	NM_001318735	18387	Mm.7977	NM_011011	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	opioid receptor, kappa 1	protein-coding
Merged-chr10-106921107-1	chr10	106921029	106921186	+	1	NA	intron (NM_001359698, intron 27 of 28)	L1_Mm|LINE|L1	202557	NM_198636	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
Merged-chr13-23684551-1	chr13	23684462	23684640	+	1	NA	promoter-TSS (NM_178189)	promoter-TSS (NM_178189)	352	NM_001290380	68024	Mm.261676	NM_023422	ENSMUSG00000018102	Hist1h2bc	2610022J01Rik|H2bfs|R74621	histone cluster 1, H2bc	protein-coding
Merged-chr1-94142242-1	chr1	94142163	94142321	+	1	NA	Intergenic	L1Md_A|LINE|L1	-89689	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
Merged-chr3-9733406-1	chr3	9733324	9733488	+	1	NA	intron (NM_053182, intron 2 of 7)	IAPEz-int|LTR|ERVK	100273	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
Merged-chr4-62520682-1	chr4	62520602	62520762	+	1	NA	promoter-TSS (NM_008525)	promoter-TSS (NM_008525)	-619	NM_008525	17025	Mm.6988	NM_008525	ENSMUSG00000028393	Alad	ALADH|Lv	aminolevulinate, delta-, dehydratase	protein-coding
Merged-chr19-8913781-1	chr19	8913703	8913859	+	1	NA	intron (NM_001293621, intron 17 of 23)	intron (NM_001293621, intron 17 of 23)	-6612	NM_024256	72727	Mm.259	NM_024256	ENSMUSG00000071649	B3gat3	2810405M13Rik	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	protein-coding
Merged-chr15-55683930-1	chr15	55683843	55684017	+	1	NA	intron (NM_016667, intron 3 of 6)	L1Md_T|LINE|L1	126522	NM_134092	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
Merged-chr5-145632108-1	chr5	145631960	145632256	+	1	NA	Intergenic	Intergenic	-47378	NM_001105159	100041375	Mm.489591	NM_001105159	ENSMUSG00000075552	Cyp3a41b	-	cytochrome P450, family 3, subfamily a, polypeptide 41B	protein-coding
Merged-chr17-38560524-1	chr17	38560389	38560659	+	1	NA	TTS (NM_001177585)	TTS (NM_001177585)	6332	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr17-27378190-1	chr17	27378057	27378323	+	1	NA	Intergenic	Intergenic	20093	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
Merged-chr12-68560170-1	chr12	68560053	68560288	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	599016	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
Merged-chr10-38259310-1	chr10	38259222	38259398	+	1	NA	Intergenic	L1Md_T|LINE|L1	83536	NR_131035	75877	Mm.402094	NR_131035	ENSMUSG00000111234	4930591E09Rik	-	RIKEN cDNA 4930591E09 gene	ncRNA
Merged-chr17-34850491-1	chr17	34850382	34850601	+	1	NA	promoter-TSS (NM_001045864)	promoter-TSS (NM_001045864)	100	NM_001045864	27632	Mm.653	NM_138580	ENSMUSG00000024369	Nelfe	D17H6S45|NELF-E|RD|Rdbp	negative elongation factor complex member E, Rdbp	protein-coding
Merged-chr13-68051376-1	chr13	68051286	68051467	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	180444	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr1-25666703-1	chr1	25666594	25666813	+	1	NA	intron (NM_175642, intron 2 of 30)	L1Md_T|LINE|L1	163004	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
Merged-chr11-27383917-1	chr11	27383755	27384080	+	1	NA	Intergenic	L1Md_T|LINE|L1	598809	NR_002890	654472	Mm.347777	NR_002890		Gm12070	-	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
Merged-chr10-65386514-1	chr10	65386378	65386651	+	1	NA	Intergenic	L1Md_T|LINE|L1	-266147	NR_152621	102632700		NR_152621	ENSMUSG00000100528	Gm28881	-	predicted gene 28881	ncRNA
Merged-chr10-97181283-1	chr10	97181102	97181465	+	1	NA	Intergenic	L1Md_T|LINE|L1	145515	NR_045358	75301	Mm.108650	NR_045358	ENSMUSG00000111924	4930556N09Rik	-	RIKEN cDNA 4930556N09 gene	ncRNA
Merged-chr10-45691183-1	chr10	45691073	45691293	+	1	NA	intron (NM_172473, intron 20 of 23)	L1Md_A|LINE|L1	113354	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
Merged-chr10-118344732-1	chr10	118344642	118344822	+	1	NA	Intergenic	MusHAL1|LINE|L1	-49694	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
Merged-chr12-60537163-1	chr12	60537039	60537288	+	1	NA	Intergenic	L1Md_T|LINE|L1	984657	NR_045049	100504101	Mm.235026	NR_045049	ENSMUSG00000113429	Gm20063	-	predicted gene, 20063	ncRNA
Merged-chr1-11778304-1	chr1	11778149	11778459	+	1	NA	intron (NM_001160369, intron 8 of 13)	L1Md_T|LINE|L1	364199	NM_001160369	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
Merged-chr19-46434555-1	chr19	46434475	46434635	+	1	NA	intron (NM_001025391, intron 3 of 11)	intron (NM_001025391, intron 3 of 11)	37659	NM_015752	24069	Mm.41210	NM_015752	ENSMUSG00000025231	Sufu	Su(fu)	SUFU negative regulator of hedgehog signaling	protein-coding
Merged-chr1-150278210-1	chr1	150277911	150278509	+	1	NA	Intergenic	L1Md_T|LINE|L1	-41207	NM_024458	20028	Mm.440883	NM_024458	ENSMUSG00000006007	Pdc	Rpr-1|Rpr1	phosducin	protein-coding
Merged-chr1-112844740-1	chr1	112844658	112844822	+	1	NA	Intergenic	L1Md_T|LINE|L1	-979822	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
Merged-chr14-43713090-1	chr14	43712992	43713188	+	1	NA	Intergenic	Intergenic	-105077	NM_001098269	100042342	Mm.429750	NM_001098269	ENSMUSG00000095528	Gm10375	-	predicted gene 10375	protein-coding
Merged-chr1-145783384-1	chr1	145783268	145783500	+	1	NA	Intergenic	L1Md_T|LINE|L1	-712245	NM_001357571	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr9-88482044-1	chr9	88481961	88482127	+	1	NA	intron (NM_001284328, intron 1 of 11)	CpG	353	NM_019796	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
Merged-chr11-120824375-1	chr11	120824250	120824500	+	1	NA	5' UTR (NM_007988, exon 1 of 43)	5' UTR (NM_007988, exon 1 of 43)	172	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
Merged-chr7-59480374-1	chr7	59480242	59480506	+	1	NA	intron (NR_146211, intron 106 of 171)	intron (NR_146211, intron 106 of 171)	-132950	NR_146600	102642160		NR_146600		Gm22496	-	predicted gene, 22496	snoRNA
Merged-chr19-46324361-1	chr19	46324263	46324459	+	1	NA	exon (NM_001347454, exon 3 of 18)	exon (NM_001347454, exon 3 of 18)	2505	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
Merged-chr11-40968196-1	chr11	40968111	40968282	+	1	NA	Intergenic	L1Md_T|LINE|L1	-212910	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
Merged-chr4-95511230-1	chr4	95511110	95511350	+	1	NA	Intergenic	L1Md_A|LINE|L1	-46277	NM_001113412	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
Merged-chr1-162066389-1	chr1	162066192	162066587	+	1	NA	intron (NM_172646, intron 16 of 19)	L1Md_T|LINE|L1	61420	NR_040562	72753	Mm.452125	NR_040562	ENSMUSG00000090260	2810442N19Rik	-	RIKEN cDNA 2810442N19 gene	ncRNA
Merged-chr1-171546787-1	chr1	171546439	171547136	+	1	NA	Intergenic	RMER21B|LTR|ERV1	-11493	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
Merged-chr12-38042018-1	chr12	38041913	38042123	+	1	NA	intron (NM_178681, intron 2 of 24)	L1Md_T|LINE|L1	161501	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
Merged-chr1-9178572-1	chr1	9178470	9178675	+	1	NA	intron (NM_027671, intron 2 of 20)	L1Md_A|LINE|L1	121305	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
Merged-chr10-15965145-1	chr10	15964958	15965332	+	1	NA	Intergenic	L1Md_A|LINE|L1	173368	NR_131087	77538	Mm.128235	NR_131087	ENSMUSG00000112227	C330004P14Rik	-	RIKEN cDNA C330004P14 gene	ncRNA
Merged-chr1-61499358-1	chr1	61499231	61499485	+	1	NA	Intergenic	L1Md_T|LINE|L1	120926	NR_040483	77341	Mm.402964	NR_040483	ENSMUSG00000085447	9530026F06Rik	-	RIKEN cDNA 9530026F06 gene	ncRNA
Merged-chr1-166916032-1	chr1	166915951	166916114	+	1	NA	Intergenic	L1Md_T|LINE|L1	83698	NR_037988	100503962	Mm.216842	NR_037988	ENSMUSG00000102548	Gm16701	-	predicted gene, 16701	ncRNA
Merged-chr1-118585044-1	chr1	118584960	118585128	+	1	NA	intron (NM_001359330, intron 36 of 39)	L1Md_A|LINE|L1	-42901	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
Merged-chr13-66743104-1	chr13	66743011	66743198	+	1	NA	Intergenic	Intergenic	162246	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr19-41504132-1	chr19	41503975	41504290	+	1	NA	Intergenic	Intergenic	-21120	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
Merged-chr1-76879713-1	chr1	76879618	76879809	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	370153	NR_105761	102465175		NR_105761	ENSMUSG00000098611	Mir6343	Gm27304|mmu-mir-6343	microRNA 6343	ncRNA
Merged-chr19-5973140-1	chr19	5973052	5973229	+	1	NA	intron (NM_198650, intron 6 of 9)	intron (NM_198650, intron 6 of 9)	-8934	NM_001164057	18969	Mm.209931	NM_008893	ENSMUSG00000024833	Pola2	AI573378	polymerase (DNA directed), alpha 2	protein-coding
Merged-chr1-164728545-1	chr1	164728351	164728740	+	1	NA	Intergenic	L1Md_A|LINE|L1	-68118	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
Merged-chr1-140515170-1	chr1	140515025	140515316	+	1	NA	intron (NM_001081027, intron 17 of 27)	L1Md_T|LINE|L1	141232	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr1-121037522-1	chr1	121037428	121037616	+	1	NA	Intergenic	L1Md_T|LINE|L1	-49883	NR_110450	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
Merged-chr1-19376086-1	chr1	19375920	19376253	+	1	NA	Intergenic	L1Md_T|LINE|L1	164032	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
Merged-chr1-61515283-1	chr1	61515178	61515388	+	1	NA	Intergenic	L1Md_T|LINE|L1	-123541	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
Merged-chr13-66795037-1	chr13	66794930	66795144	+	1	NA	Intergenic	MurSatRep1|Unknown|Unknown	110313	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr17-91220212-1	chr17	91220110	91220315	+	1	NA	Intergenic	Intergenic	-127410	NM_177284	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
Merged-chr10-126702031-1	chr10	126701881	126702181	+	1	NA	Intergenic	L1Md_T|LINE|L1	8360	NR_105841	102465224		NR_105841	ENSMUSG00000098756	Mir378d	Gm27650|mmu-mir-378d	microRNA 378d	ncRNA
Merged-chr8-19955458-1	chr8	19955379	19955538	+	1	NA	intron (NM_001270553, intron 6 of 9)	Lx3C|LINE|L1	225882	NM_001039553	626415	Mm.425517	NM_001039553	ENSMUSG00000096265	4930467E23Rik	TSAP	RIKEN cDNA 4930467E23 gene	protein-coding
Merged-chr5-26007299-1	chr5	26007029	26007569	+	1	NA	Intergenic	Intergenic	-2572	NM_001281519	100038949		NM_001281519	ENSMUSG00000091049	Gm1979	-	predicted gene 1979	protein-coding
Merged-chr1-84124589-1	chr1	84124462	84124716	+	1	NA	intron (NM_001003948, intron 2 of 2)	L1Md_A|LINE|L1	94372	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
Merged-chr1-162342744-1	chr1	162342639	162342849	+	1	NA	intron (NM_001038619, intron 4 of 20)	L1Md_T|LINE|L1	119376	NR_029796	387210		NR_029796	ENSMUSG00000065516	Mir214	Mirn214|mir-214|mmu-mir-214	microRNA 214	ncRNA
Merged-chr1-77785293-1	chr1	77785195	77785391	+	1	NA	Intergenic	L1Md_A|LINE|L1	-270205	NM_007936	13838	Mm.400747	NM_007936	ENSMUSG00000026235	Epha4	2900005C20Rik|AI385584|Cek8|Hek8|Sek|Sek1|Tyro1|rb	Eph receptor A4	protein-coding
Merged-chr6-23511849-1	chr6	23511764	23511934	+	1	NA	intron (NM_153163, intron 7 of 29)	L1Md_T|LINE|L1	138456	NM_198251	386611	Mm.436547	NM_198251	ENSMUSG00000051956	Rnf133	Greul2	ring finger protein 133	protein-coding
Merged-chr19-6061368-1	chr19	6061246	6061490	+	1	NA	exon (NM_013859, exon 1 of 1)	exon (NM_013859, exon 1 of 1)	161	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
Merged-chr15-25843319-1	chr15	25843130	25843509	+	1	NA	promoter-TSS (NM_001034851)	promoter-TSS (NM_001034851)	21	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Retreg1	1810015C04Rik|AU015349|Fam134b|Retreg1d	reticulophagy regulator 1	protein-coding
Merged-chr11-86179937-1	chr11	86179808	86180067	+	1	NA	intron (NM_178309, intron 6 of 19)	L1Md_A|LINE|L1	21256	NM_178309	237911	Mm.186143	NM_178309	ENSMUSG00000034329	Brip1	3110009N10Rik|8030460J03Rik|Bach1|FACJ|Fancj|OF	BRCA1 interacting protein C-terminal helicase 1	protein-coding
Merged-chr1-46584544-1	chr1	46584437	46584651	+	1	NA	intron (NM_001310335, intron 19 of 64)	L1Md_T|LINE|L1	159026	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
Merged-chr17-38534397-1	chr17	38534227	38534568	+	1	NA	Intergenic	Intergenic	-19795	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr7-28658752-1	chr7	28658594	28658910	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-27737	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
Merged-chr10-8549544-1	chr10	8549327	8549761	+	1	NA	Intergenic	RLTR4_MM-int|LTR|ERV1	-30719	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
Merged-chr15-83156129-1	chr15	83156034	83156225	+	1	NA	intron (NM_029787, intron 8 of 8)	intron (NM_029787, intron 8 of 8)	6484	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
Merged-chr18-20622196-1	chr18	20622072	20622321	+	1	NA	intron (NR_155534, intron 1 of 2)	L1M3e|LINE|L1	-43054	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
Merged-chr5-26112579-1	chr5	26112441	26112717	+	1	NA	Intergenic	Lx3A|LINE|L1	-7265	NM_207657	381622	Mm.226878	NM_207657	ENSMUSG00000051940	5031410I06Rik	-	RIKEN cDNA 5031410I06 gene	protein-coding
Merged-chr2-55789039-1	chr2	55788924	55789154	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	353069	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
Merged-chr13-31545067-1	chr13	31544961	31545173	+	1	NA	Intergenic	L1Md_T|LINE|L1	-13103	NM_008239	15220	Mm.44235	NM_008239	ENSMUSG00000038415	Foxq1	HFH-1|Hfh1|Hfh1l|sa	forkhead box Q1	protein-coding
Merged-chr1-108408242-1	chr1	108408150	108408335	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	490983	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr19-8820326-1	chr19	8820226	8820427	+	1	NA	exon (NM_001081196, exon 1 of 14)	exon (NM_001081196, exon 1 of 14)	925	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
Merged-chr7-38183726-1	chr7	38183617	38183836	+	1	NA	promoter-TSS (NM_028166)	promoter-TSS (NM_028166)	-61	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
Merged-chr8-7041040-1	chr8	7040804	7041277	+	1	NA	Intergenic	Intergenic	1619733	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr15-77841781-1	chr15	77841694	77841868	+	1	NA	intron (NM_022410, intron 1 of 40)	CpG	394	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
Merged-chr1-108325141-1	chr1	108324975	108325307	+	1	NA	Intergenic	L1Md_T|LINE|L1	407882	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr1-73649799-1	chr1	73649688	73649910	+	1	NA	intron (NR_045311, intron 7 of 8)	L1Md_A|LINE|L1	205776	NR_105769	102465179		NR_105769	ENSMUSG00000098504	Mir6351	Gm27936|mmu-mir-6351	microRNA 6351	ncRNA
Merged-chr9-59757072-1	chr9	59756977	59757168	+	1	NA	intron (NM_173018, intron 1 of 43)	B2_Mm1a|SINE|B2	5898	NM_173018	270163	Mm.249545	NM_173018	ENSMUSG00000039585	Myo9a	4732465J09Rik|C130068I12Rik|C230003M11	myosin IXa	protein-coding
Merged-chr11-10441640-1	chr11	10441514	10441767	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-672376	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
Merged-chr1-48927173-1	chr1	48927024	48927323	+	1	NA	Intergenic	L1Md_T|LINE|L1	-317443	NR_151585	442837	Mm.337149	NM_001002792	ENSMUSG00000051616	C230029F24Rik	-	RIKEN cDNA C230029F24 gene	ncRNA
Merged-chr6-101643534-1	chr6	101643392	101643676	+	1	NA	Intergenic	L1Md_T|LINE|L1	-130715	NR_027989	207157	Mm.57632	NM_177579	ENSMUSG00000052236	Gm9871	0610005I04|EG207157	predicted gene 9871	ncRNA
Merged-chr19-47322956-1	chr19	47322870	47323043	+	1	NA	intron (NM_008018, intron 6 of 14)	intron (NM_008018, intron 6 of 14)	-49367	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
Merged-chr17-35286172-1	chr17	35286063	35286282	+	1	NA	Intergenic	MurERV4-int|LTR|ERVK	23049	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
Merged-chr1-84122843-1	chr1	84122745	84122942	+	1	NA	intron (NM_001003948, intron 2 of 2)	L1Md_A|LINE|L1	96118	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
Merged-chr10-30217739-1	chr10	30217574	30217904	+	1	NA	Intergenic	L1Md_T|LINE|L1	-17199	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding
Merged-chr13-66696481-1	chr13	66696385	66696578	+	1	NA	Intergenic	Intergenic	208869	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr12-6772600-1	chr12	6772477	6772723	+	1	NA	Intergenic	L1Md_A|LINE|L1	607730	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
Merged-chr8-84903563-1	chr8	84903453	84903673	+	1	NA	intron (NM_010635, intron 2 of 2)	CpG-14292	1635	NM_010635	16596	Mm.4847	NM_010635	ENSMUSG00000054191	Klf1	Eklf|Nan	Kruppel-like factor 1 (erythroid)	protein-coding
Merged-chrX-17476902-1	chrX	17476730	17477075	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	95105	NM_001313746	72018	Mm.41558	NM_028058	ENSMUSG00000025040	Fundc1	1500005J14Rik|1810033P05Rik	FUN14 domain containing 1	protein-coding
Merged-chr12-35867513-1	chr12	35867398	35867628	+	1	NA	Intergenic	L1Md_A|LINE|L1	-58108	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding
Merged-chr13-68002912-1	chr13	68002811	68003014	+	1	NA	Intergenic	RLTR1B-int|LTR|ERV1	139586	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr17-81064869-1	chr17	81064764	81064975	+	1	NA	intron (NM_028138, intron 1 of 9)	intron (NM_028138, intron 1 of 9)	216	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
Merged-chr9-38960923-1	chr9	38960836	38961011	+	1	NA	Intergenic	L1Md_T|LINE|L1	-14755	NM_146441	258433	Mm.271361	NM_146441	ENSMUSG00000058515	Olfr933	MOR171-22	olfactory receptor 933	protein-coding
Merged-chr1-173977115-1	chr1	173976973	173977258	+	1	NA	intron (NM_008327, intron 2 of 6)	intron (NM_008327, intron 2 of 6)	5729	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
Merged-chr17-32559371-1	chr17	32559271	32559471	+	1	NA	Intergenic	L1Md_F2|LINE|L1	22814	NM_001356303	70101	Mm.30504	NM_024442	ENSMUSG00000048440	Cyp4f16	2310021J05Rik|AI746515	cytochrome P450, family 4, subfamily f, polypeptide 16	protein-coding
Merged-chr13-66492990-1	chr13	66492902	66493079	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-51872	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr1-104219925-1	chr1	104219840	104220011	+	1	NA	Intergenic	Intergenic	-548595	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr1-40200688-1	chr1	40200547	40200829	+	1	NA	Intergenic	L1Md_T|LINE|L1	-24392	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
Merged-chr5-91250658-1	chr5	91250521	91250795	+	1	NA	Intergenic	L1Md_F2|LINE|L1	32418	NR_040428	100503265	Mm.125059	NR_040428	ENSMUSG00000107198	Gm19619	-	predicted gene, 19619	ncRNA
Merged-chr10-48233351-1	chr10	48233272	48233430	+	1	NA	Intergenic	L1Md_T|LINE|L1	1554586	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
Merged-chr8-94601505-1	chr8	94601394	94601616	+	1	NA	promoter-TSS (NM_026274)	promoter-TSS (NM_026274)	221	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
Merged-chr6-95214844-1	chr6	95214744	95214944	+	1	NA	Intergenic	L1Md_T|LINE|L1	96964	NM_001008785	243574	Mm.333275	NM_001008785	ENSMUSG00000030031	Kbtbd8	AU040152|SSEC-51|SSEC51|Takrp|mKIAA1842	kelch repeat and BTB (POZ) domain containing 8	protein-coding
Merged-chr15-79510676-1	chr15	79510520	79510832	+	1	NA	Intergenic	Intergenic	-5435	NM_008427	16520	Mm.39759	NM_008427	ENSMUSG00000044216	Kcnj4	IRK3|Kcnf2|MB-IRK3	potassium inwardly-rectifying channel, subfamily J, member 4	protein-coding
Merged-chr12-90839320-1	chr12	90839220	90839421	+	1	NA	Intergenic	L1Md_T|LINE|L1	-100283	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
Merged-chr5-89292721-1	chr5	89292615	89292828	+	1	NA	Intergenic	L1Md_F2|LINE|L1	165177	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	vitamin D binding protein	protein-coding
Merged-chr10-22337672-1	chr10	22337522	22337823	+	1	NA	intron (NM_009018, intron 6 of 6)	ERVB7_4-LTR_MM|LTR|ERVK	-24222	NM_020030	56554	Mm.458004	NM_020030	ENSMUSG00000078452	Raet1d	RAE-1delta	retinoic acid early transcript delta	protein-coding
Merged-chr7-59365183-1	chr7	59365098	59365268	+	1	NA	intron (NR_146211, intron 147 of 171)	intron (NR_146211, intron 147 of 171)	-17759	NR_146600	102642160		NR_146600		Gm22496	-	predicted gene, 22496	snoRNA
Merged-chr12-115105610-1	chr12	115105518	115105702	+	1	NA	Intergenic	L1Md_T|LINE|L1	590184	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr17-38587199-1	chr17	38587084	38587314	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	33007	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr1-47085675-1	chr1	47085579	47085772	+	1	NA	Intergenic	L1Md_T|LINE|L1	-159899	NM_001356417	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|Zip10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
Merged-chr1-124144937-1	chr1	124144824	124145050	+	1	NA	Intergenic	L1Md_T|LINE|L1	-99378	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
Merged-chr8-120605872-1	chr8	120605688	120606057	+	1	NA	Intergenic	Intergenic	-16797	NM_178856	272551	Mm.275910	NM_178856	ENSMUSG00000031821	Gins2	2210013I18Rik|4833427B12Rik|AI323585|Pfs2	GINS complex subunit 2 (Psf2 homolog)	protein-coding
Merged-chr10-53898451-1	chr10	53898340	53898563	+	1	NA	Intergenic	L1Md_A|LINE|L1	-147542	NM_001081428	75906	Mm.436785	NM_001081428	ENSMUSG00000019856	Fam184a	3110012E06Rik|4930438C08Rik|4930589M24Rik	family with sequence similarity 184, member A	protein-coding
Merged-chr8-70997704-1	chr8	70997594	70997814	+	1	NA	Intergenic	Intergenic	29051	NR_045487	69419	Mm.188688	NR_045487	ENSMUSG00000101854	1700026F02Rik	-	RIKEN cDNA 1700026F02 gene	ncRNA
Merged-chr8-91901417-1	chr8	91901334	91901501	+	1	NA	Intergenic	Intergenic	-99763	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
Merged-chr4-88794899-1	chr4	88794694	88795104	+	1	NA	exon (NM_001085533, exon 1 of 1)	exon (NM_001085533, exon 1 of 1)	412	NM_001161609	545654	Mm.478784	NM_001161609	ENSMUSG00000095101	Gm13285	limitin	predicted gene 13285	protein-coding
Merged-chr7-129015815-1	chr7	129015699	129015931	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-241279	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding
Merged-chr17-38487211-1	chr17	38487118	38487305	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-66981	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr1-139119292-1	chr1	139119207	139119378	+	1	NA	intron (NM_001166501, intron 14 of 21)	L1Md_T|LINE|L1	141635	NR_108103	78229	Mm.437838	NR_108103	ENSMUSG00000104900	4930596I21Rik	-	RIKEN cDNA 4930596I21 gene	ncRNA
Merged-chr4-74139456-1	chr4	74139376	74139536	+	1	NA	intron (NM_172869, intron 6 of 13)	(GGAAA)n|Simple_repeat|Simple_repeat	-103041	NM_001172095	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
Merged-chr12-115638051-1	chr12	115637913	115638190	+	1	NA	Intergenic	L1_Mus4|LINE|L1	57743	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr8-7082303-1	chr8	7082193	7082414	+	1	NA	Intergenic	L1_Mur2|LINE|L1	1578470	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
Merged-chr1-171554869-1	chr1	171554768	171554971	+	1	NA	Intergenic	MER77|LTR|ERVL	-4324	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
Merged-chr7-59614215-1	chr7	59614004	59614427	+	1	NA	intron (NR_146211, intron 91 of 171)	intron (NR_146211, intron 91 of 171)	61864	NR_033778	64244		NR_033778	ENSMUSG00000096475	Snord116l1	Pwcr1l1	small nucleolar RNA, C/D box 116-like 1	snoRNA
Merged-chr10-105812204-1	chr10	105812116	105812292	+	1	NA	intron (NM_001359642, intron 6 of 12)	L1Md_T|LINE|L1	29176	NM_001359640	216292	Mm.250875	NM_207522	ENSMUSG00000036009	Mettl25	-	methyltransferase like 25	protein-coding
Merged-chr10-28041729-1	chr10	28041643	28041815	+	1	NA	Intergenic	L1Md_T|LINE|L1	-33091	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
Merged-chr2-82427092-1	chr2	82427013	82427172	+	1	NA	Intergenic	L1Md_A|LINE|L1	-34890	NR_152125	228116	Mm.246588	NR_152125	ENSMUSG00000087061	A130030D18Rik	Gm558	RIKEN cDNA A130030D18 gene	ncRNA
Merged-chr8-72077611-1	chr8	72077523	72077699	+	1	NA	Intergenic	Lx5c|LINE|L1	19951	NM_207555	404315	Mm.377936	NM_207555	ENSMUSG00000069998	Olfr372	MOR282-1	olfactory receptor 372	protein-coding
Merged-chr8-79820533-1	chr8	79820363	79820703	+	1	NA	Intergenic	L1Md_F2|LINE|L1	108684	NM_001357235	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
Merged-chr1-29370637-1	chr1	29370557	29370717	+	1	NA	Intergenic	L1Md_A|LINE|L1	-50851	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
Merged-chr13-66692277-1	chr13	66692135	66692419	+	1	NA	Intergenic	L1_Mur2|LINE|L1	213073	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr12-77772163-1	chr12	77772075	77772251	+	1	NA	Intergenic	L1Md_T|LINE|L1	362022	NM_001252616	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
Merged-chr12-77769520-1	chr12	77769395	77769646	+	1	NA	Intergenic	L1Md_T|LINE|L1	359379	NM_001252616	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
Merged-chr17-93285708-1	chr17	93285582	93285835	+	1	NA	Intergenic	L1Md_T|LINE|L1	86540	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
Merged-chr12-38992492-1	chr12	38992358	38992626	+	1	NA	Intergenic	L1Md_T|LINE|L1	208781	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
Merged-chr11-120237643-1	chr11	120237523	120237764	+	1	NA	intron (NM_198423, intron 2 of 27)	CpG-2934	4696	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
Merged-chr10-8313961-1	chr10	8313862	8314061	+	1	NA	intron (NM_177387, intron 3 of 7)	L1Md_T|LINE|L1	204864	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
Merged-chr3-10810472-1	chr3	10810367	10810577	+	1	NA	Intergenic	L1Md_A|LINE|L1	-370342	NM_029068	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding
Merged-chr10-105921217-1	chr10	105921114	105921321	+	1	NA	Intergenic	L1Md_A|LINE|L1	79738	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding
Merged-chr7-59472121-1	chr7	59472026	59472216	+	1	NA	intron (NR_146211, intron 108 of 171)	intron (NR_146211, intron 108 of 171)	-124697	NR_146600	102642160		NR_146600		Gm22496	-	predicted gene, 22496	snoRNA
Merged-chr1-55367756-1	chr1	55367644	55367869	+	1	NA	Intergenic	L1Md_T|LINE|L1	-4287	NM_029267	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	boule homolog, RNA binding protein	protein-coding
Merged-chr1-166917576-1	chr1	166917458	166917694	+	1	NA	Intergenic	L1Md_T|LINE|L1	82154	NR_037988	100503962	Mm.216842	NR_037988	ENSMUSG00000102548	Gm16701	-	predicted gene, 16701	ncRNA
Merged-chr19-36669820-1	chr19	36669741	36669900	+	1	NA	intron (NR_033510, intron 2 of 4)	MIRb|SINE|MIR	19659	NR_033510	668215	Mm.394223	NR_033510	ENSMUSG00000087579	Hectd2os	1500017E21Rik	Hectd2, opposite strand	ncRNA
Merged-chr17-23297927-1	chr17	23297842	23298013	+	1	NA	intron (NM_001102584, intron 4 of 5)	intron (NM_001102584, intron 4 of 5)	14386	NM_001102584	666002	Mm.469838	NM_001102584	ENSMUSG00000091945	Vmn2r114	EG666002|V2Rp3	vomeronasal 2, receptor 114	protein-coding
Merged-chr1-94653884-1	chr1	94653780	94653989	+	1	NA	Intergenic	L1Md_A|LINE|L1	-143558	NR_040473	74689	Mm.399187	NR_040473	ENSMUSG00000100518	4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	ncRNA
Merged-chr15-98497888-1	chr15	98497800	98497976	+	1	NA	exon (NM_001001807, exon 1 of 1)	exon (NM_001001807, exon 1 of 1)	414	NM_001001807	258502	Mm.377539	NM_001001807	ENSMUSG00000054036	Olfr279	MOR122-1|Olfr234|Olfr234-ps1|Olfr279-ps1	olfactory receptor 279	protein-coding
Merged-chr19-3348279-1	chr19	3348195	3348363	+	1	NA	intron (NM_013495, intron 1 of 18)	intron (NM_013495, intron 1 of 18)	24978	NM_013495	12894	Mm.18522	NM_013495	ENSMUSG00000024900	Cpt1a	C730027G07|CPTI|Cpt1	carnitine palmitoyltransferase 1a, liver	protein-coding
Merged-chr1-141698801-1	chr1	141698586	141699016	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1042399	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr17-57656767-1	chr17	57656649	57656885	+	1	NA	Intergenic	L1Md_T|LINE|L1	-111453	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
Merged-chr1-23888347-1	chr1	23888171	23888524	+	1	NA	intron (NM_001357395, intron 2 of 10)	L1Md_A|LINE|L1	21389	NM_001290683	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
Merged-chr13-75206508-1	chr13	75206371	75206646	+	1	NA	Intergenic	L1Md_A|LINE|L1	116651	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
Merged-chr16-66524358-1	chr16	66524280	66524437	+	1	NA	Intergenic	L1Md_T|LINE|L1	-132760	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
Merged-chr3-150072992-1	chr3	150072868	150073116	+	1	NA	Intergenic	Intergenic	798255	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
Merged-chr19-41502361-1	chr19	41502210	41502513	+	1	NA	Intergenic	B1_Mm|SINE|Alu	-22891	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
Merged-chr6-3819177-1	chr6	3819095	3819260	+	1	NA	Intergenic	L1Md_T|LINE|L1	-54464	NM_007588	12311	Mm.4642	NM_007588	ENSMUSG00000023964	Calcr	Clr|Ct-r	calcitonin receptor	protein-coding
Merged-chr1-114228454-1	chr1	114228365	114228543	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1456683	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr1-66577862-1	chr1	66577738	66577986	+	1	NA	intron (NM_175510, intron 23 of 64)	L1Md_A|LINE|L1	109415	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
Merged-chr17-13486709-1	chr17	13486613	13486805	+	1	NA	TTS (NR_045436)	TTS (NR_045436)	-34747	NR_030763	272667	Mm.444718	NR_030763	ENSMUSG00000079711	Smok4a	4930513D10Rik|Smok2c	sperm motility kinase 4A	pseudo
Merged-chr1-14648600-1	chr1	14648491	14648709	+	1	NA	Intergenic	L1Md_F2|LINE|L1	107366	NM_001360810	17681	Mm.5820	NM_010827	ENSMUSG00000025930	Msc	MyoR|bHLHa22	musculin	protein-coding
Merged-chr15-83253162-1	chr15	83253042	83253283	+	1	NA	Intergenic	Intergenic	-1388	NM_001004150	239559	Mm.323805	NM_001004150	ENSMUSG00000047878	A4galt	-	alpha 1,4-galactosyltransferase	protein-coding
Merged-chr1-140927678-1	chr1	140927429	140927927	+	1	NA	Intergenic	L1Md_T|LINE|L1	-271276	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr8-71617457-1	chr8	71617344	71617570	+	1	NA	intron (NM_146211, intron 3 of 11)	intron (NM_146211, intron 3 of 11)	6433	NM_146211	234407	Mm.240885	NM_146211	ENSMUSG00000034807	Colgalt1	2810024B22Rik|Glt25d1	collagen beta(1-O)galactosyltransferase 1	protein-coding
Merged-chr12-119514181-1	chr12	119514072	119514291	+	1	NA	Intergenic	L1Md_T|LINE|L1	70771	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding
Merged-chr3-108445176-1	chr3	108445091	108445261	+	1	NA	promoter-TSS (NM_001204979)	promoter-TSS (NM_001204979)	83	NM_011319	20226	Mm.28688	NM_011319	ENSMUSG00000068739	Sars	Sars1|Strs|serRS	seryl-aminoacyl-tRNA synthetase	protein-coding
Merged-chr1-23886472-1	chr1	23886375	23886570	+	1	NA	intron (NM_001357395, intron 2 of 10)	L1Md_A|LINE|L1	23264	NM_001290683	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
Merged-chr10-35515436-1	chr10	35515327	35515546	+	1	NA	Intergenic	L1Md_T|LINE|L1	-991371	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding