Nfil3 (nuclear factor, interleukin 3 regulated)

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Gene: Nfil3 (nuclear factor, interleukin 3 regulated) Rattus norvegicus

Analyze

Symbol:

Nfil3

Name:

nuclear factor, interleukin 3 regulated

RGD ID:

620972

Description:

Enables DNA-binding transcription factor activity. Predicted to be involved in circadian rhythm; natural killer cell differentiation; and regulation of transcription, DNA-templated. Predicted to act upstream of or within cellular response to interleukin-4 and positive regulation of gene expression. Predicted to be active in nucleus. Orthologous to human NFIL3 (nuclear factor, interleukin 3 regulated); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

E4 promoter binding-protein 4; E4 promoter-binding protein 4; E4BP4; nuclear factor interleukin-3-regulated protein; nuclear factor, interleukin 3, regulated

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	17	12,280,499 - 12,295,728 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	17	12,280,484 - 12,295,858 (+)	Ensembl
Rnor_6.0	17	12,261,102 - 12,276,316 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	17	12,261,102 - 12,276,315 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	17	14,359,252 - 14,374,102 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	18,092,489 - 18,107,708 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	17	18,092,488 - 18,107,707 (+)	NCBI
Celera	17	12,046,069 - 12,061,335 (+)	NCBI		Celera
Cytogenetic Map	17	p14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

advanced sleep phase syndrome (ISO)

inflammatory bowel disease (ISS)

severe acute respiratory syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

(R)-noradrenaline (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

2-hydroxypropanoic acid (ISO)

3-chloropropane-1,2-diol (EXP)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

acrylamide (EXP,ISO)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

amphetamine (EXP)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

azoxystrobin (EXP,ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

Benzo[ghi]perylene (ISO)

benzoates (ISO)

beta-naphthoflavone (EXP)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

Butylbenzyl phthalate (EXP)

C60 fullerene (EXP)

cadmium atom (ISO)

cannabidiol (ISO)

captan (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

cefaloridine (EXP)

chlordecone (ISO)

chlorohydrocarbon (EXP)

chloroprene (EXP,ISO)

chlorpyrifos (EXP)

choline (ISO)

chrysene (ISO)

cisplatin (ISO)

clofibrate (ISO)

cobalt dichloride (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

coumestrol (ISO)

crocidolite asbestos (ISO)

CU-O LINKAGE (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dibenz[a,h]anthracene (ISO)

dibutyl phthalate (EXP,ISO)

dichloroacetic acid (ISO)

dichloromethane (ISO)

diclofenac (ISO)

dioxygen (ISO)

doxorubicin (ISO)

endosulfan (EXP)

Enterolactone (ISO)

fenpyroximate (ISO)

fluoranthene (ISO)

flusilazole (ISO)

folic acid (ISO)

folpet (ISO)

furan (EXP)

genistein (EXP)

geraniol (ISO)

glyphosate (EXP)

hexaconazole (ISO)

hexadecanoic acid (ISO)

hydrogen peroxide (ISO)

imidacloprid (EXP)

Indeno[1,2,3-cd]pyrene (ISO)

indole-3-methanol (EXP)

iron atom (ISO)

iron(0) (ISO)

isoprenaline (ISO)

ketamine (EXP)

kojic acid (ISO)

L-methionine (ISO)

leflunomide (ISO)

lipopolysaccharide (ISO)

methamphetamine (EXP)

methotrexate (ISO)

methylmercury chloride (EXP)

methylseleninic acid (ISO)

mitomycin C (ISO)

monosodium L-glutamate (ISO)

N-acetyl-L-cysteine (EXP)

N-nitrosodiethylamine (EXP)

nefazodone (EXP)

nickel dichloride (EXP,ISO)

nickel sulfate (ISO)

nimesulide (EXP)

ozone (ISO)

paracetamol (ISO)

paraquat (EXP)

perfluorononanoic acid (ISO)

phenobarbital (ISO)

phenylephrine (ISO)

picoxystrobin (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

progesterone (ISO)

quercetin (ISO)

rac-lactic acid (ISO)

raloxifene (ISO)

rotenone (EXP,ISO)

SCH 23390 (EXP)

sevoflurane (EXP)

silicon dioxide (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

sodium dichromate (ISO)

Soman (EXP)

styrene (ISO)

sulindac (ISO)

tamoxifen (ISO)

tebufenpyrad (ISO)

testosterone (ISO)

tetrachloromethane (ISO)

tetraphene (ISO)

thapsigargin (ISO)

thiabendazole (EXP)

titanium dioxide (EXP,ISO)

torcetrapib (ISO)

triadimefon (ISO)

tributylstannane (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (EXP)

troglitazone (ISO)

tunicamycin (ISO)

undecane (EXP)

valproic acid (ISO)

valsartan (ISO)

vinclozolin (EXP)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to interleukin-4 (ISO)

circadian rhythm (IBA)

immune response (IEA)

natural killer cell differentiation (ISO,ISS)

negative regulation of transcription by RNA polymerase II (ISO)

negative regulation of transcription, DNA-templated (ISO,ISS)

positive regulation of gene expression (ISO)

positive regulation of transcription, DNA-templated (ISO,ISS)

regulation of transcription, DNA-templated (IBA)

transcription by RNA polymerase II (IEA)

Cellular Component

nucleus (IBA)

Molecular Function

DNA-binding transcription factor activity (IDA)

DNA-binding transcription repressor activity, RNA polymerase II-specific (ISO)

identical protein binding (ISO)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Kong SL, etal., Virus Res. 2009 Nov;145(2):260-9. Epub 2009 Jul 25.
4.	MGD data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	Nishimura Y and Tanaka T, J Biol Chem 2001 Jun 8;276(23):19921-8.
7.	RGD automated data pipeline
8.	RGD automated import pipeline for gene-chemical interactions
9.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:9798653	PMID:12805554	PMID:15306565	PMID:20093779	PMID:20102225	PMID:21112399	PMID:21212137	PMID:21460847	PMID:21635892	PMID:25536374	PMID:25993115	PMID:29653076
PMID:30555544

Genomics

Comparative Map Data

Nfil3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	17	12,280,499 - 12,295,728 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	17	12,280,484 - 12,295,858 (+)	Ensembl
Rnor_6.0	17	12,261,102 - 12,276,316 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	17	12,261,102 - 12,276,315 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	17	14,359,252 - 14,374,102 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	18,092,489 - 18,107,708 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	17	18,092,488 - 18,107,707 (+)	NCBI
Celera	17	12,046,069 - 12,061,335 (+)	NCBI		Celera
Cytogenetic Map	17	p14	NCBI

NFIL3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	9	91,409,045 - 91,423,832 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	9	91,409,045 - 91,425,063 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	9	94,171,327 - 94,186,908 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	93,211,148 - 93,225,965 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	9	91,250,883 - 91,265,699	NCBI
Celera	9	64,605,969 - 64,620,785 (-)	NCBI
Cytogenetic Map	9	q22.31	NCBI
HuRef	9	63,851,695 - 63,866,454 (-)	NCBI		HuRef
CHM1_1	9	94,317,789 - 94,332,468 (-)	NCBI		CHM1_1

Nfil3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	53,121,245 - 53,136,914 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	13	53,121,245 - 53,135,109 (-)	Ensembl
GRCm38	13	52,967,209 - 52,982,878 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	52,967,209 - 52,981,073 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	13	53,062,578 - 53,076,408 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	13	52,979,641 - 52,993,471 (-)	NCBI			mm8
Celera	13	54,044,445 - 54,046,258 (-)	NCBI		Celera
Cytogenetic Map	13	B1	NCBI
cM Map	13	27.68	NCBI

Nfil3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955515	908,477 - 909,868 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955515	908,313 - 910,159 (+)	NCBI	ChiLan1.0	ChiLan1.0

NFIL3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	9	90,566,818 - 90,568,862 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	90,567,116 - 90,568,504 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	9	62,467,360 - 62,482,926 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

NFIL3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	95,508,224 - 95,510,452 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	95,508,764 - 95,510,152 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	95,949,339 - 95,964,139 (+)	NCBI
ROS_Cfam_1.0	1	96,095,964 - 96,110,820 (+)	NCBI
UMICH_Zoey_3.1	1	95,728,371 - 95,743,174 (+)	NCBI
UNSW_CanFamBas_1.0	1	95,448,017 - 95,462,797 (+)	NCBI
UU_Cfam_GSD_1.0	1	96,207,896 - 96,222,747 (+)	NCBI

Nfil3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404944	13,047,007 - 13,049,623 (-)	NCBI
SpeTri2.0	NW_004936796	367,461 - 369,469 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NFIL3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	2,588,891 - 2,603,255 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	2,588,887 - 2,603,774 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	3,264,864 - 3,279,973 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NFIL3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	12	101,845,294 - 101,860,844 (-)	NCBI
ChlSab1.1	12	101,845,294 - 101,860,844 (-)	NCBI
ChlSab1.1 Ensembl	12	101,845,592 - 101,846,980 (-)	Ensembl
Vero_WHO_p1.0	NW_023666038	90,166,784 - 90,183,191 (-)	NCBI

Nfil3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624868	1,139,575 - 1,150,370 (+)	NCBI

Position Markers

AV225605

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	12,295,604 - 12,295,722 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	12,276,193 - 12,276,310	NCBI	Rnor6.0
Rnor_5.0	17	14,373,979 - 14,374,096	UniSTS	Rnor5.0
RGSC_v3.4	17	18,107,585 - 18,107,702	UniSTS	RGSC3.4
Celera	17	12,061,212 - 12,061,329	UniSTS
Cytogenetic Map	17	p14	UniSTS

RH133089

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	12,295,452 - 12,295,663 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	12,276,041 - 12,276,251	NCBI	Rnor6.0
Rnor_5.0	17	14,373,827 - 14,374,037	UniSTS	Rnor5.0
RGSC_v3.4	17	18,107,433 - 18,107,643	UniSTS	RGSC3.4
Celera	17	12,061,060 - 12,061,270	UniSTS
RH 3.4 Map	17	114.1	UniSTS
Cytogenetic Map	17	p14	UniSTS

BE107980

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	12,280,928 - 12,281,098 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	12,261,532 - 12,261,701	NCBI	Rnor6.0
Rnor_5.0	17	14,359,682 - 14,359,851	UniSTS	Rnor5.0
RGSC_v3.4	17	18,092,919 - 18,093,088	UniSTS	RGSC3.4
Celera	17	12,046,499 - 12,046,668	UniSTS
RH 3.4 Map	17	115.7	UniSTS
Cytogenetic Map	17	p14	UniSTS

UniSTS:237019

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	12,295,385 - 12,295,625 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	12,275,974 - 12,276,213	NCBI	Rnor6.0
Rnor_5.0	17	14,373,760 - 14,373,999	UniSTS	Rnor5.0
RGSC_v3.4	17	18,107,366 - 18,107,605	UniSTS	RGSC3.4
Celera	17	12,060,993 - 12,061,232	UniSTS
Cytogenetic Map	17	p14	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
9590316	Scort21	Serum corticosterone level QTL 21	4.75	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	17	1	22871563	Rat
10401807	Kidm52	Kidney mass QTL 52			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	17	1	31701463	Rat
70184	BpQTLcluster14	Blood pressure QTL cluster 14	3.38		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	17	1	31990913	Rat
631207	Niddm41	Non-insulin dependent diabetes mellitus QTL 41			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	17	1	37830672	Rat
1354658	Spl8	Serum phospholipid level QTL 8	3.8		blood VLDL phospholipid amount (VT:0010507)	blood very low density lipoprotein phospholipid level (CMO:0001571)	17	1	60781592	Rat
1354581	Bp247	Blood pressure QTL 247	4.5		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	17	1	69599340	Rat
1354662	Rf49	Renal function QTL 49	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	17	1	69599340	Rat
1641902	Colcr7	Colorectal carcinoma resistance QTL 7	3.35	0.0044	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	17	2115149	21881669	Rat
1300123	Bp194	Blood pressure QTL 194	2.82		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	17	2115149	34551001	Rat
631499	Stl1	Serum triglyceride level QTL 1	3.6		blood triglyceride amount (VT:0002644)	blood triglyceride level (CMO:0000118)	17	3271398	27389946	Rat
2324619	Coatc4	Coat color QTL 4		0.001	coat/hair pigmentation trait (VT:0010463)	pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)	17	4299130	21293263	Rat
2324619	Coatc4	Coat color QTL 4		0.001	coat/hair pigmentation trait (VT:0010463)	pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)	17	4299130	21293263	Rat
1354613	Kidm14	Kidney mass QTL 14	6.2		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	17	4299130	35837242	Rat
1354596	Bw32	Body weight QTL 32	4.5		body mass (VT:0001259)	body weight (CMO:0000012)	17	4299130	60781592	Rat
1354630	Cm34	Cardiac mass QTL 34	8.7		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	17	4299130	69599340	Rat
1354638	Insul1	Insulin level QTL 1	4.8		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	17	4299130	69599340	Rat
1354651	Lmblg2	Limb length QTL 2	6		tibia length (VT:0004357)	tibia length (CMO:0000450)	17	4299130	69599340	Rat
2293648	Bmd31	Bone mineral density QTL 31	4.5	0.0001	femur size trait (VT:1000369)	femoral neck cortical cross-sectional area (CMO:0001702)	17	4354487	27028127	Rat
2293664	Bmd28	Bone mineral density QTL 28	5.1	0.0001	femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	17	4354487	27028127	Rat
2303627	Vencon8	Ventilatory control QTL 8		0.001	respiration trait (VT:0001943)	tidal volume (CMO:0000222)	17	4528038	49528038	Rat
10054088	Scort28	Serum corticosterone level QTL 28	2.04	0.0102	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	17	4528038	49528038	Rat
1581553	Pur14	Proteinuria QTL 14	5.3	0.0001	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	17	7979968	16317111	Rat
2303561	Bw91	Body weight QTL 91	2		body mass (VT:0001259)	body weight (CMO:0000012)	17	8868462	53868462	Rat
1582199	Insul5	Insulin level QTL 5	3.4	0.0119	blood insulin amount (VT:0001560)	calculated serum insulin level (CMO:0000359)	17	9201365	23653323	Rat
1582208	Kidm32	Kidney mass QTL 32	3.9	0.0018	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	17	9201365	23653323	Rat
1582224	Epfw4	Epididymal fat weight QTL 4	3.5	0.0058	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	17	9201365	23653323	Rat
1582225	Bw67	Body weight QTL 67	6.2	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
1582226	Bw64	Body weight QTL 64	4.2	0.0017	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
1582241	Bw70	Body weight QTL 70	4.6	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
1582245	Bw73	Body weight QTL 73	4.6	0.0004	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
1582258	Bw76	Body weight QTL 76	4.6	0.0005	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
2300002	Iddm36	Insulin dependent diabetes mellitus QTL 36	1.98		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	17	9991286	40540197	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	101
Count of miRNA genes:	83
Interacting mature miRNAs:	93
Transcripts:	ENSRNOT00000015525
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	1	28	33	30		30		3	55	20	32
Low	2	15	24	11	19	11	8	8	19	15	9	11	8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053727	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006253667	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006253669	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006253670	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039095285	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AY004663	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC072527	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473977	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000287	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000015525 ⟹ ENSRNOP00000015525

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	17	12,280,484 - 12,295,858 (+)	Ensembl
Rnor_6.0 Ensembl	17	12,261,102 - 12,276,315 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000096237 ⟹ ENSRNOP00000093138

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	17	12,284,693 - 12,295,858 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000096697 ⟹ ENSRNOP00000090522

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	17	12,284,007 - 12,295,662 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000112357 ⟹ ENSRNOP00000089110

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	17	12,282,205 - 12,295,858 (+)	Ensembl

RefSeq Acc Id:

NM_053727 ⟹ NP_446179

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	12,280,499 - 12,295,728 (+)	NCBI
Rnor_6.0	17	12,261,102 - 12,276,316 (+)	NCBI
Rnor_5.0	17	14,359,252 - 14,374,102 (+)	NCBI
RGSC_v3.4	17	18,092,489 - 18,107,708 (+)	RGD
Celera	17	12,046,069 - 12,061,335 (+)	RGD

Sequence:

show sequence

CACGAATGTGGTGGAGGCTCAGTGTGGACTGCCCCCCGGGAATGAAGACAGGCATCAGATTTCA
AAATTCAGTCGAAAGAACAGCTTCGTGGGTCACAGCCATCCGTTCGTTCCTCCGCTGGCAACCT
TGGATAACCCATAAAAGGCTCCTGACAGGTTCACCCTCTGCCGGACAGCAGAAGGAATATTGAT
GGATTCGAGAAGCTGAAGCCCTTACAACCTGAAAGAAGACTGGGGAAGTGATTCGTCTCCTCCT
CCATCGGGTCTGTAGGACGGGGAGGTCCTTTCTGATGCAGCTGAGAAAAATGCAGGCCATCAAA
AAGGAGCCTGCATCCCTGGATCCTACCGGCAGCTCAGACAAGATGTTGCTGCTGAACTCTGCCT
TAGCTGAGGTGGCTGAGGACCTAGCCTCAGGGGAAGATCTGCTCCTGAATGAAGGGAGCATGGG
GAAAAACAAGTCCTCTGCCTGTCGGAGAAAACGGGAATTCATCCCGGATGAGAAGAAGGACGCC
ATGTATTGGGAGAAACGGCGGAAAAACAACGAGGCTGCCAAAAGGTCTCGGGAGAAGCGTCGCC
TCAATGACCTGGTTCTGGAGAACAAGCTGATCGCCCTGGGAGAAGAAAATGCCACTTTAAAAGC
TGAGCTGCTCTCCCTGAAATTAAAGTTTGGCTTAATTAGCTCCACGGTGTACGCCCAAGAAATC
CAGAAACTCAGTAATTCCACAGCTGTGTATTTTCAGGACTACCAGACATCCAAGGCTGCCGTGA
GCTCTTACGTGGACGAGCATGAGCCTGCGATGGTAGCCGGAAGTTGCATCTCTGTCATCAAGCA
CTCTCCTCAGAGCTCGCTCTCGGATGTGTCTGAGGTGTCCTCTGTGGAGCACACACAGGAAAGC
CCCGCACAGGGAGGCTGCCGGAGCCCTGAGAACAAGTTCCCTGTGATCAAGCAGGAGCCCGTGG
AGTTGGAGAGCTTTGCCAGGGAGTCCAGAGAGGAGCGGGGTGCCTATTCCGCCTCCATCTACCA
GAGCTACATGGGTAGCTCTTTCTCCACCTACTCCCACTCCCCTCCCCTCCTGCAGGTCCACGGC
TCCACCAGCAACTCCCCGAGAACCTCGGAGGCCGACGAGGGTGTGGTGGGCAAGTCTTCTGATG
GGGAAGACGAGCAGCAGGTCCCCAAAGGCCCCATCCATTCTCCAGTGGAGCTGCAGCGGGTGCA
CGCCACGGTGGTGAAGGTTCCGGAAGTGAACCCTTCCGCCTTACCGCACAAGCTCCGGATTAAA
GCCAAGGCCATGCAGGTCAAAGTGGAAGCTTTGGACAGTGAGTTCGAAGGCATGCAGAAACTCT
CTTCACCGGCAGATGCGCTAGCCAAAAGACATTTTGACCTGGAGAAGCATGGCGCTTCGGGTAC
GGCCCATTCCTCCCTCCCTCCTTTCTCGGTGCAGGTGACGAACATTCAAGATTGGTCCCTCAGA
TCGGAACACTGGCATCACAAAGAACTGGGCGGCAAAACTCAGGGTACCTTCAAAACGGGTGTGG
TGGAAGTCAAAGACAGTGGCTATAAGGTTTCCGAGGCTGAGAATTTGTATTTGAAGCAGGGGGT
GGCAAACTTATCCGCAGAGGTGGTCTCGCTCAAGAGATTCATAGCCACACAGCCTATCTCGGCT
TCGGACTCCAGGTAAATGGCTACTGACTGAGCTATGCGTGGAAGAGGATGCTCTTGGTACCATA
CTGAATTTCCCACTGGACCTCTAAAGTCATTTCACTGTAGTGTGCACAACGGTGTCTGTCTGGT
GTCCTTGTGTACACAACGCTGAAGACTTGATGCCCTCACTCTGCCTGGCGTGTAGTCAGATAGC
CCTTCCCTCCCCACCCCCCAGAGGCTGTACATACCGAACGTTATTTTTGCTCTATGATAAAGTG
TGTACGTTGCCAGTTTCAATAAAGGATTGGTGGCAAACACAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAA

hide sequence

RefSeq Acc Id:

XM_006253667 ⟹ XP_006253729

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	12,285,463 - 12,295,728 (+)	NCBI
Rnor_6.0	17	12,265,389 - 12,276,316 (+)	NCBI
Rnor_5.0	17	14,359,252 - 14,374,102 (+)	NCBI

Sequence:

show sequence

GCCCGGTGGCCTGAGGCGGAGAGCGGGCGTGCTTCCTGGGCGCAGGCTCCGGCAGTGATGGGCC
TCGGGACAGCGCAGCCTCAGACGGACACATCCAGTAGCTGACTCCACTCCGGAGCATCGCTAGC
TGCGACCCCCACAGATACCTTTGTTTCTGGAGTCTCCGTTGAATTTCAGAGGCAAGCTCTTCTC
CATTCGCGGAGTGAAAAAGCAAGACCTCTAAATAGCTACTGAAAGGAGGGAGGGCATTCTTGAC
CGTGATGAAAAGGGGGGTCCCTGCTTGAAAGAGGCCAGTCAAGCCCAAGTTTTTATTATTTCCT
ATATCTAAAGTTTATTTGGTCAAAGGCCCAAGATTATATATATATGGTCGGAAGTCCCTAATTC
AAAATCACCCACATAGTTGCAGCTGGCTCTCCTGTAAAAGTACCTCTCTACTTCATCAGAACTT
CAGGTTTCTCTGGATGGCCTTCTGACGTCACAGCAAAGCCTCCGGTGTTTGGAGGGTGATCAGC
TCAGGCTGCTCTCTGGGGATGGTAAGCCTGGAATTCAGCATCAAATGATGCTATTGGTACCTAG
GGACCCTTTTTAAGCTAAAGATGGCTTTGGCAGGTGTAGGTGCTGCCCAGGCGTGTCTCTACCC
AGTATATGATAGGCCTTCGCTGGCTTCCAGGGAAACTTAGGAGAAGCCTGGGGAGCGGGGCAGT
TAGAAGGAGCTCAATAAATGTTTCCCATATGAATGCTTATGTTTGAGCTGGCTTTCCTTGGCTG
AACCGGATCTCCCAGGAAGACCGAAGACAGATAACCCATAAAAGGCTCCTGACAGGTTCACCCT
CTGCCGGACAGCAGAAGGAATATTGATGGATTCGAGAAGCTGAAGCCCTTACAACCTGAAAGAA
GACTGGGGAAGTGATTCGTCTCCTCCTCCATCGGGTCTGTAGGACGGGGAGGTCCTTTCTGATG
CAGCTGAGAAAAATGCAGGCCATCAAAAAGGAGCCTGCATCCCTGGATCCTACCGGCAGCTCAG
ACAAGATGTTGCTGCTGAACTCTGCCTTAGCTGAGGTGGCTGAGGACCTAGCCTCAGGGGAAGA
TCTGCTCCTGAATGAAGGGAGCATGGGGAAAAACAAGTCCTCTGCCTGTCGGAGAAAACGGGAA
TTCATCCCGGATGAGAAGAAGGACGCCATGTATTGGGAGAAACGGCGGAAAAACAACGAGGCTG
CCAAAAGGTCTCGGGAGAAGCGTCGCCTCAATGACCTGGTTCTGGAGAACAAGCTGATCGCCCT
GGGAGAAGAAAATGCCACTTTAAAAGCTGAGCTGCTCTCCCTGAAATTAAAGTTTGGCTTAATT
AGCTCCACGGTGTACGCCCAAGAAATCCAGAAACTCAGTAATTCCACAGCTGTGTATTTTCAGG
ACTACCAGACATCCAAGGCTGCCGTGAGCTCTTACGTGGACGAGCATGAGCCTGCGATGGTAGC
CGGAAGTTGCATCTCTGTCATCAAGCACTCTCCTCAGAGCTCGCTCTCGGATGTGTCTGAGGTG
TCCTCTGTGGAGCACACACAGGAAAGCCCCGCACAGGGAGGCTGCCGGAGCCCTGAGAACAAGT
TCCCTGTGATCAAGCAGGAGCCCGTGGAGTTGGAGAGCTTTGCCAGGGAGTCCAGAGAGGAGCG
GGGTGCCTATTCCGCCTCCATCTACCAGAGCTACATGGGTAGCTCTTTCTCCACCTACTCCCAC
TCCCCTCCCCTCCTGCAGGTCCACGGCTCCACCAGCAACTCCCCGAGAACCTCGGAGGCCGACG
AGGGTGTGGTGGGCAAGTCTTCTGATGGGGAAGACGAGCAGCAGGTCCCCAAAGGCCCCATCCA
TTCTCCAGTGGAGCTGCAGCGGGTGCACGCCACGGTGGTGAAGGTTCCGGAAGTGAACCCTTCC
GCCTTACCGCACAAGCTCCGGATTAAAGCCAAGGCCATGCAGGTCAAAGTGGAAGCTTTGGACA
GTGAGTTCGAAGGCATGCAGAAACTCTCTTCACCGGCAGATGCGCTAGCCAAAAGACATTTTGA
CCTGGAGAAGCATGGCGCTTCGGGTACGGCCCATTCCTCCCTCCCTCCTTTCTCGGTGCAGGTG
ACGAACATTCAAGATTGGTCCCTCAGATCGGAACACTGGCATCACAAAGAACTGGGCGGCAAAA
CTCAGGGTACCTTCAAAACGGGTGTGGTGGAAGTCAAAGACAGTGGCTATAAGGTTTCCGAGGC
TGAGAATTTGTATTTGAAGCAGGGGGTGGCAAACTTATCCGCAGAGGTGGTCTCGCTCAAGAGA
TTCATAGCCACACAGCCTATCTCGGCTTCGGACTCCAGGTAAATGGCTACTGACTGAGCTATGC
GTGGAAGAGGATGCTCTTGGTACCATACTGAATTTCCCACTGGACCTCTAAAGTCATTTCACTG
TAGTGTGCACAACGGTGTCTGTCTGGTGTCCTTGTGTACACAACGCTGAAGACTTGATGCCCTC
ACTCTGCCTGGCGTGTAGTCAGATAGCCCTTCCCTCCCCACCCCCCAGAGGCTGTACATACCGA
ACGTTATTTTTGCTCTATGATAAAGTGTGTACGTTGCCAGTTTCAATAAAGGATTGGTGGCAAA
CACA

hide sequence

RefSeq Acc Id:

XM_006253669 ⟹ XP_006253731

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	12,283,331 - 12,295,728 (+)	NCBI
Rnor_6.0	17	12,263,284 - 12,276,316 (+)	NCBI
Rnor_5.0	17	14,359,252 - 14,374,102 (+)	NCBI

Sequence:

show sequence

TGATTGCAGCGCCCTGGCGCCCGCACGTAGCCGGGGCTGCCGCGGGCTCCCTCCTCCTCCCCGC
TATTGCATAATGTCTCCGGATTTCAGGAAAATTGATGTTTCGGTGGCGAAGAGCGCGCCGGGGA
GGCGGAGTGGAGGCCGATCCTTTTAGCAGCCTGACGTGCCCTGCTCTCCGGGGTCTCTCCGCGC
TAGTCCCCAATCCGGGCCGGCCAGTGGGAGGGTTGAGTCTTGGGGAGCCGTCTTGATTTGCTTA
GGAGGGTTGGGAGTGCGAACGGTGACGGCAATCGGAGGTGCCTGCGCGGCGTTTGTTTGTGTCA
GGCGCTGTGTCGGCACCGACGTTTTCCAACCCGTTTGTCGTCACCGTGTTTTACGAGCCCTCGG
GAAGGTGGAGGGATGTGTCCTTTCTTACGTTGCATAATGGGCTAGCGGTGAAACGTGGGCACCG
AGGACGAGCTGATGTGAGAATGTGCGCCTATGTGTGCAATGATTTGGTCATTTTAGCGCAGCGT
TTGGTGCCTCTGTATCGTCCCAAATAAGCATATTTTAAAAACGAGTCTATGAAATTCATTATTA
AGAAAGGAGAAATCCTAGTGTTGGACACTAATGCGCGCGGGAGGGCGAGTTGGGGGGGGGGGCT
CCTTAAATGTTCCGAGGTGTTATTTTTAAAACCCGGAGGAGCCATTGTGACGTTTGCCTCCCCA
CTTTTCCCAACCGTTTCATCAGCTTTTTTTTTCTTCTCACCTTATCGTCATTGGCTTTTTTTTT
TTTTTTAATAAAGACACCACAAGACAAATCATTAATAGATTCCTGGAAATGTGAGGTTACGTAA
CTGCCGAATTTGCTGGCTGTTGAGCATAGAAAGGGAGCTAATTACGTGATTTTATAATCTTGCC
ACAAAGAAAGTAGGGCAATCTCAGCGTTTAAGAATGTCACAATCAACAGGGGTTTTGTTGGTTC
TTTTAAAGGATATTTTAAGCCGGAAAGTGACGACCAACTAAGCTTTGACATAGCTCGTGCTTGC
CAAATGGGTGTCTTTTACCCTAAATGAAATGTACGTCTTTCTAAATTTAGCCCCATCACATTTT
AACAATCCTGGCCTCGGTGCTATTTCTGGTTTCTCCAGGGCTGTGTGCAAATACGAGCTCAAGG
CCATTTGCTGTAGTTTTAACTCCACGCCTTCCAAGACCTCTGATAAGACTGTATTTTTAGGAAG
GCATTTCGCAGCGCCCAGTGACTGCTGGTGAACGCGGGGGCCCCATTTATCATTTTAAAGGACA
CTTAGGAGGAACTGCTACGTTCAGAGGCCAACAGGGAATGGACAAGTGTCACCTTCTCTGGCTC
TTGTAAATAACAACAGCTAATGAGATAACCCATAAAAGGCTCCTGACAGGTTCACCCTCTGCCG
GACAGCAGAAGGAATATTGATGGATTCGAGAAGCTGAAGCCCTTACAACCTGAAAGAAGACTGG
GGAAGTGATTCGTCTCCTCCTCCATCGGGTCTGTAGGACGGGGAGGTCCTTTCTGATGCAGCTG
AGAAAAATGCAGGCCATCAAAAAGGAGCCTGCATCCCTGGATCCTACCGGCAGCTCAGACAAGA
TGTTGCTGCTGAACTCTGCCTTAGCTGAGGTGGCTGAGGACCTAGCCTCAGGGGAAGATCTGCT
CCTGAATGAAGGGAGCATGGGGAAAAACAAGTCCTCTGCCTGTCGGAGAAAACGGGAATTCATC
CCGGATGAGAAGAAGGACGCCATGTATTGGGAGAAACGGCGGAAAAACAACGAGGCTGCCAAAA
GGTCTCGGGAGAAGCGTCGCCTCAATGACCTGGTTCTGGAGAACAAGCTGATCGCCCTGGGAGA
AGAAAATGCCACTTTAAAAGCTGAGCTGCTCTCCCTGAAATTAAAGTTTGGCTTAATTAGCTCC
ACGGTGTACGCCCAAGAAATCCAGAAACTCAGTAATTCCACAGCTGTGTATTTTCAGGACTACC
AGACATCCAAGGCTGCCGTGAGCTCTTACGTGGACGAGCATGAGCCTGCGATGGTAGCCGGAAG
TTGCATCTCTGTCATCAAGCACTCTCCTCAGAGCTCGCTCTCGGATGTGTCTGAGGTGTCCTCT
GTGGAGCACACACAGGAAAGCCCCGCACAGGGAGGCTGCCGGAGCCCTGAGAACAAGTTCCCTG
TGATCAAGCAGGAGCCCGTGGAGTTGGAGAGCTTTGCCAGGGAGTCCAGAGAGGAGCGGGGTGC
CTATTCCGCCTCCATCTACCAGAGCTACATGGGTAGCTCTTTCTCCACCTACTCCCACTCCCCT
CCCCTCCTGCAGGTCCACGGCTCCACCAGCAACTCCCCGAGAACCTCGGAGGCCGACGAGGGTG
TGGTGGGCAAGTCTTCTGATGGGGAAGACGAGCAGCAGGTCCCCAAAGGCCCCATCCATTCTCC
AGTGGAGCTGCAGCGGGTGCACGCCACGGTGGTGAAGGTTCCGGAAGTGAACCCTTCCGCCTTA
CCGCACAAGCTCCGGATTAAAGCCAAGGCCATGCAGGTCAAAGTGGAAGCTTTGGACAGTGAGT
TCGAAGGCATGCAGAAACTCTCTTCACCGGCAGATGCGCTAGCCAAAAGACATTTTGACCTGGA
GAAGCATGGCGCTTCGGGTACGGCCCATTCCTCCCTCCCTCCTTTCTCGGTGCAGGTGACGAAC
ATTCAAGATTGGTCCCTCAGATCGGAACACTGGCATCACAAAGAACTGGGCGGCAAAACTCAGG
GTACCTTCAAAACGGGTGTGGTGGAAGTCAAAGACAGTGGCTATAAGGTTTCCGAGGCTGAGAA
TTTGTATTTGAAGCAGGGGGTGGCAAACTTATCCGCAGAGGTGGTCTCGCTCAAGAGATTCATA
GCCACACAGCCTATCTCGGCTTCGGACTCCAGGTAAATGGCTACTGACTGAGCTATGCGTGGAA
GAGGATGCTCTTGGTACCATACTGAATTTCCCACTGGACCTCTAAAGTCATTTCACTGTAGTGT
GCACAACGGTGTCTGTCTGGTGTCCTTGTGTACACAACGCTGAAGACTTGATGCCCTCACTCTG
CCTGGCGTGTAGTCAGATAGCCCTTCCCTCCCCACCCCCCAGAGGCTGTACATACCGAACGTTA
TTTTTGCTCTATGATAAAGTGTGTACGTTGCCAGTTTCAATAAAGGATTGGTGGCAAACACA

hide sequence

RefSeq Acc Id:

XM_006253670 ⟹ XP_006253732

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	12,285,206 - 12,295,728 (+)	NCBI
Rnor_6.0	17	12,265,389 - 12,276,316 (+)	NCBI
Rnor_5.0	17	14,359,252 - 14,374,102 (+)	NCBI

Sequence:

show sequence

GCCCGGTGGCCTGAGGCGGAGAGCGGGCGTGCTTCCTGGGCGCAGGCTCCGGCAGTGATGGGCC
TCGGGACAGCGCAGCCTCAGACGGACACATCCAGTAGCTGACTCCACTCCGGAGCATCGCTAGC
TGCGACCCCCACAGATACCTTTGTTTCTGGAGTCTCCGTTGAATTTCAGAGGCAAGCTCTTCTC
CATTCGCGGAGTGAAAAAGCAAGACCTCTAAATAGCTACTGAAAGGAGGGAGGGCATTCTTGAC
CGTGATGAAAAGGGGGGTCCCTGCTTGAAAGAGGCCAGTCAAGCCCAAGTTTTTATTATTTCCT
ATATCTAAAGTTTATTTGGTCAAAGGCCCAAGATTATATATATATGGTCGGAAGTCCCTAATTC
AAAATCACCCACATAGTTGCAGCTGGCTCTCCTGTAAAAGTACCTCTCTACTTCATCAGAACTT
CAGGTTTCTCTGGATGGCCTTCTGACGTCACAGCAAAGCCTCCGGTGTTTGGAGGGTGATCAGC
TCAGGCTGCTCTCTGGGGATGATAACCCATAAAAGGCTCCTGACAGGTTCACCCTCTGCCGGAC
AGCAGAAGGAATATTGATGGATTCGAGAAGCTGAAGCCCTTACAACCTGAAAGAAGACTGGGGA
AGTGATTCGTCTCCTCCTCCATCGGGTCTGTAGGACGGGGAGGTCCTTTCTGATGCAGCTGAGA
AAAATGCAGGCCATCAAAAAGGAGCCTGCATCCCTGGATCCTACCGGCAGCTCAGACAAGATGT
TGCTGCTGAACTCTGCCTTAGCTGAGGTGGCTGAGGACCTAGCCTCAGGGGAAGATCTGCTCCT
GAATGAAGGGAGCATGGGGAAAAACAAGTCCTCTGCCTGTCGGAGAAAACGGGAATTCATCCCG
GATGAGAAGAAGGACGCCATGTATTGGGAGAAACGGCGGAAAAACAACGAGGCTGCCAAAAGGT
CTCGGGAGAAGCGTCGCCTCAATGACCTGGTTCTGGAGAACAAGCTGATCGCCCTGGGAGAAGA
AAATGCCACTTTAAAAGCTGAGCTGCTCTCCCTGAAATTAAAGTTTGGCTTAATTAGCTCCACG
GTGTACGCCCAAGAAATCCAGAAACTCAGTAATTCCACAGCTGTGTATTTTCAGGACTACCAGA
CATCCAAGGCTGCCGTGAGCTCTTACGTGGACGAGCATGAGCCTGCGATGGTAGCCGGAAGTTG
CATCTCTGTCATCAAGCACTCTCCTCAGAGCTCGCTCTCGGATGTGTCTGAGGTGTCCTCTGTG
GAGCACACACAGGAAAGCCCCGCACAGGGAGGCTGCCGGAGCCCTGAGAACAAGTTCCCTGTGA
TCAAGCAGGAGCCCGTGGAGTTGGAGAGCTTTGCCAGGGAGTCCAGAGAGGAGCGGGGTGCCTA
TTCCGCCTCCATCTACCAGAGCTACATGGGTAGCTCTTTCTCCACCTACTCCCACTCCCCTCCC
CTCCTGCAGGTCCACGGCTCCACCAGCAACTCCCCGAGAACCTCGGAGGCCGACGAGGGTGTGG
TGGGCAAGTCTTCTGATGGGGAAGACGAGCAGCAGGTCCCCAAAGGCCCCATCCATTCTCCAGT
GGAGCTGCAGCGGGTGCACGCCACGGTGGTGAAGGTTCCGGAAGTGAACCCTTCCGCCTTACCG
CACAAGCTCCGGATTAAAGCCAAGGCCATGCAGGTCAAAGTGGAAGCTTTGGACAGTGAGTTCG
AAGGCATGCAGAAACTCTCTTCACCGGCAGATGCGCTAGCCAAAAGACATTTTGACCTGGAGAA
GCATGGCGCTTCGGGTACGGCCCATTCCTCCCTCCCTCCTTTCTCGGTGCAGGTGACGAACATT
CAAGATTGGTCCCTCAGATCGGAACACTGGCATCACAAAGAACTGGGCGGCAAAACTCAGGGTA
CCTTCAAAACGGGTGTGGTGGAAGTCAAAGACAGTGGCTATAAGGTTTCCGAGGCTGAGAATTT
GTATTTGAAGCAGGGGGTGGCAAACTTATCCGCAGAGGTGGTCTCGCTCAAGAGATTCATAGCC
ACACAGCCTATCTCGGCTTCGGACTCCAGGTAAATGGCTACTGACTGAGCTATGCGTGGAAGAG
GATGCTCTTGGTACCATACTGAATTTCCCACTGGACCTCTAAAGTCATTTCACTGTAGTGTGCA
CAACGGTGTCTGTCTGGTGTCCTTGTGTACACAACGCTGAAGACTTGATGCCCTCACTCTGCCT
GGCGTGTAGTCAGATAGCCCTTCCCTCCCCACCCCCCAGAGGCTGTACATACCGAACGTTATTT
TTGCTCTATGATAAAGTGTGTACGTTGCCAGTTTCAATAAAGGATTGGTGGCAAACACA

hide sequence

RefSeq Acc Id:

XM_039095285 ⟹ XP_038951213

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	12,282,351 - 12,295,728 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_446179	(Get FASTA)	NCBI Sequence Viewer
	XP_006253729	(Get FASTA)	NCBI Sequence Viewer
	XP_006253731	(Get FASTA)	NCBI Sequence Viewer
	XP_006253732	(Get FASTA)	NCBI Sequence Viewer
	XP_038951213	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF86615	(Get FASTA)	NCBI Sequence Viewer
	AAH72527	(Get FASTA)	NCBI Sequence Viewer
	EDL98064	(Get FASTA)	NCBI Sequence Viewer
	Q6IMZ0	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_446179 ⟸ NM_053727

- UniProtKB:

Q6IMZ0 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MQLRKMQAIKKEPASLDPTGSSDKMLLLNSALAEVAEDLASGEDLLLNEGSMGKNKSSACRRKR
EFIPDEKKDAMYWEKRRKNNEAAKRSREKRRLNDLVLENKLIALGEENATLKAELLSLKLKFGL
ISSTVYAQEIQKLSNSTAVYFQDYQTSKAAVSSYVDEHEPAMVAGSCISVIKHSPQSSLSDVSE
VSSVEHTQESPAQGGCRSPENKFPVIKQEPVELESFARESREERGAYSASIYQSYMGSSFSTYS
HSPPLLQVHGSTSNSPRTSEADEGVVGKSSDGEDEQQVPKGPIHSPVELQRVHATVVKVPEVNP
SALPHKLRIKAKAMQVKVEALDSEFEGMQKLSSPADALAKRHFDLEKHGASGTAHSSLPPFSVQ
VTNIQDWSLRSEHWHHKELGGKTQGTFKTGVVEVKDSGYKVSEAENLYLKQGVANLSAEVVSLK
RFIATQPISASDSR

hide sequence

RefSeq Acc Id:	XP_006253731 ⟸ XM_006253669
- Peptide Label:	isoform X1
- UniProtKB:	Q6IMZ0 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MQLRKMQAIKKEPASLDPTGSSDKMLLLNSALAEVAEDLASGEDLLLNEGSMGKNKSSACRRKR EFIPDEKKDAMYWEKRRKNNEAAKRSREKRRLNDLVLENKLIALGEENATLKAELLSLKLKFGL ISSTVYAQEIQKLSNSTAVYFQDYQTSKAAVSSYVDEHEPAMVAGSCISVIKHSPQSSLSDVSE VSSVEHTQESPAQGGCRSPENKFPVIKQEPVELESFARESREERGAYSASIYQSYMGSSFSTYS HSPPLLQVHGSTSNSPRTSEADEGVVGKSSDGEDEQQVPKGPIHSPVELQRVHATVVKVPEVNP SALPHKLRIKAKAMQVKVEALDSEFEGMQKLSSPADALAKRHFDLEKHGASGTAHSSLPPFSVQ VTNIQDWSLRSEHWHHKELGGKTQGTFKTGVVEVKDSGYKVSEAENLYLKQGVANLSAEVVSLK RFIATQPISASDSR hide sequence

RefSeq Acc Id:	XP_006253732 ⟸ XM_006253670
- Peptide Label:	isoform X1
- UniProtKB:	Q6IMZ0 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MQLRKMQAIKKEPASLDPTGSSDKMLLLNSALAEVAEDLASGEDLLLNEGSMGKNKSSACRRKR EFIPDEKKDAMYWEKRRKNNEAAKRSREKRRLNDLVLENKLIALGEENATLKAELLSLKLKFGL ISSTVYAQEIQKLSNSTAVYFQDYQTSKAAVSSYVDEHEPAMVAGSCISVIKHSPQSSLSDVSE VSSVEHTQESPAQGGCRSPENKFPVIKQEPVELESFARESREERGAYSASIYQSYMGSSFSTYS HSPPLLQVHGSTSNSPRTSEADEGVVGKSSDGEDEQQVPKGPIHSPVELQRVHATVVKVPEVNP SALPHKLRIKAKAMQVKVEALDSEFEGMQKLSSPADALAKRHFDLEKHGASGTAHSSLPPFSVQ VTNIQDWSLRSEHWHHKELGGKTQGTFKTGVVEVKDSGYKVSEAENLYLKQGVANLSAEVVSLK RFIATQPISASDSR hide sequence

RefSeq Acc Id:	XP_006253729 ⟸ XM_006253667
- Peptide Label:	isoform X1
- UniProtKB:	Q6IMZ0 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MQLRKMQAIKKEPASLDPTGSSDKMLLLNSALAEVAEDLASGEDLLLNEGSMGKNKSSACRRKR EFIPDEKKDAMYWEKRRKNNEAAKRSREKRRLNDLVLENKLIALGEENATLKAELLSLKLKFGL ISSTVYAQEIQKLSNSTAVYFQDYQTSKAAVSSYVDEHEPAMVAGSCISVIKHSPQSSLSDVSE VSSVEHTQESPAQGGCRSPENKFPVIKQEPVELESFARESREERGAYSASIYQSYMGSSFSTYS HSPPLLQVHGSTSNSPRTSEADEGVVGKSSDGEDEQQVPKGPIHSPVELQRVHATVVKVPEVNP SALPHKLRIKAKAMQVKVEALDSEFEGMQKLSSPADALAKRHFDLEKHGASGTAHSSLPPFSVQ VTNIQDWSLRSEHWHHKELGGKTQGTFKTGVVEVKDSGYKVSEAENLYLKQGVANLSAEVVSLK RFIATQPISASDSR hide sequence

RefSeq Acc Id:

ENSRNOP00000015525 ⟸ ENSRNOT00000015525

RefSeq Acc Id:	XP_038951213 ⟸ XM_039095285
- Peptide Label:	isoform X1

RefSeq Acc Id:

ENSRNOP00000090522 ⟸ ENSRNOT00000096697

RefSeq Acc Id:

ENSRNOP00000093138 ⟸ ENSRNOT00000096237

RefSeq Acc Id:

ENSRNOP00000089110 ⟸ ENSRNOT00000112357

Protein Domains

bZIP

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13700333

Promoter ID:

EPDNEW_R10857

Type:

multiple initiation site

Name:

Nfil3_1

Description:

nuclear factor, interleukin 3 regulated

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	17	12,261,071 - 12,261,131	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN-Lx/CubMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BUF/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

DA/OlaHsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620972	AgrOrtholog
Ensembl Genes	ENSRNOG00000011668	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000015525	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000015525	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7097417	IMAGE-MGC_LOAD
InterPro	bZIP	UniProtKB/Swiss-Prot
	NFIL3/E4BP4	UniProtKB/Swiss-Prot
	Vert_IL3-reg_TF	UniProtKB/Swiss-Prot
KEGG Report	rno:114519	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:91562	IMAGE-MGC_LOAD
NCBI Gene	114519	ENTREZGENE
PANTHER	PTHR15284:SF1	UniProtKB/Swiss-Prot
Pfam	bZIP_2	UniProtKB/Swiss-Prot
	Vert_IL3-reg_TF	UniProtKB/Swiss-Prot
PhenoGen	Nfil3	PhenoGen
PIRSF	bZIP_E4BP4	UniProtKB/Swiss-Prot
PROSITE	BZIP	UniProtKB/Swiss-Prot
	BZIP_BASIC	UniProtKB/Swiss-Prot
SMART	BRLZ	UniProtKB/Swiss-Prot
UniProt	NFIL3_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	Q923M2	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-12-14	Nfil3	nuclear factor, interleukin 3 regulated		nuclear factor, interleukin 3, regulated	Name updated	1299863	APPROVED
2002-08-07	Nfil3	nuclear factor, interleukin 3, regulated			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_regulation	expression regulated in a Ca2+ dependent manner by both calcineurin/NFAT and CaM kinase	633353

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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