Nr4a1 (nuclear receptor subfamily 4, group A, member 1) - Rat Genome Database

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Gene: Nr4a1 (nuclear receptor subfamily 4, group A, member 1) Rattus norvegicus
Analyze
Symbol: Nr4a1
Name: nuclear receptor subfamily 4, group A, member 1
RGD ID: 620029
Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific; glucocorticoid receptor binding activity; and protein heterodimerization activity. Involved in several processes, including neurotransmitter secretion involved in regulation of skeletal muscle contraction; response to amphetamine; and response to lipopolysaccharide. Located in nucleus. Used to study Parkinson's disease and chronic kidney disease. Biomarker of mesangial proliferative glomerulonephritis. Orthologous to human NR4A1 (nuclear receptor subfamily 4 group A member 1); PARTICIPATES IN mitogen activated protein kinase signaling pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 17beta-estradiol; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: HMR; immediate early gene transcription factor NGFI-B; nerve growth factor induced protein I-B; nerve growth factor-induced protein I-B; Ngfi-b; nuclear receptor subfamily 4 group A member 1; Nur77; Orphan nuclear receptor HMR
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Nr4a1m1Mcwi  
Genetic Models: FHH-Nr4a1m1Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27132,368,399 - 132,389,300 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7132,374,840 - 132,389,297 (+)Ensembl
Rnor_6.07142,899,358 - 142,920,216 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,905,758 - 142,920,216 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07140,700,242 - 140,721,073 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47140,012,807 - 140,020,590 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17140,089,243 - 140,097,024 (+)NCBI
Celera7128,846,928 - 128,854,640 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(R)-pantothenic acid  (ISO)
(S)-amphetamine  (ISO)
(S)-nicotine  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (ISO)
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
2-methoxyethanol  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3,5-dichloro-N-[[(2S)-1-ethyl-2-pyrrolidinyl]methyl]-2-hydroxy-6-methoxybenzamide  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3-methylcholanthrene  (ISO)
3-Nitrobenzanthrone  (ISO)
4,4'-sulfonyldiphenol  (EXP)
4,5,6,7-TETRABROMOBENZOTRIAZOLE  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (ISO)
8-Br-cAMP  (ISO)
8-OH-DPAT  (EXP)
acetaldehyde  (ISO)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (EXP,ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
alpha-amanitin  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
ATP  (EXP)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (ISO)
bisphenol F  (EXP)
bucladesine  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
C.I. Natural Red 20  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
cadmium sulfate  (ISO)
Calcimycin  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
chloroprene  (ISO)
chlorpyrifos  (EXP)
Chorionic gonadotropin  (EXP)
cisplatin  (ISO)
clozapine  (EXP)
cocaine  (EXP)
colforsin daropate hydrochloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
Cuprizon  (EXP)
cycloheximide  (EXP)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
D-glucopyranose 6-phosphate  (ISO)
D-penicillamine  (EXP)
daidzein  (ISO)
daidzein 7-O-beta-D-glucoside  (ISO)
dapsone  (ISO)
DDE  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dichlorine  (EXP)
dicrotophos  (ISO)
dieldrin  (ISO)
dimethylselenide  (ISO)
dinophysistoxin 1  (ISO)
dipentyl phthalate  (EXP)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenofibrate  (ISO)
fenthion  (ISO)
fluoranthene  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP)
genistein  (ISO)
genistein 7-O-beta-D-glucoside  (ISO)
glutathione  (ISO)
glycerol  (ISO)
glycidol  (EXP)
glycitein  (ISO)
glycitin  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
haloperidol  (EXP,ISO)
hydrogen peroxide  (ISO)
Ibotenic acid  (EXP)
indole-3-methanol  (EXP)
indometacin  (ISO)
isoprenaline  (ISO)
kainic acid  (EXP,ISO)
kenpaullone  (EXP)
ketorolac  (EXP)
lead diacetate  (EXP)
leflunomide  (ISO)
leptomycin B  (ISO)
linsidomine  (EXP)
lipopolysaccharide  (EXP,ISO)
maneb  (ISO)
menadione  (ISO)
mercury atom  (EXP)
mercury(0)  (EXP)
metformin  (EXP)
methamphetamine  (EXP)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
morphine  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-[2-[4-(2-methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl)cyclohexanecarboxamide  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodimethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (EXP)
naphthalenes  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotinamide  (ISO)
nicotine  (ISO)
nitric oxide  (EXP)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
paracetamol  (ISO)
paraquat  (ISO)
paricalcitol  (ISO)
pentetrazol  (ISO)
pentobarbital  (EXP)
perfluorooctanoic acid  (EXP)
phenformin  (EXP)
phenobarbital  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosphorus atom  (ISO)
phosphorus(.)  (ISO)
pioglitazone  (ISO)
potassium atom  (EXP)
potassium chloride  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
proanthocyanidin  (ISO)
progesterone  (ISO)
pyridaben  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
ranitidine  (EXP)
reactive oxygen species  (ISO)
Rebamipide  (EXP)
rotenone  (EXP)
ryanodine  (ISO)
SB 203580  (ISO)
scopolamine  (EXP)
sevoflurane  (EXP)
Shikonin  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
Soman  (EXP)
styrene  (ISO)
succinic acid  (ISO)
sulforaphane  (ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thalidomide  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
topotecan  (EXP)
torcetrapib  (ISO)
triazolam  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (EXP,ISO)
trichostatin A  (ISO)
triphenylstannane  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (EXP,ISO)
undecane  (EXP)
urethane  (ISO)
vinclozolin  (EXP)
zearalenone  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA)
cytosol  (IEA,ISO)
mitochondrion  (IEA)
nuclear membrane  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA,IEA,ISO)
presynapse  (IEA)
transcription regulator complex  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View

References

References - curated
1. Balasubramanian S, etal., J Am Soc Nephrol. 2012 Apr;23(4):674-86. doi: 10.1681/ASN.2011070646. Epub 2012 Feb 16.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. GOA data from the GO Consortium
4. Lee S and Rivier C, Brain Res Mol Brain Res. 1998 Jun 1;57(1):54-62.
5. Lee S, etal., Brain Res. 1995 Dec 24;705(1-2):136-48. doi: 10.1016/0006-8993(95)01142-0.
6. Maira M, etal., Mol Cell Biol. 1999 Nov;19(11):7549-57.
7. Martens C, etal., Mol Endocrinol. 2005 Apr;19(4):885-97. Epub 2004 Dec 9.
8. MGD data from the GO Consortium
9. Milbrandt J Neuron 1988 May;1(3):183-8.
10. NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. Pipeline to import KEGG annotations from KEGG into RGD
12. Rambaud J, etal., J Biol Chem. 2009 May 22;284(21):14147-56. doi: 10.1074/jbc.M809023200. Epub 2009 Mar 25.
13. RGD automated data pipeline
14. RGD automated import pipeline for gene-chemical interactions
15. Rouillard C, etal., Exp Neurol. 2018 Jun;304:143-153. doi: 10.1016/j.expneurol.2018.03.008. Epub 2018 Mar 9.
16. Shakib K, etal., Proteomics. 2005 Jul;5(11):2819-38.
17. Tessem JS, etal., Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5242-7. doi: 10.1073/pnas.1320953111. Epub 2014 Mar 24.
18. Westbrook L, etal., J Am Soc Nephrol. 2014 Nov;25(11):2499-510. doi: 10.1681/ASN.2013070786. Epub 2014 Apr 10.
19. Xu JH, etal., Cell Tissue Res. 2006 Oct;326(1):159-68. doi: 10.1007/s00441-006-0214-4. Epub 2006 May 31.
Additional References at PubMed
PMID:1314418   PMID:8227042   PMID:8395013   PMID:8961274   PMID:9155013   PMID:10331876   PMID:12030839   PMID:12477932   PMID:12770726   PMID:12815108   PMID:14657025   PMID:14769794  
PMID:15016657   PMID:15155786   PMID:15358368   PMID:15486232   PMID:15525348   PMID:15701640   PMID:15707695   PMID:15716272   PMID:16951544   PMID:17032584   PMID:17416458   PMID:17434920  
PMID:17550977   PMID:18059339   PMID:18163434   PMID:18292087   PMID:18388149   PMID:18945812   PMID:18987158   PMID:18996961   PMID:19150624   PMID:19270309   PMID:19359610   PMID:19412742  
PMID:19447175   PMID:19789410   PMID:20375114   PMID:20411306   PMID:21048074   PMID:21357543   PMID:21442465   PMID:21505978   PMID:21908547   PMID:22097717   PMID:22128883   PMID:22147266  
PMID:22427340   PMID:22525717   PMID:23028064   PMID:23197407   PMID:23663895   PMID:24047441   PMID:24584059   PMID:24680679   PMID:24737679   PMID:25957997   PMID:26003139   PMID:26008781  
PMID:26195821   PMID:26276525   PMID:26465200   PMID:26497037   PMID:26498924   PMID:26884829   PMID:27221116   PMID:27765761   PMID:29295823   PMID:29850786   PMID:30006349   PMID:31273046  
PMID:31939452   PMID:31993850   PMID:32919804   PMID:33562500  


Genomics

Comparative Map Data
Nr4a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27132,368,399 - 132,389,300 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7132,374,840 - 132,389,297 (+)Ensembl
Rnor_6.07142,899,358 - 142,920,216 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,905,758 - 142,920,216 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07140,700,242 - 140,721,073 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47140,012,807 - 140,020,590 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17140,089,243 - 140,097,024 (+)NCBI
Celera7128,846,928 - 128,854,640 (+)NCBICelera
Cytogenetic Map7q36NCBI
NR4A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1252,022,832 - 52,059,507 (+)EnsemblGRCh38hg38GRCh38
GRCh381252,022,832 - 52,059,507 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371252,416,616 - 52,453,287 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361250,731,458 - 50,739,554 (+)NCBINCBI36hg18NCBI36
Build 341250,723,762 - 50,736,019NCBI
Celera1251,247,867 - 51,255,961 (+)NCBI
Cytogenetic Map12q13.13NCBI
HuRef1249,449,770 - 49,486,519 (+)NCBIHuRef
CHM1_11252,382,884 - 52,419,560 (+)NCBICHM1_1
Nr4a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915101,151,788 - 101,172,676 (+)NCBIGRCm39mm39
GRCm39 Ensembl15101,152,150 - 101,172,676 (+)Ensembl
GRCm3815101,253,902 - 101,274,795 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15101,254,269 - 101,274,795 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715101,097,277 - 101,105,226 (+)NCBIGRCm37mm9NCBIm37
MGSCv3615101,094,896 - 101,102,826 (+)NCBImm8
Celera15103,414,983 - 103,422,853 (+)NCBICelera
Cytogenetic Map15F1NCBI
Nr4a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555472,404,532 - 2,431,050 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555472,404,532 - 2,426,882 (+)NCBIChiLan1.0ChiLan1.0
NR4A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11237,480,300 - 37,498,290 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1237,480,300 - 37,501,188 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01236,703,903 - 36,740,211 (-)NCBIMhudiblu_PPA_v0panPan3
NR4A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1272,947,729 - 2,965,045 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl272,891,053 - 2,955,655 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2743,300,499 - 43,308,433 (+)NCBI
ROS_Cfam_1.0272,944,790 - 2,966,939 (-)NCBI
UMICH_Zoey_3.1272,961,332 - 2,969,256 (-)NCBI
UNSW_CanFamBas_1.0272,947,820 - 2,955,733 (-)NCBI
UU_Cfam_GSD_1.02743,698,715 - 43,706,655 (+)NCBI
Nr4a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494563,656,496 - 63,678,740 (-)NCBI
SpeTri2.0NW_0049365129,486,096 - 9,508,338 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NR4A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11148,208,354 - 48,232,857 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1148,208,587 - 48,233,063 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037197,859,302 - 197,884,070 (-)NCBIVero_WHO_p1.0
Nr4a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624816271,345 - 288,265 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat


Genetic Models
This gene Nr4a1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:337
Count of miRNA genes:193
Interacting mature miRNAs:217
Transcripts:ENSRNOT00000010171
Prediction methods:Microtar, Miranda, Rnahybrid
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 4 7 5 2 5 17 9 5 2
Low 2 39 36 27 14 27 6 6 57 35 32 6 6
Below cutoff 14 14 14

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010171   ⟹   ENSRNOP00000010171
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7132,381,391 - 132,389,297 (+)Ensembl
Rnor_6.0 Ensembl7142,912,316 - 142,920,216 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078663   ⟹   ENSRNOP00000070558
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7132,374,840 - 132,385,097 (+)Ensembl
Rnor_6.0 Ensembl7142,905,758 - 142,916,017 (+)Ensembl
RefSeq Acc Id: NM_024388   ⟹   NP_077364
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,381,391 - 132,389,300 (+)NCBI
Rnor_6.07142,912,309 - 142,920,216 (+)NCBI
Rnor_5.07140,700,242 - 140,721,073 (+)NCBI
RGSC_v3.47140,012,807 - 140,020,590 (+)RGD
Celera7128,846,928 - 128,854,640 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006242358   ⟹   XP_006242420
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,374,841 - 132,389,300 (+)NCBI
Rnor_6.07142,905,064 - 142,920,216 (+)NCBI
Rnor_5.07140,700,242 - 140,721,073 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595130   ⟹   XP_017450619
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,368,399 - 132,389,300 (+)NCBI
Rnor_6.07142,899,358 - 142,920,216 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_077364   ⟸   NM_024388
- UniProtKB: P22829 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242420   ⟸   XM_006242358
- Peptide Label: isoform X1
- UniProtKB: P22829 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017450619   ⟸   XM_017595130
- Peptide Label: isoform X1
- UniProtKB: P22829 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010171   ⟸   ENSRNOT00000010171
RefSeq Acc Id: ENSRNOP00000070558   ⟸   ENSRNOT00000078663
Protein Domains
NR LBD

Transcriptome

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

Promoters
RGD ID:13695673
Promoter ID:EPDNEW_R6191
Type:single initiation site
Name:Nr4a1_2
Description:nuclear receptor subfamily 4, group A, member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6192  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07142,905,759 - 142,905,819EPDNEW
RGD ID:13695667
Promoter ID:EPDNEW_R6192
Type:multiple initiation site
Name:Nr4a1_1
Description:nuclear receptor subfamily 4, group A, member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6191  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07142,912,303 - 142,912,363EPDNEW

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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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

Database Acc Id Source(s)
AGR Gene RGD:620029 AgrOrtholog
Ensembl Genes ENSRNOG00000007607 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010171 UniProtKB/Swiss-Prot
  ENSRNOP00000070558 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010171 UniProtKB/Swiss-Prot
  ENSRNOT00000078663 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot
  3.30.50.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7458540 IMAGE-MGC_LOAD
InterPro NHR-like_dom_sf UniProtKB/Swiss-Prot
  Nuc_orp_HMR_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuc_orph_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot
  Nuclear_hrmn_rcpt UniProtKB/Swiss-Prot
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot
  Znf_NHR/GATA UniProtKB/Swiss-Prot
KEGG Report rno:79240 UniProtKB/Swiss-Prot
MGC_CLONE MGC:114310 IMAGE-MGC_LOAD
NCBI Gene 79240 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot
  zf-C4 UniProtKB/Swiss-Prot
PhenoGen Nr4a1 PhenoGen
PRINTS HMRNUCRECPTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEARECPTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STRDHORMONER UniProtKB/Swiss-Prot
  STROIDFINGER UniProtKB/Swiss-Prot
PROSITE NR_LBD UniProtKB/Swiss-Prot
  NUCLEAR_REC_DBD_1 UniProtKB/Swiss-Prot
  NUCLEAR_REC_DBD_2 UniProtKB/Swiss-Prot
SMART HOLI UniProtKB/Swiss-Prot
  ZnF_C4 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot
UniProt A0A0G2JY86_RAT UniProtKB/TrEMBL
  NR4A1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q4V8M4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Nr4a1  nuclear receptor subfamily 4, group A, member 1    immediate early gene transcription factor NGFI-B  Name updated 1299863 APPROVED
2002-08-07 Nr4a1  immediate early gene transcription factor NGFI-B      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation expression is induced by NGF in PC12 cells 728970