Nr1d1 (nuclear receptor subfamily 1, group D, member 1) - Rat Genome Database

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Gene: Nr1d1 (nuclear receptor subfamily 1, group D, member 1) Rattus norvegicus
Analyze
Symbol: Nr1d1
Name: nuclear receptor subfamily 1, group D, member 1
RGD ID: 628827
Description: Exhibits transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including photoperiodism; positive regulation of circadian rhythm; and regulation of hepatic stellate cell activation. Localizes to cytoplasm; dendrite; and neuronal cell body. Biomarker of hyperthyroidism; hypothyroidism; portal hypertension; and type 2 diabetes mellitus. Orthologous to human NR1D1 (nuclear receptor subfamily 1 group D member 1); INTERACTS WITH 1,2,4-trimethylbenzene; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: EAR-1; nuclear receptor subfamily 1 group D member 1; rev-erb alpha; rev-erbA-alpha; REV-ERBAALPHA; V-erbA-related protein 1; V-erbA-related protein EAR-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21083,728,348 - 83,735,562 (-)NCBI
Rnor_6.0 Ensembl1086,683,875 - 86,690,815 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01086,683,875 - 86,690,815 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01086,479,868 - 86,486,808 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41087,541,246 - 87,548,186 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11087,555,629 - 87,560,471 (-)NCBI
Celera1082,476,555 - 82,483,495 (-)NCBICelera
Cytogenetic Map10q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-amino-4,6-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
aristolochic acid  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[ghi]perylene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
cefaloridine  (EXP)
CGS-21680  (ISO)
chenodeoxycholic acid  (ISO)
chloroprene  (EXP,ISO)
chrysene  (ISO)
clofibrate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
cypermethrin  (ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dichloroacetic acid  (ISO)
dichloromethane  (ISO)
dicrotophos  (ISO)
diethyl maleate  (EXP)
dioxygen  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenvalerate  (EXP)
fluoranthene  (ISO)
folic acid  (ISO)
furan  (EXP)
genistein  (ISO)
geraniol  (ISO)
haloperidol  (EXP)
hexachlorobenzene  (EXP)
hyaluronic acid  (ISO)
hypochlorous acid  (ISO)
indole-3-methanol  (EXP)
ketamine  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
lithium atom  (ISO)
lithium hydride  (ISO)
luteolin  (ISO)
manganese(II) chloride  (EXP)
metformin  (EXP)
methotrexate  (ISO)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
naphthalenes  (EXP)
nevirapine  (EXP)
orphenadrine  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
phenformin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
prednisolone  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
progesterone  (EXP)
propiconazole  (ISO)
quercetin  (EXP)
raloxifene  (ISO)
resveratrol  (EXP)
rotenone  (EXP)
SCH-351591  (EXP)
scopolamine  (EXP)
sevoflurane  (EXP)
silicon dioxide  (EXP,ISO)
simvastatin  (ISO)
sodium dichromate  (ISO)
streptozocin  (EXP)
styrene  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
titanium dioxide  (EXP,ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
undecane  (EXP)
urethane  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell differentiation  (IBA)
cellular glucose homeostasis  (IEA,ISO,ISS)
cellular response to interleukin-1  (IEA,ISO,ISS)
cellular response to lipopolysaccharide  (IEA,ISO)
cellular response to tumor necrosis factor  (IEA,ISO,ISS)
cholesterol homeostasis  (IEA,ISO,ISS)
circadian regulation of gene expression  (IEA,ISO,ISS)
circadian rhythm  (IEP,ISO)
circadian temperature homeostasis  (IEA,ISO,ISS)
glycogen biosynthetic process  (IEA,ISO,ISS)
hormone-mediated signaling pathway  (IBA)
intracellular receptor signaling pathway  (IEA)
negative regulation of astrocyte activation  (IEA,ISO,ISS)
negative regulation of cold-induced thermogenesis  (ISO,ISS)
negative regulation of I-kappaB kinase/NF-kappaB signaling  (IEA,ISO,ISS)
negative regulation of inflammatory response  (ISO,ISS)
negative regulation of microglial cell activation  (IEA,ISO,ISS)
negative regulation of neuroinflammatory response  (ISO,ISS)
negative regulation of toll-like receptor 4 signaling pathway  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IBA,IEA,ISO)
negative regulation of transcription, DNA-templated  (ISO,ISS)
photoperiodism  (IEP)
positive regulation of bile acid biosynthetic process  (IEA,ISO,ISS)
positive regulation of circadian rhythm  (IDA)
positive regulation of transcription by RNA polymerase II  (IBA)
positive regulation of transcription, DNA-templated  (IDA,IEA,ISO)
proteasomal protein catabolic process  (IEA,ISO,ISS)
protein destabilization  (IEA,ISO,ISS)
regulation of circadian rhythm  (IDA,ISO)
regulation of circadian sleep/wake cycle  (IEA,ISO,ISS)
regulation of fat cell differentiation  (IEA,ISO,ISS)
regulation of hepatic stellate cell activation  (IDA)
regulation of insulin secretion involved in cellular response to glucose stimulus  (IEA,ISO,ISS)
regulation of lipid metabolic process  (ISO,ISS)
regulation of transcription, DNA-templated  (IEA,ISO)
regulation of type B pancreatic cell proliferation  (IEA,ISO,ISS)
response to leptin  (IBA,IEA,ISO,ISS)

Cellular Component
chromatin  (IEA,ISO)
cytoplasm  (IDA,IEA,ISO,ISS)
dendrite  (IDA,ISO,ISS)
dendritic spine  (IEA,ISO,ISS)
neuronal cell body  (IDA)
nuclear body  (IEA,ISO)
nucleus  (IEA,ISO,ISS)

References

References - curated
1. Chen H, etal., Biochem Biophys Res Commun. 2012 Apr 6;420(2):374-9. doi: 10.1016/j.bbrc.2012.02.164. Epub 2012 Mar 8.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Gerhart-Hines Z, etal., Nature. 2013 Nov 21;503(7476):410-413. doi: 10.1038/nature12642. Epub 2013 Oct 27.
4. GOA data from the GO Consortium
5. Harding HP and Lazar MA, Mol Cell Biol. 1993 May;13(5):3113-21.
6. Hu J and Wang C, Nan Fang Yi Ke Da Xue Xue Bao. 2013 Oct;33(10):1544-6.
7. Jannini EA, etal., Biochem Biophys Res Commun. 1992 Apr 30;184(2):739-45.
8. Lazar MA, etal., Mol Cell Biol 1989 Mar;9(3):1128-36.
9. Li T, etal., Hepatology. 2014 Jun;59(6):2383-96. doi: 10.1002/hep.27049. Epub 2014 Apr 29.
10. Medici M, etal., Thyroid. 2012 Nov;22(11):1181-6. doi: 10.1089/thy.2012.0198. Epub 2012 Oct 19.
11. Meng QJ, etal., J Cell Sci. 2008 Nov 1;121(Pt 21):3629-35. doi: 10.1242/jcs.035048.
12. MGD data from the GO Consortium
13. RGD automated data pipeline
14. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. RGD automated import pipeline for gene-chemical interactions
16. Spanjaard RA, etal., Mol Endocrinol. 1994 Mar;8(3):286-95.
17. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
18. Szantoova K, etal., Mol Cell Biochem. 2011 Feb;348(1-2):53-60. doi: 10.1007/s11010-010-0636-x. Epub 2010 Nov 14.
19. Valnegri P, etal., Nat Neurosci. 2011 Aug 28;14(10):1293-301. doi: 10.1038/nn.2911.
20. Zhang R, etal., Am J Physiol Regul Integr Comp Physiol. 2013 Jul 15;305(2):R134-46. doi: 10.1152/ajpregu.00520.2012. Epub 2013 May 1.
Additional References at PubMed
PMID:7838158   PMID:8622974   PMID:12150932   PMID:12821652   PMID:14645221   PMID:15761026   PMID:18006707   PMID:18227153   PMID:18511497   PMID:18565334   PMID:19721697   PMID:19955433  
PMID:20070857   PMID:20159955   PMID:20424134   PMID:21628546   PMID:21952132   PMID:22166979   PMID:23398316   PMID:24030830   PMID:24355794   PMID:24794873   PMID:25588874   PMID:25648833  
PMID:26102301   PMID:26811051   PMID:27686098   PMID:29508494   PMID:29533925   PMID:29653076   PMID:30096135   PMID:30555544   PMID:30792350  


Genomics

Comparative Map Data
Nr1d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21083,728,348 - 83,735,562 (-)NCBI
Rnor_6.0 Ensembl1086,683,875 - 86,690,815 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01086,683,875 - 86,690,815 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01086,479,868 - 86,486,808 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41087,541,246 - 87,548,186 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11087,555,629 - 87,560,471 (-)NCBI
Celera1082,476,555 - 82,483,495 (-)NCBICelera
Cytogenetic Map10q31NCBI
NR1D1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1740,092,793 - 40,100,589 (-)EnsemblGRCh38hg38GRCh38
GRCh381740,092,793 - 40,100,589 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371738,249,046 - 38,256,842 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361735,502,567 - 35,510,499 (-)NCBINCBI36hg18NCBI36
Build 341735,502,566 - 35,510,499NCBI
Celera1734,909,147 - 34,917,084 (-)NCBI
Cytogenetic Map17q21.1NCBI
HuRef1734,042,773 - 34,050,715 (-)NCBIHuRef
CHM1_11738,484,740 - 38,492,682 (-)NCBICHM1_1
Nr1d1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391198,658,758 - 98,666,233 (-)NCBIGRCm39mm39
GRCm39 Ensembl1198,658,758 - 98,666,159 (-)Ensembl
GRCm381198,767,932 - 98,775,377 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1198,767,932 - 98,775,333 (-)EnsemblGRCm38mm10GRCm38
MGSCv371198,629,249 - 98,636,556 (-)NCBIGRCm37mm9NCBIm37
MGSCv361198,584,022 - 98,590,912 (-)NCBImm8
Celera11108,422,591 - 108,429,908 (-)NCBICelera
Cytogenetic Map11DNCBI
Nr1d1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545114,742,735 - 14,750,999 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545114,743,763 - 14,750,903 (-)NCBIChiLan1.0ChiLan1.0
NR1D1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11717,409,669 - 17,417,600 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1717,409,669 - 17,417,600 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01717,188,390 - 17,196,315 (+)NCBIMhudiblu_PPA_v0panPan3
NR1D1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1922,461,556 - 22,469,243 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl922,461,705 - 22,469,053 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha921,933,902 - 21,941,575 (+)NCBI
ROS_Cfam_1.0923,254,745 - 23,262,432 (+)NCBI
UMICH_Zoey_3.1922,028,188 - 22,035,862 (+)NCBI
UNSW_CanFamBas_1.0922,287,169 - 22,294,857 (+)NCBI
UU_Cfam_GSD_1.0922,411,920 - 22,419,594 (+)NCBI
Nr1d1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560221,861,286 - 21,868,939 (+)NCBI
SpeTri2.0NW_00493649015,206,194 - 15,213,858 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NR1D1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1222,263,657 - 22,271,643 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11222,263,549 - 22,274,131 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
NR1D1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11666,078,990 - 66,086,927 (+)NCBI
ChlSab1.1 Ensembl1666,079,089 - 66,090,685 (+)Ensembl
Nr1d1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247953,102,424 - 3,109,497 (+)NCBI

Position Markers
RH133144  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,729,162 - 83,729,353 (+)MAPPER
Rnor_6.01086,684,690 - 86,684,880NCBIRnor6.0
Rnor_5.01086,480,683 - 86,480,873UniSTSRnor5.0
RGSC_v3.41087,542,061 - 87,542,251UniSTSRGSC3.4
Celera1082,477,370 - 82,477,560UniSTS
RH 3.4 Map10858.6UniSTS
Cytogenetic Map10q31UniSTS
AW259572  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,729,114 - 83,729,206 (+)MAPPER
Rnor_6.01086,684,642 - 86,684,733NCBIRnor6.0
Rnor_5.01086,480,635 - 86,480,726UniSTSRnor5.0
RGSC_v3.41087,542,013 - 87,542,104UniSTSRGSC3.4
Celera1082,477,322 - 82,477,413UniSTS
Cytogenetic Map10q31UniSTS
BF387429  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,732,373 - 83,732,559 (+)MAPPER
Rnor_6.01086,687,901 - 86,688,086NCBIRnor6.0
Rnor_5.01086,483,894 - 86,484,079UniSTSRnor5.0
RGSC_v3.41087,545,272 - 87,545,457UniSTSRGSC3.4
Celera1082,480,581 - 82,480,766UniSTS
RH 3.4 Map10876.09UniSTS
Cytogenetic Map10q31UniSTS
D17S1644E  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,729,253 - 83,729,324 (+)MAPPER
Rnor_6.01086,684,781 - 86,684,851NCBIRnor6.0
Rnor_5.01086,480,774 - 86,480,844UniSTSRnor5.0
RGSC_v3.41087,542,152 - 87,542,222UniSTSRGSC3.4
Celera1082,477,461 - 82,477,531UniSTS
Cytogenetic Map10q31UniSTS
MARC_5497-5498:996690469:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,728,799 - 83,729,539 (+)MAPPER
Rnor_6.01086,684,327 - 86,685,066NCBIRnor6.0
Rnor_5.01086,480,320 - 86,481,059UniSTSRnor5.0
RGSC_v3.41087,541,698 - 87,542,437UniSTSRGSC3.4
Celera1082,477,007 - 82,477,746UniSTS
Cytogenetic Map10q31UniSTS
RH125185  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,728,377 - 83,728,548 (+)MAPPER
Rnor_6.01086,683,905 - 86,684,075NCBIRnor6.0
Rnor_5.01086,479,898 - 86,480,068UniSTSRnor5.0
RGSC_v3.41087,541,276 - 87,541,446UniSTSRGSC3.4
Celera1082,476,585 - 82,476,755UniSTS
Cytogenetic Map10q31UniSTS
NR1D1_2626  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,728,163 - 83,728,854 (+)MAPPER
Rnor_6.01086,683,691 - 86,684,381NCBIRnor6.0
Rnor_5.01086,479,684 - 86,480,374UniSTSRnor5.0
RGSC_v3.41087,541,062 - 87,541,752UniSTSRGSC3.4
Celera1082,476,371 - 82,477,061UniSTS
Cytogenetic Map10q31UniSTS
THRA_2263  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,728,582 - 83,729,339 (+)MAPPER
Rnor_6.01086,684,110 - 86,684,866NCBIRnor6.0
Rnor_5.01086,480,103 - 86,480,859UniSTSRnor5.0
RGSC_v3.41087,541,481 - 87,542,237UniSTSRGSC3.4
Celera1082,476,790 - 82,477,546UniSTS
Cytogenetic Map10q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1041260363106105607Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104370495588704955Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104659302198939209Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104684834691848346Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104684834691848346Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104684834691848346Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)105063833795638337Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105310471898104718Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105362581598939209Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105363748594807701Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)1055224855100224855Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)1055679084102427604Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1056698730101698730Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1060450007105450007Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1060875260105875260Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1060875260105875260Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1060875260105875260Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1062096293107096293Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)1064648175101691360Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1064648175102149713Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1064648175102149713Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1069123603101482600Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107504539197308358Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)107705574186962563Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107705574198282519Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107834302790042115Rat
2325836Bp346Blood pressure QTL 3460.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027986962563Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027998282519Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1078970279112626471Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1079927661112626471Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1080239190112626471Rat
724516Uae17Urinary albumin excretion QTL 173.6urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)108094611088200662Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1081515116101758478Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)108164977590297007Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)108267523388141097Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108338982894488181Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1083389828104994768Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1085079943112626471Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108551382295638337Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1086566908112626471Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:187
Count of miRNA genes:98
Interacting mature miRNAs:104
Transcripts:ENSRNOT00000012537, ENSRNOT00000055333
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 3 17 15 5 6 5 7 10 29 15 14 11 7
Low 26 36 30 13 30 1 1 45 20 27 1
Below cutoff 6 6 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012537   ⟹   ENSRNOP00000012537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1086,683,875 - 86,690,815 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000055333   ⟹   ENSRNOP00000052200
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1086,683,875 - 86,688,730 (-)Ensembl
RefSeq Acc Id: NM_001113422   ⟹   NP_001106893
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,728,348 - 83,735,562 (-)NCBI
Rnor_6.01086,683,875 - 86,690,815 (-)NCBI
Rnor_5.01086,479,868 - 86,486,808 (-)NCBI
RGSC_v3.41087,541,246 - 87,548,186 (-)RGD
Celera1082,476,555 - 82,483,495 (-)RGD
Sequence:
RefSeq Acc Id: NM_145775   ⟹   NP_665718
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,728,348 - 83,733,204 (-)NCBI
Rnor_6.01086,683,875 - 86,688,730 (-)NCBI
Rnor_5.01086,479,868 - 86,486,808 (-)NCBI
RGSC_v3.41087,541,246 - 87,548,186 (-)RGD
Celera1082,476,555 - 82,481,410 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_665718   ⟸   NM_145775
- Peptide Label: isoform 2
- UniProtKB: Q63503 (UniProtKB/Swiss-Prot),   G3V9L8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001106893   ⟸   NM_001113422
- Peptide Label: isoform 1
- Sequence:
RefSeq Acc Id: ENSRNOP00000052200   ⟸   ENSRNOT00000055333
RefSeq Acc Id: ENSRNOP00000012537   ⟸   ENSRNOT00000012537
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13697671
Promoter ID:EPDNEW_R8195
Type:single initiation site
Name:Nr1d1_1
Description:nuclear receptor subfamily 1, group D, member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01086,690,773 - 86,690,833EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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
BBDP/Wor (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
BN/SsN (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
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)
F344/NCrl (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
F344/NRrrc (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
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)
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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
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 (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/NCrlBR (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
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
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
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
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
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)
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 (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
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)
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: 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)
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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
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 (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 (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 (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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 86480422 86480423 G T snv SBH/Ygl (MCW), MR/N (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), IS-Tlk/Kyo (KyushuU), LEW/NCrl (KNAW), IS/Kyo (KyushuU), HTX/Kyo (KyushuU), LEW/Crl (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 86684429 86684430 G T snv SBH/Ygl (MCW), MR/N (MCW), SBH/Ygl (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), BBDP/Wor (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 87541800 87541801 G T snv MR/N (KNAW), BBDP/WorN (ICL), SBH/Ygl (ICL), LEW/NCrl (ICL), LEW/Crl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628827 AgrOrtholog
Ensembl Genes ENSRNOG00000009329 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012537 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000052200 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012537 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000055333 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5598020 IMAGE-MGC_LOAD
InterPro NHR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:252917 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72288 IMAGE-MGC_LOAD
NCBI Gene 252917 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nr1d1 PhenoGen
PRINTS STRDHORMONER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V770_RAT UniProtKB/TrEMBL
  G3V9L8 ENTREZGENE, UniProtKB/TrEMBL
  NR1D1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6P6S7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Nr1d1  nuclear receptor subfamily 1, group D, member 1      Symbol and Name status set to approved 625702 APPROVED
2003-02-27 Nr1d1  nuclear receptor subfamily 1, group D, member 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression highly expressed in skeletal muscle and brown fat 728950
gene_other gene overlaps with r-erbA alpha-2 gene 728950