Nr1i3 (nuclear receptor subfamily 1, group I, member 3) - Rat Genome Database

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Gene: Nr1i3 (nuclear receptor subfamily 1, group I, member 3) Rattus norvegicus
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Symbol: Nr1i3
Name: nuclear receptor subfamily 1, group I, member 3
RGD ID: 621400
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and nuclear receptor activity. Involved in osteoblast differentiation. Located in cytoplasm and nucleus. Biomarker of cholestasis. Orthologous to human NR1I3 (nuclear receptor subfamily 1 group I member 3); INTERACTS WITH (+)-artemisinin; 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 1,1,1-Trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CAR; constitutive androstane receptor; MGC108525; nuclear receptor constitutive active receptor; nuclear receptor subfamily 1 group I member 3; strain Fischer nuclear receptor (CAR)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Nr1i3em1Sage  
Genetic Models: SD-Nr1i2em1Sage Nr1i3em1Sage SD-Nr1i2em1Sage Nr1i3em1Sage Ahrem1Sage SD-Nr1i3em1Sage
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21383,632,940 - 83,638,193 (+)NCBI
Rnor_6.0 Ensembl1389,586,283 - 89,591,277 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01389,585,072 - 89,591,278 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01394,211,961 - 94,218,143 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41387,104,241 - 87,108,563 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11387,292,773 - 87,297,730 (+)NCBI
Celera1383,264,145 - 83,269,088 (+)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-artemisinin  (EXP,ISO)
(-)-anisomycin  (ISO)
(E)-azobenzene  (ISO)
(E,E)-germacrone  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,1,1-Trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dihydrostilbene  (ISO)
1,3-Diphenylpropane  (ISO)
1,4-dichlorobenzene  (ISO)
1-\{2-[(4-chlorobenzyl)sulfanyl]-2-(2,4-dichlorophenyl)ethyl\}-1H-imidazole  (ISO)
1-Amino-2,4-dibromoanthraquinone  (ISO)
1-benzofuran  (ISO)
1-benzylpiperazine  (EXP)
1-Hydroxypyrene  (ISO)
1-naphthol  (EXP)
1-naphthyl isothiocyanate  (ISO)
1-tert-Butoxy-2-propanol  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP,ISO)
2,2'-Dihydroxy-4-methoxybenzophenone  (ISO)
2,2-(2-Chlorophenyl-4'-chlorophenyl)-1,1-dichloroethene  (ISO)
2,3',5-trichlorobiphenyl  (ISO)
2,3,3',4,4',5-Hexachlorobiphenyl  (ISO)
2,3,4,3',4'-Pentachlorobiphenyl  (ISO)
2,3,4,4'-tetrachlorobiphenyl  (ISO)
2,3,4,5-Tetrachloro-4'-biphenylol  (ISO)
2,3,4,5-tetrachlorobiphenyl  (ISO)
2,3,5,6-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4'-dichlorobiphenyl  (ISO)
2,4,4',6-tetrachlorobiphenyl  (ISO)
2,4-Dihydroxybenzophenone  (ISO)
2,4-dinitrotoluene  (EXP)
2,5-dichlorobiphenyl  (ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-(tert-butylimino)-5-phenyl-3-(propan-2-yl)-1,3,5-thiadiazinan-4-one  (ISO)
2-chlorobiphenyl  (ISO)
2-Hydroxy-2',3',4',5,5'-pentachlorobiphenyl  (ISO)
2-hydroxypropanoic acid  (ISO)
2-tert-butylhydroquinone  (ISO)
2-tert-Butylphenol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP,ISO)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3,6-diaminoacridine  (ISO)
3-chlorobiphenyl  (ISO)
3-methylcholanthrene  (EXP,ISO)
3-Pentadecylphenol  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-ethylphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-nitrophenol  (ISO)
4-nonylphenol  (ISO)
4-octylphenol  (ISO)
4-tert-butylphenol  (ISO)
4-tert-Octylphenol  (ISO)
5,6,7,8-tetrahydro-2-naphthol  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP,ISO)
5alpha-androst-16-en-3alpha-ol  (ISO)
5alpha-pregnane-3,20-dione  (ISO)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (EXP,ISO)
6-propyl-2-thiouracil  (EXP,ISO)
8-(4-chlorophenylthio)-cAMP  (ISO)
8-Br-cAMP  (ISO)
9-cis-retinal  (ISO)
9-cis-retinoic acid  (ISO)
acenaphthene  (ISO)
acetamide  (EXP)
acetic acid [2-[[(5-nitro-2-thiazolyl)amino]-oxomethyl]phenyl] ester  (ISO)
acifluorfen  (ISO)
aclonifen  (ISO)
aflatoxin B1  (ISO)
AICA ribonucleotide  (EXP)
alachlor  (ISO)
aldehydo-D-glucose  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (ISO)
allethrin  (ISO)
allyl isothiocyanate  (ISO)
alpha-naphthoflavone  (EXP)
amiodarone  (EXP)
ammonium chloride  (EXP)
androst-4-ene-3,17-dione  (ISO)
androstane  (ISO)
androstane-3,17-diol  (ISO)
anthracene  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
artemether  (ISO)
artemotil  (ISO)
aspartame  (ISO)
atazanavir sulfate  (ISO)
atorvastatin calcium  (EXP,ISO)
azobenzene  (ISO)
baicalein  (ISO)
benfuracarb  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzophenone  (ISO)
Benzyl parahydroxybenzoate  (ISO)
berberine  (ISO)
bergomottin  (ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP,ISO)
bezafibrate  (EXP)
bilirubin IXalpha  (ISO)
bioresmethrin  (EXP)
biphenyl  (ISO)
biphenyl-2-ol  (ISO)
biphenyl-4-ol  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (ISO)
bisphenol A dimethacrylate  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
Bromophos-ethyl  (ISO)
bromothymol blue  (ISO)
bromuconazole  (EXP)
bupirimate  (ISO)
buprofezin  (ISO)
bupropion  (ISO)
Butamifos  (ISO)
butylated hydroxyanisole  (ISO)
Butylbenzyl phthalate  (ISO)
Butylparaben  (EXP)
cadmium atom  (ISO)
calcipotriol  (ISO)
captan  (ISO)
carbamazepine  (EXP,ISO)
carbaryl  (EXP)
carbon nanotube  (ISO)
carbosulfan  (ISO)
cefuroxime  (ISO)
cerivastatin  (EXP,ISO)
chenodeoxycholic acid  (ISO)
Chlomethoxyfen  (ISO)
chlormidazole  (ISO)
chlornitrofen  (ISO)
chlorpromazine  (ISO)
chlorpyrifos  (ISO)
chlorpyrifos-methyl  (ISO)
cholesterol  (ISO)
chromium(6+)  (ISO)
chrysin  (ISO)
ciguatoxin CTX1B  (ISO)
cimetidine  (ISO)
ciprofibrate  (EXP,ISO)
clemizole  (ISO)
clofibrate  (EXP,ISO)
clopidogrel  (ISO)
clotrimazole  (EXP,ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
cobicistat  (ISO)
cocaine  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (ISO)
crotamiton  (ISO)
cyclobutanes  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cypermethrin  (ISO)
cyproconazole  (ISO)
cyproterone acetate  (ISO)
D-glucose  (ISO)
DDD  (ISO)
DDE  (EXP,ISO)
DDT  (ISO)
decabromodiphenyl ether  (EXP,ISO)
deoxycholic acid  (ISO)
dexamethasone  (EXP,ISO)
Di-n-hexyl phthalate  (ISO)
Diallyl sulfide  (EXP,ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP,ISO)
Dichlofenthion  (ISO)
diclofenac  (ISO)
dicofol  (ISO)
Dicyclohexyl phthalate  (ISO)
dieldrin  (ISO)
dienestrol  (ISO)
diethyl phthalate  (ISO)
diethylstilbestrol  (ISO)
difenoconazole  (ISO)
diiodine  (ISO)
diisobutyl phthalate  (ISO)
diisononyl phthalate  (ISO)
Dimethametryn  (ISO)
Dimethyl phthalate  (ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (ISO)
dipentyl phthalate  (ISO)
Diphenamid  (ISO)
diphenhydramine  (ISO)
diphenyl ether  (ISO)
dipropyl phthalate  (ISO)
doxorubicin  (ISO)
doxylamine  (ISO)
drometrizole  (ISO)
edifenphos  (ISO)
efavirenz  (EXP,ISO)
ellagic acid  (ISO)
endosulfan  (ISO)
endrin  (ISO)
enilconazole  (ISO)
enzacamene  (ISO)
EPN  (ISO)
epoxiconazole  (ISO)
erlotinib hydrochloride  (ISO)
estrone  (EXP,ISO)
ethanol  (EXP,ISO)
ethion  (ISO)
etofenprox  (EXP,ISO)
etoposide  (ISO)
everolimus  (ISO)
fenofibrate  (EXP,ISO)
fenoxycarb  (ISO)
fenvalerate  (EXP,ISO)
fipronil  (ISO)
flavanone  (ISO)
flavone  (ISO)
flavonoids  (EXP)
fluazifop-butyl  (ISO)
fluconazole  (ISO)
fludioxonil  (ISO)
fluoranthene  (ISO)
fluorene  (ISO)
fluvastatin  (EXP,ISO)
folpet  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
furathiocarb  (ISO)
galangin  (ISO)
gamma-hexachlorocyclohexane  (EXP,ISO)
gemfibrozil  (ISO)
glafenine  (EXP)
glucose  (ISO)
glutathione  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycogen  (ISO)
guggulsterone  (ISO)
GW 4064  (ISO)
GW 7647  (EXP,ISO)
heptachlor  (ISO)
Heptachlor epoxide  (ISO)
herbicide  (ISO)
hexachlorobenzene  (ISO)
hexestrol  (ISO)
imidazoles  (EXP,ISO)
imperatorin  (ISO)
indole-3-methanol  (ISO)
iprobenfos  (ISO)
isofenphos  (ISO)
isoniazide  (ISO)
isopimpinellin  (ISO)
isoxazoles  (ISO)
kaempferol  (ISO)
ketoconazole  (ISO)
kojic acid  (EXP)
L-ethionine  (EXP)
lactacystin  (ISO)
Lasiocarpine  (ISO)
leflunomide  (EXP,ISO)
leptophos  (ISO)
Licochalcone B  (ISO)
lipopolysaccharide  (ISO)
lithocholic acid  (ISO)
loperamide  (ISO)
malathion  (ISO)
MC-4379  (ISO)
Meclizine  (EXP,ISO)
metformin  (EXP)
methapyrilene  (EXP,ISO)
methotrexate  (EXP)
methoxychlor  (EXP,ISO)
metoprolol  (ISO)
metyrapone  (ISO)
miconazole  (EXP,ISO)
midazolam  (ISO)
mifepristone  (ISO)
Mitotane  (ISO)
molinate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monobenzyl phthalate  (ISO)
monocrotophos  (ISO)
monoethyl phthalate  (ISO)
Monomethyl phenylphosphonate  (ISO)
monosodium L-glutamate  (ISO)
N,N-dimethyl-3-phenyl-3-(2-pyridinyl)-1-propanamine  (ISO)
N-(1-naphthyl)ethylenediamine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-Nitrosopyrrolidine  (ISO)
naphthalene-1,5-diamine  (ISO)
nefazodone  (EXP,ISO)
neticonazole  (ISO)
nevirapine  (ISO)
niclosamide  (ISO)
nitrapyrin  (ISO)
nitrofen  (ISO)
nonan-1-ol  (ISO)
Nonylphenol  (ISO)
O-methyleugenol  (ISO)
Octachlorostyrene  (ISO)
octamethylcyclotetrasiloxane  (ISO)
oleanolic acid  (ISO)
oleic acid  (ISO)
oltipraz  (ISO)
omeprazole  (EXP,ISO)
orlistat  (ISO)
ortho-Aminoazotoluene  (ISO)
Oxadiazon  (ISO)
oxazepam  (ISO)
oxolane  (ISO)
oxybenzone  (ISO)
oxycodone  (EXP)
p-menthan-3-ol  (ISO)
p-tert-Amylphenol  (ISO)
Padimate O  (ISO)
paracetamol  (ISO)
paraoxon  (ISO)
paraquat  (ISO)
parathion  (ISO)
PCB138  (EXP,ISO)
pencycuron  (ISO)
pendimethalin  (ISO)
pentachloronitrobenzene  (ISO)
pentobarbital  (ISO)
perfluorodecanoic acid  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
permethrin  (EXP,ISO)
phenacetin  (ISO)
phenanthrene  (ISO)
phenobarbital  (EXP,ISO)
phenolphthalein  (ISO)
phenols  (ISO)
phenothrin  (EXP,ISO)
Phenoxybenzamine  (ISO)
phenthoate  (ISO)
phenylhydrazine  (ISO)
phenytoin  (EXP,ISO)
phosalone  (ISO)
piperonyl butoxide  (ISO)
Piperophos  (ISO)
pirinixic acid  (EXP,ISO)
PK-11195  (ISO)
pregnenolone  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
prochloraz  (ISO)
profenofos  (ISO)
progesterone  (ISO)
propiconazole  (EXP,ISO)
propylparaben  (ISO)
propyzamide  (ISO)
prothiofos  (ISO)
protoporphyrin  (ISO)
pterostilbene  (ISO)
pyrene  (EXP,ISO)
pyriproxyfen  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
reactive oxygen species  (ISO)
reserpine  (ISO)
resmethrin  (ISO)
resveratrol  (ISO)
retinyl acetate  (ISO)
rifampicin  (EXP,ISO)
romidepsin  (ISO)
rotenone  (EXP)
senecionine  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (ISO)
sodium cholate  (ISO)
sodium dichromate  (ISO)
stilbene oxide  (ISO)
stilbenoid  (ISO)
Sudan III  (ISO)
sulconazole  (ISO)
sulfoxaflor  (ISO)
tamoxifen  (ISO)
Tanshinone I  (ISO)
taurocholic acid  (ISO)
tebuconazole  (EXP,ISO)
teriflunomide  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
Tetrachlorobisphenol A  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
thiacloprid  (ISO)
thioacetamide  (EXP)
Thiobencarb  (ISO)
thiophanate-methyl  (ISO)
thyroxine  (ISO)
tiracizine  (ISO)
titanium dioxide  (ISO)
tolclofos-methyl  (ISO)
toluene  (EXP)
toxaphene  (ISO)
TRAM-34  (ISO)
triadimefon  (ISO)
triazoles  (EXP,ISO)
tribufos  (ISO)
Tributyltin oxide  (ISO)
triclocarban  (ISO)
triclosan  (EXP,ISO)
trifloxystrobin  (ISO)
trifluralin  (ISO)
trifluridine  (ISO)
triphenyl phosphate  (ISO)
triphenylmethane  (ISO)
Tris(2,3-dibromopropyl) phosphate  (ISO)
troglitazone  (EXP,ISO)
tunicamycin  (ISO)
uranium atom  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vatalanib  (ISO)
vinclozolin  (EXP,ISO)
voriconazole  (ISO)
zearalenone  (ISO)
ziram  (ISO)
Zoxazolamine  (ISO)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:11114890   PMID:11891224   PMID:12477932   PMID:12885400   PMID:15953603   PMID:16055207   PMID:16153763   PMID:16272689   PMID:17904126   PMID:18023279   PMID:19162173   PMID:19435144  
PMID:20478346   PMID:22066269   PMID:23331901   PMID:24090815   PMID:24368200   PMID:24603056   PMID:25489928   PMID:25989892   PMID:26053941   PMID:27665777  


Genomics

Comparative Map Data
Nr1i3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21383,632,940 - 83,638,193 (+)NCBI
Rnor_6.0 Ensembl1389,586,283 - 89,591,277 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01389,585,072 - 89,591,278 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01394,211,961 - 94,218,143 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41387,104,241 - 87,108,563 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11387,292,773 - 87,297,730 (+)NCBI
Celera1383,264,145 - 83,269,088 (+)NCBICelera
Cytogenetic Map13q24NCBI
NR1I3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1161,229,666 - 161,238,244 (-)EnsemblGRCh38hg38GRCh38
GRCh381161,229,666 - 161,238,623 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371161,199,459 - 161,207,993 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361159,466,080 - 159,474,624 (-)NCBINCBI36hg18NCBI36
Build 341158,012,527 - 158,021,028NCBI
Celera1134,266,598 - 134,275,155 (-)NCBI
Cytogenetic Map1q23.3NCBI
HuRef1132,556,384 - 132,564,950 (-)NCBIHuRef
CHM1_11162,595,690 - 162,604,231 (-)NCBICHM1_1
Nr1i3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391171,041,503 - 171,046,414 (+)NCBIGRCm39mm39
GRCm39 Ensembl1171,041,539 - 171,048,270 (+)Ensembl
GRCm381171,213,934 - 171,218,845 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1171,213,970 - 171,220,701 (+)EnsemblGRCm38mm10GRCm38
MGSCv371173,144,101 - 173,148,975 (+)NCBIGRCm37mm9NCBIm37
MGSCv361173,050,645 - 173,055,519 (+)NCBImm8
Celera1173,662,106 - 173,666,983 (+)NCBICelera
Cytogenetic Map1H3NCBI
cM Map179.21NCBI
Nr1i3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495546812,985,105 - 13,002,850 (-)NCBIChiLan1.0ChiLan1.0
NR1I3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11140,553,938 - 140,562,799 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1140,553,951 - 140,562,799 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01136,642,126 - 136,651,074 (-)NCBIMhudiblu_PPA_v0panPan3
NR1I3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13821,252,874 - 21,257,951 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3821,253,089 - 21,258,827 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3821,327,778 - 21,332,809 (+)NCBI
ROS_Cfam_1.03821,370,731 - 21,375,765 (+)NCBI
UMICH_Zoey_3.13821,267,845 - 21,272,874 (+)NCBI
UNSW_CanFamBas_1.03821,673,095 - 21,678,115 (+)NCBI
UU_Cfam_GSD_1.03822,082,201 - 22,087,226 (+)NCBI
Nr1i3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244050587,319,081 - 7,325,712 (-)NCBI
SpeTri2.0NW_004936903527,838 - 533,930 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NR1I3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl489,226,690 - 89,236,450 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1489,226,314 - 89,231,781 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2497,082,997 - 97,088,463 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NR1I3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1202,724,843 - 2,752,999 (+)NCBI
ChlSab1.1 Ensembl202,744,908 - 2,756,658 (+)Ensembl
Vero_WHO_p1.0NW_0236660381,793,181 - 1,801,362 (+)NCBI
Nr1i3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624794141,316 - 158,059 (+)NCBI

Position Markers
RH141655  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21383,636,714 - 83,636,901 (+)MAPPER
Rnor_6.01389,590,099 - 89,590,285NCBIRnor6.0
Rnor_5.01394,216,964 - 94,217,150UniSTSRnor5.0
RGSC_v3.41387,107,668 - 87,107,854UniSTSRGSC3.4
Celera1383,267,909 - 83,268,095UniSTS
RH 3.4 Map13551.9UniSTS
Cytogenetic Map13q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)135157782490675199Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)136500824591629354Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)137456837892916783Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)137456837892916783Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)137456837892916783Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)138040355991629354Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat


Genetic Models
This gene Nr1i3 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:159
Count of miRNA genes:116
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000049873
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 3 23 23 23 10 2
Low 2 8 32 16 19 16 8 11 1 11 9 9 8
Below cutoff 2 2 2 16 9

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001270838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_022941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598930 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091080 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492287 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB104736 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB105071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB105072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204897 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204898 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204900 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC099236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF133094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF133095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF233431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000049873   ⟹   ENSRNOP00000048836
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1389,586,336 - 89,591,277 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079355   ⟹   ENSRNOP00000072813
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1389,586,283 - 89,591,277 (+)Ensembl
RefSeq Acc Id: NM_001270838   ⟹   NP_001257767
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,952 - 83,637,894 (+)NCBI
Rnor_6.01389,586,336 - 89,591,278 (+)NCBI
Rnor_5.01394,211,961 - 94,218,143 (+)NCBI
Celera1383,264,145 - 83,269,088 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270839   ⟹   NP_001257768
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,952 - 83,637,894 (+)NCBI
Rnor_6.01389,586,336 - 89,591,278 (+)NCBI
Rnor_5.01394,211,961 - 94,218,143 (+)NCBI
Celera1383,264,145 - 83,269,088 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270840   ⟹   NP_001257769
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,952 - 83,637,894 (+)NCBI
Rnor_6.01389,586,336 - 89,591,278 (+)NCBI
Rnor_5.01394,211,961 - 94,218,143 (+)NCBI
Celera1383,264,145 - 83,269,088 (+)NCBI
Sequence:
RefSeq Acc Id: NM_022941   ⟹   NP_075230
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,952 - 83,637,894 (+)NCBI
Rnor_6.01389,586,336 - 89,591,278 (+)NCBI
Rnor_5.01394,211,961 - 94,218,143 (+)NCBI
RGSC_v3.41387,104,241 - 87,108,563 (+)RGD
Celera1383,264,145 - 83,269,088 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091080   ⟹   XP_038947008
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,940 - 83,638,193 (+)NCBI
RefSeq Acc Id: XM_039091081   ⟹   XP_038947009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,940 - 83,638,193 (+)NCBI
RefSeq Acc Id: XM_039091082   ⟹   XP_038947010
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,940 - 83,637,617 (+)NCBI
RefSeq Acc Id: XM_039091084   ⟹   XP_038947012
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,940 - 83,636,371 (+)NCBI
RefSeq Acc Id: XM_039091085   ⟹   XP_038947013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,940 - 83,636,345 (+)NCBI
RefSeq Acc Id: XR_005492284
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,940 - 83,637,617 (+)NCBI
RefSeq Acc Id: XR_005492285
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,940 - 83,636,625 (+)NCBI
RefSeq Acc Id: XR_005492286
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,940 - 83,636,620 (+)NCBI
RefSeq Acc Id: XR_005492287
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,632,940 - 83,636,543 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_075230   ⟸   NM_022941
- Peptide Label: isoform 1
- UniProtKB: Q9QUS1 (UniProtKB/Swiss-Prot),   Q5FVU7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257767   ⟸   NM_001270838
- Peptide Label: isoform 3
- UniProtKB: Q402C1 (UniProtKB/TrEMBL),   Q5FVU7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257768   ⟸   NM_001270839
- Peptide Label: isoform 4
- UniProtKB: Q402C0 (UniProtKB/TrEMBL),   Q5FVU7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257769   ⟸   NM_001270840
- Peptide Label: isoform 2
- UniProtKB: Q5FVU7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072813   ⟸   ENSRNOT00000079355
RefSeq Acc Id: ENSRNOP00000048836   ⟸   ENSRNOT00000049873
RefSeq Acc Id: XP_038947008   ⟸   XM_039091080
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947009   ⟸   XM_039091081
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038947010   ⟸   XM_039091082
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947012   ⟸   XM_039091084
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038947013   ⟸   XM_039091085
- Peptide Label: isoform X5
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13699009
Promoter ID:EPDNEW_R9521
Type:initiation region
Name:Nr1i3_1
Description:nuclear receptor subfamily 1, group I, member 3
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_6.01389,586,312 - 89,586,372EPDNEW

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)
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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
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)
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)
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/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)
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
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
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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 (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 (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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621400 AgrOrtholog
Ensembl Genes ENSRNOG00000003260 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000048836 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072813 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049873 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000079355 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:7324318 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
  ThyrH_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:65035 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:108525 IMAGE-MGC_LOAD
NCBI Gene 65035 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB NR1I3 RGD
PhenoGen Nr1i3 PhenoGen
PRINTS STRDHORMONER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  THYROIDHORMR 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 NR1I3_RAT UniProtKB/Swiss-Prot
  Q402B9_RAT UniProtKB/TrEMBL
  Q402C0 ENTREZGENE, UniProtKB/TrEMBL
  Q402C1 ENTREZGENE, UniProtKB/TrEMBL
  Q5FVU7 ENTREZGENE, UniProtKB/TrEMBL
  Q76FN2_RAT UniProtKB/TrEMBL
  Q9QUS1 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Nr1i3  nuclear receptor subfamily 1, group I, member 3    strain Fischer nuclear receptor (CAR)  Name updated 1299863 APPROVED
2002-08-07 Nr1i3  strain Fischer nuclear receptor (CAR)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation accumulated in the liver nucleus of male rats in response to phenobarbital treatment 633380