Nr1h4 (nuclear receptor subfamily 1, group H, member 4) - Rat Genome Database

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Gene: Nr1h4 (nuclear receptor subfamily 1, group H, member 4) Mus musculus
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Symbol: Nr1h4
Name: nuclear receptor subfamily 1, group H, member 4
RGD ID: 734104
MGI Page MGI
Description: Enables DNA-binding transcription factor activity, RNA polymerase II-specific; bile acid binding activity; and nuclear retinoid X receptor binding activity. Involved in several processes, including intracellular receptor signaling pathway; negative regulation of cytokine production; and regulation of signal transduction. Acts upstream of or within several processes, including bile acid metabolic process; negative regulation of very-low-density lipoprotein particle remodeling; and positive regulation of transcription by RNA polymerase II. Predicted to be located in euchromatin. Predicted to be part of RNA polymerase II transcription regulator complex and receptor complex. Predicted to be active in nucleus. Is expressed in several structures, including branchial arch; central nervous system; genitourinary system; gut; and sensory organ. Used to study hepatocellular carcinoma. Human ortholog(s) of this gene implicated in extrahepatic cholestasis; hepatocellular carcinoma; and progressive familial intrahepatic cholestasis 5. Orthologous to human NR1H4 (nuclear receptor subfamily 1 group H member 4).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AI957360; bile acid receptor; farnesoid X activated receptor; farnesoid X receptor; farnesoid X-activated receptor; farnesol receptor HRR-1; FX; Fxr; HR; HRR1; nuclear receptor subfamily 1 group H member 4; retinoid X receptor-interacting protein 14; RI; RIP14; Rxr; RXR-interacting protein 14; Rxrip14
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391089,290,096 - 89,369,484 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1089,290,096 - 89,369,447 (-)EnsemblGRCm39 Ensembl
GRCm381089,454,234 - 89,533,645 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1089,454,234 - 89,533,585 (-)EnsemblGRCm38mm10GRCm38
MGSCv371088,916,979 - 88,996,367 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361088,884,177 - 88,936,426 (-)NCBIMGSCv36mm8
Celera1091,441,224 - 91,574,747 (-)NCBICelera
Cytogenetic Map10C2NCBI
cM Map1044.98NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-epicatechin-3-O-gallate  (ISO)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(S)-colchicine  (ISO)
1,2-dimethylhydrazine  (EXP)
1,3,7,9-tetramethyluric acid  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
22,23-dihydroavermectin B1a  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,6-diaminoacridine  (ISO)
3-chloropropane-1,2-diol  (ISO)
3alpha-hydroxy-5beta-pregnan-20-one  (EXP)
4'-epidoxorubicin  (ISO)
4'-hydroxyacetophenone  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (EXP)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
6-propyl-2-thiouracil  (ISO)
8-Br-cAMP  (ISO)
9-aminoacridine  (ISO)
abamectin  (ISO)
acadesine  (EXP,ISO)
acrylamide  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (EXP,ISO)
AICA ribonucleotide  (ISO)
albendazole  (ISO)
albendazole S-oxide  (ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (ISO)
Alisol B  (ISO)
Alisol C 23-acetate  (ISO)
all-trans-retinoic acid  (ISO)
alpha-linolenic acid  (ISO)
alvocidib  (ISO)
ammonium chloride  (ISO)
ampicillin  (EXP)
angelicin  (ISO)
Ankaflavin  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
apigenin  (ISO)
arachidonic acid  (ISO)
arjunolic acid  (ISO)
arotinoid acid  (ISO)
arsenite(3-)  (EXP)
atazanavir sulfate  (ISO)
Atractylenolide II  (ISO)
Azoxymethane  (EXP)
benazepril  (ISO)
benidipine  (ISO)
benomyl  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (ISO)
beta-hexachlorocyclohexane  (EXP,ISO)
beta-lapachone  (EXP)
beta-naphthoflavone  (ISO)
bezafibrate  (EXP,ISO)
bifenthrin  (ISO)
biochanin A  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol AF  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (EXP)
Boldine  (ISO)
bortezomib  (ISO)
bosentan  (ISO)
bromuconazole  (ISO)
butachlor  (ISO)
butanal  (ISO)
Butylbenzyl phthalate  (EXP)
carbendazim  (ISO)
carbon nanotube  (EXP)
carvedilol  (EXP)
CGP 52608  (ISO)
chenodeoxycholic acid  (EXP,ISO)
chlorogenic acid  (ISO)
chlorpromazine  (ISO)
cholanic acid  (ISO)
cholate  (ISO)
cholesterol  (EXP,ISO)
cholic acid  (EXP,ISO)
choline  (ISO)
chrysin  (ISO)
ciclobendazole  (ISO)
cilnidipine  (ISO)
cisplatin  (ISO)
citric acid  (EXP)
clevidipine  (ISO)
clofibrate  (EXP)
clofibric acid  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corilagin  (ISO)
corn oil  (ISO)
Cyclopamine  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (EXP,ISO)
cyfluthrin  (ISO)
cyhalothrin  (ISO)
cypermethrin  (ISO)
D-glucose  (ISO)
daunorubicin  (ISO)
DDE  (ISO)
deoxycholic acid  (EXP,ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (EXP)
dibutyl phthalate  (EXP)
dichloroacetic acid  (EXP)
dicrotophos  (ISO)
diethyl phthalate  (EXP)
digoxin  (ISO)
dihydroartemisinin  (ISO)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dimethyl sulfoxide  (ISO)
Diosbulbin B  (EXP,ISO)
dioscin  (ISO)
diosgenin  (ISO)
Diphenadione  (ISO)
dipyridamole  (ISO)
dobutamine  (ISO)
Doramectin  (ISO)
dorsomorphin  (EXP,ISO)
doxorubicin  (EXP,ISO)
emamectin  (ISO)
emetine  (ISO)
emodin  (EXP)
endosulfan  (ISO)
enilconazole  (EXP)
epoxiconazole  (EXP)
eprinomectin  (ISO)
ethacridine  (ISO)
ethambutol  (ISO)
ethanol  (EXP,ISO)
ethylestrenol  (ISO)
farnesol  (ISO)
felodipine  (ISO)
fenbendazole  (ISO)
fenofibrate  (ISO)
fenvalerate  (ISO)
Fexaramine  (ISO)
flucythrinate  (ISO)
fluoranthene  (EXP)
fluoxastrobin  (ISO)
fluvalinate  (ISO)
fulvestrant  (EXP,ISO)
furan  (EXP,ISO)
gallocatechin  (ISO)
Geniposide  (ISO)
genistein  (EXP,ISO)
Gentiopicrin  (ISO)
ginsenoside Rg1  (ISO)
glafenine  (ISO)
glucose  (ISO)
glyburide  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycyrrhetinic acid  (ISO)
glyphosate  (EXP)
griseofulvin  (ISO)
guggulsterone  (EXP,ISO)
GW 3965  (EXP)
GW 4064  (EXP,ISO)
GW 7647  (ISO)
hexadecanoic acid  (EXP,ISO)
high-density lipoprotein cholesterol  (EXP)
hydrogen peroxide  (ISO)
ibuprofen  (EXP)
icariside II  (EXP,ISO)
idarubicin  (ISO)
imazamox  (ISO)
imazapyr  (ISO)
Imazethapyr  (ISO)
isoniazide  (ISO)
isoprenaline  (ISO)
isotretinoin  (ISO)
Isradipine  (ISO)
ivermectin  (EXP,ISO)
juvenile hormone III  (ISO)
kadethrin  (ISO)
kaempferol  (ISO)
ketoconazole  (ISO)
L-methionine  (ISO)
lacidipine  (ISO)
lercanidipine  (ISO)
lipopolysaccharide  (EXP,ISO)
liquiritin  (EXP)
lithocholic acid  (EXP,ISO)
malic acid  (EXP)
manidipine  (ISO)
mebendazole  (ISO)
mechlorethamine  (EXP)
menadione  (ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
methidathion  (EXP)
methotrexate  (ISO)
methoxsalen  (ISO)
methyl 2-methylpropyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate  (ISO)
methylmercury chloride  (ISO)
metronidazole  (EXP)
milbemycin  (ISO)
mitomycin C  (ISO)
monascin  (EXP)
mono(2-ethylhexyl) phthalate  (EXP)
montelukast  (ISO)
Muraglitazar  (ISO)
N,N-diethyl-m-toluamide  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
naphthalenes  (ISO)
nefazodone  (ISO)
nemorubicin  (ISO)
neomycin  (EXP)
nicardipine  (ISO)
nifedipine  (ISO)
nimesulide  (ISO)
nimodipine  (ISO)
nisoldipine  (ISO)
nitrendipine  (ISO)
nitrofen  (ISO)
nocodazole  (ISO)
obeticholic acid  (EXP,ISO)
oleanolic acid  (EXP)
oleic acid  (ISO)
oxfendazole  (ISO)
ozone  (EXP,ISO)
papaverine  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
parbendazole  (ISO)
pentamidine  (ISO)
pentanal  (ISO)
perfluorohexanesulfonic acid  (EXP)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
permethrin  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (EXP)
phenothrin  (ISO)
picoxystrobin  (ISO)
picropodophyllotoxin  (ISO)
Picroside ii  (EXP)
Pirarubicin  (ISO)
pirinixic acid  (EXP)
platycodin D  (ISO)
podophyllotoxin  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
procymidone  (EXP)
propanal  (ISO)
prothioconazole  (EXP)
Prothioconazole-desthio  (EXP)
psoralen  (ISO)
pyrazinecarboxamide  (ISO)
quercetin  (ISO)
quinolines  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
rifaximin  (ISO)
ritonavir  (ISO)
rosuvastatin  (ISO)
rotenone  (ISO)
Salidroside  (EXP)
scoparone  (ISO)
Selamectin  (ISO)
senecionine  (EXP,ISO)
silibinin  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sirolimus  (ISO)
sodium arsenite  (EXP,ISO)
stigmasterol  (EXP)
streptozocin  (EXP)
tamibarotene  (ISO)
tamoxifen  (ISO)
tartrazine  (ISO)
taurine  (EXP)
tauro-beta-muricholic acid  (EXP)
taurocholic acid  (EXP,ISO)
taurodeoxycholic acid  (ISO)
tauroursodeoxycholic acid  (EXP)
tectorigenin  (EXP)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
Tetrachlorobisphenol A  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
thioacetamide  (ISO)
thiram  (ISO)
titanium dioxide  (EXP)
topotecan  (ISO)
trichloroethene  (ISO)
triclosan  (ISO)
trifloxystrobin  (ISO)
triphenyl phosphate  (EXP)
Triptolide  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
tris(2-chloroethyl) phosphate  (EXP)
uranium atom  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (EXP,ISO)
valproic acid  (EXP,ISO)
vancomycin  (EXP)
vincaleukoblastine  (ISO)
vincristine  (ISO)
vinorelbine  (ISO)
Yangonin  (EXP,ISO)
zinc acetate  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
bile acid and bile salt transport  (ISO)
bile acid metabolic process  (IMP,ISO)
cell differentiation  (IBA)
cell-cell junction assembly  (IMP)
cellular response to bile acid  (IMP,ISO)
cellular response to fatty acid  (IEA,ISO)
cellular response to lipopolysaccharide  (IMP)
cellular response to xenobiotic stimulus  (ISO)
cholesterol homeostasis  (IMP,ISO)
defense response to bacterium  (IDA)
digestive tract development  (ISO)
fatty acid homeostasis  (IMP)
glucose homeostasis  (IDA)
inflammatory response  (IEA)
innate immune response  (IEA)
intracellular glucose homeostasis  (IDA)
intracellular receptor signaling pathway  (IBA)
intracellular triglyceride homeostasis  (IEA,ISO)
negative regulation of apoptotic process  (IEA,ISO)
negative regulation of canonical NF-kappaB signal transduction  (IMP,ISO)
negative regulation of collagen biosynthetic process  (ISO)
negative regulation of inflammatory response  (IBA,IMP)
negative regulation of interleukin-1 production  (IMP)
negative regulation of interleukin-2 production  (IMP)
negative regulation of interleukin-6 production  (IDA)
negative regulation of monocyte chemotactic protein-1 production  (IMP)
negative regulation of NF-kappaB transcription factor activity  (IMP)
negative regulation of transcription by RNA polymerase II  (IBA,IMP,ISO)
negative regulation of triglyceride biosynthetic process  (ISO)
negative regulation of tumor necrosis factor production  (IMP,ISO)
negative regulation of tumor necrosis factor-mediated signaling pathway  (IMP)
negative regulation of type II interferon production  (IMP,ISO)
negative regulation of very-low-density lipoprotein particle remodeling  (IDA,ISO)
Notch signaling pathway  (IDA)
nuclear receptor-mediated bile acid signaling pathway  (IMP,ISO)
positive regulation of adipose tissue development  (IMP)
positive regulation of ammonia assimilation cycle  (IMP)
positive regulation of DNA-templated transcription  (IDA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of glutamate metabolic process  (IMP)
positive regulation of insulin receptor signaling pathway  (IDA)
positive regulation of insulin secretion involved in cellular response to glucose stimulus  (IMP)
positive regulation of interleukin-17 production  (IEA,ISO)
positive regulation of phosphatidic acid biosynthetic process  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IBA,IDA,IMP,ISO)
regulation of carbohydrate metabolic process  (ISO)
regulation of DNA-templated transcription  (ISO)
regulation of insulin secretion involved in cellular response to glucose stimulus  (ISO)
regulation of low-density lipoprotein particle clearance  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IGI,ISO)
regulation of urea metabolic process  (IMP)
response to cholesterol  (ISO)
response to estrogen  (ISO)
response to ethanol  (ISO)
response to glucose  (ISO)
response to lipopolysaccharide  (ISO)
response to norepinephrine  (ISO)
response to nutrient levels  (ISO)
response to xenobiotic stimulus  (ISO)
toll-like receptor 9 signaling pathway  (IMP)
transcription by RNA polymerase II  (IDA)
triglyceride homeostasis  (IDA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal bile composition  (IAGP)
abnormal bile salt homeostasis  (IAGP)
abnormal bile salt level  (IAGP)
abnormal bile secretion  (IAGP)
abnormal blood homeostasis  (IAGP)
abnormal hepatocyte morphology  (IAGP)
abnormal liver morphology  (IAGP)
abnormal liver perisinusoidal space morphology  (IAGP)
abnormal liver physiology  (IAGP)
abnormal liver sinusoid morphology  (IAGP)
cachexia  (IAGP)
decreased body temperature  (IAGP)
decreased body weight  (IAGP)
decreased bone mineral content  (IAGP)
decreased bone mineral density  (IAGP)
decreased circulating free fatty acids level  (IAGP)
decreased circulating glucose level  (IAGP)
decreased circulating insulin level  (IAGP)
decreased epididymal fat pad weight  (IAGP)
decreased interscapular fat pad weight  (IAGP)
decreased retroperitoneal fat pad weight  (IAGP)
decreased susceptibility to weight gain  (IAGP)
decreased total body fat amount  (IAGP)
decreased white fat cell size  (IAGP)
enlarged gallbladder  (IAGP)
enlarged liver  (IAGP)
focal hepatic necrosis  (IAGP)
hepatic steatosis  (IAGP)
impaired glucose tolerance  (IAGP)
increased bile salt level  (IAGP)
increased cecum weight  (IAGP)
increased circulating alanine transaminase level  (IAGP)
increased circulating aspartate transaminase level  (IAGP)
increased circulating bilirubin level  (IAGP)
increased circulating cholesterol level  (IAGP)
increased circulating phospholipid level  (IAGP)
increased circulating triglyceride level  (IAGP)
increased energy expenditure  (IAGP)
increased fluid intake  (IAGP)
increased food intake  (IAGP)
increased hepatocellular carcinoma incidence  (IAGP)
increased hepatocyte apoptosis  (IAGP)
increased hepatocyte proliferation  (IAGP)
increased liver adenoma incidence  (IAGP)
increased liver cholesterol level  (IAGP)
increased liver triglyceride level  (IAGP)
increased liver tumor incidence  (IAGP)
increased liver weight  (IAGP)
increased spleen weight  (IAGP)
increased susceptibility to induced morbidity/mortality  (IAGP)
jaundice  (IAGP)
liver degeneration  (IAGP)
liver inflammation  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Reduced hepatic expression of farnesoid X receptor in hereditary cholestasis associated to mutation in ATP8B1. Alvarez L, etal., Hum Mol Genet. 2004 Oct 15;13(20):2451-60. Epub 2004 Aug 18.
2. Immunomodulatory glycan LNFPIII alleviates hepatosteatosis and insulin resistance through direct and indirect control of metabolic pathways. Bhargava P, etal., Nat Med. 2012 Nov;18(11):1665-72. doi: 10.1038/nm.2962. Epub 2012 Oct 28.
3. Ageing Fxr deficient mice develop increased energy expenditure, improved glucose control and liver damage resembling NASH. Bjursell M, etal., PLoS One. 2013 May 20;8(5):e64721. doi: 10.1371/journal.pone.0064721. Print 2013.
4. Searching QTL by gene expression: analysis of diabesity. Brown AC, etal., BMC Genet 2005 Mar 10;6(1):12.
5. Postprandial FGF19-induced phosphorylation by Src is critical for FXR function in bile acid homeostasis. Byun S, etal., Nat Commun. 2018 Jul 3;9(1):2590. doi: 10.1038/s41467-018-04697-5.
6. Bile salt export pump is dysregulated with altered farnesoid X receptor isoform expression in patients with hepatocellular carcinoma. Chen Y, etal., Hepatology. 2013 Apr;57(4):1530-41. doi: 10.1002/hep.26187. Epub 2013 Feb 15.
7. Impaired VLDL assembly: a novel mechanism contributing to hepatic lipid accumulation following ovariectomy and high-fat/high-cholesterol diets? Côté I, etal., Br J Nutr. 2014 Nov 28;112(10):1592-600. doi: 10.1017/S0007114514002517. Epub 2014 Sep 29.
8. An atherogenic diet decreases liver FXR gene expression and causes severe hepatic steatosis and hepatic cholesterol accumulation: effect of endurance training. Côté I, etal., Eur J Nutr. 2013 Aug;52(5):1523-32. doi: 10.1007/s00394-012-0459-5. Epub 2012 Nov 2.
9. Prevention of spontaneous hepatocarcinogenesis in farnesoid X receptor-null mice by intestinal-specific farnesoid X receptor reactivation. Degirolamo C, etal., Hepatology. 2015 Jan;61(1):161-70. doi: 10.1002/hep.27274. Epub 2014 Oct 30.
10. Glucose regulates the expression of the farnesoid X receptor in liver. Duran-Sandoval D, etal., Diabetes. 2004 Apr;53(4):890-8.
11. Protective effects of 6-ethyl chenodeoxycholic acid, a farnesoid X receptor ligand, in estrogen-induced cholestasis. Fiorucci S, etal., J Pharmacol Exp Ther. 2005 May;313(2):604-12. Epub 2005 Jan 11.
12. Cross-talk between farnesoid-X-receptor (FXR) and peroxisome proliferator-activated receptor gamma contributes to the antifibrotic activity of FXR ligands in rodent models of liver cirrhosis. Fiorucci S, etal., J Pharmacol Exp Ther. 2005 Oct;315(1):58-68. Epub 2005 Jun 24.
13. Effects of Farnesoid X Receptor Activation on Arachidonic Acid Metabolism, NF-kB Signaling, and Hepatic Inflammation. Gai Z, etal., Mol Pharmacol. 2018 Aug;94(2):802-811. doi: 10.1124/mol.117.111047. Epub 2018 May 9.
14. Effect of a high-fat diet on the hepatic expression of nuclear receptors and their target genes: relevance to drug disposition. Ghoneim RH, etal., Br J Nutr. 2015 Feb 14;113(3):507-16. doi: 10.1017/S0007114514003717. Epub 2015 Jan 23.
15. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, etal., Science 2004 Dec 24;306(5705):2255-7.
16. Exploration of Hepatoprotective Effect of Gentiopicroside on Alpha-Naphthylisothiocyanate-Induced Cholestatic Liver Injury in Rats by Comprehensive Proteomic and Metabolomic Signatures. Han H, etal., Cell Physiol Biochem. 2018;49(4):1304-1319. doi: 10.1159/000493409. Epub 2018 Sep 17.
17. Disrupted coordinate regulation of farnesoid X receptor target genes in a patient with cerebrotendinous xanthomatosis. Honda A, etal., J Lipid Res. 2005 Feb;46(2):287-96. Epub 2004 Dec 1.
18. Farnesoid X receptor agonist INT-767 attenuates liver steatosis and inflammation in rat model of nonalcoholic steatohepatitis. Hu YB, etal., Drug Des Devel Ther. 2018 Jul 16;12:2213-2221. doi: 10.2147/DDDT.S170518. eCollection 2018.
19. Reduced triglyceride accumulation due to overactivation of farnesoid X receptor signaling contributes to impaired liver regeneration following 50% hepatectomy in extra‑cholestatic liver tissue. Jia WJ, etal., Mol Med Rep. 2018 Jan;17(1):1545-1554. doi: 10.3892/mmr.2017.8025. Epub 2017 Nov 10.
20. Suppressed hepatic bile acid signalling despite elevated production of primary and secondary bile acids in NAFLD. Jiao N, etal., Gut. 2018 Oct;67(10):1881-1891. doi: 10.1136/gutjnl-2017-314307. Epub 2017 Aug 3.
21. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
22. Spontaneous hepatocarcinogenesis in farnesoid X receptor-null mice. Kim I, etal., Carcinogenesis. 2007 May;28(5):940-6. doi: 10.1093/carcin/bgl249. Epub 2006 Dec 20.
23. Serum omentin and vaspin levels in cirrhotic patients with and without portal vein thrombosis. Kukla M, etal., World J Gastroenterol. 2017 Apr 14;23(14):2613-2624. doi: 10.3748/wjg.v23.i14.2613.
24. Activation of the farnesoid X receptor provides protection against acetaminophen-induced hepatic toxicity. Lee FY, etal., Mol Endocrinol. 2010 Aug;24(8):1626-36. doi: 10.1210/me.2010-0117. Epub 2010 Jun 23.
25. Small heterodimer partner overexpression partially protects against liver tumor development in farnesoid X receptor knockout mice. Li G, etal., Toxicol Appl Pharmacol. 2013 Oct 15;272(2):299-305. doi: 10.1016/j.taap.2013.06.016. Epub 2013 Jun 26.
26. Role of AMP-activated protein kinase α1 in 17α-ethinylestradiol-induced cholestasis in rats. Li X, etal., Arch Toxicol. 2017 Jan;91(1):481-494. doi: 10.1007/s00204-016-1697-8. Epub 2016 Apr 18.
27. In vitro efficacy of pro- and anticoagulant strategies in compensated and acutely ill patients with cirrhosis. Lisman T, etal., Liver Int. 2018 Nov;38(11):1988-1996. doi: 10.1111/liv.13882. Epub 2018 May 30.
28. Hepatoprotection by the farnesoid X receptor agonist GW4064 in rat models of intra- and extrahepatic cholestasis. Liu Y, etal., J Clin Invest. 2003 Dec;112(11):1678-87. Epub 2003 Nov 17.
29. Cocarcinogenic effects of intrahepatic bile acid accumulation in cholangiocarcinoma development. Lozano E, etal., Mol Cancer Res. 2014 Jan;12(1):91-100. doi: 10.1158/1541-7786.MCR-13-0503. Epub 2013 Nov 19.
30. Farnesoid X receptor is essential for normal glucose homeostasis. Ma K, etal., J Clin Invest. 2006 Apr;116(4):1102-9. Epub 2006 Mar 23.
31. Insights into hepatic and renal FXR/DDAH-1/eNOS pathway and its role in the potential benefit of rosuvastatin and silymarin in hepatic nephropathy. Magdy YM, etal., Exp Mol Pathol. 2018 Dec;105(3):293-310. doi: 10.1016/j.yexmp.2018.10.004. Epub 2018 Oct 9.
32. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
33. MGDs mouse GO annotations MGD data from the GO Consortium
34. MGD IEA MGD IEA
35. Selective activation of nuclear bile acid receptor FXR in the intestine protects mice against cholestasis. Modica S, etal., Gastroenterology. 2012 Feb;142(2):355-65.e1-4. doi: 10.1053/j.gastro.2011.10.028. Epub 2011 Nov 2.
36. The decrease in farnesoid X receptor, pregnane X receptor and constitutive androstane receptor in the liver after intestinal ischemia-reperfusion. Ogura J, etal., J Pharm Pharm Sci. 2012;15(5):616-31. doi: 10.18433/j38c88.
37. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
38. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
39. Dysregulation of BSEP and MRP2 May Play an Important Role in Isoniazid-Induced Liver Injury via the SIRT1/FXR Pathway in Rats and HepG2 Cells. Qu X, etal., Biol Pharm Bull. 2018;41(8):1211-1218. doi: 10.1248/bpb.b18-00028.
40. Bile-acid-activated farnesoid X receptor regulates hydrogen sulfide production and hepatic microcirculation. Renga B, etal., World J Gastroenterol. 2009 May 7;15(17):2097-108. doi: 10.3748/wjg.15.2097.
41. Mouse MP Annotation Import Pipeline RGD automated import pipeline
42. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
43. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
44. Enhanced expression of monocyte tissue factor in patients with liver cirrhosis. Saliola M, etal., Gut. 1998 Sep;43(3):428-32. doi: 10.1136/gut.43.3.428.
45. The FXR agonist PX20606 ameliorates portal hypertension by targeting vascular remodelling and sinusoidal dysfunction. Schwabl P, etal., J Hepatol. 2017 Apr;66(4):724-733. doi: 10.1016/j.jhep.2016.12.005. Epub 2016 Dec 18.
46. Dose-related liver injury of Geniposide associated with the alteration in bile acid synthesis and transportation. Tian J, etal., Sci Rep. 2017 Aug 21;7(1):8938. doi: 10.1038/s41598-017-09131-2.
47. Curative effect of arjunolic acid from Terminalia arjuna in non-alcoholic fatty liver disease models. Toppo E, etal., Biomed Pharmacother. 2018 Nov;107:979-988. doi: 10.1016/j.biopha.2018.08.019. Epub 2018 Aug 23.
48. Evidence of normal thrombin generation in cirrhosis despite abnormal conventional coagulation tests. Tripodi A, etal., Hepatology. 2005 Mar;41(3):553-8. doi: 10.1002/hep.20569.
49. Obeticholic acid, a farnesoid X receptor agonist, improves portal hypertension by two distinct pathways in cirrhotic rats. Verbeke L, etal., Hepatology. 2014 Jun;59(6):2286-98. doi: 10.1002/hep.26939. Epub 2014 Apr 14.
50. Association between low-grade disseminated intravascular coagulation and endotoxemia in patients with liver cirrhosis. Violi F, etal., Gastroenterology. 1995 Aug;109(2):531-9. doi: 10.1016/0016-5085(95)90342-9.
51. Role of farnesoid X receptor in determining hepatic ABC transporter expression and liver injury in bile duct-ligated mice. Wagner M, etal., Gastroenterology. 2003 Sep;125(3):825-38. doi: 10.1016/s0016-5085(03)01068-0.
52. 18β-Glycyrrhetinic acid protects against alpha-naphthylisothiocyanate-induced cholestasis through activation of the Sirt1/FXR signaling pathway. Wu SY, etal., Acta Pharmacol Sin. 2018 Dec;39(12):1865-1873. doi: 10.1038/s41401-018-0110-y. Epub 2018 Jul 30.
53. Dihydroartemisinin protects against alcoholic liver injury through alleviating hepatocyte steatosis in a farnesoid X receptor-dependent manner. Xu W, etal., Toxicol Appl Pharmacol. 2017 Jan 15;315:23-34. doi: 10.1016/j.taap.2016.12.001. Epub 2016 Dec 6.
54. Levels of vitamin K, immunoreactive prothrombin, des-gamma-carboxy prothrombin and gamma-glutamyl carboxylase activity in hepatocellular carcinoma tissue. Yamagata H, etal., J Gastroenterol Hepatol. 1995 Jan-Feb;10(1):8-13. doi: 10.1111/j.1440-1746.1995.tb01040.x.
55. Effects of corilagin on alleviating cholestasis via farnesoid X receptor-associated pathways in vitro and in vivo. Yang F, etal., Br J Pharmacol. 2018 Mar;175(5):810-829. doi: 10.1111/bph.14126. Epub 2018 Jan 25.
56. Spontaneous development of liver tumors in the absence of the bile acid receptor farnesoid X receptor. Yang F, etal., Cancer Res. 2007 Feb 1;67(3):863-7. doi: 10.1158/0008-5472.CAN-06-1078.
57. The ileum-liver Farnesoid X Receptor signaling axis mediates the compensatory mechanism of 17α-ethynylestradiol-induced cholestasis via increasing hepatic biosynthesis of chenodeoxycholic acids in rats. Zhang F, etal., Eur J Pharm Sci. 2018 Oct 15;123:404-415. doi: 10.1016/j.ejps.2018.08.005. Epub 2018 Aug 2.
58. Promotion of liver regeneration/repair by farnesoid X receptor in both liver and intestine in mice. Zhang L, etal., Hepatology. 2012 Dec;56(6):2336-43. doi: 10.1002/hep.25905.
59. Protective effect of dioscin against thioacetamide-induced acute liver injury via FXR/AMPK signaling pathway in vivo. Zheng L, etal., Biomed Pharmacother. 2018 Jan;97:481-488. doi: 10.1016/j.biopha.2017.10.153. Epub 2017 Nov 6.
60. Modulation of transport and metabolism of bile acids and bilirubin by chlorogenic acid against hepatotoxicity and cholestasis in bile duct ligation rats: involvement of SIRT1-mediated deacetylation of FXR and PGC-1α. Zhu L, etal., J Hepatobiliary Pancreat Sci. 2018 Mar;25(3):195-205. doi: 10.1002/jhbp.537.
61. Role of nuclear bile acid receptor, FXR, in adaptive ABC transporter regulation by cholic and ursodeoxycholic acid in mouse liver, kidney and intestine. Zollner G, etal., J Hepatol. 2003 Oct;39(4):480-8. doi: 10.1016/s0168-8278(03)00228-9.
Additional References at PubMed
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Genomics

Comparative Map Data
Nr1h4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391089,290,096 - 89,369,484 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1089,290,096 - 89,369,447 (-)EnsemblGRCm39 Ensembl
GRCm381089,454,234 - 89,533,645 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1089,454,234 - 89,533,585 (-)EnsemblGRCm38mm10GRCm38
MGSCv371088,916,979 - 88,996,367 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361088,884,177 - 88,936,426 (-)NCBIMGSCv36mm8
Celera1091,441,224 - 91,574,747 (-)NCBICelera
Cytogenetic Map10C2NCBI
cM Map1044.98NCBI
NR1H4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812100,473,866 - 100,564,414 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12100,473,708 - 100,564,414 (+)EnsemblGRCh38hg38GRCh38
GRCh3712100,867,644 - 100,958,192 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361299,391,810 - 99,481,774 (+)NCBINCBI36Build 36hg18NCBI36
Build 341299,370,146 - 99,460,111NCBI
Celera12100,532,992 - 100,622,995 (+)NCBICelera
Cytogenetic Map12q23.1NCBI
HuRef1297,928,334 - 98,018,410 (+)NCBIHuRef
CHM1_112100,833,597 - 100,923,679 (+)NCBICHM1_1
T2T-CHM13v2.012100,435,311 - 100,525,835 (+)NCBIT2T-CHM13v2.0
Nr1h4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8725,733,471 - 25,829,440 (-)NCBIGRCr8
mRatBN7.2723,846,122 - 23,942,085 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl723,846,122 - 23,942,047 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx725,840,659 - 25,936,578 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0728,003,082 - 28,099,010 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0727,780,396 - 27,876,311 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0730,003,429 - 30,162,095 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl730,003,429 - 30,162,056 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0730,170,397 - 30,214,796 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0730,104,960 - 30,107,142 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4726,189,759 - 26,307,061 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1726,210,029 - 26,327,332 (-)NCBI
Celera720,992,814 - 21,085,820 (-)NCBICelera
Cytogenetic Map7q13NCBI
Nr1h4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540536,160,049 - 36,237,751 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540536,160,360 - 36,236,258 (+)NCBIChiLan1.0ChiLan1.0
NR1H4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v210108,557,041 - 108,627,402 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan112108,553,438 - 108,623,792 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01298,052,778 - 98,144,085 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112101,457,885 - 101,548,058 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12101,457,885 - 101,548,058 (+)Ensemblpanpan1.1panPan2
NR1H4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11539,497,313 - 39,608,120 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1539,536,290 - 39,608,116 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1539,876,387 - 39,987,365 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01540,161,103 - 40,272,109 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1540,200,071 - 40,271,741 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11539,418,531 - 39,529,420 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01539,525,061 - 39,636,033 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01539,799,183 - 39,910,169 (+)NCBIUU_Cfam_GSD_1.0
Nr1h4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494520,304,852 - 20,379,409 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649213,315,265 - 13,374,034 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649213,315,265 - 13,365,186 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NR1H4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl583,604,294 - 83,684,604 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1583,607,222 - 83,732,668 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2587,754,914 - 87,828,507 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NR1H4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11195,792,428 - 95,877,989 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1195,792,996 - 95,878,293 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037149,156,310 - 149,247,016 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nr1h4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247507,219,251 - 7,303,834 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247507,222,306 - 7,303,809 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nr1h4
2758 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:383
Count of miRNA genes:138
Interacting mature miRNAs:157
Transcripts:ENSMUST00000058126, ENSMUST00000105296, ENSMUST00000105297
Prediction methods: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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302035Lmb4_mlupus in MRL and B6 F2 cross (mouse)Not determined106684818792258673Mouse
12910789Pwgrq19_mpost-weaning growth rate QTL 19 (mouse)108282870092169056Mouse
1301520Uvbi1_mUVB induced immunosuppression 1 (mouse)Not determined1086909085120909229Mouse
4142137Femwf3_mfemur work to failure 3 (mouse)Not determined75338568109338767Mouse
1301787Bsc1_mbrain size control 1 (mouse)Not determined105851696992517096Mouse
27226772Tibl13_mtibia length 13, 10 week (mouse)1018875748129635869Mouse
4142386Tgq20_mtriglyceride QTL 20 (mouse)Not determined88836456122836456Mouse
1357594Estoq3_membryo survival total QTL 3 (mouse)Not determined1084079650122041528Mouse
27226764Tibl19_mtibia length 19, 16 week (mouse)1039175996129635869Mouse
1357831Igf1sl2_mIGF-1 serum levels 2 (mouse)Not determined108769412799936278Mouse
4141479W10q8_mweight 10 weeks QTL 8 (mouse)Not determined84079650122041528Mouse
14747004Mancz8_mmandible centroid size 8 (mouse)1082078412116078412Mouse
4142496W6q8_mweight 6 weeks QTL 8 (mouse)Not determined84079650122041528Mouse
1302067Scc9_mcolon tumor susceptibility 9 (mouse)Not determined1018259333125575232Mouse
26884411Bzwq8_mbi-zygomatic width QTL 8, 10 week (mouse)1044876096115935905Mouse
11039497Ltpr5a_mLeishmania tropica response 5a (mouse)1073506901107507047Mouse
1357622Espq3_membryo survival preimplantation QTL 3 (mouse)Not determined1084079650122041528Mouse
4142365Egq9_mearly growth QTL 9 (mouse)Not determined84079650122041528Mouse
1300533Aem3_manti-erythrocyte autoantibody modifier 3 (mouse)Not determined106549093899491121Mouse
26884403Cvht8_mcranial vault height 8, 16 week (mouse)102287589991035862Mouse
1300921Skl4_mskeletal size (tail length) 4 (mouse)Not determined1088088254122088391Mouse
26884407Bzwq14_mbi-zygomatic width QTL 14, 16 wee (mouse)1045476096120635905Mouse
11251717Siim1_mstress induced immobility 1 (mouse)1078381268112381268Mouse
1300797Sluc22_msusceptibility to lung cancer 22 (mouse)Not determined1086713608120713756Mouse
26884405Huml2_mhumerus length 2, 5 week (mouse)1069735830130430862Mouse
1357740Obsty3_mobesity 3 (mouse)Not determined108235478116190980Mouse
13208560Wght9_mweight 9 (mouse)1059835822120835905Mouse
1301165Lith7_mlithogenic gene 7 (mouse)Not determined1082309418116309657Mouse
1302060El3_mepilepsy 3 (mouse)Not determined106549093899491121Mouse
1300908Insq4_minsulin QTL 4 (mouse)Not determined1086909085120909229Mouse
4141054mwfh_mmodifier of white forlock hypopigmentation (mouse)Not determined83017003117017136Mouse
26884447Sklq9_mskull length QTL 9, 10 week (mouse)1067335830111735905Mouse
11353832Pcholq4_mplasma cholesterol QTL 4 (mouse)1073987216125515907Mouse
1357779Tesq3_mtestis weight QTL 3 (mouse)Not determined1084079650122041528Mouse
11059553Lmr32d_mleishmaniasis resistance 32d (mouse)1082309418116309657Mouse
11059554Lmr32e_mleishmaniasis resistance 32e (mouse)1082309418116309657Mouse
11059555Lmr32f_mleishmaniasis resistance 32f (mouse)1082309418116309657Mouse
26884426Cvht1_mcranial vault height 1, 5 week (mouse)1024675898121035905Mouse
26884424Zlq9_mzygomatic length QTL 9, 16 week (mouse)1063935779115935905Mouse
1357638Cia29_mcollagen induced arthritis 29 (mouse)Not determined1085454982118497353Mouse
26884430Zlq5_mzygomatic length QTL 5, 10 week (mouse)1067835830124835905Mouse
1357632Vtbt9_mvertebral trabecular bone trait 9 (mouse)Not determined1075338568109338767Mouse
11353843Gluq1_mblood glucose QTL 1 (mouse)1073987216125515907Mouse
10043881Adip24_madiposity 24 (mouse)Not determined1082392803116392952Mouse
1558757Eae34_mexperimental allergic encephalomyelitis susceptibility 34 (mouse)Not determined1021408154114217230Mouse
4141387Lgaq5_mlate growth adjusted QTL 5 (mouse)Not determined84079650122041528Mouse
11059550Lmr32a_mleishmaniasis resistance 32a (mouse)1082309418116309657Mouse
11059551Lmr32b_mleishmaniasis resistance 32b (mouse)1082309418116309657Mouse
26884450Sklq15_mskull length QTL 15, 16 week (mouse)1059335822122335905Mouse
4141382Ssrq4_mstress response QTL 4 (mouse)Not determined8249093890856102Mouse
27095911Pglq15_mpelvic girdle length QTL 15, 16 week (mouse)1039175996129635869Mouse
1301737Insq9_minsulin QTL 9 (mouse)Not determined106549093899491121Mouse
1300975Fembrs3_mfemur breaking strength 3 (mouse)Not determined1075338568109338767Mouse
13524528Bodwtq9_mbody wweight QTL 9 (mouse)108764311793193117Mouse

Markers in Region
AI646847  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38444,991,325 - 44,991,430UniSTSGRCm38
MGSCv37445,004,197 - 45,004,302UniSTSGRCm37
Celera1091,541,750 - 91,541,855UniSTS
Celera445,011,385 - 45,011,490UniSTS
Cytogenetic Map4B1UniSTS
Cytogenetic Map10C2UniSTS
cM Map1050.0UniSTS
Whitehead/MRC_RH4753.23UniSTS
AI957360  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381089,454,585 - 89,454,729UniSTSGRCm38
MGSCv371088,917,330 - 88,917,474UniSTSGRCm37
Celera1091,441,575 - 91,441,719UniSTS
Cytogenetic Map10C2UniSTS
cM Map1050.0UniSTS
Whitehead/MRC_RH101026.69UniSTS
U09416  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381089,454,585 - 89,454,679UniSTSGRCm38
MGSCv371088,917,330 - 88,917,424UniSTSGRCm37
Celera1091,441,575 - 91,441,669UniSTS
Cytogenetic Map10C2UniSTS
cM Map1050.0UniSTS
Whitehead/MRC_RH101028.22UniSTS
UniSTS:234914  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38444,991,700 - 44,991,944UniSTSGRCm38
MGSCv37445,004,572 - 45,004,816UniSTSGRCm37
Celera1091,542,124 - 91,542,379UniSTS
Celera445,011,760 - 45,012,004UniSTS
Cytogenetic Map4B1UniSTS
Cytogenetic Map10C2UniSTS
cM Map1050.0UniSTS
UniSTS:236437  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38444,993,195 - 44,993,332UniSTSGRCm38
GRCm381089,554,905 - 89,555,042UniSTSGRCm38
MGSCv371089,017,650 - 89,017,787UniSTSGRCm37
MGSCv37445,006,067 - 45,006,204UniSTSGRCm37
Celera445,013,255 - 45,013,392UniSTS
Celera1091,543,648 - 91,543,785UniSTS
Cytogenetic Map4B1UniSTS
Cytogenetic Map10C2UniSTS
cM Map1050.0UniSTS
Nr1h4  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map10C2UniSTS
cM Map1050.0UniSTS


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001163504 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001163700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001385711 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_009108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006513391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_030244963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001779493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC152417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF293370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK002513 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK050566 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK132255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY366407 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY366408 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC015261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSMUST00000058126   ⟹   ENSMUSP00000053092
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1089,290,096 - 89,342,511 (-)Ensembl
GRCm38.p6 Ensembl1089,454,234 - 89,506,649 (-)Ensembl
Ensembl Acc Id: ENSMUST00000105296   ⟹   ENSMUSP00000100933
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1089,290,096 - 89,342,520 (-)Ensembl
GRCm38.p6 Ensembl1089,454,234 - 89,506,658 (-)Ensembl
Ensembl Acc Id: ENSMUST00000105297   ⟹   ENSMUSP00000100934
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1089,290,235 - 89,369,447 (-)Ensembl
GRCm38.p6 Ensembl1089,454,373 - 89,533,585 (-)Ensembl
RefSeq Acc Id: NM_001163504   ⟹   NP_001156976
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,096 - 89,369,484 (-)NCBI
GRCm381089,454,234 - 89,533,622 (-)NCBI
MGSCv371088,916,979 - 88,996,367 (-)RGD
Celera1091,441,224 - 91,574,747 (-)RGD
cM Map10 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001163700   ⟹   NP_001157172
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,096 - 89,342,520 (-)NCBI
GRCm381089,454,234 - 89,506,658 (-)NCBI
MGSCv371088,916,979 - 88,996,367 (-)RGD
Celera1091,441,224 - 91,574,747 (-)RGD
cM Map10 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001385711   ⟹   NP_001372640
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,235 - 89,369,465 (-)NCBI
Sequence:
RefSeq Acc Id: NM_009108   ⟹   NP_033134
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,096 - 89,342,520 (-)NCBI
GRCm381089,454,234 - 89,506,658 (-)NCBI
MGSCv371088,916,979 - 88,996,367 (-)RGD
Celera1091,441,224 - 91,574,747 (-)RGD
cM Map10 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006513391   ⟹   XP_006513454
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,235 - 89,353,334 (-)NCBI
GRCm381089,454,373 - 89,517,472 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030244963   ⟹   XP_030100823
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,235 - 89,352,646 (-)NCBI
GRCm381089,454,373 - 89,516,785 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001779493
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,338 - 89,342,542 (-)NCBI
GRCm381089,454,476 - 89,506,680 (-)NCBI
Sequence:
RefSeq Acc Id: NP_033134   ⟸   NM_009108
- Peptide Label: isoform 3
- UniProtKB: Q3V1T8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001156976   ⟸   NM_001163504
- Peptide Label: isoform 2
- UniProtKB: Q60641 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001157172   ⟸   NM_001163700
- Peptide Label: isoform 1
- UniProtKB: Q60643 (UniProtKB/Swiss-Prot),   Q60642 (UniProtKB/Swiss-Prot),   Q60641 (UniProtKB/Swiss-Prot),   E9QJW2 (UniProtKB/Swiss-Prot),   D3YTT2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006513454   ⟸   XM_006513391
- Peptide Label: isoform X1
- UniProtKB: Q60641 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_030100823   ⟸   XM_030244963
- Peptide Label: isoform X1
Ensembl Acc Id: ENSMUSP00000100933   ⟸   ENSMUST00000105296
Ensembl Acc Id: ENSMUSP00000100934   ⟸   ENSMUST00000105297
Ensembl Acc Id: ENSMUSP00000053092   ⟸   ENSMUST00000058126
RefSeq Acc Id: NP_001372640   ⟸   NM_001385711
- Peptide Label: isoform 4
Protein Domains
NR LBD   Nuclear receptor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q60641-F1-model_v2 AlphaFold Q60641 1-488 view protein structure

Promoters
RGD ID:6819674
Promoter ID:MM_KWN:5305
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney,   Liver
Transcripts:NM_001163700,   OTTMUST00000054480,   UC007GSI.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361088,969,124 - 88,969,624 (-)MPROMDB
RGD ID:8673010
Promoter ID:EPDNEW_M14535
Type:multiple initiation site
Name:Nr1h4_1
Description:Mus musculus nuclear receptor subfamily 1, group H, member 4, transcript variant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M14536  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381089,506,638 - 89,506,698EPDNEW
RGD ID:8673012
Promoter ID:EPDNEW_M14536
Type:initiation region
Name:Nr1h4_2
Description:Mus musculus nuclear receptor subfamily 1, group H, member 4, transcript variant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M14535  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381089,533,563 - 89,533,623EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1352464 AgrOrtholog
Ensembl Genes ENSMUSG00000047638 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000058126 ENTREZGENE
  ENSMUST00000058126.15 UniProtKB/Swiss-Prot
  ENSMUST00000105296 ENTREZGENE
  ENSMUST00000105296.9 UniProtKB/Swiss-Prot
  ENSMUST00000105297 ENTREZGENE
  ENSMUST00000105297.2 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro NHR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NR_LBD_NR1H4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_hormone_rcpt_NR1 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 mmu:20186 UniProtKB/Swiss-Prot
MGD MGI:1352464 ENTREZGENE
NCBI Gene Nr1h4 ENTREZGENE
PANTHER BILE ACID RECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR HORMONE RECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nr1h4 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 Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D3YTT2 ENTREZGENE
  E9QJW2 ENTREZGENE
  NR1H4_MOUSE UniProtKB/Swiss-Prot
  Q3V1T8 ENTREZGENE, UniProtKB/TrEMBL
  Q60641 ENTREZGENE
  Q60642 ENTREZGENE
  Q60643 ENTREZGENE
  Q99MT9_MOUSE UniProtKB/TrEMBL
UniProt Secondary D3YTT2 UniProtKB/Swiss-Prot
  E9QJW2 UniProtKB/Swiss-Prot
  Q60642 UniProtKB/Swiss-Prot
  Q60643 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-08-21 Nr1h4  nuclear receptor subfamily 1, group H, member 4  Fxr  farnesoid X receptor  Symbol and/or name change 5135510 APPROVED
2024-08-21 Fxr  farnesoid X receptor  Nr1h4  nuclear receptor subfamily 1, group H, member 4  Symbol and/or name change 5135510 APPROVED