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) Rattus norvegicus
Symbol: Nr1h4
Name: nuclear receptor subfamily 1, group H, member 4
RGD ID: 628831
Description: Enables several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; bile acid receptor activity; and chenodeoxycholic acid binding activity. Contributes to double-stranded DNA binding activity. Involved in several processes, including cellular response to bile acid; liver development; and regulation of cellular biosynthetic process. Part of receptor complex. Used to study extrahepatic cholestasis; intrahepatic cholestasis; and portal hypertension. Biomarker of bile duct disease (multiple); liver disease (multiple); obesity; and premature menopause. 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); PARTICIPATES IN bile acid signaling pathway; bile acid signaling pathway; bile acid signaling pathway; INTERACTS WITH 1,3,7,9-tetramethyluric acid; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
Previously known as: bile acid receptor; farnesoid X activated receptor; farnesoid X-activated receptor; farnesol receptor HRR-1; Fxr; MGC94878; nuclear receptor subfamily 1 group H member 4; retinoid X receptor-interacting protein 14; RXR-interacting protein 14
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
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
JBrowse: View Region in Genome Browser (JBrowse)

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

Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component
euchromatin  (IEA,ISO)
nucleus  (IEA)
receptor complex  (IDA,IEA,ISO)

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

Mammalian Phenotype
liver fibrosis  (IDA,IMP)

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. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. Lipopolysaccharide represses cholesterol 7-alpha hydroxylase and induces binding activity to the bile acid response element II. Dikopoulos N, etal., Eur J Clin Invest. 2003 Jan;33(1):58-64.
10. Glucose regulates the expression of the farnesoid X receptor in liver. Duran-Sandoval D, etal., Diabetes. 2004 Apr;53(4):890-8.
11. A synthetic farnesoid X receptor (FXR) agonist promotes cholesterol lowering in models of dyslipidemia. Evans MJ, etal., Am J Physiol Gastrointest Liver Physiol. 2009 Mar;296(3):G543-52. doi: 10.1152/ajpgi.90585.2008. Epub 2009 Jan 8.
12. A farnesoid x receptor-small heterodimer partner regulatory cascade modulates tissue metalloproteinase inhibitor-1 and matrix metalloprotease expression in hepatic stellate cells and promotes resolution of liver fibrosis. Fiorucci S, etal., J Pharmacol Exp Ther. 2005 Aug;314(2):584-95. Epub 2005 Apr 28.
13. 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.
14. 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.
15. Identification of a nuclear receptor that is activated by farnesol metabolites. Forman BM, etal., Cell 1995 Jun 2;81(5):687-93.
16. 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.
17. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
18. 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.
19. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
20. 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.
21. 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.
22. Farnesoid X receptor agonist reduces serum asymmetric dimethylarginine levels through hepatic dimethylarginine dimethylaminohydrolase-1 gene regulation. Hu T, etal., J Biol Chem. 2006 Dec 29;281(52):39831-8. Epub 2006 Oct 25.
23. 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.
24. Bile acids regulate the ontogenic expression of ileal bile acid binding protein in the rat via the farnesoid X receptor. Hwang ST, etal., Gastroenterology. 2002 May;122(5):1483-92.
25. 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.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. 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.
37. Identification of a nuclear receptor for bile acids. Makishima M, etal., Science. 1999 May 21;284(5418):1362-5. doi: 10.1126/science.284.5418.1362.
38. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
39. Structural basis for bile acid binding and activation of the nuclear receptor FXR. Mi LZ, etal., Mol Cell. 2003 Apr;11(4):1093-100.
40. 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.
41. 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.
42. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
43. Farnesoid X receptor regulates bile acid-amino acid conjugation. Pircher PC, etal., J Biol Chem. 2003 Jul 25;278(30):27703-11. Epub 2003 May 16.
44. 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.
45. 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.
46. GOA pipeline RGD automated data pipeline
47. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
48. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
49. 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.
50. 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.
51. Dehydroepiandrosterone sulfotransferase gene induction by bile acid activated farnesoid X receptor. Song CS, etal., J Biol Chem 2001 Nov 9;276(45):42549-56.
52. Regulation of carbohydrate metabolism by the farnesoid X receptor. Stayrook KR, etal., Endocrinology. 2005 Mar;146(3):984-91. Epub 2004 Nov 24.
53. 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.
54. 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.
55. 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.
56. Discovery of Tropifexor (LJN452), a Highly Potent Non-bile Acid FXR Agonist for the Treatment of Cholestatic Liver Diseases and Nonalcoholic Steatohepatitis (NASH). Tully DC, etal., J Med Chem. 2017 Dec 28;60(24):9960-9973. doi: 10.1021/acs.jmedchem.7b00907. Epub 2017 Dec 8.
57. 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.
58. 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.
59. 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.
60. 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.
61. 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.
62. 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.
63. The relationship between bile acid concentration, glucagon-like-peptide 1, fibroblast growth factor 15 and bile acid receptors in rats during progression of glucose intolerance. Yan X, etal., BMC Endocr Disord. 2017 Sep 25;17(1):60. doi: 10.1186/s12902-017-0211-5.
64. 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.
65. 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.
66. 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.
67. 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.
68. 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.
69. 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.
70. 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
PMID:7760852   PMID:12421815   PMID:12477932   PMID:12660231   PMID:12815072   PMID:12891557   PMID:12917447   PMID:14729567   PMID:14990788   PMID:15471871   PMID:15521018   PMID:15590640  
PMID:15721319   PMID:16357303   PMID:16446356   PMID:16473946   PMID:18006431   PMID:18006476   PMID:18029909   PMID:18467501   PMID:18510855   PMID:18972444   PMID:19027009   PMID:19864602  
PMID:20026603   PMID:20155456   PMID:20305288   PMID:20447400   PMID:21205480   PMID:21242261   PMID:21757002   PMID:21924881   PMID:22661717   PMID:23070085   PMID:23372731   PMID:23410061  
PMID:23767959   PMID:23835330   PMID:23861371   PMID:24211198   PMID:24266967   PMID:25446530   PMID:25771127   PMID:26392308   PMID:26782298   PMID:26888176   PMID:27050864   PMID:27190252  
PMID:27896916   PMID:29198707   PMID:32443832   PMID:33092050   PMID:38036169   PMID:38135007  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
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
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
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
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_00495540536,160,049 - 36,237,751 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540536,160,360 - 36,236,258 (+)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
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
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
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
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
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
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
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
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
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
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
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 in Nr1h4
1015 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:244
Count of miRNA genes:154
Interacting mature miRNAs:172
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 (
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)71816950526029351Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)72055570529891047Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2723,846,173 - 23,846,345 (+)MAPPERmRatBN7.2
Rnor_6.0730,003,481 - 30,003,652NCBIRnor6.0
Rnor_5.0730,105,012 - 30,105,183UniSTSRnor5.0
RGSC_v3.4726,189,811 - 26,189,982UniSTSRGSC3.4
Celera720,992,866 - 20,993,037UniSTS
Cytogenetic Map7q13UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2723,846,369 - 23,846,561 (+)MAPPERmRatBN7.2
Rnor_6.0730,003,677 - 30,003,868NCBIRnor6.0
Rnor_5.0730,105,208 - 30,105,399UniSTSRnor5.0
RGSC_v3.4726,190,007 - 26,190,198UniSTSRGSC3.4
Celera720,993,062 - 20,993,253UniSTS
RH 3.4 Map7108.9UniSTS
Cytogenetic Map7q13UniSTS


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
Medium 3 23 23 23 23
Low 24 34 18 16 18 1 1 32 10 37 9 1
Below cutoff 19 3 7 7 42 2 4 2 7


RefSeq Acc Id: ENSRNOT00000009910   ⟹   ENSRNOP00000009910
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl723,846,122 - 23,942,047 (-)Ensembl
Rnor_6.0 Ensembl730,003,429 - 30,162,056 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091227   ⟹   ENSRNOP00000073765
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl723,846,351 - 23,903,525 (-)Ensembl
Rnor_6.0 Ensembl730,003,586 - 30,105,132 (-)Ensembl
RefSeq Acc Id: NM_021745   ⟹   NP_068513
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,846,122 - 23,942,047 (-)NCBI
Rnor_6.0730,003,429 - 30,162,056 (-)NCBI
Rnor_5.0730,104,960 - 30,107,142 (-)NCBI
Rnor_5.0730,170,397 - 30,214,796 (-)NCBI
RGSC_v3.4726,189,759 - 26,307,061 (-)RGD
Celera720,992,814 - 21,085,820 (-)RGD
RefSeq Acc Id: XM_008765260   ⟹   XP_008763482
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,846,354 - 23,904,247 (-)NCBI
Rnor_6.0730,003,578 - 30,105,682 (-)NCBI
RefSeq Acc Id: XM_008765261   ⟹   XP_008763483
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,846,350 - 23,904,242 (-)NCBI
Rnor_6.0730,003,594 - 30,105,681 (-)NCBI
RefSeq Acc Id: XM_008765262   ⟹   XP_008763484
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,846,354 - 23,942,085 (-)NCBI
Rnor_6.0730,003,578 - 30,162,095 (-)NCBI
RefSeq Acc Id: XM_039079832   ⟹   XP_038935760
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,872,295 - 23,904,238 (-)NCBI
RefSeq Acc Id: XR_005486714
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,872,176 - 23,904,237 (-)NCBI
RefSeq Acc Id: NP_068513   ⟸   NM_021745
- UniProtKB: Q62735 (UniProtKB/Swiss-Prot),   A6IFR2 (UniProtKB/TrEMBL),   A6IFR3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763484   ⟸   XM_008765262
- Peptide Label: isoform X3
- UniProtKB: A0A8L2Q4E9 (UniProtKB/TrEMBL),   A6IFR3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763482   ⟸   XM_008765260
- Peptide Label: isoform X1
- UniProtKB: A6IFR3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763483   ⟸   XM_008765261
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K6D2 (UniProtKB/TrEMBL),   A6IFR3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073765   ⟸   ENSRNOT00000091227
RefSeq Acc Id: ENSRNOP00000009910   ⟸   ENSRNOT00000009910
RefSeq Acc Id: XP_038935760   ⟸   XM_039079832
- Peptide Label: isoform X4
Protein Domains
NR LBD   Nuclear receptor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q62735-F1-model_v2 AlphaFold Q62735 1-469 view protein structure


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

RGD ID:13695135
Promoter ID:EPDNEW_R5660
Type:multiple initiation site
Description:nuclear receptor subfamily 1, group H, member 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Experiment Methods:Single-end sequencing.
Rat AssemblyChrPosition (strand)Source
Rnor_6.0730,162,060 - 30,162,120EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628831 AgrOrtholog
BioCyc Gene G2FUF-34492 BioCyc
Ensembl Genes ENSRNOG00000007197 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009910 ENTREZGENE
  ENSRNOT00000009910.5 UniProtKB/TrEMBL
  ENSRNOT00000091227.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL 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_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:60351 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nr1h4 PhenoGen
  NUCLEAR_REC_DBD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007197 RatGTEx
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
  NR1H4_RAT UniProtKB/Swiss-Prot

Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Nr1h4  nuclear receptor subfamily 1, group H, member 4      Symbol and Name status set to approved 625702 APPROVED
2003-02-27 Nr1h4        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction interacts with the retinoid X receptor to form a heterodimeric complex 729010