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
Symbol: Nr1h4
Name: nuclear receptor subfamily 1, group H, member 4
RGD ID: 734104
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 lipid homeostasis; negative regulation of cytokine production; and regulation of signal transduction. Acts upstream of or within several processes, including Notch signaling pathway; bile acid metabolic process; and negative regulation of very-low-density lipoprotein particle remodeling. Predicted to be located in euchromatin and nucleus. Predicted to be part of receptor complex. Is expressed in several structures, including 1st branchial arch; central nervous system; liver; sensory organ; and urinary system. 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-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
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
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
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  (EXP,ISO)
(S)-colchicine  (ISO)
1,2-dimethylhydrazine  (EXP)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (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)
3,6-diaminoacridine  (ISO)
3-chloropropane-1,2-diol  (ISO)
3alpha-hydroxy-5beta-pregnan-20-one  (EXP)
4'-epidoxorubicin  (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  (ISO)
AICA ribonucleotide  (ISO)
albendazole  (ISO)
albendazole S-oxide  (ISO)
aldehydo-D-glucosamine  (ISO)
all-trans-retinoic acid  (ISO)
alpha-linolenic acid  (ISO)
alvocidib  (ISO)
ammonium chloride  (ISO)
angelicin  (ISO)
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)
benazepril  (ISO)
benidipine  (ISO)
benomyl  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (ISO)
beta-hexachlorocyclohexane  (EXP,ISO)
beta-naphthoflavone  (ISO)
bezafibrate  (EXP,ISO)
bifenthrin  (ISO)
biochanin A  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
Boldine  (ISO)
bortezomib  (ISO)
bosentan  (ISO)
butachlor  (ISO)
butanal  (ISO)
carbendazim  (ISO)
carbon nanotube  (EXP)
CGP 52608  (ISO)
chenodeoxycholic acid  (EXP,ISO)
chlorpromazine  (ISO)
cholanic acid  (ISO)
cholate  (ISO)
cholesterol  (EXP,ISO)
cholic acid  (EXP,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)
Cyclopamine  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (EXP,ISO)
cyfluthrin  (ISO)
cyhalothrin  (ISO)
cypermethrin  (ISO)
daunorubicin  (ISO)
deoxycholic acid  (EXP,ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (EXP)
dichloroacetic acid  (EXP)
dicrotophos  (ISO)
digoxin  (ISO)
dihydroartemisinin  (ISO)
dimethyl sulfoxide  (ISO)
Diosbulbin B  (EXP)
dioscin  (ISO)
diosgenin  (ISO)
Diphenadione  (ISO)
dipyridamole  (ISO)
dobutamine  (ISO)
Doramectin  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
emamectin  (ISO)
emetine  (ISO)
emodin  (EXP)
endosulfan  (ISO)
enilconazole  (EXP)
epoxiconazole  (EXP)
eprinomectin  (ISO)
ethacridine  (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)
glyburide  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycyrrhetinic acid  (ISO)
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)
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)
ketoconazole  (ISO)
lacidipine  (ISO)
lercanidipine  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (EXP,ISO)
malic acid  (EXP)
manidipine  (ISO)
mebendazole  (ISO)
menadione  (ISO)
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)
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)
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)
papaverine  (ISO)
paracetamol  (EXP,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)
propanal  (ISO)
psoralen  (ISO)
pyrazinecarboxamide  (ISO)
quercetin  (ISO)
quinolines  (ISO)
resveratrol  (ISO)
rifaximin  (ISO)
ritonavir  (ISO)
rosuvastatin  (ISO)
rotenone  (ISO)
Salidroside  (EXP)
Selamectin  (ISO)
senecionine  (ISO)
silibinin  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sirolimus  (ISO)
sodium arsenite  (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)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
thioacetamide  (ISO)
titanium dioxide  (EXP)
topotecan  (ISO)
trichloroethene  (ISO)
triclosan  (ISO)
trifloxystrobin  (ISO)
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)
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)
bile acid signaling pathway  (IBA,IMP,ISO)
cell differentiation  (IBA)
cell-cell junction assembly  (IMP)
cellular glucose homeostasis  (IDA)
cellular response to bile acid  (ISO)
cellular response to fatty acid  (ISO)
cellular response to lipopolysaccharide  (IMP)
cellular response to organonitrogen compound  (IMP)
cellular response to xenobiotic stimulus  (ISO)
cellular triglyceride homeostasis  (ISO)
cholesterol homeostasis  (IMP,ISO)
defense response to bacterium  (IDA)
digestive tract development  (ISO)
DNA-templated transcription  (ISO)
fatty acid homeostasis  (IMP)
glucose homeostasis  (IDA,ISO)
hepatocyte proliferation  (ISO)
histone H3-R17 methylation  (ISO)
immune system process  (IEA)
inflammatory response  (IEA)
innate immune response  (IEA)
intracellular bile acid receptor signaling pathway  (ISO)
intracellular receptor signaling pathway  (IMP,ISO)
leukocyte migration involved in inflammatory response  (ISO)
lipid localization  (ISO)
liver regeneration  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of collagen biosynthetic process  (ISO)
negative regulation of I-kappaB kinase/NF-kappaB signaling  (IMP,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)
nitrogen catabolite activation of transcription from RNA polymerase II promoter  (IC)
Notch signaling pathway  (IDA)
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  (ISO)
positive regulation of phosphatidic acid biosynthetic process  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,IDA,IMP,ISO)
regulation of bile acid secretion  (ISO)
regulation of carbohydrate metabolic process  (ISO)
regulation of DNA-templated transcription  (ISO)
regulation of gene expression  (ISO)
regulation of insulin secretion involved in cellular response to glucose stimulus  (ISO)
regulation of lipid storage  (ISO)
regulation of low-density lipoprotein particle clearance  (ISO)
regulation of transcription by RNA polymerase II  (IGI,ISO)
regulation of urea metabolic process  (IMP)
response to 17alpha-ethynylestradiol  (ISO)
response to cholesterol  (ISO)
response to ethanol  (ISO)
response to fenofibrate  (ISO)
response to glucose  (ISO)
response to lipopolysaccharide  (ISO)
response to norepinephrine  (ISO)
response to nutrient levels  (ISO)
response to organic cyclic compound  (ISO)
response to xenobiotic stimulus  (ISO)
toll-like receptor 4 signaling pathway  (ISO)
toll-like receptor 9 signaling pathway  (IMP)
transcription by RNA polymerase II  (IDA)
triglyceride homeostasis  (IDA,ISO)

Cellular Component
chromatin  (IC,ISO)
euchromatin  (ISO)
nucleus  (ISO)
receptor complex  (ISO)

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 sensitivity to induced morbidity/mortality  (IAGP)
increased spleen weight  (IAGP)
jaundice  (IAGP)
liver degeneration  (IAGP)
liver inflammation  (IAGP)

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
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
PMID:7760852   PMID:8835541   PMID:10349636   PMID:11030617   PMID:11042159   PMID:11076861   PMID:11208732   PMID:11279518   PMID:12004058   PMID:12062799   PMID:12393883   PMID:12421815  
PMID:12456679   PMID:12477932   PMID:12519762   PMID:12529392   PMID:12718892   PMID:12891557   PMID:12917447   PMID:12923173   PMID:12949731   PMID:14592843   PMID:14681479   PMID:14729567  
PMID:15371561   PMID:15466244   PMID:15489334   PMID:15558057   PMID:15564327   PMID:15590640   PMID:15611112   PMID:15721319   PMID:15817812   PMID:15899888   PMID:15981587   PMID:16002565  
PMID:16023103   PMID:16141072   PMID:16141073   PMID:16186601   PMID:16224116   PMID:16251721   PMID:16269825   PMID:16284190   PMID:16327028   PMID:16357057   PMID:16410358   PMID:16423920  
PMID:16446356   PMID:16473946   PMID:16606610   PMID:16609145   PMID:16614213   PMID:16682417   PMID:16778009   PMID:16825595   PMID:16844773   PMID:16912278   PMID:16971476   PMID:16973757  
PMID:17110163   PMID:17205580   PMID:17289919   PMID:17426284   PMID:17440045   PMID:17521389   PMID:17545158   PMID:17622954   PMID:17624466   PMID:17660268   PMID:17720959   PMID:17931734  
PMID:17950284   PMID:17963822   PMID:18287559   PMID:18436567   PMID:18448072   PMID:18495661   PMID:18562803   PMID:18648086   PMID:18703564   PMID:18820241   PMID:18842595   PMID:18948497  
PMID:18972444   PMID:18988759   PMID:19028791   PMID:19030180   PMID:19047134   PMID:19056864   PMID:19072826   PMID:19118524   PMID:19182371   PMID:19204003   PMID:19386638   PMID:19407337  
PMID:19556342   PMID:19605523   PMID:19608735   PMID:19718444   PMID:19776172   PMID:19805516   PMID:19815629   PMID:19864602   PMID:19880446   PMID:19883617   PMID:19910507   PMID:19965601  
PMID:19965603   PMID:19996107   PMID:20026603   PMID:20059953   PMID:20060466   PMID:20091679   PMID:20185821   PMID:20211986   PMID:20233723   PMID:20373033   PMID:20375256   PMID:20444884  
PMID:20447400   PMID:20483916   PMID:20531290   PMID:20699418   PMID:20842631   PMID:20850540   PMID:20851881   PMID:20868235   PMID:20957146   PMID:21081494   PMID:21123943   PMID:21195347  
PMID:21224055   PMID:21242261   PMID:21267068   PMID:21296199   PMID:21386911   PMID:21430080   PMID:21431940   PMID:21504366   PMID:21593203   PMID:21619550   PMID:21642744   PMID:21690373  
PMID:21757002   PMID:21804189   PMID:21862726   PMID:21873635   PMID:22135065   PMID:22144677   PMID:22178739   PMID:22261820   PMID:22268101   PMID:22278336   PMID:22285937   PMID:22290433  
PMID:22296850   PMID:22447981   PMID:22467244   PMID:22474109   PMID:22474125   PMID:22492528   PMID:22540009   PMID:22542490   PMID:22565294   PMID:22643070   PMID:22661717   PMID:22730081  
PMID:22952826   PMID:23051670   PMID:23056173   PMID:23172628   PMID:23178280   PMID:23205607   PMID:23348961   PMID:23372731   PMID:23395169   PMID:23460643   PMID:23462932   PMID:23507574  
PMID:23519696   PMID:23530060   PMID:23541942   PMID:23549084   PMID:23609136   PMID:23747249   PMID:23861371   PMID:23916961   PMID:24004655   PMID:24007921   PMID:24037988   PMID:24038130  
PMID:24043304   PMID:24064762   PMID:24091600   PMID:24146773   PMID:24211198   PMID:24268772   PMID:24269813   PMID:24291500   PMID:24333182   PMID:24338587   PMID:24365583   PMID:24389307  
PMID:24464484   PMID:24531544   PMID:24656817   PMID:24670636   PMID:24721598   PMID:24875360   PMID:24952961   PMID:25138215   PMID:25156247   PMID:25183423   PMID:25184625   PMID:25278094  
PMID:25339829   PMID:25363753   PMID:25383523   PMID:25400456   PMID:25425577   PMID:25446530   PMID:25460735   PMID:25470824   PMID:25496033   PMID:25500885   PMID:25506828   PMID:25545350  
PMID:25559344   PMID:25593129   PMID:25599407   PMID:25651182   PMID:25655198   PMID:25719402   PMID:25870546   PMID:26134028   PMID:26238153   PMID:26241054   PMID:26332085   PMID:26474702  
PMID:26482353   PMID:26505219   PMID:26554605   PMID:26620317   PMID:26655953   PMID:26670557   PMID:26728993   PMID:26740296   PMID:26811456   PMID:26812075   PMID:26848619   PMID:26899873  
PMID:27146480   PMID:27170759   PMID:27358174   PMID:27376807   PMID:27383204   PMID:27471003   PMID:27531557   PMID:27624003   PMID:27639801   PMID:27758768   PMID:27820600   PMID:27821667  
PMID:27889186   PMID:27896916   PMID:27956139   PMID:28065787   PMID:28125709   PMID:28130067   PMID:28181583   PMID:28223344   PMID:28380377   PMID:28400119   PMID:28446510   PMID:28449117  
PMID:28478385   PMID:28496104   PMID:28505368   PMID:28586124   PMID:28596381   PMID:28647362   PMID:28669602   PMID:28711154   PMID:28714273   PMID:28787755   PMID:28852062   PMID:28891815  
PMID:28894223   PMID:28895119   PMID:28951211   PMID:28956216   PMID:29028769   PMID:29089371   PMID:29107284   PMID:29142166   PMID:29377207   PMID:29718219   PMID:29730159   PMID:29739889  
PMID:29771182   PMID:29925501   PMID:29929982   PMID:29940597   PMID:29976576   PMID:29981427   PMID:30098335   PMID:30122655   PMID:30208322   PMID:30260705   PMID:30337250   PMID:30354208  
PMID:30445014   PMID:30464200   PMID:30520052   PMID:30536462   PMID:30580099   PMID:30653340   PMID:30794774   PMID:30803859   PMID:30862680   PMID:30967475   PMID:30996006   PMID:31298930  
PMID:31387746   PMID:31470114   PMID:31485455   PMID:31506275   PMID:31673703   PMID:31776512   PMID:31862954   PMID:31875848   PMID:31911428   PMID:31932588   PMID:32006644   PMID:32034442  
PMID:32145254   PMID:32170842   PMID:32305491   PMID:32325033   PMID:32446390   PMID:32450881   PMID:32461639   PMID:32661285   PMID:32712104   PMID:32914211   PMID:33029504   PMID:33029898  
PMID:33068587   PMID:33318189   PMID:33368684   PMID:33462514   PMID:33482151   PMID:33526687   PMID:33568795   PMID:33594777   PMID:33737325   PMID:33767132   PMID:33857491   PMID:33895309  
PMID:33938457   PMID:33980856   PMID:34010595   PMID:34164827   PMID:34246806   PMID:34270928   PMID:34505013   PMID:34708236   PMID:34862975   PMID:34869329   PMID:35216094   PMID:35251469  
PMID:35447541   PMID:35526796   PMID:35767918   PMID:35780502  


Comparative Map Data
(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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh3812100,473,866 - 100,564,414 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 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
(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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0728,003,082 - 28,099,010 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0727,780,396 - 27,876,311 (-)NCBIRnor_WKY
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
(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
PanPan1.112101,457,885 - 101,548,058 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12101,457,885 - 101,548,058 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01298,052,778 - 98,144,085 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
(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
SpeTri2.0NW_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

Position Markers
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
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
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
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
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
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map10C2UniSTS
cM Map1050.0UniSTS

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

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID

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 (
For more information about miRGate, see PMID:25858286 or access the full paper here.



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

Reference Sequences
RefSeq Acc Id: ENSMUST00000058126   ⟹   ENSMUSP00000053092
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1089,290,096 - 89,342,511 (-)Ensembl
GRCm38.p6 Ensembl1089,454,234 - 89,506,649 (-)Ensembl
RefSeq Acc Id: ENSMUST00000105296   ⟹   ENSMUSP00000100933
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1089,290,096 - 89,342,520 (-)Ensembl
GRCm38.p6 Ensembl1089,454,234 - 89,506,658 (-)Ensembl
RefSeq Acc Id: ENSMUST00000105297   ⟹   ENSMUSP00000100934
RefSeq Status:
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
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
RefSeq Acc Id: NM_001163700   ⟹   NP_001157172
RefSeq Status: VALIDATED
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
RefSeq Acc Id: NM_001385711   ⟹   NP_001372640
RefSeq Status: VALIDATED
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,235 - 89,369,465 (-)NCBI
RefSeq Acc Id: NM_009108   ⟹   NP_033134
RefSeq Status: VALIDATED
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
RefSeq Acc Id: XM_006513391   ⟹   XP_006513454
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,235 - 89,353,334 (-)NCBI
GRCm381089,454,373 - 89,517,472 (-)NCBI
RefSeq Acc Id: XM_030244963   ⟹   XP_030100823
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,235 - 89,352,646 (-)NCBI
GRCm381089,454,373 - 89,516,785 (-)NCBI
RefSeq Acc Id: XR_001779493
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm391089,290,338 - 89,342,542 (-)NCBI
GRCm381089,454,476 - 89,506,680 (-)NCBI
Reference Sequences
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),   Q60641 (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
RefSeq Acc Id: ENSMUSP00000100933   ⟸   ENSMUST00000105296
RefSeq Acc Id: ENSMUSP00000100934   ⟸   ENSMUST00000105297
RefSeq 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

RGD ID:6819674
Promoter ID:MM_KWN:5305
SO ACC ID:SO:0000170
Tissues & Cell Lines:Kidney,   Liver
Transcripts:NM_001163700,   OTTMUST00000054480,   UC007GSI.1
Mouse AssemblyChrPosition (strand)Source
MGSCv361088,969,124 - 88,969,624 (-)MPROMDB
RGD ID:8673010
Promoter ID:EPDNEW_M14535
Type:multiple initiation site
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,
Alternative Promoters:null; see alsoEPDNEW_M14536  
Experiment Methods:Single-end sequencing.
Mouse AssemblyChrPosition (strand)Source
GRCm381089,506,638 - 89,506,698EPDNEW
RGD ID:8673012
Promoter ID:EPDNEW_M14536
Type:initiation region
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,
Alternative Promoters:null; see alsoEPDNEW_M14535  
Experiment Methods:Single-end sequencing.
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 Protein ENSMUSP00000053092 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000100933 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000100934 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000058126 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000105296 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000105297 ENTREZGENE, UniProtKB/Swiss-Prot
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 mmu:20186 UniProtKB/Swiss-Prot
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
SMART HOLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt NR1H4_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary D3YTT2 UniProtKB/Swiss-Prot
  E9QJW2 UniProtKB/Swiss-Prot
  Q60642 UniProtKB/Swiss-Prot
  Q60643 UniProtKB/Swiss-Prot