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Nr1h4 nuclear receptor subfamily 1, group H, member 4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 60351, updated on 2-Nov-2024

Summary

Official Symbol
Nr1h4provided by RGD
Official Full Name
nuclear receptor subfamily 1, group H, member 4provided by RGD
Primary source
RGD:628831
See related
EnsemblRapid:ENSRNOG00000007197 AllianceGenome:RGD:628831
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Fxr
Summary
Enables several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chenodeoxycholic acid binding activity. Contributes to double-stranded DNA binding activity. Involved in several processes, including cellular response to bile acid; negative regulation of biosynthetic process; and regulation of gene expression. Part of receptor complex. Used to study extrahepatic cholestasis; intrahepatic cholestasis; and portal hypertension. Biomarker of bile duct disease (multiple); liver disease (multiple); and obesity. 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). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Liver (RPKM 265.5) and Kidney (RPKM 198.2) See more
Orthologs
NEW
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Try the new Transcript table

Genomic context

See Nr1h4 in Genome Data Viewer
Location:
7q13
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (25733471..25829440, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (23846122..23942085, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (30003429..30162095, complement)

Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene 60S ribosomal protein L9 pseudogene Neighboring gene growth arrest-specific 2 like 3 Neighboring gene U7 small nuclear RNA Neighboring gene Annexin A7, pseudogene 2 Neighboring gene solute carrier family 17 member 8 Neighboring gene SCY1 like pseudokinase 2

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

General gene information

Markers

Clone Names

  • MGC94878

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables bile acid binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables bile acid binding IDA
Inferred from Direct Assay
more info
PubMed 
enables bile acid binding IEA
Inferred from Electronic Annotation
more info
 
enables bile acid binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables bile acid binding ISO
Inferred from Sequence Orthology
more info
 
enables bile acid nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables bile acid nuclear receptor activity IEA
Inferred from Electronic Annotation
more info
 
enables bile acid nuclear receptor activity ISO
Inferred from Sequence Orthology
more info
 
enables chenodeoxycholic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
enables chenodeoxycholic acid binding IEA
Inferred from Electronic Annotation
more info
 
enables chenodeoxycholic acid binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor activity IEA
Inferred from Electronic Annotation
more info
 
enables nuclear receptor activity ISO
Inferred from Sequence Orthology
more info
 
enables nuclear retinoid X receptor binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear retinoid X receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables peptide binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription coregulator binding IEA
Inferred from Electronic Annotation
more info
 
enables transcription coregulator binding ISO
Inferred from Sequence Orthology
more info
 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within Notch signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in bile acid and bile salt transport IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in bile acid metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in bile acid metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in bile acid metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within bile acid metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in bile acid signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cell-cell junction assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in cell-cell junction assembly ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to bile acid IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to bile acid IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to bile acid ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to fatty acid IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to fatty acid ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to lipopolysaccharide ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to xenobiotic stimulus IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to xenobiotic stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cholesterol homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cholesterol homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in cholesterol homeostasis IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cholesterol homeostasis ISO
Inferred from Sequence Orthology
more info
 
involved_in defense response to bacterium IEA
Inferred from Electronic Annotation
more info
 
involved_in defense response to bacterium ISO
Inferred from Sequence Orthology
more info
 
involved_in digestive tract development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in fatty acid homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in fatty acid homeostasis ISO
Inferred from Sequence Orthology
more info
 
involved_in glucose homeostasis ISO
Inferred from Sequence Orthology
more info
 
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in intracellular glucose homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in intracellular glucose homeostasis ISO
Inferred from Sequence Orthology
more info
 
involved_in intracellular receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in intracellular receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in intracellular triglyceride homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in intracellular triglyceride homeostasis ISO
Inferred from Sequence Orthology
more info
 
involved_in leukocyte migration involved in inflammatory response IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in negative regulation of NF-kappaB transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of NF-kappaB transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of apoptotic process ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of canonical NF-kappaB signal transduction IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of canonical NF-kappaB signal transduction ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of collagen biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of inflammatory response ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of interleukin-1 production IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of interleukin-1 production ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of interleukin-2 production IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of interleukin-2 production ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of interleukin-6 production IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of interleukin-6 production ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of monocyte chemotactic protein-1 production IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of monocyte chemotactic protein-1 production ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of triglyceride biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of tumor necrosis factor production IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of tumor necrosis factor production ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of tumor necrosis factor-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of tumor necrosis factor-mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of type II interferon production IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of type II interferon production ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of very-low-density lipoprotein particle remodeling IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of very-low-density lipoprotein particle remodeling ISO
Inferred from Sequence Orthology
more info
 
involved_in nuclear receptor-mediated bile acid signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in nuclear receptor-mediated bile acid signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in nuclear receptor-mediated bile acid signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of adipose tissue development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of adipose tissue development ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of ammonia assimilation cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of ammonia assimilation cycle ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of glutamate metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of insulin receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of insulin receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of insulin secretion involved in cellular response to glucose stimulus IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of insulin secretion involved in cellular response to glucose stimulus ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of interleukin-17 production IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of interleukin-17 production ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of phosphatidic acid biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of phosphatidic acid biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of carbohydrate metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of lipid storage IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in regulation of low-density lipoprotein particle clearance IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of low-density lipoprotein particle clearance ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of urea metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of urea metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in response to cholesterol IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to estrogen IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to ethanol IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to glucose IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to lipopolysaccharide IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to norepinephrine IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to nutrient levels IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to organic cyclic compound IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to xenobiotic stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in toll-like receptor 9 signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in toll-like receptor 9 signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in triglyceride homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in triglyceride homeostasis IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in triglyceride homeostasis ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in euchromatin IEA
Inferred from Electronic Annotation
more info
 
located_in euchromatin ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
part_of receptor complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of receptor complex IEA
Inferred from Electronic Annotation
more info
 
part_of receptor complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
bile acid receptor
Names
RXR-interacting protein 14
farnesoid X-activated receptor
farnesol receptor HRR-1
retinoid X receptor-interacting protein 14

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_021745.1NP_068513.1  bile acid receptor

    See identical proteins and their annotated locations for NP_068513.1

    Status: PROVISIONAL

    Source sequence(s)
    U18374
    UniProtKB/Swiss-Prot
    Q62735
    UniProtKB/TrEMBL
    A6IFR2, A6IFR3
    Conserved Domains (2) summary
    cd06936
    Location:245464
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:121204
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086025.1 Reference GRCr8

    Range
    25733471..25829440 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_008765262.3XP_008763484.1  bile acid receptor isoform X3

    UniProtKB/TrEMBL
    A0A8L2Q4E9, A6IFR3
    Related
    ENSRNOP00000009910.4, ENSRNOT00000009910.6
    Conserved Domains (2) summary
    cd06936
    Location:249468
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:121208
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  2. XM_008765260.4XP_008763482.1  bile acid receptor isoform X1

    UniProtKB/TrEMBL
    A6IFR3
    Conserved Domains (2) summary
    cd06936
    Location:292511
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:164251
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  3. XM_008765261.4XP_008763483.1  bile acid receptor isoform X2

    UniProtKB/TrEMBL
    A0A0G2K6D2, A6IFR3
    Related
    ENSRNOP00000073765.1, ENSRNOT00000091227.3
    Conserved Domains (2) summary
    cd06936
    Location:288507
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:164247
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  4. XM_039079832.2XP_038935760.1  bile acid receptor isoform X4

    Conserved Domains (1) summary
    cl02596
    Location:164251
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

RNA

  1. XR_005486714.2 RNA Sequence