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NR1H4 nuclear receptor subfamily 1 group H member 4 [ Homo sapiens (human) ]

Gene ID: 9971, updated on 1-Aug-2020

Summary

Official Symbol
NR1H4provided by HGNC
Official Full Name
nuclear receptor subfamily 1 group H member 4provided by HGNC
Primary source
HGNC:HGNC:7967
See related
Ensembl:ENSG00000012504 MIM:603826
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BAR; FXR; HRR1; HRR-1; PFIC5; RIP14
Summary
This gene encodes a ligand-activated transcription factor that shares structural features in common with nuclear hormone receptor family members. This protein functions as a receptor for bile acids, and when bound to bile acids, binds to DNA and regulates the expression of genes involved in bile acid synthesis and transport. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Feb 2016]
Expression
Biased expression in liver (RPKM 14.7), small intestine (RPKM 8.3) and 6 other tissues See more
Orthologs

Genomic context

See NR1H4 in Genome Data Viewer
Location:
12q23.1
Exon count:
14
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (100473866..100564414)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (100867486..100957645)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene DEP domain containing 4 Neighboring gene SCY1 like pseudokinase 2 Neighboring gene solute carrier family 17 member 8 Neighboring gene growth arrest specific 2 like 3 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class A pseudogene 1 Neighboring gene anoctamin 4 Neighboring gene sorting nexin 5 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Cholestasis, progressive familial intrahepatic, 5
MedGen: C4310747 OMIM: 617049 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study identifies a novel susceptibility locus at 12q23.1 for lung squamous cell carcinoma in han chinese.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
matrix gag Treatment of human PBMCs with HIV-1 MA upregulates the expression of MCP-1, ICAM-1, CD40, CD86 and CD36 and downregulates the expression of nuclear receptors FXR and PPARgamma PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC163445

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
bile acid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bile acid binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
bile acid binding TAS
Traceable Author Statement
more info
PubMed 
bile acid receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bile acid receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
bile acid receptor activity TAS
Traceable Author Statement
more info
PubMed 
chenodeoxycholic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
nuclear receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
nuclear receptor binding TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
retinoid X receptor binding IEA
Inferred from Electronic Annotation
more info
 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
bile acid and bile salt transport TAS
Traceable Author Statement
more info
 
bile acid metabolic process IEA
Inferred from Electronic Annotation
more info
 
bile acid signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bile acid signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
bile acid signaling pathway TAS
Traceable Author Statement
more info
PubMed 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell junction assembly IEA
Inferred from Electronic Annotation
more info
 
cellular glucose homeostasis IEA
Inferred from Electronic Annotation
more info
 
cellular response to bile acid IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to fatty acid IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
cellular response to organonitrogen compound ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cellular triglyceride homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
cholesterol homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
defense response to bacterium IEA
Inferred from Electronic Annotation
more info
 
fatty acid homeostasis IEA
Inferred from Electronic Annotation
more info
 
histone H3-R17 methylation IDA
Inferred from Direct Assay
more info
PubMed 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
interleukin-17 production IDA
Inferred from Direct Assay
more info
PubMed 
intracellular bile acid receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
intracellular receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
lipid homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lipid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of I-kappaB kinase/NF-kappaB signaling IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of NF-kappaB transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
negative regulation of apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of interferon-gamma production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-1 production IEA
Inferred from Electronic Annotation
more info
 
negative regulation of interleukin-2 production IEA
Inferred from Electronic Annotation
more info
 
negative regulation of interleukin-6 production IEA
Inferred from Electronic Annotation
more info
 
negative regulation of monocyte chemotactic protein-1 production IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of tumor necrosis factor secretion IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of tumor necrosis factor-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
nitrogen catabolite activation of transcription from RNA polymerase II promoter IC
Inferred by Curator
more info
PubMed 
positive regulation of adipose tissue development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of ammonia assimilation cycle IEA
Inferred from Electronic Annotation
more info
 
positive regulation of glutamate metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of insulin receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of insulin secretion involved in cellular response to glucose stimulus IEA
Inferred from Electronic Annotation
more info
 
positive regulation of phosphatidic acid biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of bile acid biosynthetic process TAS
Traceable Author Statement
more info
PubMed 
regulation of cholesterol metabolic process TAS
Traceable Author Statement
more info
PubMed 
regulation of insulin secretion involved in cellular response to glucose stimulus IDA
Inferred from Direct Assay
more info
PubMed 
regulation of low-density lipoprotein particle clearance IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
regulation of urea metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
toll-like receptor 4 signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
toll-like receptor 9 signaling pathway IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nuclear euchromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
receptor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_029843.1 RefSeqGene

    Range
    5094..95642
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206977.2NP_001193906.1  bile acid receptor isoform 1

    See identical proteins and their annotated locations for NP_001193906.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate exon in the 5' UTR compared to variant 1. Variants 1 and 6 encode the same isoform (1, also known as FXRalpha+).
    Source sequence(s)
    AC010200, AF384555, BC035654, DA011411
    Consensus CDS
    CCDS55873.1
    UniProtKB/Swiss-Prot
    Q96RI1
    UniProtKB/TrEMBL
    F1DAL1
    Related
    ENSP00000496908.1, ENST00000648861.1
    Conserved Domains (2) summary
    cd06936
    Location:251471
    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:124211
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  2. NM_001206978.2NP_001193907.1  bile acid receptor isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an in-frame exon compared to variant 1. This results in a shorter isoform (5) than isoform 1.
    Source sequence(s)
    AC010200, BC035654, BC130573, BC144183, DA011411
    Consensus CDS
    CCDS55874.1
    UniProtKB/Swiss-Prot
    Q96RI1
    Related
    ENSP00000448978.1, ENST00000549996.5
    Conserved Domains (2) summary
    cd06936
    Location:200420
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cl02596
    Location:127149
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  3. NM_001206979.2NP_001193908.1  bile acid receptor isoform 1

    See identical proteins and their annotated locations for NP_001193908.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1 (also known as FXRalpha+). Variants 1 and 6 encode the same isoform (1).
    Source sequence(s)
    AC010200, BC035654, BC130573, DA011411
    Consensus CDS
    CCDS55873.1
    UniProtKB/Swiss-Prot
    Q96RI1
    UniProtKB/TrEMBL
    F1DAL1
    Related
    ENSP00000376712.3, ENST00000392986.8
    Conserved Domains (2) summary
    cd06936
    Location:251471
    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:124211
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  4. NM_001206992.2NP_001193921.1  bile acid receptor isoform 4

    See identical proteins and their annotated locations for NP_001193921.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs 5' UTR, lacks a portion of the 5' coding region, and uses an alternate in-frame splice site, compared to variant 1. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (4, also known as FXRbeta-) has a distinct N-terminus and is longer than isoform 1.
    Source sequence(s)
    AC010200, AF478445, BC035654
    Consensus CDS
    CCDS55875.1
    UniProtKB/Swiss-Prot
    Q96RI1
    Related
    ENSP00000188403.7, ENST00000188403.7
    Conserved Domains (2) summary
    cd06936
    Location:257477
    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:134217
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  5. NM_001206993.2NP_001193922.1  bile acid receptor isoform 3

    See identical proteins and their annotated locations for NP_001193922.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs 5' UTR and lacks a portion of the 5' coding region compared to variant 1. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (3, also known as FXRbeta+) has a distinct, longer N-terminus, compared to isoform 1.
    Source sequence(s)
    AC010200, AF478446, BC035654
    Consensus CDS
    CCDS55876.1
    UniProtKB/Swiss-Prot
    Q96RI1
    Related
    ENSP00000447149.1, ENST00000551379.5
    Conserved Domains (2) summary
    cd06936
    Location:261481
    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:134221
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  6. NM_005123.4NP_005114.1  bile acid receptor isoform 2

    See identical proteins and their annotated locations for NP_005114.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. This results in a shorter isoform (2, also known as FXRalpha-) compared to isoform 1.
    Source sequence(s)
    AC010200, BC035654, DA011411, U68233
    Consensus CDS
    CCDS9078.1
    UniProtKB/Swiss-Prot
    Q96RI1
    UniProtKB/TrEMBL
    B6ZGS9
    Related
    ENSP00000448506.1, ENST00000548884.5
    Conserved Domains (2) summary
    cd06936
    Location:247467
    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:124207
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

RNA

  1. NR_135146.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC010200, AK312959, BC035654, BC144187

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    100473866..100564414
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011539040.2XP_011537342.1  bile acid receptor isoform X1

    See identical proteins and their annotated locations for XP_011537342.1

    UniProtKB/Swiss-Prot
    Q96RI1
    UniProtKB/TrEMBL
    F1DAL1
    Conserved Domains (2) summary
    cd06936
    Location:251471
    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:124211
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  2. XM_011539041.2XP_011537343.1  bile acid receptor isoform X2

    Conserved Domains (2) summary
    cd06936
    Location:210430
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cl02596
    Location:137159
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  3. XM_006719719.2XP_006719782.1  bile acid receptor isoform X3

    Conserved Domains (1) summary
    cl02596
    Location:134221
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  4. XM_011539042.1XP_011537344.1  bile acid receptor isoform X4

    Conserved Domains (1) summary
    cl02596
    Location:134217
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
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