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

    Gene ID: 9971, updated on 8-Jul-2021

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NR1H4 in Genome Data Viewer
    Location:
    12q23.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (100473866..100564414)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (100867644..100958192)

    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
    Genome-wide association study identifies a novel susceptibility locus at 12q23.1 for lung squamous cell carcinoma in han chinese.
    GeneReviews: Not available

    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
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables bile acid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables bile acid binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables bile acid binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables bile acid receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables bile acid receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables bile acid receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables chenodeoxycholic acid binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nuclear receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables nuclear receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nuclear receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables nuclear receptor binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in bile acid signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in bile acid signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in bile acid signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cellular response to bile acid IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to fatty acid IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to organonitrogen compound ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in cellular triglyceride homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in histone H3-R17 methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular bile acid receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in intracellular receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of I-kappaB kinase/NF-kappaB signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of inflammatory response IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in negative regulation of interferon-gamma production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in negative regulation of tumor necrosis factor production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of very-low-density lipoprotein particle remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nitrogen catabolite activation of transcription from RNA polymerase II promoter IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive regulation of glutamate metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of interleukin-17 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of phosphatidic acid biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of bile acid biosynthetic process TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of cholesterol metabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of insulin secretion involved in cellular response to glucose stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of low-density lipoprotein particle clearance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of urea metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in toll-like receptor 4 signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromatin IC
    Inferred by Curator
    more info
    PubMed 
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in euchromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    part_of 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)

    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.

    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 Updated Annotation Release 109.20210514

    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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