U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    Nr1h4 nuclear receptor subfamily 1, group H, member 4 [ Mus musculus (house mouse) ]

    Gene ID: 20186, updated on 19-Jun-2024

    Summary

    Official Symbol
    Nr1h4provided by MGI
    Official Full Name
    nuclear receptor subfamily 1, group H, member 4provided by MGI
    Primary source
    MGI:MGI:1352464
    See related
    Ensembl:ENSMUSG00000047638 AllianceGenome:MGI:1352464
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Fxr; HRR1; RIP14; Rxrip14
    Summary
    Enables DNA-binding transcription factor activity, RNA polymerase II-specific; bile acid binding activity; and 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). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in large intestine adult (RPKM 22.6), liver adult (RPKM 18.8) and 10 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:
    10 C2; 10 44.98 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (89290096..89369484, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (89454234..89533645, complement)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene anoctamin 4 Neighboring gene predicted gene, 30769 Neighboring gene STARR-seq mESC enhancer starr_27517 Neighboring gene STARR-positive B cell enhancer ABC_E6898 Neighboring gene STARR-seq mESC enhancer starr_27520 Neighboring gene STARR-positive B cell enhancer ABC_E1404 Neighboring gene growth arrest-specific 2 like 3 Neighboring gene STARR-seq mESC enhancer starr_27521 Neighboring gene solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8 Neighboring gene STARR-positive B cell enhancer ABC_E5164 Neighboring gene SCY1-like 2 (S. cerevisiae)

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    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 ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    enables DNA-binding transcription factor activity IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    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 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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables bile acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chenodeoxycholic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    contributes_to double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables nuclear receptor activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    enables nuclear retinoid X receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables peptide binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within Notch signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in bile acid and bile salt transport ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within bile acid metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in 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 bile acid signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in bile acid signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell-cell junction assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to bile acid ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to fatty acid ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to lipopolysaccharide IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to organonitrogen compound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to xenobiotic stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cholesterol homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cholesterol homeostasis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in defense response to bacterium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in fatty acid homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in glucose homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within immune system process IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular glucose homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in intracellular receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular triglyceride homeostasis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of canonical NF-kappaB signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of inflammatory response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of inflammatory response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of interleukin-1 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of interleukin-2 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of interleukin-6 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of monocyte chemotactic protein-1 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 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 ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of tumor necrosis factor production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of type II interferon production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of type II interferon production ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of very-low-density lipoprotein particle remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of very-low-density lipoprotein particle remodeling ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in nitrogen catabolite activation of transcription from RNA polymerase II promoter IC
    Inferred by Curator
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in positive regulation of adipose tissue development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of ammonia assimilation cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of glutamate metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of insulin receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of insulin secretion involved in cellular response to glucose stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of interleukin-17 production ISO
    Inferred from Sequence Orthology
    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
     
    acts_upstream_of_or_within 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 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of DNA-templated transcription IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of carbohydrate metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of insulin secretion involved in cellular response to glucose stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of low-density lipoprotein particle clearance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of urea metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to norepinephrine ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in toll-like receptor 9 signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in triglyceride homeostasis IDA
    Inferred from Direct Assay
    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
     
    part_of chromatin IC
    Inferred by Curator
    more info
    PubMed 
    part_of chromatin ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    part_of euchromatin ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    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_001163504.1NP_001156976.1  bile acid receptor isoform 2

      See identical proteins and their annotated locations for NP_001156976.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2), alternatively referred to as alpha 1, differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC152417
      Consensus CDS
      CCDS48669.1
      UniProtKB/Swiss-Prot
      Q60641
      Related
      ENSMUSP00000100934.2, ENSMUST00000105297.2
      Conserved Domains (2) summary
      cd06936
      Location:250469
      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. NM_001163700.1NP_001157172.1  bile acid receptor isoform 1

      See identical proteins and their annotated locations for NP_001157172.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1), alternatively referred to as beta 1 and alpha 3, encodes the longest isoform (1).
      Source sequence(s)
      AC152417, AK002513
      Consensus CDS
      CCDS48668.1
      UniProtKB/Swiss-Prot
      D3YTT2, E9QJW2, Q60641, Q60642, Q60643
      Related
      ENSMUSP00000100933.3, ENSMUST00000105296.9
      Conserved Domains (2) summary
      cd06936
      Location:264483
      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:135222
      NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
    3. NM_001385711.1NP_001372640.1  bile acid receptor isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), alternatively referred to as alpha 2, differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC152417
      Conserved Domains (2) summary
      cd06936
      Location:246465
      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
    4. NM_009108.2NP_033134.2  bile acid receptor isoform 3

      See identical proteins and their annotated locations for NP_033134.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3), alternatively referred to as beta 2 and alpha 4, uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter isoform (2), compared to isoform 1.
      Source sequence(s)
      AC152417, AK132255
      Consensus CDS
      CCDS24116.1
      UniProtKB/TrEMBL
      Q3V1T8
      Related
      ENSMUSP00000053092.9, ENSMUST00000058126.15
      Conserved Domains (2) summary
      cd06936
      Location:260479
      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:135218
      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_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      89290096..89369484 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006513391.4XP_006513454.1  bile acid receptor isoform X1

      See identical proteins and their annotated locations for XP_006513454.1

      UniProtKB/Swiss-Prot
      Q60641
      Conserved Domains (2) summary
      cd06936
      Location:250469
      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_030244963.2XP_030100823.1  bile acid receptor isoform X1

      Conserved Domains (2) summary
      cd06936
      Location:250469
      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

    RNA

    1. XR_001779493.2 RNA Sequence