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    Hnf4a hepatic nuclear factor 4, alpha [ Mus musculus (house mouse) ]

    Gene ID: 15378, updated on 4-Jan-2025

    Summary

    Official Symbol
    Hnf4aprovided by MGI
    Official Full Name
    hepatic nuclear factor 4, alphaprovided by MGI
    Primary source
    MGI:MGI:109128
    See related
    Ensembl:ENSMUSG00000017950 AllianceGenome:MGI:109128
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Hnf4; HNF-4; MODY1; Nr2a1; Tcf14; TCF-14; Hnf4alpha
    Summary
    The protein encoded by this gene is a transcription factor involved in the development of the pancreas, liver, kidney, and intestines. The encoded protein also functions to maintain glucose homeostasis. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
    Expression
    Biased expression in large intestine adult (RPKM 148.8), kidney adult (RPKM 141.3) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Hnf4a in Genome Data Viewer
    Location:
    2 H3; 2 84.32 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (163348731..163414827)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (163506811..163572907)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 2310001K24 gene Neighboring gene STARR-positive B cell enhancer ABC_E4516 Neighboring gene fat storage-inducing transmembrane protein 2 Neighboring gene R3H domain containing-like Neighboring gene hepatic nuclear factor 4 alpha, opposite strand Neighboring gene STARR-seq mESC enhancer starr_06311 Neighboring gene predicted gene, 25881 Neighboring gene STARR-positive B cell enhancer ABC_E2652 Neighboring gene STARR-seq mESC enhancer starr_06312 Neighboring gene Crx opposite strand transcript 1 pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E9538 Neighboring gene STARR-positive B cell enhancer ABC_E2057 Neighboring gene tocopherol (alpha) transfer protein-like

    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

    General gene information

    Gene Ontology Provided by MGI

    Items 1 - 25 of 36
    Function Evidence Code Pubs
    enables DNA binding PubMed 
    enables DNA binding PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity PubMed 
    enables DNA-binding transcription factor activity PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding PubMed 
    enables arachidonate binding  
    enables chromatin binding PubMed 
    enables cis-regulatory region sequence-specific DNA binding  
    enables fatty acid binding  
    enables fatty acid binding  
    enables fatty-acyl-CoA binding  
    enables long-chain fatty acyl-CoA binding  
    enables long-chain fatty acyl-CoA hydrolase activity  
    enables nuclear receptor activity  
    enables nuclear receptor activity  
    enables protein binding PubMed 
    enables protein domain specific binding  
    enables protein homodimerization activity  
    enables protein homodimerization activity  
    enables protein-containing complex binding  
    enables sequence-specific DNA binding PubMed 
    enables sequence-specific DNA binding  
    enables sequence-specific double-stranded DNA binding  
    enables signaling receptor binding  
    enables signaling receptor binding  
    enables stearic acid binding  
    enables transcription cis-regulatory region binding PubMed 
    enables transcription cis-regulatory region binding  
    enables transcription coregulator binding  
    enables transcription corepressor binding  
    enables zinc ion binding  
    Items 1 - 25 of 36
    Items 1 - 25 of 60
    Process Evidence Code Pubs
    involved_in acyl-CoA metabolic process  
    involved_in blood coagulation  
    involved_in blood coagulation  
    involved_in cell differentiation  
    involved_in cell differentiation  
    involved_in cell-cell junction organization  
    involved_in cholesterol homeostasis PubMed 
    involved_in establishment of tissue polarity  
    involved_in glucose homeostasis PubMed 
    involved_in intracellular receptor signaling pathway  
    involved_in lipid homeostasis  
    acts_upstream_of_or_within lipid metabolic process PubMed 
    involved_in negative regulation of DNA-templated transcription  
    involved_in negative regulation of DNA-templated transcription  
    involved_in negative regulation of cell growth  
    involved_in negative regulation of cell growth  
    involved_in negative regulation of cell migration  
    involved_in negative regulation of cell population proliferation  
    involved_in negative regulation of cell population proliferation  
    involved_in negative regulation of mitotic cell cycle  
    involved_in negative regulation of protein import into nucleus  
    involved_in negative regulation of tyrosine phosphorylation of STAT protein  
    involved_in ornithine metabolic process  
    involved_in phospholipid homeostasis PubMed 
    acts_upstream_of_or_within positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of fatty acid biosynthetic process  
    involved_in positive regulation of gene expression  
    involved_in positive regulation of gluconeogenesis  
    involved_in positive regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within regulation of DNA-templated transcription PubMed 
    involved_in regulation of circadian rhythm PubMed 
    involved_in regulation of circadian rhythm  
    acts_upstream_of_or_within regulation of gastrulation PubMed 
    involved_in regulation of insulin secretion PubMed 
    involved_in regulation of lipid metabolic process  
    involved_in regulation of lipid metabolic process  
    involved_in regulation of microvillus assembly  
    involved_in regulation of ornithine metabolic process  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II PubMed 
    involved_in regulation of transcription by RNA polymerase II  
    involved_in response to glucose PubMed 
    involved_in response to glucose  
    involved_in response to trichostatin A  
    involved_in rhythmic process  
    acts_upstream_of_or_within sex differentiation PubMed 
    acts_upstream_of_or_within signal transduction involved in regulation of gene expression PubMed 
    acts_upstream_of transcription by RNA polymerase II PubMed 
    involved_in triglyceride homeostasis PubMed 
    involved_in xenobiotic metabolic process  
    involved_in xenobiotic metabolic process  
    Items 1 - 25 of 60
    Component Evidence Code Pubs
    located_in chromatin PubMed 
    located_in cytoplasm  
    located_in cytosol  
    located_in nucleoplasm  
    located_in nucleoplasm  
    located_in nucleus PubMed 
    located_in nucleus PubMed 

    General protein information

    Preferred Names
    hepatocyte nuclear factor 4-alpha
    Names
    HNF4 alpha
    Nuclear receptor 2A1
    nuclear receptor subfamily 2 group A member 1
    transcription factor 14
    transcription factor HNF-4

    NCBI Reference Sequences (RefSeq)

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    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_001312906.1NP_001299835.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha11

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (HNF4alpha11) has a shorter and distinct N-terminus compared to isoform HNF4alpha2.
      Source sequence(s)
      AL591488, BP765980, FJ608820
      UniProtKB/TrEMBL
      Z4YKX0
      Conserved Domains (2) summary
      cd06931
      Location:126348
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:35110
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    2. NM_001312907.1NP_001299836.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha10

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction in the 3' end compared to variant 1. The resulting isoform (HNF4alpha10) has a shorter and distinct N-terminus and lacks an internal segment compared to isoform HNF4alpha2.
      Source sequence(s)
      AL591488, BP765980, FJ608819
      UniProtKB/TrEMBL
      B9VVT5
      Conserved Domains (2) summary
      cd06931
      Location:126348
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:35110
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    3. NM_008261.3NP_032287.2  hepatocyte nuclear factor 4-alpha isoform HNF4alpha2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (HNF4alpha2).
      Source sequence(s)
      AK143948, AL591488, BY034048
      Consensus CDS
      CCDS17012.1
      UniProtKB/Swiss-Prot
      A2A5I5, A2ICH0, P49698, Q3UNX3, Q8CFY1
      UniProtKB/TrEMBL
      Z4YKX0
      Related
      ENSMUSP00000018094.7, ENSMUST00000018094.13
      Conserved Domains (2) summary
      cd06931
      Location:151373
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:60135
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) 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_000068.8 Reference GRCm39 C57BL/6J

      Range
      163348731..163414827
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006498788.2XP_006498851.1  hepatocyte nuclear factor 4-alpha isoform X2

      UniProtKB/TrEMBL
      Z4YKX0
      Conserved Domains (2) summary
      cd06931
      Location:129351
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:38113
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    2. XM_006498787.1XP_006498850.1  hepatocyte nuclear factor 4-alpha isoform X1

      UniProtKB/TrEMBL
      Z4YKX0
      Conserved Domains (2) summary
      cd06931
      Location:151373
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:60135
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
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