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

    Gene ID: 15378, updated on 20-Jul-2021

    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
    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
    Nr; Hnf; HNF-; Hnf4; MODY; 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
    NEW
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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
    109 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)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (163372924..163398643)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 2310001K24 gene 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 predicted gene, 25881 Neighboring gene Crx opposite strand transcript 1 pseudogene 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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    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 binding 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
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables arachidonic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables fatty acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables fatty-acyl-CoA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables long-chain fatty acyl-CoA 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
    PubMed 
    enables palmitoyl-CoA hydrolase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables signaling receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables stearic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription cis-regulatory region 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 SMAD protein signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in acyl-CoA metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in anatomical structure development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in blood coagulation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell-cell junction organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cholesterol homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in establishment of tissue polarity ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in glucose homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in hepatocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lipid homeostasis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within lipid metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of activation of Janus kinase activity ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell growth ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of protein import into nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of tyrosine phosphorylation of STAT protein ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ornithine metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in phospholipid homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of fatty acid biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of gluconeogenesis 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
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within 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 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
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of circadian rhythm ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of gastrulation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of insulin secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of lipid metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of microvillus assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to glucose IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to glucose ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within sex differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within signal transduction involved in regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in triglyceride homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in type B pancreatic cell development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in xenobiotic metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in chromatin IC
    Inferred by Curator
    more info
    PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    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)

    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_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
      B9VVT6
      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

      See identical proteins and their annotated locations for NP_032287.2

      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
      P49698
      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: Mus musculus Annotation Release 109 details...Open this link in a new tab

    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

      See identical proteins and their annotated locations for XP_006498851.1

      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/Swiss-Prot
      P49698
      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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