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

Gene ID: 15378, updated on 31-Jan-2023

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
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)

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 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 domain specific binding ISO
Inferred from Sequence Orthology
more info
 
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 transcription coregulator binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription corepressor 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 DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
PubMed 
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 DNA-templated transcription 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 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 
acts_upstream_of_or_within positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of fatty acid biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of gene expression 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 regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
PubMed 
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
 
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
 
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
 
involved_in response to trichostatin A 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 
acts_upstream_of transcription by RNA polymerase II 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, Q8CFY1
    UniProtKB/TrEMBL
    A0A6P5QXH7, A0A8C6IDS4
    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
    UniProtKB/TrEMBL
    A0A6P5QXI1
    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