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    Hnf4a hepatocyte nuclear factor 4, alpha [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25735, updated on 9-Dec-2024

    Summary

    Official Symbol
    Hnf4aprovided by RGD
    Official Full Name
    hepatocyte nuclear factor 4, alphaprovided by RGD
    Primary source
    RGD:2810
    See related
    EnsemblRapid:ENSRNOG00000008895 AllianceGenome:RGD:2810
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Hnf4; Hnf4alpha
    Summary
    Enables several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; anion binding activity; and long-chain fatty acyl-CoA hydrolase activity. Involved in several processes, including hepatocyte differentiation; negative regulation of non-membrane spanning protein tyrosine kinase activity; and positive regulation of biosynthetic process. Located in nucleus. Biomarker of hepatocellular carcinoma and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in Fanconi renotubular syndrome 4; familial combined hyperlipidemia; hypoglycemia; maturity-onset diabetes of the young type 1; and type 2 diabetes mellitus. Orthologous to human HNF4A (hepatocyte nuclear factor 4 alpha). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 1041.7) and Liver (RPKM 892.3) See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Hnf4a in Genome Data Viewer
    Location:
    3q42
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (172606220..172667758)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (152186787..152248320)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (159902441..159965003)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC103691964 Neighboring gene fat storage-inducing transmembrane protein 2 Neighboring gene uncharacterized LOC102548241 Neighboring gene R3H domain containing-like Neighboring gene uncharacterized LOC120101780 Neighboring gene ATP synthase membrane subunit c locus 2, pseudogene 4 Neighboring gene alpha tocopherol transfer protein like

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by RGD

    Items 1 - 25 of 43
    Function Evidence Code Pubs
    enables DNA binding  
    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 activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity  
    enables DNA-binding transcription factor activity  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II-specific DNA-binding transcription factor binding  
    enables RNA polymerase II-specific DNA-binding transcription factor binding  
    enables arachidonate binding PubMed 
    enables chromatin binding  
    enables chromatin binding  
    enables cis-regulatory region sequence-specific DNA binding PubMed 
    enables fatty acid binding  
    enables fatty acid binding PubMed 
    enables fatty acid binding  
    enables fatty-acyl-CoA binding PubMed 
    enables long-chain fatty acyl-CoA binding PubMed 
    enables long-chain fatty acyl-CoA hydrolase activity PubMed 
    enables nuclear receptor activity  
    enables nuclear receptor activity  
    enables nuclear receptor activity  
    enables nuclear steroid receptor activity  
    enables protein binding PubMed 
    enables protein domain specific binding PubMed 
    enables protein homodimerization activity  
    enables protein homodimerization activity  
    enables protein-containing complex binding PubMed 
    enables protein-containing complex binding PubMed 
    enables protein-containing complex binding PubMed 
    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 PubMed 
    enables transcription cis-regulatory region binding  
    enables transcription coregulator binding PubMed 
    enables transcription corepressor binding PubMed 
    enables zinc ion binding  
    Items 1 - 25 of 43
    Items 1 - 25 of 82
    Process Evidence Code Pubs
    involved_in acyl-CoA metabolic process PubMed 
    involved_in blood coagulation  
    involved_in blood coagulation  
    involved_in cell differentiation  
    involved_in cell differentiation PubMed 
    involved_in cell-cell junction organization PubMed 
    involved_in cellular response to hypoxia PubMed 
    involved_in cholesterol homeostasis  
    involved_in cholesterol homeostasis  
    involved_in establishment of tissue polarity PubMed 
    involved_in glucose homeostasis  
    involved_in glucose homeostasis  
    involved_in hepatocyte differentiation PubMed 
    involved_in intracellular receptor signaling pathway  
    involved_in lipid homeostasis  
    involved_in lipid metabolic process  
    acts_upstream_of_or_within lipid metabolic process  
    involved_in negative regulation of DNA-binding transcription factor activity PubMed 
    involved_in negative regulation of DNA-templated transcription  
    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 PubMed 
    involved_in negative regulation of cell population proliferation PubMed 
    involved_in negative regulation of cell population proliferation  
    involved_in negative regulation of cell population proliferation  
    involved_in negative regulation of mitotic cell cycle PubMed 
    involved_in negative regulation of non-membrane spanning protein tyrosine kinase activity PubMed 
    involved_in negative regulation of protein import into nucleus PubMed 
    involved_in phospholipid homeostasis  
    involved_in phospholipid homeostasis  
    involved_in positive regulation of DNA-templated transcription PubMed 
    acts_upstream_of_or_within positive regulation of DNA-templated transcription  
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of fatty acid biosynthetic process PubMed 
    involved_in positive regulation of gene expression PubMed 
    involved_in positive regulation of gene expression PubMed 
    involved_in positive regulation of gluconeogenesis PubMed 
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in regulation of DNA-templated transcription  
    acts_upstream_of_or_within regulation of DNA-templated transcription  
    involved_in regulation of circadian rhythm  
    involved_in regulation of circadian rhythm  
    involved_in regulation of circadian rhythm  
    involved_in regulation of gastrulation  
    acts_upstream_of_or_within regulation of gastrulation  
    involved_in regulation of insulin secretion  
    involved_in regulation of insulin secretion  
    involved_in regulation of lipid metabolic process  
    involved_in regulation of lipid metabolic process  
    involved_in regulation of microvillus assembly PubMed 
    involved_in regulation of ornithine metabolic process  
    involved_in regulation of ornithine metabolic process  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II  
    involved_in regulation of transcription by RNA polymerase II  
    involved_in response to cAMP PubMed 
    involved_in response to dexamethasone PubMed 
    involved_in response to glucose PubMed 
    involved_in response to glucose  
    involved_in response to glucose  
    involved_in response to lipopolysaccharide PubMed 
    involved_in response to nutrient levels PubMed 
    involved_in response to trichostatin A PubMed 
    involved_in response to xenobiotic stimulus PubMed 
    involved_in rhythmic process  
    involved_in sex differentiation  
    acts_upstream_of_or_within sex differentiation  
    involved_in signal transduction involved in regulation of gene expression  
    acts_upstream_of_or_within signal transduction involved in regulation of gene expression  
    involved_in steroid hormone receptor signaling pathway  
    involved_in transcription by RNA polymerase II  
    acts_upstream_of transcription by RNA polymerase II  
    involved_in triglyceride homeostasis  
    involved_in triglyceride homeostasis  
    involved_in xenobiotic metabolic process  
    acts_upstream_of_positive_effect xenobiotic metabolic process  
    Items 1 - 25 of 82
    Component Evidence Code Pubs
    located_in cytoplasm  
    located_in cytoplasm  
    located_in nucleoplasm  
    located_in nucleoplasm  
    located_in nucleus PubMed 
    located_in nucleus  
    located_in nucleus  

    General protein information

    Preferred Names
    hepatocyte nuclear factor 4-alpha
    Names
    HNF-4-alpha
    TCF-14
    alpha transcription factor 4
    hepatic nuclear factor 4, alpha
    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_001270931.1NP_001257860.1  hepatocyte nuclear factor 4-alpha isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) is the longest transcript. It differs in the 5' UTR and 5' coding region, compared to variant 1. The resulting isoform (2, also known as HNF4alpha11) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      EF193390, FJ608817, FQ095211, JAXUCZ010000003
      UniProtKB/TrEMBL
      A0A0G2K5P1, A6JX36
      Related
      ENSRNOP00000073501.1, ENSRNOT00000089893.3
      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_001270933.1NP_001257862.1  hepatocyte nuclear factor 4-alpha isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and has two coding region differences, compared to variant 1. The resulting isoform (3, also known as HNF4alpha10) is shorter, has a distinct N-terminus and lacks an internal segment in the C-terminal region, compared to isoform 1.
      Source sequence(s)
      EF193390, FJ608816, FQ095211, JAXUCZ010000003
      UniProtKB/TrEMBL
      A6JX36
      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_022180.2NP_071516.2  hepatocyte nuclear factor 4-alpha isoform 1

      See identical proteins and their annotated locations for NP_071516.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      CK483260, D10554, FM042560, FQ095211, JAXUCZ010000003
      UniProtKB/TrEMBL
      A0A0G2K0G1, A6JX36, A6JX37
      Related
      ENSRNOP00000071432.1, ENSRNOT00000078703.3
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      172606220..172667758
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006235516.5XP_006235578.1  hepatocyte nuclear factor 4-alpha isoform X1

      UniProtKB/TrEMBL
      A6JX36
      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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