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hnf4a hepatocyte nuclear factor 4, alpha [ Danio rerio (zebrafish) ]

Gene ID: 322358, updated on 9-Sep-2025
Official Symbol
hnf4aprovided by ZNC
Official Full Name
hepatocyte nuclear factor 4, alphaprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-1077
See related
Ensembl:ENSDARG00000021494 AllianceGenome:ZFIN:ZDB-GENE-030131-1077
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
fb58h09; sb:eu665; id:ibd1279; wu:fb58h09
Summary
Enables DNA-binding transcription factor activity. Acts upstream of or within pancreas regeneration; response to bacterium; and type B pancreatic cell development. Predicted to be located in nucleus. Is expressed in gut; intestinal bulb primordium; liver; pleuroperitoneal region; and yolk syncytial layer. 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, Jul 2025]
Orthologs
human mouse all
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See hnf4a in Genome Data Viewer
Location:
chromosome: 23
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2025_04 current GRCz12tu (GCF_049306965.1) 23 NC_133198.1 (28776583..28809919)
RS_2024_08 previous assembly GRCz11 (GCF_000002035.6) 23 NC_007134.7 (25832596..25865856)

Chromosome 23 - NC_133198.1Genomic Context describing neighboring genes Neighboring gene acyl-coenzyme A diphosphatase FITM2 pseudogene Neighboring gene uncharacterized LOC141380497 Neighboring gene R3H domain containing-like Neighboring gene uncharacterized LOC137489129 Neighboring gene tocopherol (alpha) transfer protein-like Neighboring gene protein kinase (cAMP-dependent, catalytic) inhibitor gamma Neighboring gene uncharacterized LOC137489128

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Related articles in PubMed

  1. Formation of the digestive system in zebrafish. I. Liver morphogenesis. Field HA, et al. Dev Biol, 2003 Jan 15. PMID 12645931
  2. Gamma radiation induces locus specific changes to histone modification enrichment in zebrafish and Atlantic salmon. Lindeman LC, et al. PLoS One, 2019. PMID 30759148, Free PMC Article
  3. Conserved roles for Hnf4 family transcription factors in zebrafish development and intestinal function. Heppert JK, et al. Genetics, 2022 Nov 30. PMID 36218393, Free PMC Article
  4. A feedback loop between the liver-enriched transcription factor network and miR-122 controls hepatocyte differentiation. Laudadio I, et al. Gastroenterology, 2012 Jan. PMID 21920465
  5. Identification of anti-inflammatory compounds from Zhongjing formulae by knowledge mining and high-content screening in a zebrafish model of inflammatory bowel diseases. Yu Y, et al. Chin Med, 2021 May 31. PMID 34059101, Free PMC Article

See all (77) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. These results indicate a critical and conserved role for HNF4A in maintaining intestinal homeostasis in response to microbiota.
    Title: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha.
Submit: New GeneRIF Correction

Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IGI
Inferred from Genetic Interaction
more info
 PubMed 
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 IEA
Inferred from Electronic Annotation
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 sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within endocrine pancreas development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within pancreas regeneration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
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 regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within response to bacterium IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within type B pancreatic cell development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
hepatocyte nuclear factor 4-alpha
Names
NR2A1

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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_194368.1 → NP_919349.1  hepatocyte nuclear factor 4-alpha

    See identical proteins and their annotated locations for NP_919349.1

    Status: PROVISIONAL

    Source sequence(s)
    AF473824
    UniProtKB/TrEMBL
    Q8AXB6
    Related
    ENSDARP00000112924.1, ENSDART00000145426.3
    Conserved Domains (2) summary
    cd06931
    Location:142 → 363
    NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
    cd06960
    Location:51 → 126
    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_049306965.1-RS_2025_04

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

Reference GRCz12tu Primary Assembly

Genomic

  1. NC_133198.1 Reference GRCz12tu Primary Assembly

    Range
    28776583..28809919
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021469749.2 → XP_021325424.1  hepatocyte nuclear factor 4-alpha isoform X4

    UniProtKB/TrEMBL
    A0A8M9PKL5
    Conserved Domains (2) summary
    cd06931
    Location:134 → 355
    NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
    cd06960
    Location:38 → 118
    NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers

  2. XM_073938065.1 → XP_073794166.1  hepatocyte nuclear factor 4-alpha isoform X5

  3. XM_073938064.1 → XP_073794165.1  hepatocyte nuclear factor 4-alpha isoform X2

  4. XM_073938063.1 → XP_073794164.1  hepatocyte nuclear factor 4-alpha isoform X1

  5. XM_021469748.3 → XP_021325423.2  hepatocyte nuclear factor 4-alpha isoform X3

  6. XM_009296811.5 → XP_009295086.1  hepatocyte nuclear factor 4-alpha isoform X7

    See identical proteins and their annotated locations for XP_009295086.1

    UniProtKB/TrEMBL
    A8E5K2
    Conserved Domains (2) summary
    cd06931
    Location:115 → 336
    NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
    cd06960
    Location:24 → 99
    NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers

  7. XM_068216678.2 → XP_068072779.1  hepatocyte nuclear factor 4-alpha isoform X6

    UniProtKB/TrEMBL
    A0AB32TA66
Nucleotide Protein Strain
Heading Accession and Version

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