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

    Gene ID: 322358, updated on 9-Dec-2024

    Summary

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    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, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See hnf4a in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (25832596..25865856)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (25905900..25939315)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene acyl-coenzyme A diphosphatase FITM2 pseudogene 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

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

    Bibliography

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    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 (73) 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

    Pathways from PubChem

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    General gene information

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    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    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
    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 
    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
    		  

    General protein information

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    Preferred Names
    hepatocyte nuclear factor 4-alpha
    Names
    NR2A1

    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_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
      A0A8M9P510, 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_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007134.7 Reference GRCz11 Primary Assembly

      Range
      25832596..25865856
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021469749.2 → XP_021325424.1  hepatocyte nuclear factor 4-alpha isoform X2

      UniProtKB/TrEMBL
      A0A8M9PKL5, A0A8M9PSX4
      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_021469748.2 → XP_021325423.1  hepatocyte nuclear factor 4-alpha isoform X1

      UniProtKB/TrEMBL
      A0A8M9PEX6, A0A8M9PSX4
      Conserved Domains (2) summary
      cd06931
      Location:158 → 379
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:62 → 142
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers

    3. XM_009296811.4 → XP_009295086.1  hepatocyte nuclear factor 4-alpha isoform X4

      See identical proteins and their annotated locations for XP_009295086.1

      UniProtKB/TrEMBL
      A0A8M9P510, 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

    4. XM_068216678.1 → XP_068072779.1  hepatocyte nuclear factor 4-alpha isoform X3

      UniProtKB/TrEMBL
      A0A8M9PSX4

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395153.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      283908..291058
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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