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    hdac4 histone deacetylase 4 [ Danio rerio (zebrafish) ]

    Gene ID: 568877, updated on 9-Dec-2024

    Summary

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    Official Symbol
    hdac4provided by ZNC
    Official Full Name
    histone deacetylase 4provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-061013-95
    See related
    Ensembl:ENSDARG00000098349 AllianceGenome:ZFIN:ZDB-GENE-061013-95
    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
    wu:fa96d08; wu:fc56f08; zgc:152701
    Summary
    Predicted to enable histone deacetylase activity and metal ion binding activity. Acts upstream of or within several processes, including embryonic cranial skeleton morphogenesis; perichondral ossification; and regulation of neural crest formation. Predicted to be located in nucleus. Is expressed in several structures, including cranial neural crest cell; cranium; nervous system; optic vesicle; and trigeminal placode. Human ortholog(s) of this gene implicated in ataxia telangiectasia; eating disorder; and retinal degeneration. Orthologous to human HDAC4 (histone deacetylase 4). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See hdac4 in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (45881018..46276357, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (46082097..46475908, complement)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene neurogenic differentiation factor 1 Neighboring gene twist2 Neighboring gene uncharacterized LOC137496500 Neighboring gene uncharacterized LOC137496434 Neighboring gene lactase/phlorizin hydrolase Neighboring gene lactase

    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. Expression characterization and the promoter activity analysis of zebrafish hdac4. Zhu K, et al. Fish Physiol Biochem, 2012 Apr. PMID 21773810
    2. Histone deacetylase-4 is required during early cranial neural crest development for generation of the zebrafish palatal skeleton. DeLaurier A, et al. BMC Dev Biol, 2012 Jun 7. PMID 22676467, Free PMC Article
    3. Calcium signals act through histone deacetylase to mediate pronephric kidney morphogenesis. Rothschild SC, et al. Dev Dyn, 2018 Jun. PMID 29633426
    4. Pattern of change in histone 3 lysine 9 acetylation and histone deacetylases in development of zebrafish embryo. Li Y, et al. J Genet, 2014 Aug. PMID 25189256
    5. TDP-43 Regulation of AChE Expression Can Mediate ALS-Like Phenotype in Zebrafish. Campanari ML, et al. Cells, 2021 Jan 22. PMID 33499374, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results demonstrate that Hdac4 is a regulator of cranial neural crest-derived palatal skeletal precursors during early embryogenesis.
      Title: Histone deacetylase-4 is required during early cranial neural crest development for generation of the zebrafish palatal skeleton.
    2. region between -698 and -302 might contain mild negative regulatory elements
      Title: Expression characterization and the promoter activity analysis of zebrafish hdac4.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0288

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables histone deacetylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone deacetylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within embryonic cranial skeleton morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in epigenetic regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within neural crest cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within perichondral ossification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within pronephros morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of neural crest formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of histone deacetylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    histone deacetylase 4
    NP_001034447.2
    XP_005172586.1

    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_001039358.2 → NP_001034447.2  histone deacetylase 4

      See identical proteins and their annotated locations for NP_001034447.2

      Status: PROVISIONAL

      Source sequence(s)
      BC124583
      UniProtKB/TrEMBL
      Q08BS8
      Related
      ENSDARP00000138997.1, ENSDART00000169682.2
      Conserved Domains (3) summary
      cd10162
      Location:33 → 122
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      pfam12474
      Location:39 → 158
      PKK; Polo kinase kinase
      cl17011
      Location:594 → 996
      Arginase_HDAC; Arginase-like and histone-like hydrolases

    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_007120.7 Reference GRCz11 Primary Assembly

      Range
      45881018..46276357 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005172529.5 → XP_005172586.1  histone deacetylase 4 isoform X1

      UniProtKB/TrEMBL
      A0A0R4IAH0, A0A8M2BJV4
      Related
      ENSDARP00000131327.1, ENSDART00000165238.3
      Conserved Domains (3) summary
      cd10162
      Location:62 → 151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      pfam12474
      Location:68 → 187
      PKK; Polo kinase kinase
      cl17011
      Location:623 → 1025
      Arginase_HDAC; Arginase-like and histone-like hydrolases
    Nucleotide Protein Strain
    Heading Accession and Version

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