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    hdac6 histone deacetylase 6 [ Danio rerio (zebrafish) ]

    Gene ID: 565482, updated on 9-Dec-2024

    Summary

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    Official Symbol
    hdac6provided by ZNC
    Official Full Name
    histone deacetylase 6provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-3232
    See related
    Ensembl:ENSDARG00000008384 AllianceGenome:ZFIN:ZDB-GENE-030131-3232
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    wu:fc31d02
    Summary
    Enables potassium ion binding activity; tubulin deacetylase activity; and zinc ion binding activity. Acts upstream of or within several processes, including hemopoiesis; protein deacetylation; and swimming behavior. Predicted to be part of histone deacetylase complex. Human ortholog(s) of this gene implicated in chondrodysplasia with platyspondyly, distinctive brachydactyly, hydrocephaly, and microphthalmia. Orthologous to human HDAC6 (histone deacetylase 6). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See hdac6 in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (7393435..7444466, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (7374704..7425741, complement)

    Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene ssu-2 homolog, related sequence 1 Neighboring gene selenoprotein H Neighboring gene histone H3-like centromeric protein A Neighboring gene proprotein convertase subtilisin/kexin type 1 inhibitor, like Neighboring gene LHFPL tetraspan subfamily member 4b Neighboring gene GATA binding protein 1b Neighboring gene cyclin dependent kinase 20

    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. Structural insights into HDAC6 tubulin deacetylation and its selective inhibition. Miyake Y, et al. Nat Chem Biol, 2016 Sep. PMID 27454931
    2. Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Hai Y, et al. Nat Chem Biol, 2016 Sep. PMID 27454933, Free PMC Article
    3. Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors. Porter NJ, et al. Proc Natl Acad Sci U S A, 2017 Dec 19. PMID 29203661, Free PMC Article
    4. Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates. Varga JK, et al. Sci Rep, 2022 Feb 2. PMID 35110592, Free PMC Article
    5. Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors. Sandrone G, et al. ACS Med Chem Lett, 2021 Nov 11. PMID 34795871, Free PMC Article

    See all (41) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Histone Deacetylases Cooperate with NF-kappaB to Support the Immediate Migratory Response after Zebrafish Pronephros Injury.
      Title: Histone Deacetylases Cooperate with NF-κB to Support the Immediate Migratory Response after Zebrafish Pronephros Injury.
    2. Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6.
      Title: Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6.
    3. HDAC6 inhibition and the regulation of Prx1 activity may play a significant role in protecting retinal cells and in particular photoreceptors.
      Title: HDAC6 inhibition by tubastatin A is protective against oxidative stress in a photoreceptor cell line and restores visual function in a zebrafish model of inherited blindness.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    NOT enables acetylspermidine deacetylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone deacetylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables potassium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein lysine deacetylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tubulin deacetylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within angiogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within definitive hemopoiesis 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 hematopoietic progenitor cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein deacetylation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of tubulin deacetylation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of tubulin deacetylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within swimming behavior IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of histone deacetylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    histone deacetylase 6
    XP_009302026.1
    XP_009302027.1

    NCBI Reference Sequences (RefSeq)

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    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_007119.7 Reference GRCz11 Primary Assembly

      Range
      7393435..7444466 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009303752.3 → XP_009302027.1  histone deacetylase 6

      See identical proteins and their annotated locations for XP_009302027.1

      UniProtKB/TrEMBL
      A0A8M3BBK8, A7YT55, F8W4B7
      Related
      ENSDARP00000153983.1, ENSDART00000180659.1
      Conserved Domains (3) summary
      cd10003
      Location:448 → 798
      HDAC6-dom2; Histone deacetylase 6, domain 2
      cd11682
      Location:76 → 412
      HDAC6-dom1; Histone deacetylase 6, domain 1
      pfam02148
      Location:999 → 1061
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    2. XM_009303751.4 → XP_009302026.1  histone deacetylase 6

      See identical proteins and their annotated locations for XP_009302026.1

      UniProtKB/TrEMBL
      A0A8M3BBK8, A7YT55, F8W4B7
      Related
      ENSDARP00000124246.1, ENSDART00000148993.3
      Conserved Domains (3) summary
      cd10003
      Location:448 → 798
      HDAC6-dom2; Histone deacetylase 6, domain 2
      cd11682
      Location:76 → 412
      HDAC6-dom1; Histone deacetylase 6, domain 1
      pfam02148
      Location:999 → 1061
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
    Nucleotide Protein
    Heading Accession and Version

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