U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

hdac6 histone deacetylase 6 [ Danio rerio (zebrafish) ]

Gene ID: 565482, updated on 11-Apr-2024

Summary

Go to the top of the page Help
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 angiogenesis; hemopoiesis; and protein deacetylation. Predicted to be located in nucleus. 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, Apr 2022]
Orthologs
human mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
chromosome: 8
Exon count:
28
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (7393435..7444482, 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 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. 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
  2. Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Hosseinzadeh P, et al. Nat Commun, 2021 Jun 7. PMID 34099674, Free PMC Article
  3. Unique Molecular Interaction with the Histone Deacetylase 6 Catalytic Tunnel: Crystallographic and Biological Characterization of a Model Chemotype. Olaoye OO, et al. J Med Chem, 2021 Mar 11. PMID 33576627, Free PMC Article
  4. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. Osko JD, et al. J Med Chem, 2020 Jan 9. PMID 31793776, Free PMC Article
  5. Synthesis and Biological Investigation of Phenothiazine-Based Benzhydroxamic Acids as Selective Histone Deacetylase 6 Inhibitors. Vögerl K, et al. J Med Chem, 2019 Feb 14. PMID 30645113, Free PMC Article

See all (38) 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

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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 hydrolase activity IEA
Inferred from Electronic Annotation
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 transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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

Go to the top of the page Help
Preferred Names
histone deacetylase 6
XP_009302026.1
XP_009302027.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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..7444482 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009303752.2 → 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_009303751.3 → 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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.