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hdac5 histone deacetylase 5 [ Danio rerio (zebrafish) ]

Gene ID: 557486, updated on 5-Jul-2025
Official Symbol
hdac5provided by ZNC
Official Full Name
histone deacetylase 5provided by ZNC
Primary source
ZFIN:ZDB-GENE-121219-3
See related
Ensembl:ENSDARG00000075139 AllianceGenome:ZFIN:ZDB-GENE-121219-3
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
Summary
Predicted to enable histone deacetylase activity. Acts upstream of or within pronephros morphogenesis. Predicted to be located in nucleus. Predicted to be part of histone deacetylase complex. Predicted to be active in cytoplasm. Orthologous to human HDAC5 (histone deacetylase 5). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs
human mouse all
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See hdac5 in Genome Data Viewer
Location:
chromosome: 3
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2025_04 current GRCz12tu (GCF_049306965.1) 3 NC_133178.1 (21600869..21723552)
RS_2024_08 previous assembly GRCz11 (GCF_000002035.6) 3 NC_007114.7 (22854685..22977830)

Chromosome 3 - NC_133178.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC141381186 Neighboring gene cytochrome b561 Neighboring gene uncharacterized LOC141381187 Neighboring gene si:ch211-237i5.4 Neighboring gene LSM12 homolog a

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. Calcium signals act through histone deacetylase to mediate pronephric kidney morphogenesis. Rothschild SC, et al. Dev Dyn, 2018 Jun. PMID 29633426
  2. Histone deacetylase 9 promotes angiogenesis by targeting the antiangiogenic microRNA-17-92 cluster in endothelial cells. Kaluza D, et al. Arterioscler Thromb Vasc Biol, 2013 Mar. PMID 23288173
  3. Hyperactivation of mTORC1 in a double hit mutant zebrafish model of tuberous sclerosis complex causes increased seizure susceptibility and neurodevelopmental abnormalities. De Meulemeester AS, et al. Front Cell Dev Biol, 2022. PMID 36238691, Free PMC Article
  4. Protein kinase D2 controls cardiac valve formation in zebrafish by regulating histone deacetylase 5 activity. Just S, et al. Circulation, 2011 Jul 19. PMID 21730303
  5. Zebrafish exposure to environmentally relevant concentration of depleted uranium impairs progeny development at the molecular and histological levels. Armant O, et al. PLoS One, 2017. PMID 28531178, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Proper heart valve formation in zebrafish critically depends on protein kinase D2-histone deacetylase 5-Kruppel-like factor signaling.
    Title: Protein kinase D2 controls cardiac valve formation in zebrafish by regulating histone deacetylase 5 activity.
Submit: New GeneRIF Correction

Homology

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 histone deacetylase activity, hydrolytic mechanism 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
  
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 pronephros morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
histone deacetylase 5

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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_133178.1 Reference GRCz12tu Primary Assembly

    Range
    21600869..21723552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009299384.5 → XP_009297659.1  histone deacetylase 5 isoform X5

    UniProtKB/TrEMBL
    A0A8M3AQU0, A0A8M9PXQ8
    Conserved Domains (2) summary
    cd10164
    Location:51 → 138
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:645 → 1064
    HDAC5; Histone deacetylase 5

  2. XM_073944355.1 → XP_073800456.1  histone deacetylase 5 isoform X6

    UniProtKB/TrEMBL
    A0A8M9P8E1

  3. XM_073944356.1 → XP_073800457.1  histone deacetylase 5 isoform X7

    UniProtKB/TrEMBL
    A0A8M9PJD7

  4. XM_073944357.1 → XP_073800458.1  histone deacetylase 5 isoform X8

    UniProtKB/TrEMBL
    A0A8M9PJD7

  5. XM_680567.11 → XP_685659.5  histone deacetylase 5 isoform X1

    UniProtKB/TrEMBL
    A0A8M9PXQ8, A0A8N7T5F3, E7FH14
    Related
    ENSDARP00000100072.3
    Conserved Domains (2) summary
    cd10164
    Location:94 → 181
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:688 → 1107
    HDAC5; Histone deacetylase 5

  6. XM_009299382.5 → XP_009297657.1  histone deacetylase 5 isoform X2

    UniProtKB/TrEMBL
    A0A8M3AQH0, A0A8M9P8E1
    Conserved Domains (2) summary
    cd10164
    Location:94 → 181
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:687 → 1106
    HDAC5; Histone deacetylase 5

  7. XM_009299383.5 → XP_009297658.1  histone deacetylase 5 isoform X3

    UniProtKB/TrEMBL
    A0A8M3B885, A0A8M9PJD7
    Conserved Domains (2) summary
    cd10164
    Location:94 → 181
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:685 → 1104
    HDAC5; Histone deacetylase 5

  8. XM_073944354.1 → XP_073800455.1  histone deacetylase 5 isoform X4

    UniProtKB/TrEMBL
    A0A8M9PJD7
Nucleotide Protein Strain
Heading Accession and Version

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