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hdac5 histone deacetylase 5 [ Danio rerio (zebrafish) ]

Gene ID: 557486, updated on 30-Mar-2024

Summary

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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 NAD-dependent histone deacetylase activity (H3-K14 specific) and metal ion binding activity. Acts upstream of or within pronephros morphogenesis. Predicted to be located in cytoplasm and nucleus. Predicted to be part of histone deacetylase complex. Orthologous to human HDAC5 (histone deacetylase 5). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 3
Exon count:
27
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (22854508..22976406)
105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (22724003..22846052)

Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2a Neighboring gene uncharacterized LOC110439104 Neighboring gene cytochrome b561 Neighboring gene si:ch211-237i5.4 Neighboring gene LSM12 homolog a

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. 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. 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
  4. 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
  5. Histone Deacetylase-Mediated Müller Glia Reprogramming through Her4.1-Lin28a Axis Is Essential for Retina Regeneration in Zebrafish. Mitra S, et al. iScience, 2018 Sep 28. PMID 30267687, Free PMC Article

See all (9) 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

Pathways from PubChem

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General gene information

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Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
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 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 
involved_in response to stimulus IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of histone deacetylase complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
histone deacetylase 5

NCBI Reference Sequences (RefSeq)

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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_007114.7 Reference GRCz11 Primary Assembly

    Range
    22854508..22976406
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009299384.3 → XP_009297659.1  histone deacetylase 5 isoform X4

    UniProtKB/TrEMBL
    A0A8M3AQU0
    Related
    ENSDARP00000128586.1, ENSDART00000157378.2
    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_680567.9 → XP_685659.5  histone deacetylase 5 isoform X1

    UniProtKB/TrEMBL
    A0A8N7T5F3, E7FH14
    Related
    ENSDARP00000100072.3, ENSDART00000111435.4
    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

  3. XM_009299382.3 → XP_009297657.1  histone deacetylase 5 isoform X2

    UniProtKB/TrEMBL
    A0A8M3AQH0
    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

  4. XM_009299383.3 → XP_009297658.1  histone deacetylase 5 isoform X3

    UniProtKB/TrEMBL
    A0A8M3B885
    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

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394530.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    24042..64552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021471411.1 → XP_021327086.1  histone deacetylase 5 isoform X5

    UniProtKB/TrEMBL
    A0A8M9PXQ8
    Conserved Domains (2) summary
    cd10164
    Location:34 → 121
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:628 → 1047
    HDAC5; Histone deacetylase 5

  2. XM_021471412.1 → XP_021327087.1  histone deacetylase 5 isoform X6

    UniProtKB/TrEMBL
    A0A8M9P8E1
    Conserved Domains (2) summary
    cd10164
    Location:34 → 121
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:627 → 1046
    HDAC5; Histone deacetylase 5

  3. XM_021471413.1 → XP_021327088.1  histone deacetylase 5 isoform X7

    UniProtKB/TrEMBL
    A0A8M9PJD7
    Conserved Domains (2) summary
    cd10164
    Location:34 → 121
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:625 → 1044
    HDAC5; Histone deacetylase 5
Nucleotide Protein Strain
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