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hdac4 histone deacetylase 4 [ Danio rerio (zebrafish) ]

Gene ID: 568877, updated on 27-Mar-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 NAD-dependent histone deacetylase activity (H3-K14 specific) and metal ion binding activity. Acts upstream of or within animal organ development; perichondral ossification; and regulation of neural crest formation. Predicted to be located in nucleus. Predicted to be part of histone deacetylase complex. 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; chromosome 2q37 deletion syndrome; eating disorder; and retinal degeneration. Orthologous to human HDAC4 (histone deacetylase 4). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 9
Exon count:
28
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (45883625..46276409, 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 helix-loop-helix protein 1-like Neighboring gene twist2 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. Calcium signals act through histone deacetylase to mediate pronephric kidney morphogenesis. Rothschild SC, et al. Dev Dyn, 2018 Jun. PMID 29633426
  3. 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
  4. 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
  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 (20) 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 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 
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 
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 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: 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_007120.7 Reference GRCz11 Primary Assembly

    Range
    45883625..46276409 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005172529.4 → 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

Gene LinkOut

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