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hda-3 Histone deacetylase [ Caenorhabditis elegans ]

Gene ID: 173074, updated on 4-Jan-2025

Summary

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Official Symbol
hda-3
Official Full Name
Histone deacetylase
Primary source
WormBase:WBGene00001836
Locus tag
CELE_R06C1.1
See related
AllianceGenome:WB:WBGene00001836
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Caenorhabditis elegans (strain: Bristol N2)
Lineage
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary
Predicted to enable histone deacetylase activity and transcription corepressor activity. Involved in DNA protection. Located in nucleus. Is expressed widely. Human ortholog(s) of this gene implicated in stomach cancer. Orthologous to human HDAC1 (histone deacetylase 1) and HDAC2 (histone deacetylase 2). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

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See hda-3 in Genome Data Viewer
Location:
chromosome: I
Exon count:
5
Sequence:
Chromosome: I; NC_003279.8 (11912793..11917712, complement)

Chromosome I - NC_003279.8Genomic Context describing neighboring genes Neighboring gene RRM domain-containing protein Neighboring gene NEDD8-conjugating enzyme ubc-12 Neighboring gene Protein mago nashi homolog Neighboring gene Farnesyl pyrophosphate synthase Neighboring gene WH2 domain-containing protein;Wiskott-Aldrich syndrome protein family member

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003279.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. A class I histone deacetylase HDA-2 is essential for embryonic development and size regulation of fertilized eggs in Caenorhabditis elegans. Unno T, et al. Genes Genomics, 2022 Mar. PMID 34843089
  2. The small GTPases ARL-13 and ARL-3 coordinate intraflagellar transport and ciliogenesis. Li Y, et al. J Cell Biol, 2010 Jun 14. PMID 20530210, Free PMC Article
  3. Nuclear cGMP-dependent kinase regulates gene expression via activity-dependent recruitment of a conserved histone deacetylase complex. Hao Y, et al. PLoS Genet, 2011 May. PMID 21573134, Free PMC Article
  4. Loss of spr-5 bypasses the requirement for the C.elegans presenilin sel-12 by derepressing hop-1. Eimer S, et al. EMBO J, 2002 Nov 1. PMID 12411496, Free PMC Article
  5. A CBP/p300 homolog specifies multiple differentiation pathways in Caenorhabditis elegans. Shi Y, et al. Genes Dev, 1998 Apr 1. PMID 9531533, Free PMC Article

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Mutation in histone deacetylase HDA-3 leads to shortened locomotor healthspan in Caenorhabditis elegans.
    Title: Mutation in histone deacetylase HDA-3 leads to shortened locomotor healthspan in Caenorhabditis elegans.
Submit: New GeneRIF Correction

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 WormBase

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 ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription corepressor activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA protection IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin organization ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Component Evidence Code Pubs
part_of NuRD complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone deacetylase complex ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
Histone deacetylase
NP_493026.1
  • Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_003279.8 Reference assembly

    Range
    11912793..11917712 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_060625.8 → NP_493026.1  Histone deacetylase [Caenorhabditis elegans]

    See identical proteins and their annotated locations for NP_493026.1

    Status: REVIEWED

    UniProtKB/TrEMBL
    G5ECH0
    Conserved Domains (1) summary
    cd09991
    Location:13 → 318
    HDAC_classI; Class I histone deacetylases
Nucleotide Protein
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