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    hda-3 Histone deacetylase [ Caenorhabditis elegans ]

    Gene ID: 173074, updated on 9-Dec-2024

    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, Dec 2024]
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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
    Heading Accession and Version

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