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    HDA3 histone deacetylase 3 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 823605, updated on 18-Sep-2024

    Summary

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    Official Symbol
    HDA3
    Official Full Name
    histone deacetylase 3
    Primary source
    TAIR:AT3G44750
    Locus tag
    AT3G44750
    See related
    Araport:AT3G44750
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ATHD2A; HD2A; HDT1; HISTONE DEACETYLASE 2A; histone deacetylase 3
    Summary
    Encodes a histone deacetylase. Controls the development of adaxial/abaxial leaf polarity. Two lines with RNAi-directed against this gene show reduced Agrobacterium-mediated DNA transformation of the roots.
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    Genomic context

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    See HDA3 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    8
    Sequence:
    Chromosome: 3; NC_003074.8 (16297656..16299876)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene kinesin-like protein 1 Neighboring gene PHYTOSULFOKINE 3 PRECURSOR Neighboring gene Class II aaRS and biotin synthetases superfamily protein Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein Neighboring gene miscRNA

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Role of HD2 genes in seed germination and early seedling growth in Arabidopsis. Colville A, et al. Plant Cell Rep, 2011 Oct. PMID 21739146
    2. Plant-Specific Histone Deacetylases HDT1/2 Regulate GIBBERELLIN 2-OXIDASE2 Expression to Control Arabidopsis Root Meristem Cell Number. Li H, et al. Plant Cell, 2017 Sep. PMID 28855334, Free PMC Article
    3. Combining association mapping and transcriptomics identify HD2B histone deacetylase as a genetic factor associated with seed dormancy in Arabidopsis thaliana. Yano R, et al. Plant J, 2013 Jun. PMID 23464703
    4. Arabidopsis DNA methyltransferase AtDNMT2 associates with histone deacetylase AtHD2s activity. Song Y, et al. Biochem Biophys Res Commun, 2010 May 28. PMID 20331964
    5. Histone deacetylases and ASYMMETRIC LEAVES2 are involved in the establishment of polarity in leaves of Arabidopsis. Ueno Y, et al. Plant Cell, 2007 Feb. PMID 17293570, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. These results suggest that by repressing the expression of GA2ox2, HDT1/2 likely fine-tune gibberellin metabolism.
      Title: Plant-Specific Histone Deacetylases HDT1/2 Regulate GIBBERELLIN 2-OXIDASE2 Expression to Control Arabidopsis Root Meristem Cell Number.
    2. HD2A and HD2C may have different and opposing functions in germination with the glucose/HD2A pathway acting to restrain germination and the HD2C pathway acting to enhance germination.
      Title: Role of HD2 genes in seed germination and early seedling growth in Arabidopsis.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001203083.1

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables histone deacetylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone deacetylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA-mediated transformation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within polarity specification of adaxial/abaxial axis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within root development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within seed dormancy process IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleolus HDA PubMed 
    located_in nucleolus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    histone deacetylase 3
    NP_001190012.1
    • histone deacetylase 3 (HDA3); CONTAINS InterPro DOMAIN/s: Zinc finger, C2H2-type (InterPro:IPR007087), Nucleoplasmin (InterPro:IPR004301); BEST Arabidopsis thaliana protein match is: histone deacetylase 2B (TAIR:AT5G22650.1).
    NP_566872.1
    • histone deacetylase 3 (HDA3); FUNCTIONS IN: histone deacetylase activity, zinc ion binding, nucleic acid binding; INVOLVED IN: DNA mediated transformation, polarity specification of adaxial/abaxial axis; LOCATED IN: nucleolus; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, C2H2-like (InterPro:IPR015880), Zinc finger, C2H2-type (InterPro:IPR007087); BEST Arabidopsis thaliana protein match is: histone deacetylase 2B (TAIR:AT5G22650.1); Has 5980 Blast hits to 4690 proteins in 449 species: Archae - 12; Bacteria - 394; Metazoa - 2639; Fungi - 927; Plants - 442; Viruses - 82; Other Eukaryotes - 1484 (source: NCBI BLink).

    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_003074.8 Reference assembly

      Range
      16297656..16299876
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_114344.4 → NP_566872.1  histone deacetylase 3 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_566872.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O22238, Q9FVE6
      UniProtKB/TrEMBL
      A0A5S9XIC3, A0A7G2ERJ5
      Conserved Domains (2) summary
      pfam13912
      Location:220 → 242
      zf-C2H2_6; C2H2-type zinc finger
      pfam17800
      Location:3 → 92
      NPL; Nucleoplasmin-like domain

    2. NM_001203083.1 → NP_001190012.1  histone deacetylase 3 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001190012.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A7G2ERJ5, F4J378
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9FVE6.1

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