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    HDT4 histone deacetylase-related / HD-like protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 817331, updated on 18-Sep-2024

    Summary

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    Official Symbol
    HDT4
    Official Full Name
    histone deacetylase-related / HD-like protein
    Primary source
    TAIR:AT2G27840
    Locus tag
    AT2G27840
    See related
    Araport:AT2G27840
    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
    F15K20.6; F15K20_6; HD2D; HDA13; HDT04; HISTONE DEACETYLASE; HISTONE DEACETYLASE 13; histone deacetylase 2D
    Summary
    Belongs to the plant specific HD2 type proteins; similar to nucleolar Zea mays histone deacetylase; HD2-p39
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    Genomic context

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    See HDT4 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    8
    Sequence:
    Chromosome: 2; NC_003071.7 (11861806..11863908)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene prephenate dehydratase 1 Neighboring gene uncharacterized protein Neighboring gene tRNA-Gly Neighboring gene UDP-D-apiose/UDP-D-xylose synthase 1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis. Chu Y, et al. J Plant Physiol, 2024 Jun. PMID 38614048
    2. Telomere-binding protein regulates the chromosome ends through the interaction with histone deacetylases in Arabidopsis thaliana. Lee WK, et al. Nucleic Acids Res, 2016 Jun 2. PMID 26857545, 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. NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. He XJ, et al. Genes Dev, 2009 Feb 1. PMID 19204117, Free PMC Article
    5. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Pandey R, et al. Nucleic Acids Res, 2002 Dec 1. PMID 12466527, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis.
      Title: AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis.
    2. TRB2 interacts with HD2-type histone deacetylase HDT4.HDT4 is associated with Arabidopsis telomeres.
      Title: Telomere-binding protein regulates the chromosome ends through the interaction with histone deacetylases in Arabidopsis thaliana.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001336129.1
    NM_001336130.1
    NM_179778.1

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    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 seed dormancy process IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within siRNA processing IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleolus HDA PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    histone deacetylase-related / HD-like protein
    NP_001318300.1
    • HDT4; FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: production of siRNA involved in RNA interference; LOCATED IN: nucleolus; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; BEST Arabidopsis thaliana protein match is: histone deacetylase 3 (TAIR:AT3G44750.2); Has 818 Blast hits to 747 proteins in 183 species: Archae - 0; Bacteria - 171; Metazoa - 199; Fungi - 55; Plants - 177; Viruses - 17; Other Eukaryotes - 199 (source: NCBI BLink).
    NP_850109.1
    • HDT4; FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: production of siRNA involved in RNA interference; LOCATED IN: nucleolus; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; BEST Arabidopsis thaliana protein match is: histone deacetylase 2B (TAIR:AT5G22650.2); Has 725 Blast hits to 661 proteins in 171 species: Archae - 0; Bacteria - 166; Metazoa - 184; Fungi - 55; Plants - 136; Viruses - 17; Other Eukaryotes - 167 (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_003071.7 Reference assembly

      Range
      11861806..11863908
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_128344.4 → NP_565661.2  histone deacetylase-related / HD-like protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_565661.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WN36, Q9M4T3, Q9ZUY5
      UniProtKB/TrEMBL
      A0A178VVQ4

    2. NM_001336129.1 → NP_001318300.1  histone deacetylase-related / HD-like protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A2H1ZE29

    3. NM_001336130.1 → NP_001324791.1  histone deacetylase-related / HD-like protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8B163

    4. NM_179778.1 → NP_850109.1  histone deacetylase-related / HD-like protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_850109.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VVQ4, F4IGT4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9M4T3.1

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