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    HDA05 histone deacetylase 5 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 836227, updated on 18-Sep-2024

    Summary

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    Official Symbol
    HDA05
    Official Full Name
    histone deacetylase 5
    Primary source
    TAIR:AT5G61060
    Locus tag
    AT5G61060
    See related
    Araport:AT5G61060
    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
    ATHDA5; HDA5; histone deacetylase 5; MAF19.7; MAF19_7
    Summary
    Encodes a member of the histone deacetylase family.
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    Genomic context

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    See HDA05 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    13
    Sequence:
    Chromosome: 5; NC_003076.8 (24566783..24571072, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene glycine-rich RNA-binding protein 3 Neighboring gene uncharacterized protein Neighboring gene histone deacetylase-related / HD-like protein Neighboring gene histone deacetylase of the RPD3/HDA1 superfamily 18 Neighboring gene Polynucleotidyl transferase, ribonuclease H-like superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves. Tilak P, et al. Plant J, 2023 Jul. PMID 36961081
    2. Regulation of flowering time by the histone deacetylase HDA5 in Arabidopsis. Luo M, et al. Plant J, 2015 Jun. PMID 25922987
    3. Subcellular localization of class II HDAs in Arabidopsis thaliana: nucleocytoplasmic shuttling of HDA15 is driven by light. Alinsug MV, et al. PLoS One, 2012. PMID 22363501, Free PMC Article
    4. The cold signaling attenuator HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 activates FLOWERING LOCUS C transcription via chromatin remodeling under short-term cold stress in Arabidopsis. Jung JH, et al. Plant Cell, 2013 Nov. PMID 24220632, Free PMC Article
    5. Structure of Arabidopsis HISTONE DEACETYLASE15. Chen CY, et al. Plant Physiol, 2020 Nov. PMID 32878973, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves.
      Title: Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves.
    2. Regulation of flowering time by the histone deacetylase HDA5
      Title: Regulation of flowering time by the histone deacetylase HDA5 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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    NM_001203654.1
    NM_125499.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables histone deacetylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of gene expression, epigenetic IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of timing of transition from vegetative to reproductive phase IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm HDA PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of histone deacetylase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus HDA PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    histone deacetylase 5
    NP_001190583.1
    • histone deacetylase 5 (HDA05); FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: histone deacetylation; LOCATED IN: nucleus, cytoplasm; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase of the RPD3/HDA1 superfamily 18 (TAIR:AT5G61070.1).
    NP_200914.2
    • histone deacetylase 5 (HDA05); CONTAINS InterPro DOMAIN/s: Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase of the RPD3/HDA1 superfamily 18 (TAIR:AT5G61070.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (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_003076.8 Reference assembly

      Range
      24566783..24571072 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001203654.1 → NP_001190583.1  histone deacetylase 5 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001190583.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UKB5, A0A5S9YG03, F4K1Z5
      Conserved Domains (1) summary
      cl17011
      Location:31 → 388
      Arginase_HDAC; Arginase-like and histone-like hydrolases

    2. NM_125499.5 → NP_200914.2  histone deacetylase 5 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_200914.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8RX28, Q9FNQ7, Q9FNQ8
      UniProtKB/TrEMBL
      A0A178UKB5, A0A5S9YG03, A0A654GCY7
      Conserved Domains (1) summary
      cl17011
      Location:31 → 384
      Arginase_HDAC; Arginase-like and histone-like hydrolases
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8RX28.1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.