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    HDA9 histone deacetylase 9 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 823594, updated on 15-Oct-2023

    Summary

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    Gene symbol
    HDA9
    Gene description
    histone deacetylase 9
    Primary source
    Araport:AT3G44680
    Locus tag
    AT3G44680
    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
    AtHDA9; HDA09; HISTONE DEACETYLASE; histone deacetylase 9
    Summary
    Class I RPD3 type protein
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    Genomic context

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    Location:
    chromosome: 3
    Exon count:
    14
    Sequence:
    Chromosome: 3; NC_003074.8 (16226519..16230009, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene tyrosine phosphatase Neighboring gene histone deacetylase 10 Neighboring gene Disease resistance protein (TIR-NBS-LRR class) family Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein

    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. The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation. de Rooij PGH, et al. J Exp Bot, 2020 Oct 22. PMID 32687569, Free PMC Article
    2. HISTONE DEACETYLASE 9 Functions with Polycomb Silencing to Repress FLOWERING LOCUS C Expression. Zeng X, et al. Plant Physiol, 2020 Jan. PMID 31641076, Free PMC Article
    3. Histone deacetylase HDA9 negatively regulates salt and drought stress responsiveness in Arabidopsis. Zheng Y, et al. J Exp Bot, 2016 Mar. PMID 26733691
    4. HISTONE DEACETYLASE 9 represses seedling traits in Arabidopsis thaliana dry seeds. van Zanten M, et al. Plant J, 2014 Nov. PMID 25146719
    5. HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis. Yang J, et al. J Integr Plant Biol, 2023 Jan. PMID 36165397

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis.
      Title: The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis.
    2. HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis.
      Title: HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis.
    3. The HDA9-HY5 module epigenetically regulates flowering time in Arabidopsis thaliana.
      Title: The HDA9-HY5 module epigenetically regulates flowering time in Arabidopsis thaliana.
    4. The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation.
      Title: The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation.
    5. HOS15 and HDA9 negatively regulate immunity through histone deacetylation of intracellular immune receptor NLR genes in Arabidopsis.
      Title: HOS15 and HDA9 negatively regulate immunity through histone deacetylation of intracellular immune receptor NLR genes in Arabidopsis.
    6. HISTONE DEACETYLASE 9 Functions with Polycomb Silencing to Repress FLOWERING LOCUS C Expression.
      Title: HISTONE DEACETYLASE 9 Functions with Polycomb Silencing to Repress FLOWERING LOCUS C Expression.
    7. Histone Deacetylase HDA9 and WRKY53 Transcription Factor Are Mutual Antagonists in Regulation of Plant Stress Response.
      Title: Histone Deacetylase HDA9 and WRKY53 Transcription Factor Are Mutual Antagonists in Regulation of Plant Stress Response.
    8. HY5-HDA9 Module Transcriptionally Regulates Plant Autophagy in Response to Light-to-Dark Conversion and Nitrogen Starvation.
      Title: HY5-HDA9 Module Transcriptionally Regulates Plant Autophagy in Response to Light-to-Dark Conversion and Nitrogen Starvation.
    9. HDA9 mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance.
      Title: HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion.
    10. HDA9 specifically binds to the TOC1 promoter through the interaction with ELF3. The EC-HDA9 complex promotes H3 deacetylation at the TOC1 locus, contributing to suppressing TOC1 expression during the night.
      Title: The EC-HDA9 complex rhythmically regulates histone acetylation at the TOC1 promoter in Arabidopsis.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_114336.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    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 sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of seed germination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of leaf senescence IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 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 9
    NP_190054.2
    • histone deacetylase 9 (HDA9); FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: histone deacetylation; LOCATED IN: nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Histone deacetylase (InterPro:IPR003084), Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase 1 (TAIR:AT4G38130.1); Has 8723 Blast hits to 8511 proteins in 1453 species: Archae - 219; Bacteria - 3191; Metazoa - 1512; Fungi - 548; Plants - 472; Viruses - 0; Other Eukaryotes - 2781 (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
      16226519..16230009 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_114336.4 → NP_190054.2  histone deacetylase 9 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_190054.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8H0W2, Q9M1N6
      UniProtKB/TrEMBL
      A0A5S9XHU0, A0A654FCX3
      Conserved Domains (2) summary
      PTZ00063
      Location:6 → 396
      PTZ00063; histone deacetylase; Provisional
      cl17011
      Location:6 → 384
      Arginase_HDAC; Arginase-like and histone-like hydrolases
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8H0W2.1

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