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    LOC4345332 histone deacetylase 6 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4345332, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4345332
    Gene description
    histone deacetylase 6
    Locus tag
    OSNPB_080344100
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Oryza sativa Japonica Group
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
    Also known as
    OJ1119_B10.28
    Expression
    Ubiquitous expression in flower buds (RPKM 16.8), leaves after flowering (RPKM 16.3) and 6 other tissues See more
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    Genomic context

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    See LOC4345332 in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 8 NC_089042.1 (15630941..15635954)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 8 NC_029263.1 (15554136..15559152)

    Chromosome 8 - NC_089042.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4345330 Neighboring gene berberine bridge enzyme-like D-2 Neighboring gene mitochondrial pyruvate carrier 4 Neighboring gene phosphoenolpyruvate/phosphate translocator 2, chloroplastic-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Transcriptome profiling of various organs at different developmental stages in rice
    • Description: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds
    • BioProject: PRJNA243371
    • Publication: PMID 26387578
    • Analysis date: Fri Dec 15 20:02:59 2017

    Bibliography

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    Related articles in PubMed

    1. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Rice Full-Length cDNA Consortium, et al. Science, 2003 Jul 18. PMID 12869764

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables histone deacetylase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone deacetylase 6
    Names
    Os08g0344100
    putative histone deacetylase

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_034140825.1-RS_2024_06

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference ASM3414082v1 Primary Assembly

    Genomic

    1. NC_089042.1 Reference ASM3414082v1 Primary Assembly

      Range
      15630941..15635954
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015792602.3 → XP_015648088.1  histone deacetylase 6

      UniProtKB/TrEMBL
      B8B9W7, B9G2J7, Q0J6A5, Q6ZB59
      Conserved Domains (1) summary
      cd09991
      Location:27 → 332
      HDAC_classI; Class I histone deacetylases
    Nucleotide Protein
    Heading Accession and Version

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