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    LOC4338920 histone deacetylase 8 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4338920, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4338920
    Gene description
    histone deacetylase 8
    Locus tag
    OSNPB_050440250
    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
    Expression
    Ubiquitous expression in leaves after flowering (RPKM 17.2), roots after flowering (RPKM 16.0) and 6 other tissues See more
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    Genomic context

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    See LOC4338920 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 5 NC_089039.1 (21672503..21674747, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 5 NC_029260.1 (21562013..21564601, complement)

    Chromosome 5 - NC_089039.1Genomic Context describing neighboring genes Neighboring gene U-box domain-containing protein 29 Neighboring gene uncharacterized LOC4338919 Neighboring gene protein LEAD-SENSITIVE 1 Neighboring gene histone deacetylase 8 Neighboring gene serine/threonine-protein kinase Nek4-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 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
    2. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

    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 

    General protein information

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    Preferred Names
    histone deacetylase 8
    Names
    Os05g0440250

    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_089039.1 Reference ASM3414082v1 Primary Assembly

      Range
      21672503..21674747 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015784651.3 → XP_015640137.1  histone deacetylase 8

      UniProtKB/TrEMBL
      A2Y543, A2Y544, B9FJ73, Q0DHU2, Q60DG7
      Conserved Domains (1) summary
      cd09996
      Location:24 → 366
      HDAC_classII_1; Histone deacetylases and histone-like deacetylases, classII
    Nucleotide Protein
    Heading Accession and Version

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