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    LOC4341387 histone deacetylase 1-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4341387, updated on 17-Sep-2024

    Summary

    Gene symbol
    LOC4341387
    Gene description
    histone deacetylase 1-like
    Locus tag
    OSNPB_060583400
    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 roots after flowering (RPKM 54.6), leaves after flowering (RPKM 50.1) and 6 other tissues See more
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    Genomic context

    See LOC4341387 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (23653554..23659157, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (22794346..22800216, complement)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107281331 Neighboring gene senescence-specific cysteine protease SAG39-like Neighboring gene receptor kinase-like protein Xa21 Neighboring gene uncharacterized LOC136357056

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    General gene information

    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

    Preferred Names
    histone deacetylase 1-like
    Names
    Os06g0583400
    P0498C03.28-1
    P0498C03.28-2
    histone deacetylase HDAC1
    probable histone deacetylase 19
    putative histone deacetylase HDAC1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_089040.1 Reference ASM3414082v1 Primary Assembly

      Range
      23653554..23659157 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015788295.3XP_015643781.1  histone deacetylase 1-like

      UniProtKB/Swiss-Prot
      Q5VP94, Q7Y0Y8
      UniProtKB/TrEMBL
      A0A678RZE2, B9FTW9
      Conserved Domains (1) summary
      cl17011
      Location:22399
      Arginase_HDAC; Arginase-like and histone-like hydrolases