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

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

    Summary

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    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

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    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

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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. Unveiling the mechanism of broad-spectrum blast resistance in rice: The collaborative role of transcription factor OsGRAS30 and histone deacetylase OsHDAC1. Hou J, et al. Plant Biotechnol J, 2024 Jun. PMID 38294722, Free PMC Article
    2. The histone deacetylase OsHDAC1 epigenetically regulates the OsNAC6 gene that controls seedling root growth in rice. Chung PJ, et al. Plant J, 2009 Sep. PMID 19453457
    3. 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
    4. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
    5. 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

    What's a GeneRIF?
    1. Unveiling the mechanism of broad-spectrum blast resistance in rice: The collaborative role of transcription factor OsGRAS30 and histone deacetylase OsHDAC1.
      Title: Unveiling the mechanism of broad-spectrum blast resistance in rice: The collaborative role of transcription factor OsGRAS30 and histone deacetylase OsHDAC1.
    2. OsHDAC1 epigenetically regulates the OsNAC6 gene, and that this is primarily responsible for the alteration of root development in rice seedlings.
      Title: The histone deacetylase OsHDAC1 epigenetically regulates the OsNAC6 gene that controls seedling root growth in rice.
    Submit: New GeneRIF Correction

    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 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)

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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_089040.1 Reference ASM3414082v1 Primary Assembly

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

    mRNA and Protein(s)

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

      UniProtKB/Swiss-Prot
      Q5VP94, Q7Y0Y8
      UniProtKB/TrEMBL
      A0A678RZE2, B9FTW9
      Conserved Domains (1) summary
      cl17011
      Location:22 → 399
      Arginase_HDAC; Arginase-like and histone-like hydrolases
    Nucleotide Protein
    Heading Accession and Version

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