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    LOC4333378 DEK domain-containing chromatin-associated protein 4 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4333378, updated on 10-Oct-2024

    Summary

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    Gene symbol
    LOC4333378
    Gene description
    DEK domain-containing chromatin-associated protein 4
    Locus tag
    OSNPB_030596900
    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 110.6), leaves before flowering (RPKM 90.9) and 6 other tissues See more
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    Genomic context

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    See LOC4333378 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (23077951..23085849, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (22219265..22227216, complement)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC9266875 Neighboring gene uncharacterized LOC4333377 Neighboring gene pentatricopeptide repeat-containing protein At3g53700, chloroplastic Neighboring gene uncharacterized LOC4333380

    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 DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables histone binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in regulation of double-strand break repair 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
    DEK domain-containing chromatin-associated protein 4
    Names
    Os03g0596900
    protein DEK

    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_089037.1 Reference ASM3414082v1 Primary Assembly

      Range
      23077951..23085849 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_066309133.1 → XP_066165230.1  DEK domain-containing chromatin-associated protein 4

      UniProtKB/TrEMBL
      Q0DQH0, Q10H93

    2. XM_015775737.3 → XP_015631223.1  DEK domain-containing chromatin-associated protein 4

      UniProtKB/TrEMBL
      Q0DQH0, Q10H93, Q84TZ6
      Conserved Domains (2) summary
      COG5271
      Location:30 → 276
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      pfam08766
      Location:616 → 669
      DEK_C; DEK C terminal domain
    Nucleotide Protein
    Heading Accession and Version

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