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    LOC4348939 pre-mRNA-processing protein 40C [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4348939, updated on 10-Oct-2024

    Summary

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    Gene symbol
    LOC4348939
    Gene description
    pre-mRNA-processing protein 40C
    Locus tag
    OSNPB_100485000
    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 15.0), leaves before flowering (RPKM 12.7) and 6 other tissues See more
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    Genomic context

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    See LOC4348939 in Genome Data Viewer
    Location:
    chromosome: 10
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 10 NC_089044.1 (18989583..19000210, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 10 NC_029265.1 (18321126..18331776, complement)

    Chromosome 10 - NC_089044.1Genomic Context describing neighboring genes Neighboring gene type III polyketide synthase A Neighboring gene small ribosomal subunit protein mS86 (rPPR1) Neighboring gene uncharacterized LOC4348940 Neighboring gene protein EXECUTER 1, 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 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 RNA polymerase binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables transcription coregulator activity 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
    pre-mRNA-processing protein 40C
    Names
    Os10g0485000

    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_089044.1 Reference ASM3414082v1 Primary Assembly

      Range
      18989583..19000210 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015759154.3 → XP_015614640.1  pre-mRNA-processing protein 40C isoform X2

      UniProtKB/TrEMBL
      B9G6B9
      Conserved Domains (5) summary
      COG2811
      Location:771 → 891
      NtpH; Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]
      cd00201
      Location:424 → 451
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam01846
      Location:643 → 692
      FF; FF domain
      pfam12200
      Location:53 → 84
      DUF3597; Domain of unknown function (DUF3597)
      pfam13863
      Location:814 → 868
      DUF4200; Domain of unknown function (DUF4200)

    2. XM_066304878.1 → XP_066160975.1  pre-mRNA-processing protein 40C isoform X3

    3. XM_015759153.3 → XP_015614639.1  pre-mRNA-processing protein 40C isoform X1

      UniProtKB/TrEMBL
      B9G6B9, Q0IWV8, Q337J6
      Conserved Domains (2) summary
      PHA03247
      Location:4 → 409
      PHA03247; large tegument protein UL36; Provisional
      COG5104
      Location:473 → 1054
      PRP40; Splicing factor [RNA processing and modification]
    Nucleotide Protein
    Heading Accession and Version

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