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    LOC4334816 cleavage and polyadenylation specificity factor subunit 3-I [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4334816, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4334816
    Gene description
    cleavage and polyadenylation specificity factor subunit 3-I
    Locus tag
    OSNPB_030852900
    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 flower buds (RPKM 27.2), leaves before flowering (RPKM 23.5) and 6 other tissues See more
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    Genomic context

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    See LOC4334816 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (36887485..36890470, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (35908705..35911711, complement)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized protein ycf20 Neighboring gene pentatricopeptide repeat-containing protein At4g25270, chloroplastic Neighboring gene non-specific phospholipase C4 Neighboring gene protein TORNADO 2 Neighboring gene tetraspanin-3

    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 5'-3' RNA exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables RNA endonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA 3'-end processing by stem-loop binding and cleavage IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of mRNA cleavage and polyadenylation specificity factor complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cleavage and polyadenylation specificity factor subunit 3-I
    Names
    Os03g0852900

    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
      36887485..36890470 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015776727.3 → XP_015632213.1  cleavage and polyadenylation specificity factor subunit 3-I

      UniProtKB/TrEMBL
      A2XP63, Q0DLP6, Q7G6G7, Q84JJ2
      Conserved Domains (3) summary
      COG1236
      Location:33 → 471
      YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
      cd16292
      Location:31 → 224
      CPSF3-like_MBL-fold; cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; MBL-fold metallo-hydrolase domain
      pfam11718
      Location:495 → 694
      CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term
    Nucleotide Protein
    Heading Accession and Version

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