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    LOC9266269 probable cleavage and polyadenylation specificity factor subunit 1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 9266269, updated on 10-Oct-2024

    Summary

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    Gene symbol
    LOC9266269
    Gene description
    probable cleavage and polyadenylation specificity factor subunit 1
    Locus tag
    OSNPB_040252200
    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 15.7), leaves before flowering (RPKM 15.4) and 6 other tissues See more
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    Genomic context

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    See LOC9266269 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 4 NC_089038.1 (10083640..10111036, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 4 NC_029259.1 (9888812..9916286, complement)

    Chromosome 4 - NC_089038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC136356161 Neighboring gene uncharacterized LOC136356162 Neighboring gene uncharacterized LOC136355961 Neighboring gene uncharacterized LOC136356163

    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. 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
    3. 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 nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein binding 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
    probable cleavage and polyadenylation specificity factor subunit 1
    Names
    Os04g0252200

    NCBI Reference Sequences (RefSeq)

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    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_089038.1 Reference ASM3414082v1 Primary Assembly

      Range
      10083640..10111036 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015780254.3 → XP_015635740.1  probable cleavage and polyadenylation specificity factor subunit 1 isoform X2

      UniProtKB/Swiss-Prot
      Q7XWP1
      Conserved Domains (2) summary
      COG5161
      Location:253 → 1440
      SFT1; Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]
      pfam03178
      Location:1080 → 1406
      CPSF_A; CPSF A subunit region

    2. XM_066309577.1 → XP_066165674.1  probable cleavage and polyadenylation specificity factor subunit 1 isoform X3

    3. XM_015780259.3 → XP_015635745.1  probable cleavage and polyadenylation specificity factor subunit 1 isoform X4

      UniProtKB/Swiss-Prot
      Q7XWP1
      Conserved Domains (2) summary
      pfam03178
      Location:1042 → 1330
      CPSF_A; CPSF A subunit region
      pfam10433
      Location:188 → 706
      MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term

    4. XM_015780253.3 → XP_015635739.1  probable cleavage and polyadenylation specificity factor subunit 1 isoform X1

      UniProtKB/Swiss-Prot
      Q7XWP1
      UniProtKB/TrEMBL
      B9FE37
      Conserved Domains (2) summary
      COG5161
      Location:253 → 1441
      SFT1; Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]
      pfam03178
      Location:1081 → 1407
      CPSF_A; CPSF A subunit region

    5. XM_015780260.3 → XP_015635746.1  probable cleavage and polyadenylation specificity factor subunit 1 isoform X5

      UniProtKB/Swiss-Prot
      Q7XWP1
      Conserved Domains (2) summary
      pfam03178
      Location:841 → 1167
      CPSF_A; CPSF A subunit region
      pfam10433
      Location:53 → 466
      MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term
    Nucleotide Protein
    Heading Accession and Version

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