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    LOC4340248 pre-mRNA-processing-splicing factor 8A [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4340248, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4340248
    Gene description
    pre-mRNA-processing-splicing factor 8A
    Locus tag
    OSNPB_060167000
    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 leaves before flowering (RPKM 58.4), roots after flowering (RPKM 56.7) and 6 other tissues See more
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    Genomic context

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    See LOC4340248 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (3526704..3536726, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (3363867..3373877, complement)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene transfer RNA alanine (anticodon AGC) Neighboring gene PTI1-like tyrosine-protein kinase At3g15890 Neighboring gene AP-1 complex subunit gamma-2 Neighboring gene RING-H2 finger protein ATL46

    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
    • 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

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables U1 snRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables U2 snRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables U5 snRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables U6 snRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables metallopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables pre-mRNA intronic binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in spliceosomal tri-snRNP complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of U5 snRNP IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    part_of catalytic step 2 spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pre-mRNA-processing-splicing factor 8A
    Names
    Os06g0167000
    P0680A03.20-1
    pre-mRNA-processing-splicing factor 8
    putative splicing factor Prp8

    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
      3526704..3536726 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015787378.3 → XP_015642864.2  pre-mRNA-processing-splicing factor 8A

      UniProtKB/TrEMBL
      Q5WAB4
      Conserved Domains (1) summary
      COG5178
      Location:52 → 2371
      PRP8; U5 snRNP spliceosome subunit [RNA processing and modification]
    Nucleotide Protein
    Heading Accession and Version

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