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    LOC9268632 nuclear poly(A) polymerase 4 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 9268632, updated on 10-Oct-2024

    Summary

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    Gene symbol
    LOC9268632
    Gene description
    nuclear poly(A) polymerase 4
    Locus tag
    OSNPB_060558700
    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 109.0), leaves before flowering (RPKM 85.5) and 6 other tissues See more
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    Genomic context

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    See LOC9268632 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (22202079..22209100, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (21343396..21350357, complement)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene protein DETOXIFICATION 51 Neighboring gene verprolin-like Neighboring gene protein OXIDATIVE STRESS 3 Neighboring gene acid phosphatase 1 Neighboring gene uncharacterized LOC136356838

    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 RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables poly(A) RNA polymerase 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
    nuclear poly(A) polymerase 4
    Names
    OSJNBa0090E14.29
    Os06g0558700
    Os06g0558766
    putative poly(A) polymerase

    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
      22202079..22209100 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015787674.3 → XP_015643160.1  nuclear poly(A) polymerase 4 isoform X6

      UniProtKB/TrEMBL
      C7J4C8, Q5G7K1
      Conserved Domains (2) summary
      pfam04926
      Location:368 → 500
      PAP_RNA-bind; Poly(A) polymerase predicted RNA binding domain
      pfam04928
      Location:21 → 365
      PAP_central; Poly(A) polymerase central domain

    2. XM_015787671.3 → XP_015643157.1  nuclear poly(A) polymerase 4 isoform X6

      UniProtKB/TrEMBL
      C7J4C8, Q5G7K1
      Conserved Domains (2) summary
      pfam04926
      Location:368 → 500
      PAP_RNA-bind; Poly(A) polymerase predicted RNA binding domain
      pfam04928
      Location:21 → 365
      PAP_central; Poly(A) polymerase central domain

    3. XM_015787670.3 → XP_015643156.1  nuclear poly(A) polymerase 4 isoform X5

      UniProtKB/TrEMBL
      Q5G7K1
      Conserved Domains (2) summary
      pfam04926
      Location:368 → 500
      PAP_RNA-bind; Poly(A) polymerase predicted RNA binding domain
      pfam04928
      Location:21 → 365
      PAP_central; Poly(A) polymerase central domain

    4. XM_015787669.3 → XP_015643155.1  nuclear poly(A) polymerase 4 isoform X5

      UniProtKB/TrEMBL
      Q5G7K1
      Conserved Domains (2) summary
      pfam04926
      Location:368 → 500
      PAP_RNA-bind; Poly(A) polymerase predicted RNA binding domain
      pfam04928
      Location:21 → 365
      PAP_central; Poly(A) polymerase central domain

    5. XM_015787667.3 → XP_015643153.1  nuclear poly(A) polymerase 4 isoform X4

      UniProtKB/TrEMBL
      Q5G7K1
      Conserved Domains (3) summary
      PTZ00418
      Location:20 → 556
      PTZ00418; Poly(A) polymerase; Provisional
      pfam04926
      Location:368 → 500
      PAP_RNA-bind; Poly(A) polymerase predicted RNA binding domain
      pfam04928
      Location:21 → 365
      PAP_central; Poly(A) polymerase central domain

    6. XM_015787666.3 → XP_015643152.1  nuclear poly(A) polymerase 4 isoform X3

      UniProtKB/TrEMBL
      Q5G7K1, Q5Z7G3
      Conserved Domains (3) summary
      PTZ00418
      Location:20 → 556
      PTZ00418; Poly(A) polymerase; Provisional
      pfam04926
      Location:368 → 500
      PAP_RNA-bind; Poly(A) polymerase predicted RNA binding domain
      pfam04928
      Location:21 → 365
      PAP_central; Poly(A) polymerase central domain

    7. XM_015787665.3 → XP_015643151.1  nuclear poly(A) polymerase 4 isoform X2

      UniProtKB/TrEMBL
      Q5G7K1
      Conserved Domains (3) summary
      PTZ00418
      Location:20 → 556
      PTZ00418; Poly(A) polymerase; Provisional
      pfam04926
      Location:368 → 500
      PAP_RNA-bind; Poly(A) polymerase predicted RNA binding domain
      pfam04928
      Location:21 → 365
      PAP_central; Poly(A) polymerase central domain

    8. XM_066311344.1 → XP_066167441.1  nuclear poly(A) polymerase 4 isoform X1

    9. XM_066311346.1 → XP_066167443.1  nuclear poly(A) polymerase 4 isoform X5

    RNA

    1. XR_001546760.3 RNA Sequence

    2. XR_001546759.3 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version

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