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    LOC4335187 pentatricopeptide repeat-containing protein At5g16860 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4335187, updated on 10-Oct-2024

    Summary

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    Gene symbol
    LOC4335187
    Gene description
    pentatricopeptide repeat-containing protein At5g16860
    Locus tag
    OSNPB_040218100
    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 flowers (RPKM 15.3), roots after flowering (RPKM 14.5) and 6 other tissues See more
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    Genomic context

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    See LOC4335187 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 4 NC_089038.1 (7994497..8006562, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 4 NC_029259.1 (7893476..7901856, complement)

    Chromosome 4 - NC_089038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107280503 Neighboring gene uncharacterized LOC9267213 Neighboring gene uncharacterized LOC136356119 Neighboring gene probable methyltransferase PMT20

    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

    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 protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA modification IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pentatricopeptide repeat-containing protein At5g16860
    Names
    Os04g0218100

    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_089038.1 Reference ASM3414082v1 Primary Assembly

      Range
      7994497..8006562 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015780136.3 → XP_015635622.1  pentatricopeptide repeat-containing protein At5g16860 isoform X1

      UniProtKB/TrEMBL
      A0A0P0W7X4, Q0JER4
      Conserved Domains (3) summary
      PLN03077
      Location:73 → 881
      PLN03077; Protein ECB2; Provisional
      sd00004
      Location:298 → 323
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:359 → 406
      PPR_2; PPR repeat family

    2. XM_066310130.1 → XP_066166227.1  pentatricopeptide repeat-containing protein At5g16860 isoform X3

    3. XM_066310128.1 → XP_066166225.1  pentatricopeptide repeat-containing protein At5g16860 isoform X2

    4. XM_015780131.3 → XP_015635617.1  pentatricopeptide repeat-containing protein At5g16860 isoform X1

      UniProtKB/TrEMBL
      A0A0P0W7X4, Q0JER4
      Conserved Domains (3) summary
      PLN03077
      Location:73 → 881
      PLN03077; Protein ECB2; Provisional
      sd00004
      Location:298 → 323
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:359 → 406
      PPR_2; PPR repeat family

    5. XM_066310129.1 → XP_066166226.1  pentatricopeptide repeat-containing protein At5g16860 isoform X2

    6. XM_066310127.1 → XP_066166224.1  pentatricopeptide repeat-containing protein At5g16860 isoform X1

    RNA

    1. XR_010741092.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version

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