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    LOC4338940 protein ROS1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4338940, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4338940
    Gene description
    protein ROS1
    Locus tag
    OSNPB_050445900
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Oryza sativa Japonica Group
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
    Also known as
    ROS1C; DNG701; OsJ_18723
    Expression
    Ubiquitous expression in flowers (RPKM 10.0), leaves before flowering (RPKM 9.9) and 6 other tissues See more
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    Genomic context

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    See LOC4338940 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 5 NC_089039.1 (21954926..21968062, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 5 NC_029260.1 (21843283..21856446, complement)

    Chromosome 5 - NC_089039.1Genomic Context describing neighboring genes Neighboring gene large ribosomal subunit protein P2B Neighboring gene uncharacterized LOC4338939 Neighboring gene protein BUD31 homolog 2-like Neighboring gene uncharacterized LOC4338943

    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. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice. La H, et al. Proc Natl Acad Sci U S A, 2011 Sep 13. PMID 21896764, Free PMC Article
    2. 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 4 iron, 4 sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables DNA N-glycosylase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables DNA demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in base-excision repair IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein ROS1C
    Names
    DNA glycosylase 701
    DNA glycosylase/lyase 701
    LOC_Os05g37350
    Os05g0446000
    P0615D12.11
    Protein REPRESSOR OF SILENCING 1 homolog c
    Protein ROS1C
    NP_001389491.1
    XP_015640368.1
    XP_066166360.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001402562.1 → NP_001389491.1  protein ROS1C

      Status: VALIDATED

      Source sequence(s)
      AK070640, AK103871, AP014961, FJ536320
      UniProtKB/Swiss-Prot
      A0A0P0WMX3, B8YIE8, B9FPV3, Q0DHS4, Q65WT4

    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_089039.1 Reference ASM3414082v1 Primary Assembly

      Range
      21954926..21968062 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015784882.3 → XP_015640368.1  protein ROS1C isoform X1

      UniProtKB/Swiss-Prot
      A0A0P0WMX3, B8YIE8, B9FPV3, Q0DHS4, Q65WT4
      Conserved Domains (2) summary
      pfam15628
      Location:1693 → 1794
      RRM_DME; RRM in Demeter
      cl23768
      Location:1281 → 1462
      ENDO3c; endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

    2. XM_066310263.1 → XP_066166360.1  protein ROS1C isoform X2

    RNA

    1. XR_010741210.1 RNA Sequence

    2. XR_010741209.1 RNA Sequence

    3. XR_010741208.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B8YIE8.2 GenPept UniProtKB/Swiss-Prot:B8YIE8

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