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    LOC4333719 phosphomethylpyrimidine synthase, chloroplastic [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4333719, updated on 1-Aug-2024

    Summary

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    Gene symbol
    LOC4333719
    Gene description
    phosphomethylpyrimidine synthase, chloroplastic
    Locus tag
    OSNPB_030679700
    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
    Biased expression in leaves before flowering (RPKM 1113.6), roots after flowering (RPKM 269.3) and 3 other tissues See more
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    Genomic context

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    See LOC4333719 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (27824719..27831707)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (26952005..26958989)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC136355849 Neighboring gene probable ubiquitin-conjugating enzyme E2 25 Neighboring gene uncharacterized LOC107280492 Neighboring gene uncharacterized LOC4333720 Neighboring gene uncharacterized LOC107275267

    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. The Nucleotide-Dependent Interactome of Rice Heterotrimeric G-Protein α -Subunit. Biswal AK, et al. Proteomics, 2019 May. PMID 30866160
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables carbon-carbon lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables iron-sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in thiamine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    phosphomethylpyrimidine synthase, chloroplastic
    Names
    Os03g0679700

    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_089037.1 Reference ASM3414082v1 Primary Assembly

      Range
      27824719..27831707
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_066309015.1 → XP_066165112.1  phosphomethylpyrimidine synthase, chloroplastic

      UniProtKB/TrEMBL
      Q0DPM7, Q10F62, Q9AUL7

    2. XM_015777486.3 → XP_015632972.1  phosphomethylpyrimidine synthase, chloroplastic

      UniProtKB/TrEMBL
      Q0DPM7, Q10F62, Q9AUL7
      Conserved Domains (1) summary
      PLN02444
      Location:2 → 639
      PLN02444; HMP-P synthase

    3. XM_015777485.3 → XP_015632971.1  phosphomethylpyrimidine synthase, chloroplastic

      UniProtKB/TrEMBL
      Q0DPM7, Q10F62, Q9AUL7
      Conserved Domains (1) summary
      PLN02444
      Location:2 → 639
      PLN02444; HMP-P synthase

    RNA

    1. XR_001544821.3 RNA Sequence

    2. XR_001544819.3 RNA Sequence

    3. XR_001544820.3 RNA Sequence

    4. XR_003241398.2 RNA Sequence

    5. XR_010740370.1 RNA Sequence

    6. XR_010740368.1 RNA Sequence

    7. XR_010740369.1 RNA Sequence

    8. XR_001544822.3 RNA Sequence

    9. XR_010740371.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version

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