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    LOC4333407 glycerophosphodiester phosphodiesterase GDPD6 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4333407, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4333407
    Gene description
    glycerophosphodiester phosphodiesterase GDPD6
    Locus tag
    OSNPB_030603600
    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
    Broad expression in roots after flowering (RPKM 29.0), roots before flowering (RPKM 23.1) and 5 other tissues See more
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    Genomic context

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    See LOC4333407 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (23475192..23478691)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (22615885..22619557)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene transfer RNA arginine (anticodon ACG) Neighboring gene mitochondrial import receptor subunit TOM5 homolog Neighboring gene pentatricopeptide repeat-containing protein At5g55840 Neighboring gene presenilin-like protein At2g29900

    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 glycerophosphodiester phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    glycerophosphodiester phosphodiesterase GDPD6
    Names
    Os03g0603600

    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
      23475192..23478691
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015772504.3 → XP_015627990.1  glycerophosphodiester phosphodiesterase GDPD6

      UniProtKB/TrEMBL
      A2XJB6, A3AK86, Q6AUZ6
      Conserved Domains (1) summary
      cd08602
      Location:44 → 355
      GDPD_ScGlpQ1_like; Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins
    Nucleotide Protein
    Heading Accession and Version

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