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    LOC4335625 violaxanthin de-epoxidase, chloroplastic [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4335625, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4335625
    Gene description
    violaxanthin de-epoxidase, chloroplastic
    Locus tag
    OSNPB_040379700
    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
    Also known as
    RVDE1
    Expression
    Broad expression in leaves before flowering (RPKM 28.8), roots after flowering (RPKM 12.5) and 4 other tissues See more
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    Genomic context

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    See LOC4335625 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 (18905179..18907673, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 4 NC_029259.1 (18551315..18553850, complement)

    Chromosome 4 - NC_089038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4335622 Neighboring gene uncharacterized LOC9268951 Neighboring gene RPM1-interacting protein 4 Neighboring gene uncharacterized LOC4335626 Neighboring gene stearoyl-[acyl-carrier-protein] 9-desaturase 5, chloroplastic-like

    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 violaxanthin de-epoxidase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chlorophyll metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in xanthophyll cycle IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    violaxanthin de-epoxidase, chloroplastic
    Names
    Os04g0379700

    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
      18905179..18907673 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015780856.3 → XP_015636342.1  violaxanthin de-epoxidase, chloroplastic

      UniProtKB/TrEMBL
      Q0JDT1, Q945R7
      Conserved Domains (1) summary
      PLN02372
      Location:1 → 465
      PLN02372; violaxanthin de-epoxidase
    Nucleotide Protein
    Heading Accession and Version

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