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    LOC4333909 vacuolar sorting protein 39 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4333909, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4333909
    Gene description
    vacuolar sorting protein 39
    Locus tag
    OSNPB_030715500
    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 flower buds (RPKM 14.1), flowers (RPKM 14.0) and 6 other tissues See more
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    Genomic context

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    See LOC4333909 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (29842741..29853392, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (28964615..28975276, complement)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107280335 Neighboring gene protein POLLEN DEFECTIVE IN GUIDANCE 1 Neighboring gene uncharacterized LOC9270836 Neighboring gene PHD finger protein MALE MEIOCYTE DEATH 1

    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

    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in endosomal vesicle fusion IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vacuolar sorting protein 39
    Names
    Os03g0715500
    vam6/Vps39-like protein

    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
      29842741..29853392 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_026023817.2 → XP_025879602.1  vacuolar sorting protein 39 isoform X2

      UniProtKB/TrEMBL
      Q307Q8
      Conserved Domains (4) summary
      pfam00637
      Location:617 → 779
      Clathrin; Region in Clathrin and VPS
      pfam10366
      Location:495 → 605
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:858 → 966
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:54 → 276
      CNH; CNH domain

    2. XM_015775937.3 → XP_015631423.1  vacuolar sorting protein 39 isoform X1

      UniProtKB/TrEMBL
      B8AQN8, Q0DP47, Q10DX1, Q307Q8
      Conserved Domains (4) summary
      pfam10366
      Location:496 → 606
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam00637
      Location:618 → 780
      Clathrin; Region in Clathrin and VPS
      pfam10367
      Location:859 → 968
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:54 → 276
      CNH; CNH domain

    RNA

    1. XR_010740046.1 RNA Sequence

    2. XR_010740045.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version

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