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    LOC4335642 vacuolar protein-sorting-associated protein 11 homolog [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4335642, updated on 21-Dec-2023

    Summary

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    Gene symbol
    LOC4335642
    Gene description
    vacuolar protein-sorting-associated protein 11 homolog
    Locus tag
    OSNPB_040382700
    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 12.0), flowers (RPKM 10.6) and 6 other tissues See more
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    Genomic context

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    See LOC4335642 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    102 current IRGSP-1.0 (GCF_001433935.1) 4 NC_029259.1 (18769013..18776207)

    Chromosome 4 - NC_029259.1Genomic Context describing neighboring genes Neighboring gene SNF1-related protein kinase regulatory subunit gamma-1 Neighboring gene uncharacterized LOC4335641 Neighboring gene uncharacterized LOC112938706 Neighboring gene uncharacterized LOC9269109 Neighboring gene uncharacterized LOC4335644

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_029259.1 Chromosome 4 Reference IRGSP-1.0 Primary Assembly

    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. 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 protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein-macromolecule adaptor activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endosome organization IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in organelle fusion IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in vacuole organization IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in vesicle docking involved in exocytosis 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
    part_of HOPS complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vacuolar protein-sorting-associated protein 11 homolog
    Names
    Os04g0382700

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs of Annotated Genomes: Oryza sativa Japonica Group Annotation Release 102 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference IRGSP-1.0 Primary Assembly

    Genomic

    1. NC_029259.1 Reference IRGSP-1.0 Primary Assembly

      Range
      18769013..18776207
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_026024881.1 → XP_025880666.1  vacuolar protein-sorting-associated protein 11 homolog isoform X2

      Conserved Domains (6) summary
      pfam00637
      Location:357 → 473
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:855 → 897
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
      pfam13966
      Location:8 → 32
      zf-RVT; zinc-binding in reverse transcriptase
      cd16688
      Location:814 → 854
      RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
      cl21453
      Location:312 → 391
      PKc_like; Protein Kinases, catalytic domain
      cl26078
      Location:651 → 723
      Clathrin; Region in Clathrin and VPS

    2. XM_015781416.2 → XP_015636902.1  vacuolar protein-sorting-associated protein 11 homolog isoform X1

      UniProtKB/TrEMBL
      B9FEU4, Q7XVC4
      Conserved Domains (5) summary
      smart00299
      Location:395 → 511
      CLH; Clathrin heavy chain repeat homology
      pfam00637
      Location:395 → 511
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:891 → 935
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
      cl17238
      Location:854 → 889
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      cl21453
      Location:350 → 429
      PKc_like; Protein Kinases, catalytic domain
    Nucleotide Protein
    Heading Accession and Version

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