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    LOC4324475 vacuolar protein sorting-associated protein 55 homolog [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4324475, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4324475
    Gene description
    vacuolar protein sorting-associated protein 55 homolog
    Locus tag
    OSNPB_010966500
    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 leaves after flowering (RPKM 13.5), roots after flowering (RPKM 12.9) and 6 other tissues See more
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    Genomic context

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    See LOC4324475 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 1 NC_089035.1 (43274262..43277180)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 1 NC_029256.1 (42621762..42624751)

    Chromosome 1 - NC_089035.1Genomic Context describing neighboring genes Neighboring gene mitochondrial-processing peptidase subunit alpha Neighboring gene uncharacterized LOC4324474 Neighboring gene transfer RNA leucine (anticodon UAG) Neighboring gene beta-fructofuranosidase, insoluble isoenzyme 4-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
    2. 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 late endosome to vacuole transport via multivesicular body sorting pathway IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    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 55 homolog
    Names
    Os01g0966500
    P0458E05.31
    vacuolar protein sorting 55 family-like

    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_089035.1 Reference ASM3414082v1 Primary Assembly

      Range
      43274262..43277180
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015793734.3 → XP_015649220.1  vacuolar protein sorting-associated protein 55 homolog isoform X1

      UniProtKB/TrEMBL
      A6N1U6
      Conserved Domains (1) summary
      pfam04133
      Location:7 → 124
      Vps55; Vacuolar protein sorting 55

    2. XM_015793740.2 → XP_015649226.1  vacuolar protein sorting-associated protein 55 homolog isoform X2

      UniProtKB/TrEMBL
      A0A5S6R9F8, A6N1U6, B7E813, B8A9U9, Q0JFR1, Q5JJV1
      Conserved Domains (1) summary
      pfam04133
      Location:1 → 112
      Vps55; Vacuolar protein sorting 55
    Nucleotide Protein
    Heading Accession and Version

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