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    LOC4327586 TOM1-like protein 6 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4327586, updated on 21-Dec-2023

    Summary

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    Gene symbol
    LOC4327586
    Gene description
    TOM1-like protein 6
    Locus tag
    OSNPB_010825700
    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
    vhs2
    Expression
    Ubiquitous expression in roots before flowering (RPKM 17.7), roots after flowering (RPKM 17.6) and 6 other tissues See more
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    Genomic context

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    See LOC4327586 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    102 current IRGSP-1.0 (GCF_001433935.1) 1 NC_029256.1 (35314402..35318850, complement)

    Chromosome 1 - NC_029256.1Genomic Context describing neighboring genes Neighboring gene protein NUCLEAR FUSION DEFECTIVE 4 Neighboring gene EP1-like glycoprotein 3 Neighboring gene amino acid transporter AVT6C Neighboring gene uncharacterized LOC112937451 Neighboring gene uncharacterized LOC4327516

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_029256.1 Chromosome 1 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. Development of an efficient method for the isolation of factors involved in gene transcription during rice embryo development. Ye R, et al. Plant J, 2004 Apr. PMID 15078336
    2. 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 phosphatidylinositol binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables ubiquitin binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    TOM1-like protein 6
    Names
    Os01g0825700
    P0439E11.17
    putative VHS2 protein
    target of Myb protein 1

    NCBI Reference Sequences (RefSeq)

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    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_029256.1 Reference IRGSP-1.0 Primary Assembly

      Range
      35314402..35318850 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015766947.2 → XP_015622433.1  TOM1-like protein 6

      UniProtKB/TrEMBL
      A0A0P0V9X8, B8ABL8, B9EU84, Q5QMB2
      Conserved Domains (2) summary
      cd03561
      Location:22 → 148
      VHS; VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ...
      cd14231
      Location:200 → 278
      GAT_GGA_like_plant; GAT domain found in uncharacterized Golgi-localized gamma ear-containing Arf-binding protein (GGA)-like proteins mainly found in plants
    Nucleotide Protein
    Heading Accession and Version

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