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    LOC4339839 U-box domain-containing protein 12-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4339839, updated on 10-Oct-2024

    Summary

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    Gene symbol
    LOC4339839
    Gene description
    U-box domain-containing protein 12-like
    Locus tag
    OSNPB_060102700
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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
    PUB12; OsPUB12
    Expression
    Ubiquitous expression in roots before flowering (RPKM 34.2), roots after flowering (RPKM 30.2) and 6 other tissues See more
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    Genomic context

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    See LOC4339839 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (341665..346278)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (185625..191527)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene glutathione gamma-glutamylcysteinyltransferase 1 Neighboring gene sec-independent protein translocase protein TATB, chloroplastic-like Neighboring gene uncharacterized LOC124625845 Neighboring gene uncharacterized LOC4339840 Neighboring gene zinc finger protein CONSTANS-LIKE 13

    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. Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. Jantasuriyarat C, et al. Plant Physiol, 2005 May. PMID 15888683, Free PMC Article
    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
    3. 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

    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 ubiquitin-protein transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    U-box domain-containing protein 12
    Names
    LOC_Os06g01304
    OSJNBa0075G19.19-1
    OSJNBa0075G19.19-2
    Plant U-box protein 12
    RING-type E3 ubiquitin transferase PUB12
    putative cell death-related protein SPL11
    putative spotted leaf 11
    NP_001389605.1
    XP_066167215.1
    XP_066167216.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001402676.1 → NP_001389605.1  U-box domain-containing protein 12

      Status: VALIDATED

      Source sequence(s)
      AK071080, CB663113, CI103869, CI595153

    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_089040.1 Reference ASM3414082v1 Primary Assembly

      Range
      341665..346278
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_066311119.1 → XP_066167216.1  U-box domain-containing protein 12 isoform X3

    2. XM_066311118.1 → XP_066167215.1  U-box domain-containing protein 12 isoform X2

      UniProtKB/TrEMBL
      A3B7I6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VRH9.1 GenPept UniProtKB/Swiss-Prot:Q5VRH9

    Gene LinkOut

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