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    LOC4347500 E3 ubiquitin-protein ligase RNF4 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4347500, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4347500
    Gene description
    E3 ubiquitin-protein ligase RNF4
    Locus tag
    OSNPB_090504700
    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
    Expression
    Ubiquitous expression in roots after flowering (RPKM 51.5), leaves after flowering (RPKM 48.4) and 6 other tissues See more
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    Genomic context

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    See LOC4347500 in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 9 NC_089043.1 (23914225..23917856, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 9 NC_029264.1 (19503356..19506992, complement)

    Chromosome 9 - NC_089043.1Genomic Context describing neighboring genes Neighboring gene UDP-glucuronate 4-epimerase 6 Neighboring gene cyclin-C1-1-like Neighboring gene uncharacterized LOC4347501 Neighboring gene uncharacterized LOC4347502

    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
    • 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. A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping: an example using rice root-growth QTLs. Norton GJ, et al. Genomics, 2008 Nov. PMID 18755262
    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 SUMO-ubiquitin ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RNF4
    Names
    Os09g0504700
    NP_001391860.1
    XP_015611765.1

    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_001404931.1 → NP_001391860.1  E3 ubiquitin-protein ligase RNF4

      Status: VALIDATED

      Source sequence(s)
      AU163266, CF280105, CF318488, CI153849, CI647138
      UniProtKB/TrEMBL
      A0A5S6R9Z1, B7EMU6, Q0J0N2

    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_089043.1 Reference ASM3414082v1 Primary Assembly

      Range
      23914225..23917856 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015756279.3 → XP_015611765.1  E3 ubiquitin-protein ligase RNF4 isoform X1

      UniProtKB/TrEMBL
      A0A5S6R9Z1, B7EMU6, Q0J0N2
      Conserved Domains (1) summary
      cl17238
      Location:135 → 176
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
    Nucleotide Protein
    Heading Accession and Version

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