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    LOC4340699 ubiquitin receptor RAD23d [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4340699, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4340699
    Gene description
    ubiquitin receptor RAD23d
    Locus tag
    OSNPB_060264300
    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
    OJ1001_B06.1
    Expression
    Ubiquitous expression in leaves after flowering (RPKM 161.7), roots after flowering (RPKM 141.4) and 6 other tissues See more
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    Genomic context

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    See LOC4340699 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (8896115..8902120)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (8720563..8726647)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene 3-ketoacyl-CoA synthase 5 Neighboring gene zinc finger protein CONSTANS-LIKE 16 Neighboring gene uncharacterized LOC136357064 Neighboring gene protein NRT1/ PTR FAMILY 3.1

    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. 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
    3. 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

    Function Evidence Code Pubs
    enables damaged DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables polyubiquitin modification-dependent protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables proteasome 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 nucleotide-excision repair IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ubiquitin receptor RAD23d
    Names
    OSJNBa0037N01.48
    Os06g0264300
    putative RAD23 protein

    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_089040.1 Reference ASM3414082v1 Primary Assembly

      Range
      8896115..8902120
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015788441.2 → XP_015643927.1  ubiquitin receptor RAD23d

      UniProtKB/TrEMBL
      A2YBG8, A3BAG6, Q5Z6P9
      Conserved Domains (1) summary
      TIGR00601
      Location:1 → 408
      rad23; UV excision repair protein Rad23
    Nucleotide Protein
    Heading Accession and Version

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