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    LOC4330868 E3 ubiquitin-protein ligase COP1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4330868, updated on 13-Jul-2024

    Summary

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    Gene symbol
    LOC4330868
    Gene description
    E3 ubiquitin-protein ligase COP1
    Locus tag
    OSNPB_020771100
    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
    PPS; COP1; rCOP1; OJ1353_F08.9-2
    Expression
    Ubiquitous expression in roots before flowering (RPKM 13.7), mature seeds (RPKM 12.7) and 6 other tissues See more
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    Genomic context

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    Location:
    chromosome: 2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 2 NC_089036.1 (33023467..33028989, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 2 NC_029257.1 (32528081..32533578, complement)

    Chromosome 2 - NC_089036.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4330865 Neighboring gene separase Neighboring gene nitrate reductase [NAD(P)H] Neighboring gene probable transcription factor At1g11510 Neighboring gene LOC128684019

    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

    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 ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase COP1
    Names
    COP1, constitutive photomorphogenesis 1
    Os02g0771100
    putative COP1, constitutive photomorphogenesis 1

    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_089036.1 Reference ASM3414082v1 Primary Assembly

      Range
      33023467..33028989 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015772116.3 → XP_015627602.1  E3 ubiquitin-protein ligase COP1

      UniProtKB/TrEMBL
      A3ABS5, Q0DX70, Q6ZHH4, Q947M8, Q9MAZ5
      Conserved Domains (4) summary
      PLN00181
      Location:155 → 681
      PLN00181; protein SPA1-RELATED; Provisional
      PLN03208
      Location:35 → 172
      PLN03208; E3 ubiquitin-protein ligase RMA2; Provisional
      sd00039
      Location:385 → 429
      7WD40; WD40 repeat [structural motif]
      cd16504
      Location:57 → 101
      RING-HC_COP1; RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and similar proteins
    Nucleotide Protein
    Heading Accession and Version

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