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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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