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    LOC4333626 E3 ubiquitin ligase PARAQUAT TOLERANCE 3 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4333626, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4333626
    Gene description
    E3 ubiquitin ligase PARAQUAT TOLERANCE 3
    Locus tag
    OSNPB_030659400
    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
    Expression
    Broad expression in roots before flowering (RPKM 54.3), mature seeds (RPKM 24.9) and 6 other tissues See more
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    Genomic context

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    See LOC4333626 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (26672337..26677785, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (25805345..25810847, complement)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene ferredoxin C 1, chloroplastic Neighboring gene glyoxylase I 4 Neighboring gene acyl transferase 1-like Neighboring gene LOB domain-containing protein 4

    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 nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin ligase PARAQUAT TOLERANCE 3
    Names
    Os03g0659400

    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_089037.1 Reference ASM3414082v1 Primary Assembly

      Range
      26672337..26677785 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015777497.3 → XP_015632983.1  E3 ubiquitin ligase PARAQUAT TOLERANCE 3

      UniProtKB/TrEMBL
      A0A0P0W135, A2XK97, Q0DPV5, Q850T7
      Conserved Domains (3) summary
      COG5222
      Location:2 → 369
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
      pfam08783
      Location:4 → 81
      DWNN; DWNN domain
      pfam17228
      Location:472 → 513
      SGP; Sulphur globule protein
    Nucleotide Protein
    Heading Accession and Version

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