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    LOC4346522 E3 ubiquitin-protein ligase UPL1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4346522, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4346522
    Gene description
    E3 ubiquitin-protein ligase UPL1
    Locus tag
    OSNPB_090252700
    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
    Ubiquitous expression in leaves before flowering (RPKM 21.0), roots after flowering (RPKM 20.1) and 6 other tissues See more
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    Genomic context

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    Location:
    chromosome: 9
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 9 NC_089043.1 (8362909..8382239)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 9 NC_029264.1 (4016243..4036025)

    Chromosome 9 - NC_089043.1Genomic Context describing neighboring genes Neighboring gene exosome complex component RRP41 homolog Neighboring gene acetyl-CoA acetyltransferase 2 Neighboring gene protein NOI4 Neighboring gene uncharacterized LOC107278788

    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 transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein polyubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase UPL1
    Names
    Os09g0252700
    Os09g0252800
    P0574F11.30
    putative ubiquitin-protein ligase 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_089043.1 Reference ASM3414082v1 Primary Assembly

      Range
      8362909..8382239
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015756020.3 → XP_015611506.1  E3 ubiquitin-protein ligase UPL1 isoform X1

      UniProtKB/TrEMBL
      B9G2D0, Q6K3Y7
      Conserved Domains (5) summary
      cd00078
      Location:3354 → 3714
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
      cd14327
      Location:1286 → 1323
      UBA_atUPL1_2_like; UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins
      pfam06012
      Location:85 → 362
      DUF908; Domain of Unknown Function (DUF908)
      pfam06025
      Location:422 → 786
      DUF913; Domain of Unknown Function (DUF913)
      pfam14377
      Location:2664 → 2695
      DUF4414; Domain of unknown function (DUF4414)

    2. XM_015756022.3 → XP_015611508.1  E3 ubiquitin-protein ligase UPL1 isoform X3

      UniProtKB/TrEMBL
      B9G2D0
      Conserved Domains (6) summary
      smart00119
      Location:3342 → 3677
      HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
      cd00078
      Location:3318 → 3678
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
      cd14327
      Location:1286 → 1323
      UBA_atUPL1_2_like; UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins
      pfam06012
      Location:85 → 363
      DUF908; Domain of Unknown Function (DUF908)
      pfam06025
      Location:421 → 786
      DUF913; Domain of Unknown Function (DUF913)
      pfam14377
      Location:2597 → 2693
      DUF4414; Domain of unknown function (DUF4414)

    3. XM_015756021.3 → XP_015611507.1  E3 ubiquitin-protein ligase UPL1 isoform X2

      UniProtKB/TrEMBL
      B9G2D0
      Conserved Domains (6) summary
      smart00119
      Location:3377 → 3712
      HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
      cd00078
      Location:3353 → 3713
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
      cd14327
      Location:1285 → 1322
      UBA_atUPL1_2_like; UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins
      pfam06012
      Location:85 → 362
      DUF908; Domain of Unknown Function (DUF908)
      pfam06025
      Location:420 → 785
      DUF913; Domain of Unknown Function (DUF913)
      pfam14377
      Location:2632 → 2728
      DUF4414; Domain of unknown function (DUF4414)
    Nucleotide Protein
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