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    UBP13 ubiquitin-specific protease 13 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 820364, updated on 18-Sep-2024

    Summary

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    Official Symbol
    UBP13
    Official Full Name
    ubiquitin-specific protease 13
    Primary source
    TAIR:AT3G11910
    Locus tag
    AT3G11910
    See related
    Araport:AT3G11910
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    AtUBP13; ubiquitin-specific protease 13
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    Genomic context

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    See UBP13 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    33
    Sequence:
    Chromosome: 3; NC_003074.8 (3760724..3770563, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene transmembrane protein, putative (Protein of unknown function DUF2359, transmembrane) Neighboring gene Sterile alpha motif (SAM) domain-containing protein Neighboring gene aromatic and neutral transporter 1 Neighboring gene glutaredoxin-like protein Neighboring gene Adenine nucleotide alpha hydrolases-like superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Deubiquitinating enzymes UBP12 and UBP13 stabilize the brassinosteroid receptor BRI1. Luo Y, et al. EMBO Rep, 2022 Apr 5. PMID 35166439, Free PMC Article
    2. Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis. Kralemann LEM, et al. Genome Biol, 2020 Jun 16. PMID 32546254, Free PMC Article
    3. Ubiquitin-specific proteases UBP12 and UBP13 act in circadian clock and photoperiodic flowering regulation in Arabidopsis. Cui X, et al. Plant Physiol, 2013 Jun. PMID 23645632, Free PMC Article
    4. Ubiquitin-specific proteases UBP12 and UBP13 promote shade avoidance response by enhancing PIF7 stability. Zhou Y, et al. Proc Natl Acad Sci U S A, 2021 Nov 9. PMID 34732572, Free PMC Article
    5. Arabidopsis ubiquitin-specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency. Park SH, et al. New Phytol, 2019 Aug. PMID 31050353

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Deubiquitinating enzymes UBP12 and UBP13 stabilize the brassinosteroid receptor BRI1.
      Title: Deubiquitinating enzymes UBP12 and UBP13 stabilize the brassinosteroid receptor BRI1.
    2. Ubiquitin-specific proteases UBP12 and UBP13 promote shade avoidance response by enhancing PIF7 stability.
      Title: Ubiquitin-specific proteases UBP12 and UBP13 promote shade avoidance response by enhancing PIF7 stability.
    3. Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis.
      Title: Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis.
    4. UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2.
      Title: UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2.
    5. UBP12/UBP13 deubiquitinate ORE1 to stabilize this transcription factor and promote its activity as a positive regulator for leaf senescence under nitrogen deficiency conditions.
      Title: Arabidopsis ubiquitin-specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency.
    6. UBP12/13 are regulators of the RGF1-RGFR1-PLT1/2 signaling pathway and UBP12/13 can counteract RGF1-induced RGFR1 ubiquitination, stabilize RGFR1, and maintain root cell sensitivity to RGF1
      Title: Regulation of the stability of RGF1 receptor by the ubiquitin-specific proteases UBP12/UBP13 is critical for root meristem maintenance.
    7. UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, USP7-like proteins are essential for gene silencing in diverse genomic contexts.
      Title: H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system.
    8. The Deubiquitinating Enzymes UBP12 and UBP13 Positively Regulate MYC2 Levels in Jasmonate Responses
      Title: The Deubiquitinating Enzymes UBP12 and UBP13 Positively Regulate MYC2 Levels in Jasmonate Responses.
    9. UBP12 and UBP13 proteins play important role in the control of the circadian clock and photoperiodic flowering.
      Title: Ubiquitin-specific proteases UBP12 and UBP13 act in circadian clock and photoperiodic flowering regulation in Arabidopsis.
    10. AtUBP13 is a deubiquitinating enzyme capable of cleaving lysine-48-linked ubiquitin chains.
      Title: Deubiquitinating enzymes AtUBP12 and AtUBP13 and their tobacco homologue NtUBP12 are negative regulators of plant immunity.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001202935.1
    NM_112024.6

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables cysteine-type deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within jasmonic acid mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytosol HDA PubMed 
    located_in nucleus IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in plasmodesma HDA PubMed 

    General protein information

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    Preferred Names
    ubiquitin-specific protease 13
    NP_001319526.1
    • ubiquitin-specific protease 13 (UBP13); FUNCTIONS IN: ubiquitin-specific protease activity, ubiquitin thiolesterase activity; INVOLVED IN: ubiquitin-dependent protein catabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: TRAF-like (InterPro:IPR008974), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (InterPro:IPR018200), MATH (InterPro:IPR002083), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (InterPro:IPR001394), TRAF-type (InterPro:IPR013322); BEST Arabidopsis thaliana protein match is: ubiquitin-specific protease 12 (TAIR:AT5G06600.2).
    NP_187797.3
    • ubiquitin-specific protease 13 (UBP13); FUNCTIONS IN: ubiquitin-specific protease activity, ubiquitin thiolesterase activity; INVOLVED IN: ubiquitin-dependent protein catabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: TRAF-like (InterPro:IPR008974), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (InterPro:IPR018200), MATH (InterPro:IPR002083), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (InterPro:IPR001394), TRAF-type (InterPro:IPR013322); BEST Arabidopsis thaliana protein match is: ubiquitin-specific protease 12 (TAIR:AT5G06600.1); Has 7915 Blast hits to 7124 proteins in 272 species: Archae - 0; Bacteria - 15; Metazoa - 3654; Fungi - 1255; Plants - 1604; Viruses - 7; Other Eukaryotes - 1380 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003074.8 Reference assembly

      Range
      3760724..3770563 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001337961.1 → NP_001319526.1  ubiquitin-specific protease 13 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VCN6, A0A384L9E9, A0A654F693, F4J7I2

    2. NM_001337962.1 → NP_001326292.1  ubiquitin-specific protease 13 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WVD3, Q84WU2, Q9FU99, Q9SF08
      UniProtKB/TrEMBL
      A0A178VEE0, A0A5S9XBI0, A0A654F693
      Conserved Domains (1) summary
      COG5077
      Location:46 → 1113
      COG5077; Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

    3. NM_112024.6 → NP_187797.3  ubiquitin-specific protease 13 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_187797.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WVD3, Q84WU2, Q9FU99, Q9SF08
      UniProtKB/TrEMBL
      A0A178VEE0, A0A5S9XBI0, A0A654F693
      Conserved Domains (1) summary
      COG5077
      Location:46 → 1113
      COG5077; Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

    4. NM_001202935.1 → NP_001189864.1  ubiquitin-specific protease 13 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001189864.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VCN6, A0A384L9E9, A0A654F693, F4J7I2
      Conserved Domains (5) summary
      COG5077
      Location:45 → 1112
      COG5077; Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
      cd00121
      Location:53 → 177
      MATH; MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane ...
      cd02659
      Location:195 → 523
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
      pfam12436
      Location:622 → 873
      USP7_ICP0_bdg; ICP0-binding domain of Ubiquitin-specific protease 7
      pfam14533
      Location:882 → 1093
      USP7_C2; Ubiquitin-specific protease C-terminal
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q84WU2.1

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