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    Usp13 ubiquitin specific peptidase 13 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 310306, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Usp13provided by RGD
    Official Full Name
    ubiquitin specific peptidase 13provided by RGD
    Primary source
    RGD:1306044
    See related
    EnsemblRapid:ENSRNOG00000030639 AllianceGenome:RGD:1306044
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable several functions, including BAT3 complex binding activity; peptidase activity; and proteasome binding activity. Predicted to be involved in several processes, including maintenance of unfolded protein; regulation of DNA-templated transcription; and regulation of catabolic process. Predicted to act upstream of or within protein deubiquitination and protein stabilization. Predicted to be active in cytosol and nucleus. Orthologous to human USP13 (ubiquitin specific peptidase 13). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Muscle (RPKM 616.4), Heart (RPKM 493.7) and 2 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Usp13 in Genome Data Viewer
    Location:
    2q24
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (117502811..117617049)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (115576912..115689153)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (119197153..119317507)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA70 Neighboring gene mitochondrial ribosomal protein L47 Neighboring gene NADH:ubiquinone oxidoreductase subunit B5 Neighboring gene peroxisomal biogenesis factor 5-like Neighboring gene uncharacterized LOC134485614 Neighboring gene uncharacterized LOC134485613

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. USP13 reduces septic mediated cardiomyocyte oxidative stress and inflammation by inducing Nrf2. Wu D, et al. Allergol Immunopathol (Madr), 2023. PMID 36916102
    2. Regulation of MITF stability by the USP13 deubiquitinase. Zhao X, et al. Nat Commun, 2011 Aug 2. PMID 21811243
    3. USP13 enzyme regulates Siah2 ligase stability and activity via noncatalytic ubiquitin-binding domains. Scortegagna M, et al. J Biol Chem, 2011 Aug 5. PMID 21659512, Free PMC Article
    4. Domain analysis reveals that a deubiquitinating enzyme USP13 performs non-activating catalysis for Lys63-linked polyubiquitin. Zhang YH, et al. PLoS One, 2011. PMID 22216260, Free PMC Article
    5. Beclin1 controls the levels of p53 by regulating the deubiquitination activity of USP10 and USP13. Liu J, et al. Cell, 2011 Sep 30. PMID 21962518, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. USP13 reduces septic mediated cardiomyocyte oxidative stress and inflammation by inducing Nrf2.
      Title: USP13 reduces septic mediated cardiomyocyte oxidative stress and inflammation by inducing Nrf2.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables BAT3 complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables K48-linked deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables proteasome binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein-folding chaperone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin-like protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in maintenance of unfolded protein ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of ERAD pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein K29-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein K6-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein K63-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K63-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein stabilization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein stabilization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of protein stability IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 13
    Names
    ubiquitin specific protease 13 (isopeptidase T-3)
    ubiquitin thiolesterase 13
    NP_001101135.1
    XP_008759146.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001107665.2 → NP_001101135.1  ubiquitin carboxyl-terminal hydrolase 13

      See identical proteins and their annotated locations for NP_001101135.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/TrEMBL
      A6IHR3, D3ZDI9
      Related
      ENSRNOP00000039985.4, ENSRNOT00000048030.7
      Conserved Domains (2) summary
      COG5207
      Location:28 → 856
      UBP14; Uncharacterized Zn-finger protein, UBP-type [General function prediction only]
      cd02658
      Location:335 → 854
      Peptidase_C19B; 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 ...

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      117502811..117617049
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008760924.4 → XP_008759146.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X1

      Related
      ENSRNOP00000108074.1, ENSRNOT00000157346.1
      Conserved Domains (5) summary
      COG5207
      Location:28 → 855
      UBP14; Uncharacterized Zn-finger protein, UBP-type [General function prediction only]
      cd02658
      Location:334 → 853
      Peptidase_C19B; 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 ...
      cd14384
      Location:649 → 697
      UBA1_UBP13; UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13)
      cd14386
      Location:722 → 763
      UBA2_UBP5; UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5)
      pfam02148
      Location:208 → 281
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
    Nucleotide Protein Strain
    Heading Accession and Version

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