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    USP13 ubiquitin specific peptidase 13 [ Homo sapiens (human) ]

    Gene ID: 8975, updated on 17-Jun-2019

    Summary

    Official Symbol
    USP13provided by HGNC
    Official Full Name
    ubiquitin specific peptidase 13provided by HGNC
    Primary source
    HGNC:HGNC:12611
    See related
    Ensembl:ENSG00000058056 MIM:603591
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ISOT3; IsoT-3
    Expression
    Broad expression in heart (RPKM 16.6), adrenal (RPKM 7.5) and 21 other tissues See more
    Orthologs

    Genomic context

    See USP13 in Genome Data Viewer
    Location:
    3q26.33
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (179653040..179789401)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (179370933..179507189)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene actin like 6A Neighboring gene mitochondrial ribosomal protein L47 Neighboring gene uncharacterized LOC107986158 Neighboring gene NADH:ubiquinone oxidoreductase subunit B5 Neighboring gene peroxisomal biogenesis factor 5 like Neighboring gene PEX5L antisense RNA 2 Neighboring gene RNA, 5S ribosomal pseudogene 149

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Deubiquitination, organism-specific biosystem (from REACTOME)
      Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
    • Metabolism of proteins, organism-specific biosystem (from REACTOME)
      Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
    • Post-translational protein modification, organism-specific biosystem (from REACTOME)
      Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
    • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
      Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    BAT3 complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Lys48-specific deubiquitinase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    chaperone binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cysteine-type endopeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    proteasome binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    thiol-dependent ubiquitin-specific protease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    thiol-dependent ubiquitin-specific protease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    thiol-dependent ubiquitinyl hydrolase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    thiol-dependent ubiquitinyl hydrolase activity TAS
    Traceable Author Statement
    more info
     
    ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    ubiquitin-like protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    maintenance of unfolded protein involved in ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    melanocyte differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein K29-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein K48-linked deubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    protein K6-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein K63-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein deubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein deubiquitination TAS
    Traceable Author Statement
    more info
     
    protein stabilization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein stabilization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of autophagy IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytosol TAS
    Traceable Author Statement
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 13
    Names
    deubiquitinating enzyme 13
    ubiquitin specific peptidase 13 (isopeptidase T-3)
    ubiquitin specific protease 13 (isopeptidase T-3)
    ubiquitin thioesterase 13
    ubiquitin thiolesterase 13
    ubiquitin-specific-processing protease 13
    NP_003931.2
    XP_011511571.1
    XP_016862914.1
    XP_016862915.1
    XP_016862916.1

    NCBI Reference Sequences (RefSeq)

    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_003940.3NP_003931.2  ubiquitin carboxyl-terminal hydrolase 13

      See identical proteins and their annotated locations for NP_003931.2

      Status: VALIDATED

      Source sequence(s)
      AC007687, AC125604, BC016146
      Consensus CDS
      CCDS3235.1
      UniProtKB/Swiss-Prot
      Q92995
      UniProtKB/TrEMBL
      A0A0A6YZ17
      Related
      ENSP00000263966.3, ENST00000263966.8
      Conserved Domains (5) summary
      COG5207
      Location:30861
      UBP14; Uncharacterized Zn-finger protein, UBP-type [General function prediction only]
      cd02658
      Location:337859
      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:652700
      UBA1_UBP13; UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13)
      cd14386
      Location:728769
      UBA2_UBP5; UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5)
      pfam02148
      Location:211284
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

      Range
      179653040..179789401
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011513269.1XP_011511571.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X1

      See identical proteins and their annotated locations for XP_011511571.1

      Conserved Domains (5) summary
      COG5207
      Location:30852
      UBP14; Uncharacterized Zn-finger protein, UBP-type [General function prediction only]
      cd02658
      Location:337850
      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:643691
      UBA1_UBP13; UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13)
      cd14386
      Location:719760
      UBA2_UBP5; UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5)
      pfam02148
      Location:211284
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
    2. XM_017007426.1XP_016862915.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X3

    3. XM_017007425.1XP_016862914.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X2

      Related
      ENSP00000417146.1, ENST00000496897.5
    4. XM_017007427.1XP_016862916.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X4

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