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Aliases for USP13 Gene

Aliases for USP13 Gene

  • Ubiquitin Specific Peptidase 13 (Isopeptidase T-3) 2 3 5
  • Ubiquitin Specific Protease 13 (Isopeptidase T-3) 2 3
  • Ubiquitin-Specific-Processing Protease 13 3 4
  • Deubiquitinating Enzyme 13 3 4
  • Ubiquitin Thioesterase 13 3 4
  • IsoT-3 3 4
  • ISOT3 3 4
  • Ubiquitin Thiolesterase 13 3
  • Isopeptidase T-3 4
  • EC 3.4.19.12 4
  • EC 3.1.2.15 63

External Ids for USP13 Gene

Previous GeneCards Identifiers for USP13 Gene

  • GC03P176137
  • GC03P180213
  • GC03P180772
  • GC03P180691
  • GC03P180853
  • GC03P179370
  • GC03P176774

Summaries for USP13 Gene

GeneCards Summary for USP13 Gene

USP13 (Ubiquitin Specific Peptidase 13 (Isopeptidase T-3)) is a Protein Coding gene. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. GO annotations related to this gene include ubiquitin protein ligase binding and thiol-dependent ubiquitin-specific protease activity. An important paralog of this gene is USP5.

UniProtKB/Swiss-Prot for USP13 Gene

  • Deubiquitinase that mediates deubiquitination of target proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD). Component of a regulatory loop that controls autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-containing complexes. Also deubiquitinates USP10, an essential regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing complexes regulate USP13 stability, suggesting the existence of a regulatory system by which PIK3C3/VPS34-containing complexes regulate p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1 and mediates deubiquitination of SKP2, thereby regulating endoplasmic reticulum-associated degradation (ERAD). Mediates stabilization of SIAH2 independently of deubiquitinase activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2 autoubiquitination. Has a weak deubiquitinase activity in vitro and preferentially cleaves Lys-63-linked polyubiquitin chains. In contrast to USP5, it is not able to mediate unanchored polyubiquitin disassembly. Able to cleave ISG15 in vitro; however, additional experiments are required to confirm such data.

Gene Wiki entry for USP13 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP13 Gene

Genomics for USP13 Gene

Regulatory Elements for USP13 Gene

Enhancers for USP13 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around USP13 on UCSC Golden Path with GeneCards custom track

Promoters for USP13 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around USP13 on UCSC Golden Path with GeneCards custom track

Genomic Location for USP13 Gene

Chromosome:
3
Start:
179,652,755 bp from pter
End:
179,789,401 bp from pter
Size:
136,647 bases
Orientation:
Plus strand

Genomic View for USP13 Gene

Genes around USP13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP13 Gene

Proteins for USP13 Gene

  • Protein details for USP13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92995-UBP13_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 13
    Protein Accession:
    Q92995
    Secondary Accessions:
    • A8K2S3
    • B4DYF3
    • D3DNS2
    • Q96B25

    Protein attributes for USP13 Gene

    Size:
    863 amino acids
    Molecular mass:
    97327 Da
    Quaternary structure:
    • Interacts with UFD1. Interacts (via UBA domains) with SIAH2 (when ubiquitinated).

    Three dimensional structures from OCA and Proteopedia for USP13 Gene

    Alternative splice isoforms for USP13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP13 Gene

Proteomics data for USP13 Gene at MOPED

Post-translational modifications for USP13 Gene

  • Ubiquitination at Lys 18, Lys 176, Lys 190, Lys 259, Lys 326, Lys 328, Lys 389, Lys 405, Lys 538, Lys 565, and Lys 598
  • Modification sites at PhosphoSitePlus

Other Protein References for USP13 Gene

Domains & Families for USP13 Gene

Gene Families for USP13 Gene

Suggested Antigen Peptide Sequences for USP13 Gene

Graphical View of Domain Structure for InterPro Entry

Q92995

UniProtKB/Swiss-Prot:

UBP13_HUMAN :
  • The UBP-type zinc finger has lost its ability to bind ubiquitin and USP13 is not activated by unanchored ubiquitin. Swapping with the UBP-type zinc finger from USP5 restores ability to bind unanchored ubiquitin and subsequent activation of the protein (PubMed:22216260).
  • Belongs to the peptidase C19 family.
  • Contains 1 UBP-type zinc finger.
Domain:
  • The UBP-type zinc finger has lost its ability to bind ubiquitin and USP13 is not activated by unanchored ubiquitin. Swapping with the UBP-type zinc finger from USP5 restores ability to bind unanchored ubiquitin and subsequent activation of the protein (PubMed:22216260).
  • The UBA domains mediate binding to ubiquitin.
  • Contains 2 UBA domains.
  • Contains 1 USP domain.
Family:
  • Belongs to the peptidase C19 family.
Similarity:
  • Contains 1 UBP-type zinc finger.
genes like me logo Genes that share domains with USP13: view

Function for USP13 Gene

Molecular function for USP13 Gene

GENATLAS Biochemistry:
ubiquitin specific protease 13,expressed in testis and ovary,ubiquitin C terminal hydrolase family member,deubiquitin enzyme family
UniProtKB/Swiss-Prot CatalyticActivity:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
UniProtKB/Swiss-Prot EnzymeRegulation:
Specifically inhibited by spautin-1 (specific and potent autophagy inhibitor-1), a derivative of MBCQ that binds to USP13 and inhibits deubiquitinase activity. Regulated by PIK3C3/VPS34-containing complexes. The weak deubiquitinase activity in vitro suggests the existence of some mechanism that activates the enzyme.
UniProtKB/Swiss-Prot Function:
Deubiquitinase that mediates deubiquitination of target proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD). Component of a regulatory loop that controls autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-containing complexes. Also deubiquitinates USP10, an essential regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing complexes regulate USP13 stability, suggesting the existence of a regulatory system by which PIK3C3/VPS34-containing complexes regulate p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1 and mediates deubiquitination of SKP2, thereby regulating endoplasmic reticulum-associated degradation (ERAD). Mediates stabilization of SIAH2 independently of deubiquitinase activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2 autoubiquitination. Has a weak deubiquitinase activity in vitro and preferentially cleaves Lys-63-linked polyubiquitin chains. In contrast to USP5, it is not able to mediate unanchored polyubiquitin disassembly. Able to cleave ISG15 in vitro; however, additional experiments are required to confirm such data.

Enzyme Numbers (IUBMB) for USP13 Gene

Gene Ontology (GO) - Molecular Function for USP13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity IMP 21811243
GO:0008242 omega peptidase activity IEA --
GO:0008270 zinc ion binding IEA --
GO:0051087 chaperone binding IPI 24424410
GO:0070628 proteasome binding IDA 24424410
genes like me logo Genes that share ontologies with USP13: view
genes like me logo Genes that share phenotypes with USP13: view

Animal Model Products

  • Taconic Biosciences Mouse Models for USP13

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP13 Gene

Localization for USP13 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for USP13 Gene COMPARTMENTS Subcellular localization image for USP13 gene
Compartment Confidence
cytosol 3
nucleus 3
mitochondrion 1
peroxisome 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for USP13 Gene

Pathways & Interactions for USP13 Gene

genes like me logo Genes that share pathways with USP13: view

Pathways by source for USP13 Gene

1 Qiagen pathway for USP13 Gene

Gene Ontology (GO) - Biological Process for USP13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0006914 autophagy IEA --
GO:0008283 cell proliferation IMP 21811243
GO:0050821 protein stabilization IDA 21659512
GO:1904294 positive regulation of ERAD pathway IMP 24424410
genes like me logo Genes that share ontologies with USP13: view

No data available for SIGNOR curated interactions for USP13 Gene

Drugs & Compounds for USP13 Gene

(1) Additional Compounds for USP13 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
genes like me logo Genes that share compounds with USP13: view

Transcripts for USP13 Gene

Unigene Clusters for USP13 Gene

Ubiquitin specific peptidase 13 (isopeptidase T-3):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for USP13 Gene

No ASD Table

Relevant External Links for USP13 Gene

GeneLoc Exon Structure for
USP13
ECgene alternative splicing isoforms for
USP13

Expression for USP13 Gene

mRNA expression in normal human tissues for USP13 Gene

mRNA differential expression in normal tissues according to GTEx for USP13 Gene

This gene is overexpressed in Muscle - Skeletal (x21.0) and Heart - Left Ventricle (x5.7).

Protein differential expression in normal tissues from HIPED for USP13 Gene

This gene is overexpressed in Cerebrospinal fluid (51.2) and Testis (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for USP13 Gene



SOURCE GeneReport for Unigene cluster for USP13 Gene Hs.175322

mRNA Expression by UniProt/SwissProt for USP13 Gene

Q92995-UBP13_HUMAN
Tissue specificity: Highly expressed in ovary and testes.
genes like me logo Genes that share expression patterns with USP13: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners for USP13 Gene

Orthologs for USP13 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for USP13 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia USP13 35
  • 93.2 (n)
  • 98.03 (a)
USP13 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia USP13 35
  • 93.08 (n)
  • 98.49 (a)
USP13 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Usp13 35
  • 88.69 (n)
  • 96.15 (a)
Usp13 16
Usp13 36
  • 95 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia USP13 35
  • 99.65 (n)
  • 99.77 (a)
USP13 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usp13 35
  • 88.42 (n)
  • 95.8 (a)
oppossum
(Monodelphis domestica)
Mammalia USP13 36
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 79 (a)
OneToMany
-- 36
  • 91 (a)
OneToMany
-- 36
  • 85 (a)
OneToMany
-- 36
  • 89 (a)
OneToMany
chicken
(Gallus gallus)
Aves USP13 35
  • 78.22 (n)
  • 84.01 (a)
USP13 36
  • 83 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USP13 36
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp13 35
  • 73.91 (n)
  • 79.47 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16188 35
zebrafish
(Danio rerio)
Actinopterygii usp13 35
  • 72.36 (n)
  • 76.39 (a)
usp13 36
  • 75 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG12082 37
  • 43 (a)
CG12082 36
  • 45 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea T27A3.2 37
  • 31 (a)
usp-5 36
  • 34 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP14 36
  • 28 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9810 36
  • 46 (a)
OneToMany
Species with no ortholog for USP13:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for USP13 Gene

ENSEMBL:
Gene Tree for USP13 (if available)
TreeFam:
Gene Tree for USP13 (if available)

Paralogs for USP13 Gene

Paralogs for USP13 Gene

(1) SIMAP similar genes for USP13 Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for USP13 Gene

genes like me logo Genes that share paralogs with USP13: view

Variants for USP13 Gene

Sequence variations from dbSNP and Humsavar for USP13 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs2220 -- 179,709,983(-) AAAAC(A/C/T)ACACC intron-variant
rs15241 -- 179,789,216(-) GCACA(A/G)GAACA utr-variant-3-prime
rs721384 -- 179,670,094(+) ggagt(G/T)gggac intron-variant
rs734368 -- 179,704,552(-) GTCAT(C/T)GGTCA intron-variant
rs734778 -- 179,737,337(-) TTTCT(G/T)AACTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for USP13 Gene

Variant ID Type Subtype PubMed ID
nsv4140 CNV Loss 18451855
esv2726257 CNV Deletion 23290073
esv2656680 CNV Deletion 23128226
nsv522327 CNV Loss 19592680

Variation tolerance for USP13 Gene

Residual Variation Intolerance Score: 12.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.40; 54.34% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for USP13 Gene

Disorders for USP13 Gene

Relevant External Links for USP13

Genetic Association Database (GAD)
USP13
Human Genome Epidemiology (HuGE) Navigator
USP13
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP13

No disorders were found for USP13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP13 Gene

Publications for USP13 Gene

  1. The genomic organization of Isopeptidase T-3 (ISOT-3), a new member of the ubiquitin specific protease family (UBP). (PMID: 9841226) Timms K.M. … Gibbs R.A. (Gene 1998) 3 4 23 67
  2. Human and mouse proteases: a comparative genomic approach. (PMID: 12838346) Puente X.S. … Lopez-Otin C. (Nat. Rev. Genet. 2003) 2 3
  3. Muscle-specific RING finger-1 interacts with titin to regulate sarcomeric M-line and thick filament structure and may have nuclear functions via its interaction with glucocorticoid modulatory element binding protein-1. (PMID: 11927605) McElhinny A.S. … Gregorio C.C. (J. Cell Biol. 2002) 3 23
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  5. Deubiquitylase OTUD3 regulates PTEN stability and suppresses tumorigenesis. (PMID: 26280536) Yuan L. … Zhang L. (Nat. Cell Biol. 2015) 3

Products for USP13 Gene

Sources for USP13 Gene

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