Free for academic non-profit institutions. Other users need a Commercial license

Aliases for USP13 Gene

Aliases for USP13 Gene

  • Ubiquitin Specific Peptidase 13 2 3
  • Ubiquitin Specific Peptidase 13 (Isopeptidase T-3) 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
  • Isopeptidase T-3 2 4
  • IsoT-3 3 4
  • ISOT3 3 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 13 3
  • Ubiquitin Thiolesterase 13 3
  • EC 3.4.19.12 4
  • EC 3.1.2.15 58

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) is a Protein Coding gene. Among its related pathways are Deubiquitination and 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). Also regulates ERAD through the deubiquitination of UBL4A a component of the BAG6/BAT3 complex. 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

Additional gene information for USP13 Gene

No data available for Entrez Gene Summary , CIViC 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H179738 0.9 ENCODE 17.1 +87.0 86997 1 ELF3 FOXA2 ATF1 MLX ARID4B THRB ZSCAN9 RAD21 RARA YY1 USP13 GC03M179795
GH03H179712 0.8 Ensembl ENCODE 15.5 +63.1 63065 5 JUND POLR2A BACH1 FOS EBF1 RUNX3 MAFK USP13 GC03M179795
GH03H179680 0.7 ENCODE 17.5 +28.6 28598 1 SMARCE1 NR4A1 DPF2 ZNF592 NFIC ZNF316 BCL11A ZNF341 GLIS1 ID3 USP13 GC03M179795
GH03H179603 1.1 ENCODE 10.9 -48.2 -48159 2 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 SP3 SP5 USP13 ACTL6A NDUFB5 MRPL47 ENSG00000272660
GH03H179612 0.9 ENCODE 10.9 -38.3 -38292 3 HDAC1 ATF1 TBL1XR1 ARNT CHAMP1 TCF12 GATA2 ELK1 ATF7 CREM USP13 NDUFB5 ENSG00000239096
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000162581 845 2401 ARID4B SIN3A FEZF1 YY1 GTF3C2 SLC30A9 GLIS2 ELK1 ZNF143 FOS

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). Interacts with BAG6; the interaction is direct and may mediate UBL4A deubiquitination (PubMed:24424410). Interacts (via UBA 2 domain) with AMFR; the interaction is direct (PubMed:24424410). Interacts with UBL4A; may be indirect via BAG6 (PubMed:24424410).

    Three dimensional structures from OCA and Proteopedia for USP13 Gene

    Alternative splice isoforms for USP13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP13 Gene

Selected DME Specific Peptides for USP13 Gene

Q92995:
  • NRQQDAQEFFLHL
  • KEGRWVI
  • NLGNSCY
  • ENLWLNLTDG
  • QIKKFTFGLDWVPKK
  • ACRKAVY
  • LFAFISHMGTSTM
  • VKLGTIT
  • VFRFLVEE

Post-translational modifications for USP13 Gene

  • Ubiquitination at Lys18, posLast=176176, Lys190, posLast=259259, Lys326, posLast=328328, Lys389, posLast=405405, posLast=538538, posLast=565565, and posLast=598598
  • Modification sites at PhosphoSitePlus

Other Protein References for USP13 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for USP13 (USP13)

Domains & Families for USP13 Gene

Gene Families for USP13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

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.
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.
Family:
  • Belongs to the peptidase C19 family.
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). Also regulates ERAD through the deubiquitination of UBL4A a component of the BAG6/BAT3 complex. 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:0004843 thiol-dependent ubiquitin-specific protease activity TAS --
GO:0005515 protein binding IPI 21811243
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for USP13
  • Applied Biological Materials Clones for USP13
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

Localization for USP13 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USP13 gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for USP13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with USP13: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot 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

Gene Ontology (GO) - Biological Process for USP13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IMP 21811243
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0006914 autophagy IEA --
GO:0008283 cell proliferation IMP 21811243
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

(2) Drugs for USP13 Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Spautin-1 Pharma Novel autophagy inhibitor, USP10 and USP13 inhibitor; inhibits autophagy 0

(1) ApexBio Compounds for USP13 Gene

Compound Action Cas Number
Spautin-1 Novel autophagy inhibitor 1262888-28-7
genes like me logo Genes that share compounds with USP13: view

Drug Products

Transcripts for USP13 Gene

Unigene Clusters for USP13 Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for USP13
  • Applied Biological Materials Clones for USP13
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for USP13 Gene



NURSA nuclear receptor signaling pathways regulating expression of USP13 Gene:

USP13

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.

Evidence on tissue expression from TISSUES for USP13 Gene

  • Liver(2.1)
  • Muscle(2)
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 , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia USP13 33 34
  • 99.65 (n)
cow
(Bos Taurus)
Mammalia USP13 33 34
  • 93.2 (n)
dog
(Canis familiaris)
Mammalia USP13 33 34
  • 93.08 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 91 (a)
OneToMany
-- 34
  • 89 (a)
OneToMany
-- 34
  • 85 (a)
OneToMany
-- 34
  • 79 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Usp13 33 16 34
  • 88.69 (n)
rat
(Rattus norvegicus)
Mammalia Usp13 33
  • 88.42 (n)
oppossum
(Monodelphis domestica)
Mammalia USP13 34
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves USP13 33 34
  • 78.22 (n)
lizard
(Anolis carolinensis)
Reptilia USP13 34
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp13 33
  • 73.91 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16188 33
zebrafish
(Danio rerio)
Actinopterygii usp13 33 34
  • 72.36 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG12082 35 34
  • 43 (a)
worm
(Caenorhabditis elegans)
Secernentea usp-5 34
  • 34 (a)
OneToMany
T27A3.2 35
  • 31 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP14 34
  • 28 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9810 34
  • 46 (a)
OneToMany
Species where no ortholog for USP13 was found in the sources mined by GeneCards:
  • 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
rs1000014533 -- 179,753,611(+) AGGAG(C/T)AGTTG intron-variant
rs1000017305 -- 179,772,164(+) TCTAC(C/T)ATGTT intron-variant
rs1000037880 -- 179,729,716(+) ATCCA(C/T)CCGCC intron-variant
rs1000044421 -- 179,709,064(+) GACAG(-/C)CCAGG intron-variant
rs1000046939 -- 179,771,689(+) CCAGG(G/T)TAACA intron-variant

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

Variant ID Type Subtype PubMed ID
esv2656680 CNV deletion 23128226
esv2726257 CNV deletion 23290073
esv3562975 CNV deletion 23714750
esv3598847 CNV loss 21293372
esv3893829 CNV loss 25118596
nsv1073696 CNV deletion 25765185
nsv1074642 CNV deletion 25765185
nsv4140 CNV deletion 18451855
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)

Relevant External Links for USP13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot 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 KM … Gibbs RA (Gene 1998) 3 4 22 60
  2. USP13 antagonizes gp78 to maintain functionality of a chaperone in ER-associated degradation. (PMID: 24424410) Liu Y … Ye Y (eLife 2014) 3 4 60
  3. Domain analysis reveals that a deubiquitinating enzyme USP13 performs non-activating catalysis for Lys63-linked polyubiquitin. (PMID: 22216260) Zhang YH … Hu HY (PloS one 2011) 3 4 60
  4. Beclin1 controls the levels of p53 by regulating the deubiquitination activity of USP10 and USP13. (PMID: 21962518) Liu J … Yuan J (Cell 2011) 3 4 60
  5. Regulation of MITF stability by the USP13 deubiquitinase. (PMID: 21811243) Zhao X … Fisher DE (Nature communications 2011) 3 4 60

Products for USP13 Gene

  • Addgene plasmids for USP13

Sources for USP13 Gene

Content
Loading form....