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Aliases for USP53 Gene

Aliases for USP53 Gene

  • Ubiquitin Specific Peptidase 53 2 3 5
  • Inactive Ubiquitin-Specific Peptidase 53 4
  • Ubiquitin Specific Protease 53 2
  • KIAA1350 4

External Ids for USP53 Gene

Previous GeneCards Identifiers for USP53 Gene

  • GC04P120590
  • GC04P120619
  • GC04P120518
  • GC04P120380
  • GC04P120354
  • GC04P120133
  • GC04P115855

Summaries for USP53 Gene

GeneCards Summary for USP53 Gene

USP53 (Ubiquitin Specific Peptidase 53) is a Protein Coding gene. Diseases associated with USP53 include Cantu Syndrome. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include thiol-dependent ubiquitinyl hydrolase activity. An important paralog of this gene is USP54.

UniProtKB/Swiss-Prot for USP53 Gene

  • Tight junction-associated protein that is involved in the survival of auditory hair cells and hearing. Maybe by modulating the barrier properties and mechanical stability of tight junctions (By similarity). Has no peptidase activity (PubMed:14715245).

Gene Wiki entry for USP53 Gene

Additional gene information for USP53 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP53 Gene

Genomics for USP53 Gene

GeneHancer (GH) Regulatory Elements for USP53 Gene

Promoters and enhancers for USP53 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04I119206 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 574.9 -1.6 -1575 8.1 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 USP53 LOC101929762 LOC645513 FABP2 METTL14 LOC729218 KLHL2P1 MRPL42P1
GH04I119217 Promoter 0.6 EPDnew 550.4 +5.2 5204 0.1 ZNF189 USP53 LOC101929762 GC04P119302 PIR34278
GH04I119298 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 21.5 +87.4 87358 3.7 PKNOX1 CLOCK FOXA2 SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 C4orf3 GC04P119302 PIR34278 LOC645513 FABP2 USP53 KLHL2P1 LOC101929762
GH04I119623 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 16.7 +415.5 415499 9.8 SIN3A ZNF2 ZNF48 ZNF121 GLIS2 ZNF207 ZNF143 FOS KLF13 SP3 PDE5A LOC105377396 GC04P119639 GC04M119628 LOC645513 USP53 FABP2 KLHL2P1 ENSG00000260091
GH04I119102 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 15.3 -109.2 -109157 2.8 ATF1 FOXA2 SIN3A FEZF1 FOS ATF7 SP3 REST ZNF518A ATF4 METTL14 CICP16 USP53 MYOZ2 SNHG8 FABP2 LOC102723967 GC04P119115
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around USP53 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the USP53 gene promoter:

Genomic Locations for USP53 Gene

Genomic Locations for USP53 Gene
82,932 bases
Plus strand

Genomic View for USP53 Gene

Genes around USP53 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP53 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP53 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP53 Gene

Proteins for USP53 Gene

  • Protein details for USP53 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Inactive ubiquitin carboxyl-terminal hydrolase 53
    Protein Accession:
    Secondary Accessions:
    • Q68DA5
    • Q8WVQ5
    • Q9P2J7

    Protein attributes for USP53 Gene

    1073 amino acids
    Molecular mass:
    120806 Da
    Quaternary structure:
    • Interacts (via the C-terminal region) with the heterodimer TJP1:TJP2.
    • Sequence=AAH17382.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for USP53 Gene

Post-translational modifications for USP53 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for USP53 Gene

Domains & Families for USP53 Gene

Gene Families for USP53 Gene

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

Protein Domains for USP53 Gene

Suggested Antigen Peptide Sequences for USP53 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase C19 family.
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP53: view

Function for USP53 Gene

Molecular function for USP53 Gene

UniProtKB/Swiss-Prot Function:
Tight junction-associated protein that is involved in the survival of auditory hair cells and hearing. Maybe by modulating the barrier properties and mechanical stability of tight junctions (By similarity). Has no peptidase activity (PubMed:14715245).

Phenotypes From GWAS Catalog for USP53 Gene

Gene Ontology (GO) - Molecular Function for USP53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0036459 NOT thiol-dependent ubiquitinyl hydrolase activity IEA,IDA 14715245
genes like me logo Genes that share ontologies with USP53: view
genes like me logo Genes that share phenotypes with USP53: view

Animal Model Products

  • Taconic Biosciences Mouse Models for USP53

miRNA for USP53 Gene

miRTarBase miRNAs that target USP53

Clone Products

  • Addgene plasmids for USP53

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP53 Gene

Localization for USP53 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP53 Gene

Cell junction, tight junction.

Subcellular locations from

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 USP53 gene
Compartment Confidence
nucleus 3
cytosol 2
golgi apparatus 2
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for USP53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005911 cell-cell junction IEA --
GO:0005923 bicellular tight junction IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with USP53: view

Pathways & Interactions for USP53 Gene

genes like me logo Genes that share pathways with USP53: view

Pathways by source for USP53 Gene

1 Qiagen pathway for USP53 Gene

Gene Ontology (GO) - Biological Process for USP53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001508 action potential IEA --
GO:0006915 apoptotic process IEA --
GO:0007605 sensory perception of sound IEA --
GO:0008150 biological_process ND --
GO:0010996 response to auditory stimulus IEA --
genes like me logo Genes that share ontologies with USP53: view

No data available for SIGNOR curated interactions for USP53 Gene

Drugs & Compounds for USP53 Gene

No Compound Related Data Available

Transcripts for USP53 Gene

Unigene Clusters for USP53 Gene

Ubiquitin specific peptidase 53:
Representative Sequences:

Clone Products

  • Addgene plasmids for USP53

Alternative Splicing Database (ASD) splice patterns (SP) for USP53 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8a · 8b
SP2: - -
SP3: -
SP4: -

Relevant External Links for USP53 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for USP53 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for USP53 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for USP53 Gene

This gene is overexpressed in Nerve - Tibial (x7.0).

Protein differential expression in normal tissues from HIPED for USP53 Gene

This gene is overexpressed in Heart (36.1) and Pancreatic juice (32.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for USP53 Gene

Protein tissue co-expression partners for USP53 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of USP53 Gene:


SOURCE GeneReport for Unigene cluster for USP53 Gene:


mRNA Expression by UniProt/SwissProt for USP53 Gene:

Tissue specificity: Expressed predominantly in skeletal muscle and heart.

Evidence on tissue expression from TISSUES for USP53 Gene

  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with USP53: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for USP53 Gene

Orthologs for USP53 Gene

This gene was present in the common ancestor of animals.

Orthologs for USP53 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia USP53 33 34
  • 99.38 (n)
(Bos Taurus)
Mammalia USP53 33 34
  • 92.72 (n)
(Canis familiaris)
Mammalia USP53 33 34
  • 89.74 (n)
(Mus musculus)
Mammalia Usp53 33 16 34
  • 81.46 (n)
(Monodelphis domestica)
Mammalia USP53 34
  • 65 (a)
(Ornithorhynchus anatinus)
Mammalia USP53 34
  • 58 (a)
(Gallus gallus)
Aves USP53 33 34
  • 69.93 (n)
(Anolis carolinensis)
Reptilia USP53 34
  • 55 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia usp53 33
  • 62.5 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.32755 33
(Danio rerio)
Actinopterygii USP53 34
  • 78 (a)
fruit fly
(Drosophila melanogaster)
Insecta ec 34
  • 11 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 50 (a)
Species where no ortholog for USP53 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • rat (Rattus norvegicus)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for USP53 Gene

Gene Tree for USP53 (if available)
Gene Tree for USP53 (if available)

Paralogs for USP53 Gene

Paralogs for USP53 Gene

(1) SIMAP similar genes for USP53 Gene using alignment to 4 proteins: Pseudogenes for USP53 Gene

genes like me logo Genes that share paralogs with USP53: view

Variants for USP53 Gene

Sequence variations from dbSNP and Humsavar for USP53 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs10000726 -- 119,289,609(+) G/A intron_variant
rs1000100275 -- 119,238,624(+) A/T intron_variant
rs1000119215 -- 119,225,619(+) G/A intron_variant
rs10001498 -- 119,249,522(+) G/A intron_variant
rs1000167836 -- 119,246,150(+) TGTG/TG intron_variant

Structural Variations from Database of Genomic Variants (DGV) for USP53 Gene

Variant ID Type Subtype PubMed ID
dgv5373n100 CNV gain 25217958
esv2329745 CNV deletion 18987734
esv2728233 CNV deletion 23290073
esv2763386 CNV loss 21179565
esv3451010 CNV duplication 20981092
nsv595332 CNV loss 21841781

Variation tolerance for USP53 Gene

Residual Variation Intolerance Score: 81.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.65; 82.83% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP53 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP53 Gene

Disorders for USP53 Gene

MalaCards: The human disease database

(1) MalaCards diseases for USP53 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
cantu syndrome
  • hypertrichotic osteochondrodysplasia
- elite association - COSMIC cancer census association via MalaCards
Search USP53 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for USP53

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with USP53: view

No data available for UniProtKB/Swiss-Prot and Genatlas for USP53 Gene

Publications for USP53 Gene

  1. Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. (PMID: 14715245) Quesada V … López-Otín C (Biochemical and biophysical research communications 2004) 2 3 4 58
  2. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  3. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. (PMID: 20332099) Kalsi G … Riley BP (Human molecular genetics 2010) 3 44 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. (PMID: 26871637) Yang X … Vidal M (Cell 2016) 3 58

Products for USP53 Gene

  • Addgene plasmids for USP53

Sources for USP53 Gene

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