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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 Hypertrichotic Osteochondrodysplasia Cantu Type. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. 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

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

Regulatory Elements for USP53 Gene

Enhancers for USP53 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
GH04G119206 2 FANTOM5 Ensembl ENCODE dbSUPER 24.9 -1.6 -1576 8.1 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 LOC645513 USP53 FABP2 LOC729218 KLHL2P1 MRPL42P1
GH04G119102 1.7 FANTOM5 Ensembl ENCODE dbSUPER 15.3 -109.2 -109158 2.8 FOXA2 ATF1 SIN3A FEZF1 GATA2 FOS SP3 ZNF518A MAFF STAT3 USP53 MYOZ2 FABP2 LOC102723967 GC04P119115
GH04G119298 1.1 ENCODE 21.5 +87.4 87359 3.7 PKNOX1 FOXA2 MLX CREB3L1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 YY1 LOC645513 FABP2 USP53 KLHL2P1 PIR34278 GC04P119302 LOC101929762
GH04G119623 1.2 ENCODE dbSUPER 16.7 +415.5 415500 9.8 SIN3A ZNF2 ZNF48 ZNF121 GLIS2 ZNF143 ZNF207 FOS SP3 REST LOC645513 USP53 FABP2 KLHL2P1 ENSG00000260091 GC04P119639 LOC105377396
GH04G119105 1 Ensembl ENCODE dbSUPER 15.4 -106.1 -106089 1.2 NFIC NFIB CEBPB FOS CEBPG USP53 FABP2 GC04P119115 LOC102723967
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USP53 on UCSC Golden Path with GeneCards custom track

Promoters for USP53 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000172474 613 3601 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5

Genomic Location for USP53 Gene

Chromosome:
4
Start:
119,212,587 bp from pter
End:
119,295,518 bp from pter
Size:
82,932 bases
Orientation:
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:
    Q70EK8-UBP53_HUMAN
    Recommended name:
    Inactive ubiquitin carboxyl-terminal hydrolase 53
    Protein Accession:
    Q70EK8
    Secondary Accessions:
    • Q68DA5
    • Q8WVQ5
    • Q9P2J7

    Protein attributes for USP53 Gene

    Size:
    1073 amino acids
    Molecular mass:
    120806 Da
    Quaternary structure:
    • Interacts (via the C-terminal region) with the heterodimer TJP1:TJP2.
    SequenceCaution:
    • 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

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

Q70EK8

UniProtKB/Swiss-Prot:

UBP53_HUMAN :
  • Belongs to the peptidase C19 family.
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).

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 IDA,IEA 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

CRISPR Products

miRNA for USP53 Gene

miRTarBase miRNAs that target USP53

Inhibitory RNA Products

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

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

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:

CRISPR Products

Inhibitory RNA Products

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
SP1:
SP2: - -
SP3: -
SP4: -

Relevant External Links for USP53 Gene

GeneLoc Exon Structure for
USP53
ECgene alternative splicing isoforms for
USP53

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:

USP53

SOURCE GeneReport for Unigene cluster for USP53 Gene:

Hs.431081

mRNA Expression by UniProt/SwissProt for USP53 Gene:

Q70EK8-UBP53_HUMAN
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

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia USP53 34 35
  • 99.38 (n)
cow
(Bos Taurus)
Mammalia USP53 34 35
  • 92.72 (n)
dog
(Canis familiaris)
Mammalia USP53 34 35
  • 89.74 (n)
mouse
(Mus musculus)
Mammalia Usp53 34 16 35
  • 81.46 (n)
oppossum
(Monodelphis domestica)
Mammalia USP53 35
  • 65 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USP53 35
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves USP53 34 35
  • 69.93 (n)
lizard
(Anolis carolinensis)
Reptilia USP53 35
  • 55 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp53 34
  • 62.5 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.32755 34
zebrafish
(Danio rerio)
Actinopterygii USP53 35
  • 78 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta ec 35
  • 11 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 50 (a)
OneToMany
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

ENSEMBL:
Gene Tree for USP53 (if available)
TreeFam:
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.org 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 Sequence Context AA Info Type
rs10000726 -- 119,289,609(+) TTTCT(A/G)CTTCT intron-variant
rs1000100275 -- 119,238,624(+) GACAC(A/T)CACCT intron-variant
rs1000119215 -- 119,225,619(+) CGGGC(A/G)CCTGT intron-variant
rs10001498 -- 119,249,522(+) AGTCA(A/G)CAAAG intron-variant
rs1000167836 -- 119,246,150(+) ATGTC(-/TG)TGGAT 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)

Relevant External Links for USP53 Gene

Human Gene Mutation Database (HGMD)
USP53
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP53

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: DISEASES

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

Relevant External Links for USP53

Genetic Association Database (GAD)
USP53
Human Genome Epidemiology (HuGE) Navigator
USP53
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP53
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. … Lopez-Otin C. (Biochem. Biophys. Res. Commun. 2004) 2 3 4 64
  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 Res. 2000) 2 3 4 64
  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 B.P. (Hum. Mol. Genet. 2010) 3 46 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. (PMID: 27107012) Yachie N. … Roth F.P. (Mol. Syst. Biol. 2016) 3 64

Products for USP53 Gene

  • Addgene plasmids for USP53

Sources for USP53 Gene

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