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

Aliases for USP3 Gene

Aliases for USP3 Gene

  • Ubiquitin Specific Peptidase 3 2 3 5
  • Ubiquitin-Specific-Processing Protease 3 3 4
  • Deubiquitinating Enzyme 3 3 4
  • Ubiquitin Thioesterase 3 3 4
  • Ubiquitin Specific Protease 3 2
  • Ubiquitin Thiolesterase 3 3
  • EC 3.4.19.12 4
  • EC 3.1.2.15 63
  • SIH003 3
  • UBP 3

External Ids for USP3 Gene

Previous GeneCards Identifiers for USP3 Gene

  • GC15P059583
  • GC15P056887
  • GC15P061375
  • GC15P061512
  • GC15P061511
  • GC15P061582
  • GC15P063796
  • GC15P040621

Summaries for USP3 Gene

GeneCards Summary for USP3 Gene

USP3 (Ubiquitin Specific Peptidase 3) is a Protein Coding gene. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. GO annotations related to this gene include chromatin binding and cysteine-type endopeptidase activity. An important paralog of this gene is USP49.

UniProtKB/Swiss-Prot for USP3 Gene

  • Hydrolase that deubiquitinates monoubiquitinated target proteins such as histone H2A and H2B. Required for proper progression through S phase and subsequent mitotic entry. May regulate the DNA damage response (DDR) checkpoint through deubiquitination of H2A at DNA damage sites. Associates with the chromatin.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP3 Gene

Genomics for USP3 Gene

Regulatory Elements for USP3 Gene

Enhancers for USP3 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 USP3 on UCSC Golden Path with GeneCards custom track

Promoters for USP3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around USP3 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the USP3 gene promoter:

Genomic Location for USP3 Gene

Chromosome:
15
Start:
63,504,511 bp from pter
End:
63,594,640 bp from pter
Size:
90,130 bases
Orientation:
Plus strand

Genomic View for USP3 Gene

Genes around USP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP3 Gene

Proteins for USP3 Gene

  • Protein details for USP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y6I4-UBP3_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 3
    Protein Accession:
    Q9Y6I4
    Secondary Accessions:
    • B4DVU5
    • F5H1A6
    • Q8WVD0

    Protein attributes for USP3 Gene

    Size:
    520 amino acids
    Molecular mass:
    58897 Da
    Quaternary structure:
    • Interacts (via UBP-type domain) with H2A; the interaction is less efficient than with monoubiquitinated H2A.
    SequenceCaution:
    • Sequence=AAD42992.1; Type=Frameshift; Positions=265, 274, 299; Evidence={ECO:0000305};

    Alternative splice isoforms for USP3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP3 Gene

Proteomics data for USP3 Gene at MOPED

Selected DME Specific Peptides for USP3 Gene

Post-translational modifications for USP3 Gene

  • Ubiquitination at Lys 107, Lys 354, and Lys 423
  • Modification sites at PhosphoSitePlus

Domains & Families for USP3 Gene

Gene Families for USP3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y6I4

UniProtKB/Swiss-Prot:

UBP3_HUMAN :
  • Both protease activity and an intact zinc finger are required for H2A monodeubiquitination.
  • Belongs to the peptidase C19 family. USP3 subfamily.
  • Contains 1 UBP-type zinc finger.
Domain:
  • Both protease activity and an intact zinc finger are required for H2A monodeubiquitination.
  • Contains 1 USP domain.
Family:
  • Belongs to the peptidase C19 family. USP3 subfamily.
Similarity:
  • Contains 1 UBP-type zinc finger.
genes like me logo Genes that share domains with USP3: view

Function for USP3 Gene

Molecular function for USP3 Gene

GENATLAS Biochemistry:
ubiquitin specific protease 3,with two transcripts,both widely expressed at a low level and highly expressed in pancreas,cleaving a ubiquitin-proline bond,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 Function:
Hydrolase that deubiquitinates monoubiquitinated target proteins such as histone H2A and H2B. Required for proper progression through S phase and subsequent mitotic entry. May regulate the DNA damage response (DDR) checkpoint through deubiquitination of H2A at DNA damage sites. Associates with the chromatin.

Enzyme Numbers (IUBMB) for USP3 Gene

Gene Ontology (GO) - Molecular Function for USP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004843 thiol-dependent ubiquitin-specific protease activity TAS 10480896
GO:0008234 cysteine-type peptidase activity IEA --
genes like me logo Genes that share ontologies with USP3: view
genes like me logo Genes that share phenotypes with USP3: view

Animal Models for USP3 Gene

MGI Knock Outs for USP3:
  • Usp3 tm1a(EUCOMM)Wtsi
  • Usp3 tm1b(EUCOMM)Wtsi

Animal Model Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for USP3 Gene

Localization for USP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP3 Gene

Nucleus. Note=Localizes preferentially with monoubiquitinated H2A to chromatin.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for USP3 Gene COMPARTMENTS Subcellular localization image for USP3 gene
Compartment Confidence
nucleus 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for USP3 Gene

Pathways & Interactions for USP3 Gene

genes like me logo Genes that share pathways with USP3: view

Pathways by source for USP3 Gene

1 Qiagen pathway for USP3 Gene

Gene Ontology (GO) - Biological Process for USP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016578 histone deubiquitination IDA 17980597
genes like me logo Genes that share ontologies with USP3: view

No data available for SIGNOR curated interactions for USP3 Gene

Drugs & Compounds for USP3 Gene

(1) Additional Compounds for USP3 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 USP3: view

Transcripts for USP3 Gene

Unigene Clusters for USP3 Gene

Ubiquitin specific peptidase 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for USP3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a ·
SP1: - - - - - - -
SP2: - - - - - - -
SP3: - - - - - - - -
SP4: - - -
SP5: - - - - - -
SP6: - - - - - - -
SP7: - - - - -
SP8: - - - -
SP9: - - - - - - - - - - - - -
SP10: - -
SP11: -
SP12: -
SP13:
SP14:

ExUns: 17b ^ 18a · 18b ^ 19 ^ 20a · 20b · 20c · 20d
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: -
SP11: -
SP12:
SP13:
SP14: -

Relevant External Links for USP3 Gene

GeneLoc Exon Structure for
USP3
ECgene alternative splicing isoforms for
USP3

Expression for USP3 Gene

mRNA expression in normal human tissues for USP3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for USP3 Gene

This gene is overexpressed in Whole Blood (x6.0).

Protein differential expression in normal tissues from HIPED for USP3 Gene

This gene is overexpressed in Monocytes (17.0), Pancreatic juice (16.9), Blymphocyte (8.9), and Peripheral blood mononuclear cells (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for USP3 Gene



SOURCE GeneReport for Unigene cluster for USP3 Gene Hs.458499

mRNA Expression by UniProt/SwissProt for USP3 Gene

Q9Y6I4-UBP3_HUMAN
Tissue specificity: Expressed in all tissues examined, with strongest expression in pancreas.
genes like me logo Genes that share expression patterns with USP3: view

Protein tissue co-expression partners for USP3 Gene

Primer Products

In Situ Assay Products

Orthologs for USP3 Gene

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

Orthologs for USP3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia USP3 35
  • 94.28 (n)
  • 97.03 (a)
USP3 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia USP3 35
  • 94.94 (n)
  • 98.27 (a)
USP3 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Usp3 35
  • 90.77 (n)
  • 96.54 (a)
Usp3 16
Usp3 36
  • 97 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia USP3 35
  • 99.39 (n)
  • 99.39 (a)
USP3 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usp3 35
  • 90.06 (n)
  • 95.38 (a)
oppossum
(Monodelphis domestica)
Mammalia USP3 36
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USP3 36
  • 90 (a)
OneToOne
chicken
(Gallus gallus)
Aves USP3 35
  • 86.79 (n)
  • 95.77 (a)
USP3 36
  • 96 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USP3 36
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.18577 35
usp3 35
  • 75.95 (n)
  • 88.55 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.15490 35
zebrafish
(Danio rerio)
Actinopterygii usp3 35
  • 70.64 (n)
  • 74.23 (a)
wufe50h06 35
usp3 36
  • 71 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008805 35
  • 54.91 (n)
  • 53.68 (a)
worm
(Caenorhabditis elegans)
Secernentea usp-3 35
  • 49.8 (n)
  • 41.65 (a)
usp-3 36
  • 32 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DOA4 36
  • 12 (a)
ManyToMany
UBP5 36
  • 14 (a)
ManyToMany
Species with no ortholog for USP3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 USP3 Gene

ENSEMBL:
Gene Tree for USP3 (if available)
TreeFam:
Gene Tree for USP3 (if available)

Paralogs for USP3 Gene

Paralogs for USP3 Gene

genes like me logo Genes that share paralogs with USP3: view

Variants for USP3 Gene

Sequence variations from dbSNP and Humsavar for USP3 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs34776764 - 63,574,385(+) ATGGA(A/C)CAGTT nc-transcript-variant, reference, missense
rs4984248 -- 63,523,430(+) ATACA(A/T)GTCAC intron-variant
rs4984249 -- 63,557,327(+) GCACA(A/G)TCTTG intron-variant
rs4984250 -- 63,574,635(+) CTTTG(A/T)AATAC intron-variant
rs4984296 -- 63,525,516(+) CAGTT(C/G)CTTCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for USP3 Gene

Variant ID Type Subtype PubMed ID
nsv833034 CNV Loss 17160897

Variation tolerance for USP3 Gene

Residual Variation Intolerance Score: 8.76% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.25; 52.66% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USP3 Gene

HapMap Linkage Disequilibrium report
USP3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP3 Gene

Disorders for USP3 Gene

Relevant External Links for USP3

Genetic Association Database (GAD)
USP3
Human Genome Epidemiology (HuGE) Navigator
USP3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP3

No disorders were found for USP3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP3 Gene

Publications for USP3 Gene

  1. Characterization and chromosomal localization of USP3, a novel human ubiquitin-specific protease. (PMID: 10480896) Sloper-Mould K.E. … Baker R.T. (J. Biol. Chem. 1999) 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. Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. (PMID: 25281560) Lambert J.P. … Gingras A.C. (J Proteomics 2015) 3
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  5. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3

Products for USP3 Gene

Sources for USP3 Gene

Content