Aliases for USP3 Gene

Aliases for USP3 Gene

  • Ubiquitin Specific Peptidase 3 2 3 5
  • Ubiquitin-Specific-Processing Protease 3 3 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 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 50
  • SIH003 3
  • USP3 5
  • 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 Deubiquitination and Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include chromatin binding and cysteine-type endopeptidase activity. An important paralog of this gene is USP4.

UniProtKB/Swiss-Prot Summary 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 , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USP3 Gene

Genomics for USP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for USP3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP3

Top Transcription factor binding sites by QIAGEN in the USP3 gene promoter:
  • AML1a

Genomic Locations for USP3 Gene

Latest Assembly
chr15:63,504,511-63,594,640
(GRCh38/hg38)
Size:
90,130 bases
Orientation:
Plus strand

Previous Assembly
chr15:63,796,792-63,886,832
(GRCh37/hg19 by Entrez Gene)
Size:
90,041 bases
Orientation:
Plus strand

chr15:63,796,793-63,886,839
(GRCh37/hg19 by Ensembl)
Size:
90,047 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; Evidence={ECO:0000305};

    Alternative splice isoforms for USP3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP3 Gene

Selected DME Specific Peptides for USP3 Gene

Q9Y6I4:
  • AVVVHHG
  • GNTCFMN
  • QQDAHEF
  • NLGNTCF

Post-translational modifications for USP3 Gene

  • Ubiquitination at Lys107, Lys354, and Lys423
  • Modification sites at PhosphoSitePlus

Domains & Families for USP3 Gene

Gene Families for USP3 Gene

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

Protein Domains for USP3 Gene

InterPro:
Blocks:
  • Ubiquitin thiolesterase, family 2
  • Zn-finger in ubiquitin thiolesterase

Suggested Antigen Peptide Sequences for USP3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ12869 fis, clone NT2RP2003713, highly similar to Ubiquitin carboxyl-terminal hydrolase 3 (EC 3.1.2.15) (B3KMX7_HUMAN)
  • cDNA FLJ60902, highly similar to Ubiquitin carboxyl-terminal hydrolase 3 (EC 3.1.2.15) (B4DV65_HUMAN)
  • cDNA FLJ60359, highly similar to Ubiquitin carboxyl-terminal hydrolase 3 (EC 3.1.2.15) (B4DWJ6_HUMAN)
  • Ubiquitin carboxyl-terminal hydrolase (F5H1A6_HUMAN)
  • USP3 protein (Q498Y2_HUMAN)

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

Function for USP3 Gene

Molecular function for USP3 Gene

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=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).; EC=3.4.19.12;.
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

Enzyme Numbers (IUBMB) for USP3 Gene

Phenotypes From GWAS Catalog for USP3 Gene

Gene Ontology (GO) - Molecular Function for USP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0004843 thiol-dependent ubiquitin-specific protease activity IEA,IMP 17980597
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0008270 zinc ion binding 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 Usp3<tm1a(EUCOMM)Wtsi>
  • Usp3 Usp3<tm1b(EUCOMM)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP3

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
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 USP3 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Midbody ring (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for USP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA 17980597
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA,TAS --
GO:0005737 cytoplasm IBA 21873635
GO:0036464 cytoplasmic ribonucleoprotein granule IDA --
genes like me logo Genes that share ontologies with USP3: view

Pathways & Interactions for USP3 Gene

PathCards logo

SuperPathways 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
  • Ubiquitin-Proteasome Dependent Proteolysis

Gene Ontology (GO) - Biological Process for USP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0000278 mitotic cell cycle IMP 17980597
GO:0006281 DNA repair IMP 17980597
GO:0006325 chromatin organization IEA --
GO:0006508 proteolysis IEA --
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) Drugs for USP3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
genes like me logo Genes that share compounds with USP3: view

Transcripts for USP3 Gene

mRNA/cDNA for USP3 Gene

2 REFSEQ mRNAs :
20 NCBI additional mRNA sequence :
21 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP3

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

Expression for USP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for USP3 Gene



Protein tissue co-expression partners for USP3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for USP3

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.

Evidence on tissue expression from TISSUES for USP3 Gene

  • Skin(4.4)
  • Spleen(4.4)
  • Nervous system(4.3)
  • Eye(4.1)
  • Lung(2.4)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with USP3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for USP3 Gene

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
Chimpanzee
(Pan troglodytes)
Mammalia USP3 29 30
  • 99.39 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia USP3 30
  • 97 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia USP3 29 30
  • 94.94 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia USP3 29 30
  • 94.28 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Usp3 29 16 30
  • 90.77 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Usp3 29
  • 90.06 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia USP3 30
  • 90 (a)
OneToOne
Chicken
(Gallus gallus)
Aves USP3 29 30
  • 86.79 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia USP3 30
  • 89 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia usp3 29
  • 75.95 (n)
Str.18577 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.15490 29
Zebrafish
(Danio rerio)
Actinopterygii usp3 29 30
  • 70.64 (n)
OneToOne
wufe50h06 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008805 29
  • 54.91 (n)
Worm
(Caenorhabditis elegans)
Secernentea usp-3 29 30
  • 49.8 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP5 30
  • 14 (a)
ManyToMany
DOA4 30
  • 12 (a)
ManyToMany
Species where no ortholog for USP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for USP3: view image
Alliance of Genome Resources:
Additional Orthologs for USP3

Paralogs for USP3 Gene

(20) SIMAP similar genes for USP3 Gene using alignment to 16 proteins:

  • UBP3_HUMAN
  • B4DV65_HUMAN
  • B4DWJ6_HUMAN
  • H0YKU8_HUMAN
  • H0YL81_HUMAN
  • H0YLB7_HUMAN
  • H0YLG0_HUMAN
  • H0YLJ0_HUMAN
  • H0YM72_HUMAN
  • H0YMI4_HUMAN
  • H0YMP6_HUMAN
  • H0YMW1_HUMAN
  • H0YNK1_HUMAN
  • H0YNX9_HUMAN
  • Q498Y2_HUMAN
  • Q6JHV3_HUMAN
genes like me logo Genes that share paralogs with USP3: view

Variants for USP3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP3 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
rs146583283 Benign: not provided 63,588,415(+) C/T
NM_006537.4(USP3):c.1207C>T (p.Leu403=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs34527287 Benign: not provided 63,590,745(+) C/T
NM_006537.4(USP3):c.1482C>T (p.Asp494=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs34776764 Benign: not provided 63,574,385(+) C/Ap.Pro360Thr
NM_006537.4(USP3):c.1078C>A (p.Pro360Thr)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for USP3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
nsv1048029 CNV gain 25217958
nsv1131191 CNV deletion 24896259
nsv476887 CNV novel sequence insertion 20440878
nsv480693 CNV novel sequence insertion 20440878
nsv833034 CNV loss 17160897
nsv951974 CNV duplication 24416366

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)

Additional Variant Information for USP3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP3
Leiden Open Variation Database (LOVD)
USP3

SNP Genotyping and Copy Number Assays for research

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

Disorders for USP3 Gene

Additional Disease Information for USP3

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

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 KE … Baker RT (The Journal of biological chemistry 1999) 3 4 22
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  3. Association of genome-wide variation with the risk of incident heart failure in adults of European and African ancestry: a prospective meta-analysis from the cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium. (PMID: 20445134) Smith NL … Vasan RS (Circulation. Cardiovascular genetics 2010) 3 40
  4. Human USP3 is a chromatin modifier required for S phase progression and genome stability. (PMID: 17980597) Nicassio F … Citterio E (Current biology : CB 2007) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for USP3 Gene

Sources for USP3 Gene