Aliases for USP6 Gene

Aliases for USP6 Gene

  • Ubiquitin Specific Peptidase 6 2 3 5
  • Ubiquitin Carboxyl-Terminal Hydrolase 6 2 3 4
  • Ubiquitin Specific Peptidase 6 (Tre-2 Oncogene) 2 3
  • Ubiquitin Specific Protease 6 (Tre-2 Oncogene) 2 3
  • Ubiquitin-Specific-Processing Protease 6 3 4
  • Deubiquitinating Enzyme 6 3 4
  • Ubiquitin Thioesterase 6 3 4
  • TBC1D3 And USP32 Fusion 2 3
  • Proto-Oncogene TRE-2 3 4
  • TRE17 2 3
  • Tre-2 2 3
  • HRP1 3 4
  • TRE2 3 4
  • TRE Oncogene, Smith Magenis Syndrome Chromosome Region 2
  • Ubiquitin-Specific Protease USP6 3
  • Ubiquitin Thiolesterase 6 3
  • Hyperpolymorphic Gene 1 3
  • Tre-2 Oncogene 2
  • EC 3.4.19.12 4
  • EC 3.1.2.15 50
  • USP6-Short 3
  • TRESMCR 3
  • USP6 5
  • Tre2 2

External Ids for USP6 Gene

Previous HGNC Symbols for USP6 Gene

  • HRP1
  • TRESMCR

Previous GeneCards Identifiers for USP6 Gene

  • GC17P005451
  • GC17P005369
  • GC17P004976
  • GC17P005232
  • GC17P004972
  • GC17P004921
  • GC17P005019

Summaries for USP6 Gene

GeneCards Summary for USP6 Gene

USP6 (Ubiquitin Specific Peptidase 6) is a Protein Coding gene. Diseases associated with USP6 include Pseudosarcomatous Fibromatosis and Fasciitis. Among its related pathways are Arf6 signaling events and Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and cysteine-type endopeptidase activity. An important paralog of this gene is USP32.

UniProtKB/Swiss-Prot Summary for USP6 Gene

  • Deubiquitinase with an ATP-independent isopeptidase activity, cleaving at the C-terminus of the ubiquitin moiety. Catalyzes its own deubiquitination. In vitro, isoform 2, but not isoform 3, shows deubiquitinating activity. Promotes plasma membrane localization of ARF6 and selectively regulates ARF6-dependent endocytic protein trafficking. Is able to initiate tumorigenesis by inducing the production of matrix metalloproteinases following NF-kappa-B activation.

Gene Wiki entry for USP6 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USP6 Gene

Genomics for USP6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for USP6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J005128 Promoter 0.4 EPDnew 250.4 +12.8 12758 0.1 ZNF335 ENSG00000262855 lnc-ZNF232-1 piR-42801 piR-33033-001 piR-36645-001 piR-33659-001 piR-40159 piR-34256-001 piR-58865 piR-53959
GH17J005115 Enhancer 0.2 Ensembl 250.7 -0.7 -731 0.2 USP6 lnc-SLC52A1-3 ZNF232 ZFP3
GH17J005508 Enhancer 0.9 FANTOM5 Ensembl ENCODE 39 +392.9 392869 3 MYNN RFX1 BHLHE40 FOS POLR2A BMI1 USP6 RABEP1 MIS12 ENSG00000263272 SCIMP NUP88 RPAIN NLRP1 ENSG00000282980 LOC728392
GH17J004937 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.1 -170.0 -170006 16.5 BCLAF1 ZNF207 NCOR1 MYC ZNF600 IKZF1 SSRP1 JUND ZNF580 POLR2A ENO3 RNF167 PFN1 SLC25A11 SPAG7 ZNF232 CHRNE ZNF594-DT CAMTA2 ZZEF1
GH17J005220 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 10.4 +113.9 113905 18.7 BCLAF1 SP1 ZNF207 ZNF654 POLR2A CEBPA JUND BCL11A CTCF REST RABEP1 SCIMP ENSG00000263164 ZNF232-AS1 USP6 CAMTA2 NUP88 ENSG00000262165 ZFP3 NLRP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP6

Top Transcription factor binding sites by QIAGEN in the USP6 gene promoter:
  • AP-2alpha
  • AP-2alpha isoform 2
  • AP-2alpha isoform 3
  • AP-2alpha isoform 4
  • GR
  • GR-alpha
  • GR-beta
  • PPAR-alpha
  • YY1

Genomic Locations for USP6 Gene

Latest Assembly
chr17:5,116,032-5,175,034
(GRCh38/hg38)
Size:
59,003 bases
Orientation:
Plus strand

Previous Assembly
chr17:5,019,327-5,078,286
(GRCh37/hg19 by Entrez Gene)
Size:
58,960 bases
Orientation:
Plus strand

chr17:5,019,733-5,078,329
(GRCh37/hg19 by Ensembl)
Size:
58,597 bases
Orientation:
Plus strand

Genomic View for USP6 Gene

Genes around USP6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP6 Gene

Proteins for USP6 Gene

  • Protein details for USP6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P35125-UBP6_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 6
    Protein Accession:
    P35125
    Secondary Accessions:
    • Q15634
    • Q86WP6
    • Q8IWT4

    Protein attributes for USP6 Gene

    Size:
    1406 amino acids
    Molecular mass:
    158658 Da
    Quaternary structure:
    • Interacts with RAC1 and CDC42. Interacts (via Rab-GAP TBC domain) with ARF6. Interacts with calmodulin (CALM1, CALM2 and/or CALM3); the interaction is calcium-dependent.
    Miscellaneous:
    • The USP6 gene only exists in the primate lineage.
    • [Isoform 3]: Was shown to be tumorigenic in transfected mice and seems not to act as GTPase activating protein.

    Alternative splice isoforms for USP6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP6 Gene

Selected DME Specific Peptides for USP6 Gene

P35125:
  • FLLDGLH
  • GNTCFMN
  • QQQDSQELL
  • DGLHEDLN
  • NLGNTCF
  • LIIHLKR

Post-translational modifications for USP6 Gene

  • Monubiquitinated; ubiquitination is calmodulin and calcium dependent.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for USP6 Gene

Gene Families for USP6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for USP6 Gene

InterPro:
Blocks:
  • Ubiquitin thiolesterase, family 2
  • RabGAP/TBC domain

Suggested Antigen Peptide Sequences for USP6 Gene

GenScript: Design optimal peptide antigens:
  • Ubiquitin specific peptidase 6-short (B9A6N0_HUMAN)
  • TRE17 protein (Q9UDD3_HUMAN)
  • Ubiquitin-specific-processing protease 6 (UBP6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P35125

UniProtKB/Swiss-Prot:

UBP6_HUMAN :
  • The Rab-GAP TBC domain lacks GTPase activator activity but is necessary for interaction with ARF6.
  • Belongs to the peptidase C19 family.
Domain:
  • The Rab-GAP TBC domain lacks GTPase activator activity but is necessary for interaction with ARF6.
Family:
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP6: view

Function for USP6 Gene

Molecular function for USP6 Gene

UniProtKB/Swiss-Prot Function:
Deubiquitinase with an ATP-independent isopeptidase activity, cleaving at the C-terminus of the ubiquitin moiety. Catalyzes its own deubiquitination. In vitro, isoform 2, but not isoform 3, shows deubiquitinating activity. Promotes plasma membrane localization of ARF6 and selectively regulates ARF6-dependent endocytic protein trafficking. Is able to initiate tumorigenesis by inducing the production of matrix metalloproteinases following NF-kappa-B activation.
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 6,hyperpolymorphic gene 1,deubiquitin enzyme family

Enzyme Numbers (IUBMB) for USP6 Gene

Phenotypes From GWAS Catalog for USP6 Gene

Gene Ontology (GO) - Molecular Function for USP6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding TAS 1565468
GO:0004197 cysteine-type endopeptidase activity TAS 9827704
GO:0004843 thiol-dependent ubiquitin-specific protease activity IDA 16127172
GO:0005096 GTPase activator activity IBA 21873635
GO:0005515 protein binding IPI 12612085
genes like me logo Genes that share ontologies with USP6: view
genes like me logo Genes that share phenotypes with USP6: view

miRNA for USP6 Gene

miRTarBase miRNAs that target USP6

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP6

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP6 Gene

Localization for USP6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP6 Gene

Cell membrane. Cytoplasm. Endosome. Note=Localizes to the plasma membrane and to filamentous structures within the cell corresponding to ARF6 regulated tubular endosomes. Activation of RAC1 and CDC42 can direct the relocalization of USP6 to the plasma membrane in a manner that depends on the integrity of the actin cytoskeleton.

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 USP6 gene
Compartment Confidence
plasma membrane 5
endosome 5
lysosome 4
nucleus 3
cytosol 3
cytoskeleton 2
golgi apparatus 2
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for USP6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 12612085
GO:0005764 lysosome TAS 9827704
GO:0005768 endosome IEA --
GO:0005886 plasma membrane IEA,IDA 12612085
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with USP6: view

Pathways & Interactions for USP6 Gene

PathCards logo

SuperPathways for USP6 Gene

SuperPathway Contained pathways
1 Ubiquitin-Proteasome Dependent Proteolysis
-
2 Arf6 signaling events
genes like me logo Genes that share pathways with USP6: view

Pathways by source for USP6 Gene

1 BioSystems pathway for USP6 Gene
1 Qiagen pathway for USP6 Gene
  • Ubiquitin-Proteasome Dependent Proteolysis

SIGNOR curated interactions for USP6 Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for USP6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006464 cellular protein modification process NAS 9827704
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0006886 intracellular protein transport IBA 21873635
GO:0016579 protein deubiquitination IDA 16127172
genes like me logo Genes that share ontologies with USP6: view

Drugs & Compounds for USP6 Gene

(1) Drugs for USP6 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 USP6: view

Transcripts for USP6 Gene

mRNA/cDNA for USP6 Gene

3 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
6 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 USP6

Alternative Splicing Database (ASD) splice patterns (SP) for USP6 Gene

No ASD Table

Relevant External Links for USP6 Gene

GeneLoc Exon Structure for
USP6

Expression for USP6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for USP6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for USP6 Gene

This gene is overexpressed in Muscle - Skeletal (x17.6) and Testis (x10.9).

Protein differential expression in normal tissues from HIPED for USP6 Gene

This gene is overexpressed in Neutrophil (35.5) and Pancreatic juice (33.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for USP6 Gene



Protein tissue co-expression partners for USP6 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for USP6

SOURCE GeneReport for Unigene cluster for USP6 Gene:

Hs.448851

mRNA Expression by UniProt/SwissProt for USP6 Gene:

P35125-UBP6_HUMAN
Tissue specificity: Testis specific. Expressed in various cancer cell lines.

Evidence on tissue expression from TISSUES for USP6 Gene

  • Nervous system(2.4)
  • Kidney(2.1)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with USP6: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for USP6 Gene

Orthologs for USP6 Gene

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

Orthologs for USP6 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia USP6 29 30
  • 98.77 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia -- 30
  • 58 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia -- 30
  • 56 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia Usp32 30
  • 56 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 54 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 53 (a)
OneToMany
Chicken
(Gallus gallus)
Aves -- 30
  • 49 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 43 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.11864 29
Zebrafish
(Danio rerio)
Actinopterygii usp32 30
  • 45 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta CG8334 30
  • 24 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea H34C03.2 31
  • 51 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP12 30
  • 17 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 30 (a)
OneToMany
Species where no ortholog for USP6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 USP6 Gene

ENSEMBL:
Gene Tree for USP6 (if available)
TreeFam:
Gene Tree for USP6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for USP6: view image
Alliance of Genome Resources:
Additional Orthologs for USP6

Paralogs for USP6 Gene

(12) SIMAP similar genes for USP6 Gene using alignment to 2 proteins:

  • UBP6_HUMAN
  • L8E827_HUMAN
genes like me logo Genes that share paralogs with USP6: view

Variants for USP6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP6 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs114887037 Benign: not provided 5,139,447(+) C/T
NM_001304284.2(USP6):c.1271C>T (p.Thr424Met)
MISSENSE
rs139732460 Benign: not provided 5,162,994(+) C/T
NM_001304284.2(USP6):c.3026C>T (p.Ser1009Phe)
MISSENSE
rs145160344 Benign: not provided 5,132,426(+) G/C
NM_001304284.2(USP6):c.186G>C (p.Arg62=)
SYNONYMOUS
rs145312817 Benign: not provided 5,170,717(+) C/T
NM_001304284.2(USP6):c.3756C>T (p.Ser1252=)
SYNONYMOUS
rs150532558 Benign: not provided 5,155,520(+) A/G
NM_001304284.2(USP6):c.2742A>G (p.Lys914=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for USP6 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 USP6 Gene

Variant ID Type Subtype PubMed ID
esv25210 CNV gain 19812545
esv3639806 CNV loss 21293372
nsv1131294 CNV deletion 24896259
nsv574273 CNV gain 21841781
nsv960045 CNV duplication 23825009

Variation tolerance for USP6 Gene

Residual Variation Intolerance Score: 98.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.91; 97.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP6 Gene

Human Gene Mutation Database (HGMD)
USP6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP6
Leiden Open Variation Database (LOVD)
USP6

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP6 Gene

Disorders for USP6 Gene

MalaCards: The human disease database

(28) MalaCards diseases for USP6 Gene - From: ORP, COP, and GCD

Disorder Aliases PubMed IDs
pseudosarcomatous fibromatosis
  • fasciitis - nodular
fasciitis
myositis ossificans
  • myisitis ossificans
fibroosseous pseudotumor of digits
  • fibroosseous digital pseudotumor
telangiectatic osteogenic sarcoma
  • telangiectatic osteosarcoma
- elite association - COSMIC cancer census association via MalaCards
Search USP6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

UBP6_HUMAN
  • Note=A chromosomal aberration involving USP6 is a common genetic feature of aneurysmal bone cyst, a benign osseous neoplasm. Translocation t(16;17)(q22;p13) with CDH11. The translocation generates a fusion gene in which the strong CDH11 promoter is fused to the entire USP6 coding sequence, resulting in USP6 transcriptional up-regulation (PubMed:15026324). {ECO:0000269 PubMed:15026324}.

Additional Disease Information for USP6

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with USP6: view

No data available for Genatlas for USP6 Gene

Publications for USP6 Gene

  1. USP6 (Tre2) fusion oncogenes in aneurysmal bone cyst. (PMID: 15026324) Oliveira AM … Fletcher JA (Cancer research 2004) 3 4 22
  2. The Tre2 (USP6) oncogene is a hominoid-specific gene. (PMID: 12604796) Paulding CA … Haber DA (Proceedings of the National Academy of Sciences of the United States of America 2003) 3 4 22
  3. Expression in a RabGAP yeast mutant of two human homologues, one of which is an oncogene. (PMID: 14521938) Bizimungu C … Vandenbol M (Biochemical and biophysical research communications 2003) 3 4 22
  4. TRE17/USP6 oncogene translocated in aneurysmal bone cyst induces matrix metalloproteinase production via activation of NF-kappaB. (PMID: 20418905) Ye Y … Chou MM (Oncogene 2010) 3 4
  5. Calcium/calmodulin regulates ubiquitination of the ubiquitin-specific protease TRE17/USP6. (PMID: 16127172) Shen C … Chou MM (The Journal of biological chemistry 2005) 3 4

Products for USP6 Gene

Sources for USP6 Gene