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USP2 ubiquitin specific peptidase 2 [ Homo sapiens (human) ]

Gene ID: 9099, updated on 6-Oct-2019

Summary

Official Symbol
USP2provided by HGNC
Official Full Name
ubiquitin specific peptidase 2provided by HGNC
Primary source
HGNC:HGNC:12618
See related
Ensembl:ENSG00000036672 MIM:604725
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
USP9; UBP41
Summary
This gene encodes a member of the family of de-ubiquitinating enzymes, which belongs to the peptidase C19 superfamily. The encoded protein is a ubiquitin-specific protease which is required for TNF-alpha (tumor necrosis factor alpha) -induced NF-kB (nuclear factor kB) signaling. This protein deubiquitinates polyubiquitinated target proteins such as fatty acid synthase, murine double minute 2 (MDM2), MDM4/MDMX and cyclin D1. MDM2 and MDM4 are negative regulators of the p53 tumor suppressor and cyclin D1 is required for cell cycle G1/S transition. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]
Expression
Biased expression in testis (RPKM 31.4), kidney (RPKM 15.4) and 10 other tissues See more
Orthologs

Genomic context

See USP2 in Genome Data Viewer
Location:
11q23.3
Exon count:
17
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (119355215..119381690, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (119225925..119252436, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ring finger protein 26 Neighboring gene C1q and TNF related 5 Neighboring gene membrane frizzled-related protein Neighboring gene HNF4 motif-containing MPRA enhancer 223 Neighboring gene USP2 antisense RNA 1 (head to head) Neighboring gene major facilitator superfamily domain containing 14B pseudogene Neighboring gene Thy-1 cell surface antigen

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.
NHGRI GWA Catalog

Pathways from BioSystems

  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Death Receptor Signalling, organism-specific biosystem (from REACTOME)
    Death Receptor Signalling, organism-specific biosystemThe death receptors, all cell-surface receptors, begin the process of caspase activation. The common feature of these type 1 transmembrane proteins is the "death-domain" a conserved cytoplasmic motif...
  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Regulation of TNFR1 signaling, organism-specific biosystem (from REACTOME)
    Regulation of TNFR1 signaling, organism-specific biosystemTumor necrosis factor-alpha (TNFalpha) is an inflammatory cytokine, that activates either cell survival (e.g.,inflammation, proliferation) or cell death upon association with TNF receptor 1 (TNFR1). ...
  • Regulation of TP53 Activity, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Activity, organism-specific biosystemProtein stability and transcriptional activity of TP53 (p53) tumor suppressor are regulated by post-translational modifications that include ubiquitination, phosphorylation, acetylation, methylation,...
  • Regulation of TP53 Degradation, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Degradation, organism-specific biosystemIn unstressed cells, TP53 (p53) has a short half-life as it undergoes rapid ubiquitination and proteasome-mediated degradation. The E3 ubiquitin ligase MDM2, which is a transcriptional target of TP53...
  • Regulation of TP53 Expression and Degradation, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Expression and Degradation, organism-specific biosystemTP53 (p53) tumor suppressor protein is a transcription factor that functions as a homotetramer (Jeffrey et al. 1995). The protein levels of TP53 are low in unstressed cells due to MDM2-mediated ubiqu...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • TNF signaling, organism-specific biosystem (from REACTOME)
    TNF signaling, organism-specific biosystemThe inflammatory cytokine tumor necrosis factor alpha (TNF-alpha) is expressed in immune and nonimmune cell types including macrophages, T cells, mast cells, granulocytes, natural killer (NK) cells, ...
  • TNFR1-induced NFkappaB signaling pathway, organism-specific biosystem (from REACTOME)
    TNFR1-induced NFkappaB signaling pathway, organism-specific biosystemActivation of tumor necrosis factor receptor 1 (TNFR1) can trigger multiple signal transduction pathways to induce inflammation, cell proliferation, survival or cell death (Ward C et al. 1999; Michea...
  • TNFR1-induced proapoptotic signaling, organism-specific biosystem (from REACTOME)
    TNFR1-induced proapoptotic signaling, organism-specific biosystemActivation of tumor necrosis factor receptor 1 (TNFR1) can trigger multiple signal transduction pathways to induce cell survival or cell death (Ward C et al. 1999; Micheau O and Tschopp J 2003; Wider...
  • Transcriptional Regulation by TP53, organism-specific biosystem (from REACTOME)
    Transcriptional Regulation by TP53, organism-specific biosystemThe tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many gen...
  • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
    Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cyclin binding IPI
Inferred from Physical Interaction
more info
PubMed 
cysteine-type endopeptidase activity TAS
Traceable Author Statement
more info
PubMed 
identical protein binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IDA
Inferred from Direct Assay
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
thiol-dependent ubiquitinyl hydrolase activity TAS
Traceable Author Statement
more info
 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell cycle IEA
Inferred from Electronic Annotation
more info
 
circadian behavior ISS
Inferred from Sequence or Structural Similarity
more info
 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
entrainment of circadian clock by photoperiod ISS
Inferred from Sequence or Structural Similarity
more info
 
locomotor rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
muscle organ development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
 
protein stabilization IDA
Inferred from Direct Assay
more info
PubMed 
protein stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
centrosome IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
ubiquitin carboxyl-terminal hydrolase 2
Names
41 kDa ubiquitin-specific protease
deubiquitinating enzyme 2
ubiquitin specific protease 12
ubiquitin specific protease 9
ubiquitin thioesterase 2
ubiquitin-specific-processing protease 2
NP_001230688.1
NP_004196.4
NP_741994.1
XP_005271778.1
XP_005271779.1
XP_016874028.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029825.2 RefSeqGene

    Range
    5037..31512
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243759.2NP_001230688.1  ubiquitin carboxyl-terminal hydrolase 2 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an internal exon in the 5' region, compared to variant 1. The resulting isoform (c) has a shorter and different N-terminus compared to isoform a.
    Source sequence(s)
    AP003396, BC041366, DB065104
    Consensus CDS
    CCDS58189.1
    UniProtKB/Swiss-Prot
    O75604
    Related
    ENSP00000407842.2, ENST00000455332.6
    Conserved Domains (2) summary
    cd02674
    Location:25354
    Peptidase_C19R; A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam00443
    Location:23353
    UCH; Ubiquitin carboxyl-terminal hydrolase
  2. NM_004205.5NP_004196.4  ubiquitin carboxyl-terminal hydrolase 2 isoform a

    See identical proteins and their annotated locations for NP_004196.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AI806430, AK057225, BC002955, BC041366, DB065104, DB098786
    Consensus CDS
    CCDS8422.1
    UniProtKB/Swiss-Prot
    O75604
    Related
    ENSP00000260187.2, ENST00000260187.7
    Conserved Domains (2) summary
    cd02674
    Location:268597
    Peptidase_C19R; A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam00443
    Location:266596
    UCH; Ubiquitin carboxyl-terminal hydrolase
  3. NM_171997.3NP_741994.1  ubiquitin carboxyl-terminal hydrolase 2 isoform b

    See identical proteins and their annotated locations for NP_741994.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is missing 2 exons from the 5' end, and contains an alternate 5' terminal exon compared to transcript variant 1. This results in a shorter isoform (b) with a different N-terminus compared to isoform a.
    Source sequence(s)
    AF440755, AI806430, AK057225, AP003396, BC041366
    Consensus CDS
    CCDS8423.1
    UniProtKB/Swiss-Prot
    O75604
    Related
    ENSP00000436952.1, ENST00000525735.1
    Conserved Domains (1) summary
    pfam00443
    Location:58387
    UCH; Ubiquitin carboxyl-terminal hydrolase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    119355215..119381690 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017018539.1XP_016874028.1  ubiquitin carboxyl-terminal hydrolase 2 isoform X2

  2. XM_005271721.5XP_005271778.1  ubiquitin carboxyl-terminal hydrolase 2 isoform X1

    See identical proteins and their annotated locations for XP_005271778.1

    UniProtKB/Swiss-Prot
    O75604
    Conserved Domains (2) summary
    cd02674
    Location:268597
    Peptidase_C19R; A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam00443
    Location:266596
    UCH; Ubiquitin carboxyl-terminal hydrolase
  3. XM_005271722.2XP_005271779.1  ubiquitin carboxyl-terminal hydrolase 2 isoform X1

    See identical proteins and their annotated locations for XP_005271779.1

    UniProtKB/Swiss-Prot
    O75604
    Conserved Domains (2) summary
    cd02674
    Location:268597
    Peptidase_C19R; A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam00443
    Location:266596
    UCH; Ubiquitin carboxyl-terminal hydrolase
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