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

Gene ID: 9099, updated on 27-Nov-2024

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; AllianceGenome:HGNC:12618
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
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Genomic context

See USP2 in Genome Data Viewer
Location:
11q23.3
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119355215..119381690, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119376744..119403221, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (119225925..119252400, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119204879-119205770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3979 Neighboring gene C1q and TNF related 5 Neighboring gene ring finger protein 26 Neighboring gene membrane frizzled-related protein Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:119228534-119229733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5630 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3980 Neighboring gene HNF4 motif-containing MPRA enhancer 223 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119243670-119244170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119247037-119247615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119247932-119248520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119251478-119252467 Neighboring gene USP2 antisense RNA 1 Neighboring gene major facilitator superfamily domain containing 14B pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119290361-119290928 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119292628-119293194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119293195-119293760 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

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cyclin binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables cysteine-type deubiquitinase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables cysteine-type deubiquitinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables cysteine-type deubiquitinase activity TAS
Traceable Author Statement
more info
 
enables cysteine-type endopeptidase activity TAS
Traceable Author Statement
more info
PubMed 
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in circadian behavior ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in entrainment of circadian clock by photoperiod ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in locomotor rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in muscle organ development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in protein deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein deubiquitination TAS
Traceable Author Statement
more info
 
involved_in protein stabilization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
located_in centrosome IEA
Inferred from Electronic Annotation
more info
 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in 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
XP_054226438.1
XP_054226439.1
XP_054226440.1

NCBI Reference Sequences (RefSeq)

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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/TrEMBL
    B7Z7C2
    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
    B0YJB8, E9PPM2, O75604, Q8IUM2, Q8IW04, Q96MB9, Q9BQ21
    Related
    ENSP00000260187.2, ENST00000260187.7
    Conserved Domains (1) summary
    pfam00443
    Location:267596
    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/TrEMBL
    B7Z7C2
    Related
    ENSP00000436952.1, ENST00000525735.1
    Conserved Domains (1) summary
    pfam00443
    Location:58387
    UCH; Ubiquitin carboxyl-terminal hydrolase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_005271721.6XP_005271778.1  ubiquitin carboxyl-terminal hydrolase 2 isoform X1

    See identical proteins and their annotated locations for XP_005271778.1

    UniProtKB/Swiss-Prot
    B0YJB8, E9PPM2, O75604, Q8IUM2, Q8IW04, Q96MB9, Q9BQ21
    Conserved Domains (1) summary
    pfam00443
    Location:267596
    UCH; Ubiquitin carboxyl-terminal hydrolase
  2. XM_005271722.3XP_005271779.1  ubiquitin carboxyl-terminal hydrolase 2 isoform X1

    See identical proteins and their annotated locations for XP_005271779.1

    UniProtKB/Swiss-Prot
    B0YJB8, E9PPM2, O75604, Q8IUM2, Q8IW04, Q96MB9, Q9BQ21
    Conserved Domains (1) summary
    pfam00443
    Location:267596
    UCH; Ubiquitin carboxyl-terminal hydrolase
  3. XM_017018539.1XP_016874028.1  ubiquitin carboxyl-terminal hydrolase 2 isoform X2

    UniProtKB/TrEMBL
    B7Z7C2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    119376744..119403221 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370463.1XP_054226438.1  ubiquitin carboxyl-terminal hydrolase 2 isoform X1

    UniProtKB/Swiss-Prot
    B0YJB8, E9PPM2, O75604, Q8IUM2, Q8IW04, Q96MB9, Q9BQ21
  2. XM_054370464.1XP_054226439.1  ubiquitin carboxyl-terminal hydrolase 2 isoform X1

    UniProtKB/Swiss-Prot
    B0YJB8, E9PPM2, O75604, Q8IUM2, Q8IW04, Q96MB9, Q9BQ21
  3. XM_054370465.1XP_054226440.1  ubiquitin carboxyl-terminal hydrolase 2 isoform X2