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USP50 Gene

protein-coding   GIFtS: 36
GCID: GC15M050792

Ubiquitin Specific Peptidase 50

(Previous name: ubiquitin specific protease 50)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Ubiquitin Specific Peptidase 501 2
Ubiquitin Specific Protease 501 2
Inactive Ubiquitin-Specific Peptidase 502 3
Inactive Ubiquitin Carboxyl-Terminal Hydrolase 502

External Ids:    HGNC: 200791   Entrez Gene: 3735092   Ensembl: ENSG000001702367   UniProtKB: Q70EL33   
ORGUL members:         

Export aliases for USP50 gene to outside databases

Previous GC identifers: GC15U900216 GC15M048580 GC15M027623


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for USP50 Gene:
USP50 (ubiquitin specific peptidase 50) is a protein-coding gene. GO annotations related to this gene include ubiquitin thiolesterase activity. An important paralog of this gene is USP3.

UniProtKB/Swiss-Prot: UBP50_HUMAN, Q70EL3
Function: Has no peptidase activity




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the USP50 gene promoter:
         Nkx3-1 v4   RFX1   AML1a   Cdc5   HNF-1A   Nkx3-1 v2   HEN1   HNF-1   Nkx3-1 v3   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUSP50 promoter sequence
   Search Chromatin IP Primers for USP50

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat USP50


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 15q21.1   Ensembl cytogenetic band:  15q21.2   HGNC cytogenetic band: 15q21.1

USP50 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
USP50 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15M050792:  view genomic region     (about GC identifiers)

Start:
50,792,759 bp from pter      End:
50,838,905 bp from pter
Size:
46,147 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: UBP50_HUMAN, Q70EL3 (See protein sequence)
Recommended Name: Inactive ubiquitin carboxyl-terminal hydrolase 50  
Size: 339 amino acids; 38955 Da
Caution: Although the active site residues are conserved, lacks the conserved Asp/Asn residue which is normally
found 7-9 residues after the catalytic His

Explore the universe of human proteins at neXtProt for USP50: NX_Q70EL3

Explore proteomics data for USP50 at MOPED


See USP50 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_987090.2  
ENSEMBL proteins: 
 ENSP00000434676   ENSP00000453946   ENSP00000434014  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
USP: Ubiquitin-specific peptidases

3 InterPro protein domains:
 IPR001394 Peptidase_C19_UCH
 IPR018200 Pept_C19ubi-hydrolase_C_CS
 IPR028889 UCH/PAN2

Graphical View of Domain Structure for InterPro Entry Q70EL3

ProtoNet protein and cluster: Q70EL3

UniProtKB/Swiss-Prot: UBP50_HUMAN, Q70EL3
Similarity: Belongs to the peptidase C19 family
Similarity: Contains 1 USP domain


Find genes that share domains with USP50           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: UBP50_HUMAN, Q70EL3
Function: Has no peptidase activity

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0004221ubiquitin thiolesterase activity ----
     
Find genes that share ontologies with USP50           About GenesLikeMe


Phenotypes:
     1 MGI phenotypic allele for Usp50 (no phenotypes)

Find genes that share phenotypes with USP50           About GenesLikeMe

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for USP50

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
cytoskeleton1
extracellular1

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for USP50
Interactions:

    Search GeneGlobe Interaction Network for USP50

Selected Interacting proteins for USP50 (Q70EL33) via UniProtKB, MINT, STRING, and/or I2D (see all 23)
InteractantInteraction Details
GeneCardExternal ID(s)
ABCD3P282883I2D: score=1 
ABCE1P612213I2D: score=1 
ACADMP113103I2D: score=1 
AFG3L2Q9Y4W63I2D: score=1 
ALDH3A2P516483I2D: score=1 
About this table

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006511ubiquitin-dependent protein catabolic process IEA--

Find genes that share ontologies with USP50           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
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  Browse compounds at ApexBio 

Browse Tocris compounds for USP50 (UBP50)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for USP50 gene: 
NM_203494.4  

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000532404(uc021skx.1 uc021sky.1) ENST00000559105 ENST00000530218
ENST00000529349
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7 AceView cDNA sequences:

NM_203494 AJ583818 BN000339 BE832280 AI990110 AI990671 BE832251 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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USP50 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
USP50 Expression
About this image

USP50 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

USP50 Protein Expression

UniProtKB/Swiss-Prot: UBP50_HUMAN, Q70EL3
Tissue specificity: Weakly expressed in a few tissues

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In Situ
Assay Products:
 

 
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for USP50 gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Usp501 , 5 ubiquitin specific peptidase 501, 5 79.27(n)1
78.96(a)1
  2 (61.76 cM)5
750831  NM_029163.31  NP_083439.21 
 1267090965 
lizard
(Anolis carolinensis)
Reptilia USP506
ubiquitin specific peptidase 50
42(a)
1 ↔ 1
GL343747.1(95075-101260)
worm
(Caenorhabditis elegans)
Secernentea E01B7.16
Protein E01B7.1 (E01B7.1) mRNA, complete cds
11(a)
many ↔ many
V(17924916-17934227) WBGene00008441
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP56
DOA46
Putative ubiquitin-specific protease, closest para...
Ubiquitin isopeptidase, required for recycling ubi...
12(a)
11(a)
many ↔ many
many ↔ many
V(457806-460223) YER144C
IV(584939-587719) YDR069C


ENSEMBL Gene Tree for USP50 (if available)
TreeFam Gene Tree for USP50 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for USP50 gene
USP32  USP442  USP212  USP82  USP492  USP22  
3 SIMAP similar genes for USP50 using alignment to 5 protein entries:     UBP50_HUMAN (see all proteins):
USP15    USP8    USP11

Find genes that share paralogs with USP50           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for USP50 (see all 1037)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 15 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs667311871,2
C--30872077(+) AAAAA-/A/AA  
        
GAGTG
1 -- int12NA 4
rs1130949921,2
F--50793801(+) AGGGGA/GCTATG 1 -- int11Minor allele frequency- G:0.00CSA 1
rs1430284191,2
--50793971(+) GGCCCA/GTGGGT 1 -- int10--------
rs1838305701,2
--50793995(+) TTTTTC/GTAAGA 1 -- int10--------
rs783980671,2
F--50794058(+) AAGTAA/TTAATA 1 -- int11Minor allele frequency- T:0.03WA 118
rs1885518721,2
--50794189(+) AAACTA/GAATAG 1 -- int10--------
rs1813556411,2
--50794367(+) TGGCAC/TGATCT 1 -- int10--------
rs1413928801,2
C--50794568(+) CAAAG-/TTAT  
        
TTATT
1 -- int10--------
rs1860149621,2
--50794568(+) CAAAGC/TTATTT 1 -- int10--------
rs1903829491,2
--50794639(+) CAGCTC/TACCAC 1 -- int10--------

HapMap Linkage Disequilibrium report for USP50 (50792759 - 50838905 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for USP50:    About this table    
Variant IDTypeSubtypePubMed ID
nsv524613CNV Loss19592680
dgv317n27CNV Gain19166990
nsv471242CNV Gain18288195

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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Find genes that share disorders with USP50           About GenesLikeMe

Genetic Association Database (GAD): USP50
Human Genome Epidemiology (HuGE) Navigator: USP50 (1 document)

Export disorders for USP50 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for USP50 gene integrated from 10 sources:
(articles sorted by number of sources associating them with USP50)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
  2. A genomic analysis of rat proteases and protease inhibitors. (PubMed id 15060002)1, 2 Puente X.S. and Lopez-Otin C. (Genome Res. 2004)
  3. Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. (PubMed id 14715245)1, 2 Quesada V.... Lopez-Otin C. (Biochem. Biophys. Res. Commun. 2004)
  4. Human and mouse proteases: a comparative genomic approach. (PubMed id 12838346)1, 3 Puente X.S.... Lopez-Otin C. (Nat. Rev. Genet. 2003)
  5. A screen for deubiquitinating enzymes involved in the Ga88/M checkpoint identifies USP50 as a regulator of HSP90-dependent Wee1 stability. (PubMed id 20930503)1 Aressy B....Ducommun B. (Cell Cycle 2010)
  6. Defining the human deubiquitinating enzyme interaction landscape. (PubMed id 19615732)1 Sowa M.E....Harper J.W. (Cell 2009)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 373509 HGNC: 20079 AceView: USP50 Ensembl:ENSG00000170236 euGenes: HUgn373509
ECgene: USP50 H-InvDB: USP50

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for USP50 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for USP50 gene:
Search GeneIP for patents involving USP50

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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