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USP4 Gene

protein-coding   GIFtS: 62
GCID: GC03M049315

Ubiquitin Specific Peptidase 4 (Proto-Oncogene)

(Previous name: ubiquitin specific protease 4 (proto-oncogene))
(Previous symbol: UNP)
  See USP4-related disease
at  

(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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Aliases
Ubiquitin Specific Peptidase 4 (Proto-Oncogene)1 2     Ubiquitin Carboxyl-Terminal Hydrolase 42
UNP1 2 3 5     Ubiquitin Thiolesterase 42
Ubiquitin Specific Protease 4 (Proto-Oncogene)1 2     Ubiquitin-Specific Processing Protease 42
Deubiquitinating Enzyme 42 3     EC 3.4.19.123
Ubiquitin Thioesterase 42 3     UNPH3
Ubiquitous Nuclear Protein Homolog2 3     Ubiquitin-Specific-Processing Protease 43
Unph2     EC 3.1.2.158
Ubiquitin Carboxyl-Terminal Esterase 42     

External Ids:    HGNC: 126271   Entrez Gene: 73752   Ensembl: ENSG000001143167   OMIM: 6034865   UniProtKB: Q131073   

Export aliases for USP4 gene to outside databases

Previous GC identifers: GC03P048745 GC03P048551 GC03M049160 GC03M049274 GC03M049290


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for USP4 Gene:
The protein encoded by this gene is a protease that deubiquitinates target proteins such as ADORA2A and TRIM21.
The encoded protein shuttles between the nucleus and cytoplasm and is involved in maintaining operational
fidelity in the endoplasmic reticulum. Three transcript variants encoding different isoforms have been found for
this gene. (provided by RefSeq, Oct 2011)

GeneCards Summary for USP4 Gene:
USP4 (ubiquitin specific peptidase 4 (proto-oncogene)) is a protein-coding gene. Diseases associated with USP4 include oculopharyngeal muscular dystrophy. GO annotations related to this gene include ubiquitin-specific protease activity and identical protein binding. An important paralog of this gene is USP45.

UniProtKB/Swiss-Prot: UBP4_HUMAN, Q13107
Function: Hydrolase that deubiquitinates target proteins such as the receptor ADORA2A, PDPK1 and TRIM21.
Deubiquitination of ADORA2A increases the amount of functional receptor at the cell surface. Plays a role in the
regulation of quality control in the ER

Gene Wiki entry for USP4 Gene


(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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RefSeq DNA sequence at NCBI GenBank:
NC_000003.11  NC_018914.2  NT_022517.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the USP4 gene promoter:
         PPAR-gamma1   p53   ATF-2   PPAR-gamma2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUSP4 promoter sequence
   Search Chromatin IP Primers for USP4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat USP4


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

Entrez Gene cytogenetic band: 3p21.3   Ensembl cytogenetic band:  3p21.31   HGNC cytogenetic band: 3p21.3

USP4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
USP4 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M049315:  view genomic region     (about GC identifiers)

Start:
49,314,577 bp from pter      End:
49,378,145 bp from pter
Size:
63,569 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: UBP4_HUMAN, Q13107 (See protein sequence)
Recommended Name: Ubiquitin carboxyl-terminal hydrolase 4  
Size: 963 amino acids; 108565 Da
Subunit: Interacts with RB1 (both dephosphorylated and hypophosphorylated forms). Interacts with ADORA2A (via
cytoplasmic C-terminus); the interaction is direct. Interacts with RB1, RBL1 and RBL2
1 PDB 3D structure from and Proteopedia for USP4:
2Y6E (3D)    
Secondary accessions: A8K6Y0 C9IY91 O43452 O43453 Q08AK8
Alternative splicing: 3 isoforms:  Q13107-1   Q13107-2   Q13107-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for USP4: NX_Q13107

Explore proteomics data for USP4 at MOPED

Post-translational modifications: 

  • Monoubiquitinated by TRIM21. Ubiquitination does not lead to its proteasomal degradation. Autodeubiquitinated1
  • Ubiquitination2 at Lys186, Lys632, Lys811, Lys837
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for USP4 (Q13107) (see all 25)
     QPQKKKK  FLLDGLH  KWYYFDD  AAYVLFY 


    See USP4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001238806.1  NP_003354.2  NP_955475.1  

    ENSEMBL proteins: 
     ENSP00000341028   ENSP00000265560   ENSP00000399079   ENSP00000400623   ENSP00000408274  

    USP4 Human Recombinant Protein Products:

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    Novus Biologicals USP4 Proteins
    Novus Biologicals USP4 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for USP4

     
    Search eBioscience for Proteins for USP4 

    USP4 Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse R&D Systems for Antibodies
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    Novus Biologicals USP4 Antibodies
    Abcam antibodies for USP4 (Q13107, Q08AK8)
    Cloud-Clone Corp. Antibodies for USP4
    ThermoFisher Antibodies for USP4
    LSBio Antibodies in human, mouse, rat for USP4

    USP4 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for USP4
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for USP4
    Cloud-Clone Corp. CLIAs for USP4
    Search eBioscience for ELISAs for USP4 


    (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

    Selected InterPro protein domains (see all 6):
     IPR001394 Peptidase_C19_UCH
     IPR028134 USP
     IPR018200 Pept_C19ubi-hydrolase_C_CS
     IPR028135 Ub_USP-typ
     IPR028889 UCH/PAN2

    Graphical View of Domain Structure for InterPro Entry Q13107

    ProtoNet protein and cluster: Q13107

    3 Blocks protein domains:
    IPB001394 Ubiquitin thiolesterase
    IPB006615 Ubiquitin-specific protease DUSP
    IPB010460 Ubiquitin carboxyl-terminal hydrolase


    UniProtKB/Swiss-Prot: UBP4_HUMAN, Q13107
    Domain: The Ubiquitin-like domain 2 inserts into the catalytic domain and competes with the ubiquitin substrate,
    partially inhibiting DUB activity
    Similarity: Belongs to the peptidase C19 family. USP4 subfamily
    Similarity: Contains 1 DUSP domain
    Similarity: Contains 2 ubiquitin-like domains
    Similarity: Contains 1 USP domain


    Find genes that share domains with USP4           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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: UBP4_HUMAN, Q13107
    Function: Hydrolase that deubiquitinates target proteins such as the receptor ADORA2A, PDPK1 and TRIM21.
    Deubiquitination of ADORA2A increases the amount of functional receptor at the cell surface. Plays a role in the
    regulation of quality control in the ER
    Catalytic activity: 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)

         Genatlas biochemistry entry for USP4:
    ubiquitin-specific protease 4,homolog to murine Unp,with two tissue specific cytoplasmic isoforms,deubiquitin
    enzyme family

         Enzyme Numbers (IUBMB): EC 3.1.2.152 EC 3.4.19.121

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004221ubiquitin thiolesterase activity IMP16316627
    GO:0004843ubiquitin-specific protease activity IDA16316627
    GO:0005515protein binding IPI11461834
    GO:0031685adenosine receptor binding IPI16339847
    GO:0042802identical protein binding IPI--
         
    Find genes that share ontologies with USP4           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for USP4:
     Increased cell death in HCT116 

         5 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Usp4):
     cellular  hematopoietic system  immune system  integument  pigmentation 

    Find genes that share phenotypes with USP4           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for USP4
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for USP4

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for USP4
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for USP4

    miRNA
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    Block miRNA regulation of human, mouse, rat USP4 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate USP4 (see all 12):
    hsa-miR-136 hsa-miR-148b hsa-miR-767-3p hsa-miR-197 hsa-miR-3157-5p hsa-miR-29b-1* hsa-miR-1273d hsa-miR-152
    SwitchGear 3'UTR luciferase reporter plasmidUSP4 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for USP4
    Predesigned siRNA for gene silencing in human, mouse, rat USP4

    Gene Editing
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    Clone
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    OriGene ORF clones in mouse, rat for USP4
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): USP4 (NM_001394)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for USP4
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat USP4

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for USP4 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for USP4


    (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 UniProtKB/Swiss-Prot
    UBP4_HUMAN, Q13107: Cytoplasm (By similarity). Nucleus (By similarity). Note=Shuttles between the nucleus and
    cytoplasm. Exported to the cytoplasm in a CRM1-dependent manner and recycled back to the nucleus via the importin
    alpha/beta heterodimeric import receptor. The relative amounts found in the nucleus and cytoplasm vary according
    to the cell type (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    lysosome4
    vacuole4
    cytosol3
    plasma membrane1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA16339847
    GO:0005737cytoplasm IDA--
    GO:0005764lysosome TAS9827704
    GO:0005886plasma membrane IDA--

    Find genes that share ontologies with USP4           About GenesLikeMe


    (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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    SuperPaths for USP4 About    
    See pathways by source

    SuperPathContained pathways About
    1Cell Cycle / Checkpoint Control
    Cell Cycle / Checkpoint Control0.32
    2Ubiquitin-Proteasome Dependent Proteolysis
    Ubiquitin-Proteasome Dependent Proteolysis
    3Protein Stability
    Protein Stability


    Find genes that share SuperPaths with USP4           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for USP4
        Ubiquitin-Proteasome Dependent Proteolysis

    2 Cell Signaling Technology (CST) Pathways for USP4
        Cell Cycle / Checkpoint Control
    Protein Stability


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for USP4
    Interactions:

        GeneGlobe Interaction Network for USP4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for USP4 (Q131071, 2, 3 ENSP000002655604) via UniProtKB, MINT, STRING, and/or I2D (see all 103)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006511ubiquitin-dependent protein catabolic process IEA--
    GO:0016579protein deubiquitination IDA16316627
    GO:0031397negative regulation of protein ubiquitination IMP16472766
    GO:0031647regulation of protein stability IDA16472766
    GO:0034394protein localization to cell surface IDA16339847

    Find genes that share ontologies with USP4           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
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for USP4 (UBP4)

    1 HMDB Compound for USP4    About this table
    CompoundSynonyms CAS #PubMed Ids
    WaterDihydrogen oxide (see all 2)7732-18-5--



    (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 USP4 gene (3 alternative transcripts): 
    NM_001251877.1  NM_003363.3  NM_199443.2  

    Unigene Cluster for USP4:

    Ubiquitin specific peptidase 4 (proto-oncogene)
    Hs.77500  [show with all ESTs]
    Unigene Representative Sequence: NM_003363
    14 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000351842(uc003cwq.2 uc003cwr.2) ENST00000265560 ENST00000483212
    ENST00000485450(uc003cwp.2) ENST00000431357 ENST00000475873 ENST00000486549
    ENST00000488520 ENST00000461553 ENST00000416417(uc021wxv.1) ENST00000415188
    ENST00000462673 ENST00000464168 ENST00000491791
    miRNA
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    Block miRNA regulation of human, mouse, rat USP4 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate USP4 (see all 12):
    hsa-miR-136 hsa-miR-148b hsa-miR-767-3p hsa-miR-197 hsa-miR-3157-5p hsa-miR-29b-1* hsa-miR-1273d hsa-miR-152
    SwitchGear 3'UTR luciferase reporter plasmidUSP4 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat USP4
    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): USP4 (NM_001394)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for USP4
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat USP4
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for USP4
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat USP4
      QuantiTect SYBR Green Assays in human, mouse, rat USP4
      QuantiFast Probe-based Assays in human, mouse, rat USP4

    Additional mRNA sequence: 

    AF017305.1 AF017306.1 AK222725.1 AK223292.1 AK291795.1 BC068017.1 BC110070.1 BC125130.1 
    BC125131.1 U20657.1 

    21 DOTS entries:

    DT.86854615  DT.101954836  DT.100823354  DT.99998877  DT.105378  DT.99950324  DT.120863493  DT.99981740 
    DT.100823353  DT.75131213  DT.95095390  DT.95256634  DT.99955826  DT.120863470  DT.120863484  DT.120863486 
    DT.120863495  DT.91749359  DT.95208935  DT.99983351  DT.91673174 

    Selected AceView cDNA sequences (see all 364):

    AA451813 BU073351 AI160500 BP371283 BM014022 AL135500 CB139427 BC023586 
    BU738642 BM465554 BU741650 BQ427591 BU632996 AI401439 BM980841 AI366210 
    R77960 AW021098 W95180 AA255621 CK299344 BM710153 AW954768 AA075277 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for USP4 (see all 11)    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b · 10c ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a · 15b ^ 16 ^
    SP1:                                                              -     -     -     -     -                                                                     
    SP2:                                                              -     -     -     -     -     -     -                                                         
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                -     -                     

    ExUns: 17a · 17b ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22a · 22b · 22c ^ 23 ^ 24 ^ 25 ^ 26a · 26b
    SP1:        -     -                                                                           
    SP2:        -     -                                                                           
    SP3:        -     -                                                                           
    SP4:        -     -                 -     -     -                                             
    SP5:        -     -                                                                           


    ECgene alternative splicing isoforms for USP4

    (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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    USP4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GACACCAACT
    USP4 Expression
    About this image

    USP4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    USP4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.77500

    UniProtKB/Swiss-Prot: UBP4_HUMAN, Q13107
    Tissue specificity: Overexpressed in small cell tumors and adenocarcinomas of the lung compared to wild-type lung
    (at protein level). Expressed in the hippocampal neurons

        Custom PCR Arrays for USP4
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for USP4

    (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 eukaryotes.

    Orthologs for USP4 gene from Selected species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Usp41 , 5 ubiquitin specific peptidase 4 (proto-oncogene)1, 5 87.84(n)1
    90.85(a)1
      9 (59.25 cM)5
    222581  NM_011678.21  NP_035808.21 
     1083478315 
    chicken
    (Gallus gallus)
    Aves USP41 ubiquitin specific peptidase 4 (proto-oncogene) 70.15(n)
    71.4(a)
      415937  NM_001006134.1  NP_001006134.1 
    lizard
    (Anolis carolinensis)
    Reptilia USP46
    ubiquitin specific peptidase 4 (proto-oncogene)
    70(a)
    1 ↔ 1
    2(147443881-147491161)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3984802 similar to ubiquitin specific protease 4 (proto-oncogene) 74.66(n)    BC042353.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BQ481153.12   -- 79.7(n)   334990  BQ481153.1 
    worm
    (Caenorhabditis elegans)
    Secernentea H34C03.21 , 3 ubiquitin carboxy-terminal hydrolase3
    H34C03.21
    57(a)
    (best of 2)3
    50.19(n)1
    42.86(a)1
      IV(6757531-6761964)3
    1774371  NM_068634.51  NP_501035.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes UBP126
    Ubiquitin carboxyl-terminal hydrolase, ubiquitin-s...
    21(a)
    1 → many
    X(63805-67569) YJL197W
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons UBP51 UBP5 47.21(n)
    39.04(a)
      818691  NM_129656.3  NP_565944.1 
    barley
    (Hordeum vulgare)
    Liliopsida BU968207.12   -- 76.48(n)    BU968207.1 


    ENSEMBL Gene Tree for USP4 (if available)
    TreeFam Gene Tree for USP4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for USP4 gene
    USP452  USP192  USP62  USP152  USP112  USP162  USP312  USP432  
    USP322  
    5 SIMAP similar genes for USP4 using alignment to 5 protein entries:     UBP4_HUMAN (see all proteins):
    SSNA1    USP15    USP11    USP3    DKFZp761E10121

    Find genes that share paralogs with USP4           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for USP4
    PGOHUM00000234926


    (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 USP4 (see all 1197)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs178551131,2
    C--49246385(+) GCTGCC/AAGAGG 2 -- ds50012Minor allele frequency- A:0.00NA 4
    rs617493091,2
    C,F--49246399(+) TCTTCT/CGCAGA 2 -- ds50013Minor allele frequency- C:0.01NS NA EU 5697
    rs617493121,2
    C,F--49246417(+) GTGCAC/TGGGCA 2 -- ds50015Minor allele frequency- T:0.03NS WA EA NA 4862
    rs2009977281,2
    C--49246503(+) CAAAGG/TCCCGG 2 -- ds50011Minor allele frequency- T:0.00EU 1311
    rs1996247321,2
    --49246505(+) AAGGCC/GCGGTC 2 -- ds50010--------
    rs1457149141,2
    C,F--49246540(+) GCATCT/CTCTTA 2 -- ds50012Minor allele frequency- C:0.00NA EU 4779
    rs1822876291,2
    --49246602(+) GAAATA/GCACAG 2 -- ds50010--------
    rs1117684901,2
    C--49246617(+) ACACAA/GTAATG 2 -- ds50012Minor allele frequency- G:0.03CSA WA 119
    rs354319341,2
    C,F--49246648(+) TACCCC/ATGAAT 2 -- ds50012Minor allele frequency- A:0.25NA 8
    rs1479770371,2
    C--49246677(+) CTTGGC/TCCTGG 2 -- ds50010--------

    HapMap Linkage Disequilibrium report for USP4 (49314577 - 49378145 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for USP4:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv512800CNV Insertion21212237
    nsv507094CNV Insertion20534489

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing USP4
    DNA2.0 Custom Variant and Variant Library Synthesis for USP4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 603486    OMIM disorders: --

    1 disease for USP4:    
    About MalaCards
    oculopharyngeal muscular dystrophy


    Find genes that share disorders with USP4           About GenesLikeMe

    3 Novoseek inferred disease relationships for USP4 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    shock 0 1 15750928 (1)
    tumors 0 3 7784062 (2)
    cancer 0 1 16829531 (1)

    Genetic Association Database (GAD): USP4
    Human Genome Epidemiology (HuGE) Navigator: USP4 (2 documents)

    Export disorders for USP4 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 USP4 gene, integrated from 10 sources (see all 91):
    (articles sorted by number of sources associating them with USP4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The human UNP locus at 3p21.31 encodes two tissue-selective, cytoplasmic isoforms with deubiquitinating activity that have reduced expression in small cell lung carcinoma cell lines. (PubMed id 9464533)1, 2, 3 Frederick A.... Chiu M.I. (Oncogene 1998)
    2. Elevated expression of Unph, a proto-oncogene at 3p21.3, in human lung tumors. (PubMed id 7784062)1, 2, 9 Gray D.A.... Takahashi T. (Oncogene 1995)
    3. Ubiquitin-specific protease 4 inhibits mono-ubiquitination of the master growth factor signaling kinase PDK1. (PubMed id 22347420)1, 2 Uras I.Z.... Nijman S.M. (PLoS ONE 2012)
    4. Association analysis of 3p21 with Crohn's disease in a New Zealand population. (PubMed id 20307617)1, 4 Morgan A.R....Ferguson L.R. (Hum. Immunol. 2010)
    5. Identification of neuroglycan C and interacting partners as potential susceptibility genes for schizophrenia in a Southern Chinese population. (PubMed id 19367581)1, 4 So H.C....Sham P.C. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2010)
    6. UnpEL/Usp4 is ubiquitinated by Ro52 and deubiquitinated by itself. (PubMed id 16472766)1, 2 Wada K. and Kamitani T. (Biochem. Biophys. Res. Commun. 2006)
    7. The ubiquitin-specific protease Usp4 regulates the cell surface level of the A2A receptor. (PubMed id 16339847)1, 2 Milojevic T.... Nanoff C. (Mol. Pharmacol. 2006)
    8. Oncogenic protein UnpEL/Usp4 deubiquitinates Ro52 by its isopeptidase activity. (PubMed id 16316627)1, 2 Wada K.... Kamitani T. (Biochem. Biophys. Res. Commun. 2006)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. Human and mouse proteases: a comparative genomic approach. (PubMed id 12838346)1, 3 Puente X.S.... Lopez-Otin C. (Nat. Rev. Genet. 2003)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 7375 HGNC: 12627 AceView: FLJ43654 Ensembl:ENSG00000114316 euGenes: HUgn7375
    ECgene: USP4 H-InvDB: USP4

    (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 USP4 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for USP4 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for USP4 gene:
    Search GeneIP for patents involving USP4

    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, LSBio, eBioscience, 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
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