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USP41 Gene

protein-coding   GIFtS: 34
GCID: GC22M020704          (predicted)

Ubiquitin Specific Peptidase 41

(Previous name: ubiquitin specific protease 41)
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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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Aliases
Ubiquitin Specific Peptidase 411 2     Putative Ubiquitin Carboxyl-Terminal Hydrolase 412
Ubiquitin Specific Protease 411 2     Ubiquitin Specific Proteinase 412
Deubiquitinating Enzyme 412 3     Ubiquitin Thiolesterase 412
Ubiquitin Thioesterase 412 3     EC 3.4.19.123
Ubiquitin-Specific-Processing Protease 412 3     EC 3.1.2.158

External Ids:    HGNC: 200701   Entrez Gene: 3738562   Ensembl: ENSG000001611337   UniProtKB: Q3LFD53   

Export aliases for USP41 gene to outside databases

Previous GC identifers: GC00U909401 GC22U900095 GC22M018726 GC22M019022 GC22M003968


(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 USP41 Gene:
USP41 (ubiquitin specific peptidase 41) is a protein-coding gene. GO annotations related to this gene include cysteine-type peptidase activity and ubiquitin thiolesterase activity. An important paralog of this gene is USP24.

UniProtKB/Swiss-Prot: UBP41_HUMAN, Q3LFD5
Function: May recognize and hydrolyze the peptide bond at the C-terminal Gly of ubiquitin. Involved in the
processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins (By similarity)




(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 USP41 gene promoter:
         Spz1   COMP1   YY1   C/EBPalpha   Roaz   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for USP41

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat USP41


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

Entrez Gene cytogenetic band: 22q11.21   Ensembl cytogenetic band:  22q11.21   HGNC cytogenetic band: 22q11.22

USP41 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
USP41 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M020704:  view genomic region     (about GC identifiers)

Start:
20,704,868 bp from pter      End:
20,745,048 bp from pter
Size:
40,181 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, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: UBP41_HUMAN, Q3LFD5 (See protein sequence)
Recommended Name: Putative ubiquitin carboxyl-terminal hydrolase 41  
Size: 358 amino acids; 41394 Da
Secondary accessions: A8MXD0 Q70BM7

Explore the universe of human proteins at neXtProt for USP41: NX_Q3LFD5

Explore proteomics data for USP41 at MOPED

3 DME Specific Peptides for USP41 (Q3LFD5)
 ILKRITVPR  VDGKWFCFNDS  LLLLEKMQDSRQKA 


See USP41 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


ENSEMBL proteins: 
 ENSP00000292729   ENSP00000414922  
Reactome Protein details: Q3LFD5

USP41 Human Recombinant Protein Products:

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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 Q3LFD5

ProtoNet protein and cluster: Q3LFD5

1 Blocks protein domain: IPB001394 Ubiquitin thiolesterase

UniProtKB/Swiss-Prot: UBP41_HUMAN, Q3LFD5
Similarity: Belongs to the peptidase C19 family
Similarity: Contains 1 USP domain


Find genes that share domains with USP41           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: UBP41_HUMAN, Q3LFD5
Function: May recognize and hydrolyze the peptide bond at the C-terminal Gly of ubiquitin. Involved in the
processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins (By similarity)
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)

     Enzyme Numbers (IUBMB): EC 3.1.2.152 EC 3.4.19.121

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0004221ubiquitin thiolesterase activity ----
GO:0008234cysteine-type peptidase activity IEA--
     
Find genes that share ontologies with USP41           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for USP41:
 Increased gamma-H2AX phosphory 

Animal Models:
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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
extracellular2
cytosol1
mitochondrion1
nucleus1
peroxisome1
plasma membrane1

(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 USP41 About    
See pathways by source

SuperPathContained pathways About
1Interferon Signaling
Interferon Signaling0.59
ISG15 antiviral mechanism0.42
Cytokine Signaling in Immune system0.59
Antiviral mechanism by IFN-stimulated genes0.42
2Ubiquitin-Proteasome Dependent Proteolysis
Ubiquitin-Proteasome Dependent Proteolysis


Find genes that share SuperPaths with USP41           About GenesLikeMe

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways

1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for USP41
    Ubiquitin-Proteasome Dependent Proteolysis

1 Reactome Pathway for USP41
    ISG15 antiviral mechanism


    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for USP41
Interactions:

    Search GeneGlobe Interaction Network for USP41

STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

Selected Interacting proteins for USP41 (Q3LFD53 ENSP000004149224) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
InteractantInteraction Details
GeneCardExternal ID(s)
USP18Q9UMW83, ENSP000002157944I2D: score=1 STRING: ENSP00000215794
DUS2ENSP000003517694STRING: ENSP00000351769
HID1ENSP000004135204STRING: ENSP00000413520
PFASENSP000003134904STRING: ENSP00000313490
RPS27AENSP000002723174STRING: ENSP00000272317
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 USP41           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 USP41 (UBP41)



(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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4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000486536(uc011ahp.1) ENST00000292729 ENST00000470202 ENST00000454608(uc011ahq.1)

miRNA
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Predesigned siRNA for gene silencing in human, mouse, rat USP41
Clone
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8 AceView cDNA sequences:

BF089771 AJ586979 H55154 BG390407 BG391572 BF062298 AA303390 BQ359633 

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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USP41 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
USP41 Expression
About this image

USP41 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

USP41 Protein Expression
    Custom PCR Arrays for USP41
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for USP41

(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 USP41 gene from Selected species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves --
Ubiquitin carboxyl-terminal hydrolase
44(a)
many ↔ many
1(62215178-62227083)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
43(a)
many ↔ many
5(14357512-14377121)
zebrafish
(Danio rerio)
Actinopterygii CU571169.46
Uncharacterized protein
27(a)
many ↔ many
4(5715803-5720646) ENSDARG00000088078
fruit fly
(Drosophila melanogaster)
Insecta Ubp64E6
Ubiquitin-specific protease 64E
6(a)
1 → many
3L(5746073-5754668)
worm
(Caenorhabditis elegans)
Secernentea T05H10.16
Protein T05H10.1 (T05H10.1) mRNA, complete cds
6(a)
1 → many
II(8042589-8047446) WBGene00011507
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP156
Ubiquitin-specific protease involved in protein de...
6(a)
1 → many
XIII(874987-878679) YMR304W
        Species with no ortholog for USP41

ENSEMBL Gene Tree for USP41 (if available)
TreeFam Gene Tree for USP41 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for USP41 gene
USP242  USP182  USP482  USP402  USP72  USP472  USP342  USP9Y2  
USP9X2  
3 SIMAP similar genes for USP41 using alignment to 2 protein entries:     UBP41_HUMAN (see all proteins):
USP18    USP15    Em

Find genes that share paralogs with USP41           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 USP41 (see all 577)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs713127521,2
--3982806(+) AGTCCC/TGACCC 1 -- int11Minor allele frequency- T:0.50NA 2
rs713127531,2
--3982866(+) AACTGC/TGAAGG 1 -- int11Minor allele frequency- T:0.50NA 2
rs713127541,2
--3982898(+) AGCACG/ACAAGA 1 -- int11Minor allele frequency- A:0.50NA 2
rs713178621,2
C,F--3982997(+) TTCTGT/CTTCTC 1 -- int13Minor allele frequency- C:0.33NA 6
rs1822013271,2
--4659700(+) CCGGCA/CACAGA 1 -- ds50010--------
rs1855839381,2
--4659775(+) AATCAA/GCAAAG 1 -- ds50010--------
rs1391567611,2
--4659782(+) AAAGGC/TTTCAC 1 -- ds50010--------
rs1121750771,2
F--4659828(+) TGGGGA/GGTTGG 1 -- ds50011Minor allele frequency- G:0.00CSA 1
rs1888022351,2
--4659847(+) GTAAAC/TGAGGA 1 -- ds50010--------
rs1816040471,2
--4659994(+) GAGATG/TAGGCA 1 -- ds50010--------

HapMap Linkage Disequilibrium report for USP41 (20704868 - 20745048 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for USP41: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing USP41
DNA2.0 Custom Variant and Variant Library Synthesis for USP41

(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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  --

(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 USP41 gene integrated from 10 sources:
(articles sorted by number of sources associating them with USP41)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. Human and mouse proteases: a comparative genomic approach. (PubMed id 12838346)1, 3 Puente X.S.... Lopez-Otin C. (Nat. Rev. Genet. 2003)
  3. Defining the human deubiquitinating enzyme interaction landscape. (PubMed id 19615732)1 Sowa M.E....Harper J.W. (Cell 2009)
  4. The DNA sequence of human chromosome 22. (PubMed id 10591208)2 Dunham I.... Wright H. (Nature 1999)

(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: 373856 HGNC: 20070 AceView: USP41 Ensembl:ENSG00000161133 euGenes: HUgn373856
ECgene: USP41 H-InvDB: USP41

(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 USP41 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 USP41 gene:
Search GeneIP for patents involving USP41

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, 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 inGenious Targeting Laboratory, 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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