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Aliases for USP40 Gene

Aliases for USP40 Gene

  • Ubiquitin Specific Peptidase 40 2 3 5
  • Ubiquitin-Specific-Processing Protease 40 4
  • Ubiquitin Specific Protease 40 2
  • Deubiquitinating Enzyme 40 4
  • Ubiquitin Thioesterase 40 4
  • EC 4

External Ids for USP40 Gene

Previous GeneCards Identifiers for USP40 Gene

  • GC02M234400
  • GC02M234670
  • GC02M234168
  • GC02M234050
  • GC02M226184
  • GC02M234384

Summaries for USP40 Gene

Entrez Gene Summary for USP40 Gene

  • Modification of cellular proteins by ubiquitin is an essential regulatory mechanism controlled by the coordinated action of multiple ubiquitin-conjugating and deubiquitinating enzymes. USP40 belongs to a large family of cysteine proteases that function as deubiquitinating enzymes (Quesada et al., 2004 [PubMed 14715245]).[supplied by OMIM, Mar 2008]

GeneCards Summary for USP40 Gene

USP40 (Ubiquitin Specific Peptidase 40) is a Protein Coding gene. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. GO annotations related to this gene include cysteine-type endopeptidase activity and thiol-dependent ubiquitin-specific protease activity. An important paralog of this gene is USP47.

UniProtKB/Swiss-Prot for USP40 Gene

  • May be catalytically inactive.

Gene Wiki entry for USP40 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP40 Gene

Genomics for USP40 Gene

Regulatory Elements for USP40 Gene

Enhancers for USP40 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G234420 1.9 FANTOM5 Ensembl ENCODE dbSUPER 21.6 -858.3 -858270 9.8 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 GATA2 ZNF548 FOS ZNF202 LOC100422710 USP40 ARL4C SPP2 ENSG00000228162 GC02P234330
GH02G233412 1.8 FANTOM5 Ensembl ENCODE dbSUPER 19.1 +145.0 145014 18.4 PKNOX1 FOXA2 ARNT SIN3A CBX5 FOS REST TBX21 ZNF592 SMARCA4 USP40 SAG ATG16L1 DGKD SCARNA5 LOC105373929 INPP5D PIR59405 ENSG00000201013 GC02M233380
GH02G233485 1.2 Ensembl ENCODE dbSUPER 27.1 +79.0 78992 4.4 TBP JUN SIN3A ZIC2 GATA3 GATA2 POLR2A FOS NFE2L2 TCF7L2 USP40 UGT1A4 PIR59405 LOC100422710
GH02G233556 1.4 FANTOM5 Ensembl ENCODE 20.1 +9.4 9402 1.7 JUN BACH1 MAX GATA3 ZNF316 FOS NFE2 MAFK NFE2L2 MAFG USP40 HJURP LOC100422710
GH02G233565 1.1 ENCODE 25.5 +0.4 423 2.1 PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF207 USP40 LOC100422710
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USP40 on UCSC Golden Path with GeneCards custom track

Promoters for USP40 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for USP40 Gene

233,475,519 bp from pter
233,566,787 bp from pter
91,269 bases
Minus strand

Genomic View for USP40 Gene

Genes around USP40 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP40 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP40 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP40 Gene

Proteins for USP40 Gene

  • Protein details for USP40 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 40
    Protein Accession:
    Secondary Accessions:
    • Q6NX38
    • Q70EL0

    Protein attributes for USP40 Gene

    1235 amino acids
    Molecular mass:
    140130 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA91807.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for USP40 Gene


neXtProt entry for USP40 Gene

Post-translational modifications for USP40 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for USP40 Gene

Domains & Families for USP40 Gene

Gene Families for USP40 Gene

Protein Domains for USP40 Gene

Suggested Antigen Peptide Sequences for USP40 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase C19 family.
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP40: view

Function for USP40 Gene

Molecular function for USP40 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
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).
UniProtKB/Swiss-Prot Function:
May be catalytically inactive.

Enzyme Numbers (IUBMB) for USP40 Gene

Gene Ontology (GO) - Molecular Function for USP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity IEA --
genes like me logo Genes that share ontologies with USP40: view
genes like me logo Genes that share phenotypes with USP40: view

Animal Model Products

CRISPR Products

miRNA for USP40 Gene

miRTarBase miRNAs that target USP40

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP40 Gene

Localization for USP40 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USP40 gene
Compartment Confidence
peroxisome 2
cytosol 2
plasma membrane 1
extracellular 1
nucleus 1
endoplasmic reticulum 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for USP40 Gene

Pathways & Interactions for USP40 Gene

genes like me logo Genes that share pathways with USP40: view

Pathways by source for USP40 Gene

1 Qiagen pathway for USP40 Gene

Gene Ontology (GO) - Biological Process for USP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0016579 protein deubiquitination IEA --
genes like me logo Genes that share ontologies with USP40: view

No data available for SIGNOR curated interactions for USP40 Gene

Drugs & Compounds for USP40 Gene

(1) Drugs for USP40 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
genes like me logo Genes that share compounds with USP40: view

Transcripts for USP40 Gene

Unigene Clusters for USP40 Gene

Ubiquitin specific peptidase 40:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for USP40 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: - -

ExUns: 23a · 23b · 23c ^ 24 ^ 25 ^ 26 ^ 27a · 27b · 27c ^ 28 ^ 29 ^ 30a · 30b · 30c · 30d ^ 31 ^ 32a · 32b
SP1: - - - -
SP2: - - -
SP5: -
SP9: -

Relevant External Links for USP40 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for USP40 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for USP40 Gene

Protein differential expression in normal tissues from HIPED for USP40 Gene

This gene is overexpressed in Testis (20.9), Pancreas (12.1), and Ovary (11.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for USP40 Gene

Protein tissue co-expression partners for USP40 Gene

NURSA nuclear receptor signaling pathways regulating expression of USP40 Gene:


SOURCE GeneReport for Unigene cluster for USP40 Gene:


mRNA Expression by UniProt/SwissProt for USP40 Gene:

Tissue specificity: Broadly expressed.

Evidence on tissue expression from TISSUES for USP40 Gene

  • Liver(4.2)
genes like me logo Genes that share expression patterns with USP40: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP40 Gene

Orthologs for USP40 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for USP40 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia USP40 34 35
  • 99.28 (n)
(Bos Taurus)
Mammalia USP40 34 35
  • 86.96 (n)
(Mus musculus)
Mammalia Usp40 34 16 35
  • 83.56 (n)
(Rattus norvegicus)
Mammalia Usp40 34
  • 83.16 (n)
(Canis familiaris)
Mammalia -- 35
  • 81 (a)
-- 35
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia USP40 35
  • 66 (a)
(Monodelphis domestica)
Mammalia USP40 35
  • 59 (a)
(Gallus gallus)
Aves USP40 34 35
  • 68.58 (n)
(Anolis carolinensis)
Reptilia USP40 35
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia usp40 34
  • 58.52 (n)
(Danio rerio)
Actinopterygii usp40 34 35
  • 56.94 (n)
Dr.26632 34
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP15 35
  • 16 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 57 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.187 34
Species where no ortholog for USP40 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for USP40 Gene

Gene Tree for USP40 (if available)
Gene Tree for USP40 (if available)

Paralogs for USP40 Gene

Paralogs for USP40 Gene

(2) SIMAP similar genes for USP40 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with USP40: view

Variants for USP40 Gene

Sequence variations from dbSNP and Humsavar for USP40 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000050197 -- 233,565,559(+) TTGTG(A/G)AACTA nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs1000104114 -- 233,519,615(+) TTACC(C/T)AGTTC nc-transcript-variant, reference, synonymous-codon
rs1000209925 -- 233,477,119(+) AAGGC(A/C)GCTGG nc-transcript-variant, utr-variant-3-prime
rs1000211676 -- 233,479,354(+) GGTCA(A/G)GAGAT intron-variant
rs1000236570 -- 233,545,894(+) TCCAC(C/T)AGATA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for USP40 Gene

Variant ID Type Subtype PubMed ID
dgv768e199 CNV deletion 23128226
esv1030429 OTHER inversion 17803354
esv3397579 OTHER inversion 20981092
esv3594677 CNV loss 21293372
esv992038 OTHER inversion 20482838
nsv1136483 CNV deletion 24896259
nsv3214 CNV deletion 18451855
nsv499765 OTHER inversion 21111241
nsv508134 OTHER sequence alteration 20534489
nsv513646 OTHER inversion 21212237
nsv7336 OTHER inversion 18451855

Variation tolerance for USP40 Gene

Residual Variation Intolerance Score: 87% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 18.03; 98.43% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USP40 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP40 Gene

Disorders for USP40 Gene

Relevant External Links for USP40

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for USP40 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP40 Gene

Publications for USP40 Gene

  1. Ubiquitin specific proteases USP24 and USP40 and ubiquitin thiolesterase UCHL1 polymorphisms have synergic effect on the risk of Parkinson's disease among Taiwanese. (PMID: 20302855) Wu Y.R. … Lee-Chen G.J. (Clin. Chim. Acta 2010) 3 22 46 64
  2. Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels. (PMID: 21646302) Bielinski S.J. … Chute C.G. (Mayo Clin. Proc. 2011) 3 46 64
  3. Genetic evidence for ubiquitin-specific proteases USP24 and USP40 as candidate genes for late-onset Parkinson disease. (PMID: 16917932) Li Y. … Grupe A. (Hum. Mutat. 2006) 3 46 64
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier L.W. … Wilson R.K. (Nature 2005) 3 4 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for USP40 Gene

Sources for USP40 Gene

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