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] See more...

Aliases for USP40 Gene

Aliases for USP40 Gene

  • Ubiquitin Specific Peptidase 40 2 3 5
  • Ubiquitin-Specific-Processing Protease 40 3 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 40 3 4
  • Ubiquitin Specific Protease 40 2 3
  • Deubiquitinating Enzyme 40 3 4
  • Ubiquitin Thioesterase 40 3 4
  • Ubiquitin Thiolesterase 40 3
  • EC 3.4.19.12 4
  • FLJ10785 2
  • USP40 5

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. Diseases associated with USP40 include Inflammatory Bowel Disease 10 and Parkinson Disease, Late-Onset. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (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 Summary for USP40 Gene

Gene Wiki entry for USP40 Gene

Additional gene information for USP40 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USP40 Gene

Genomics for USP40 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for USP40 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP40 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP40

Top Transcription factor binding sites by QIAGEN in the USP40 gene promoter:
  • AML1a
  • AREB6
  • Brachyury
  • FOXF2
  • HSF2
  • Lhx3a
  • LHX3b
  • MyoD
  • Nkx6-1
  • Sox5

Genomic Locations for USP40 Gene

Genomic Locations for USP40 Gene
chr2:233,475,520-233,566,789
(GRCh38/hg38)
Size:
91,270 bases
Orientation:
Minus strand
chr2:234,384,165-234,475,428
(GRCh37/hg19)
Size:
91,264 bases
Orientation:
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:
    Q9NVE5-UBP40_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 40
    Protein Accession:
    Q9NVE5
    Secondary Accessions:
    • Q6NX38
    • Q70EL0

    Protein attributes for USP40 Gene

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

    Alternative splice isoforms for USP40 Gene

    UniProtKB/Swiss-Prot:

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

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for USP40 Gene

InterPro:
Blocks:
  • Ubiquitin thiolesterase, family 2
ProtoNet:

Suggested Antigen Peptide Sequences for USP40 Gene

GenScript: Design optimal peptide antigens:
  • Ubiquitin-specific-processing protease 40 (UBP40_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NVE5

UniProtKB/Swiss-Prot:

UBP40_HUMAN :
  • Belongs to the peptidase C19 family.
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 Function:
May be catalytically inactive.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=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).; EC=3.4.19.12;.

Enzyme Numbers (IUBMB) for USP40 Gene

Phenotypes From GWAS Catalog for USP40 Gene

Gene Ontology (GO) - Molecular Function for USP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity IBA 21873635
GO:0004843 thiol-dependent ubiquitin-specific protease activity IBA 21873635
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 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

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP40

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

COMPARTMENTS
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
cytosol 2
plasma membrane 1
extracellular 1
peroxisome 1
nucleus 1
endoplasmic reticulum 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for USP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005829 cytosol IBA 21873635
genes like me logo Genes that share ontologies with USP40: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for USP40 Gene

Pathways & Interactions for USP40 Gene

PathCards logo

SuperPathways for USP40 Gene

SuperPathway Contained pathways
1 Ubiquitin-Proteasome Dependent Proteolysis
-
genes like me logo Genes that share pathways with USP40: view

Pathways by source for USP40 Gene

1 Qiagen pathway for USP40 Gene
  • Ubiquitin-Proteasome Dependent Proteolysis

Gene Ontology (GO) - Biological Process for USP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0016579 protein deubiquitination IBA 21873635
GO:0031647 regulation of protein stability IBA 21873635
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

mRNA/cDNA for USP40 Gene

11 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
17 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP40

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: - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

ExUns: 23a · 23b · 23c ^ 24 ^ 25 ^ 26 ^ 27a · 27b · 27c ^ 28 ^ 29 ^ 30a · 30b · 30c · 30d ^ 31 ^ 32a · 32b
SP1: - - - -
SP2: - - -
SP3:
SP4:
SP5: -
SP6:
SP7:
SP8:
SP9: -

Relevant External Links for USP40 Gene

GeneLoc Exon Structure for
USP40

Expression for USP40 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for USP40 Gene



Protein tissue co-expression partners for USP40 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for USP40

SOURCE GeneReport for Unigene cluster for USP40 Gene:

Hs.96513

mRNA Expression by UniProt/SwissProt for USP40 Gene:

Q9NVE5-UBP40_HUMAN
Tissue specificity: Broadly expressed.

Evidence on tissue expression from TISSUES for USP40 Gene

  • Liver(4.2)
  • Nervous system(2.1)
genes like me logo Genes that share expression patterns with USP40: view

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
Chimpanzee
(Pan troglodytes)
Mammalia USP40 30 31
  • 99.28 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia USP40 30 31
  • 86.96 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Usp40 30 17 31
  • 83.56 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Usp40 30
  • 83.16 (n)
Dog
(Canis familiaris)
Mammalia -- 31
  • 81 (a)
OneToMany
-- 31
  • 80 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia USP40 31
  • 66 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia USP40 31
  • 59 (a)
OneToOne
Chicken
(Gallus gallus)
Aves USP40 30 31
  • 68.58 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia USP40 31
  • 63 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia usp40 30
  • 58.52 (n)
Zebrafish
(Danio rerio)
Actinopterygii usp40 30 31
  • 56.94 (n)
OneToOne
Dr.26632 30
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP15 31
  • 16 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 57 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.187 30
Species where no ortholog for USP40 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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

ENSEMBL:
Gene Tree for USP40 (if available)
TreeFam:
Gene Tree for USP40 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for USP40: view image

Paralogs for USP40 Gene

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

  • UBP40_HUMAN
  • C9JK14_HUMAN
  • H7BZ71_HUMAN
  • H7C0C4_HUMAN
  • H7C2T9_HUMAN
  • H7C307_HUMAN
  • L8EAZ2_HUMAN
genes like me logo Genes that share paralogs with USP40: view

Variants for USP40 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP40 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
770515 Benign: not provided 233,551,502(-) C/T SYNONYMOUS_VARIANT
786495 Benign: not provided 233,556,972(-) G/A SYNONYMOUS_VARIANT
rs1048603 - p.Arg1111Cys
rs34026756 - p.Thr1025Met
rs838543 - p.Val666Ala

Additional dbSNP identifiers (rs#s) for USP40 Gene

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)

Additional Variant Information for USP40 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP40

SNP Genotyping and Copy Number Assay Products

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

Disorders for USP40 Gene

MalaCards: The human disease database

(2) MalaCards diseases for USP40 Gene - From: DISEASES

Disorder Aliases PubMed IDs
inflammatory bowel disease 10
  • ibd10
parkinson disease, late-onset
  • pd
- elite association - COSMIC cancer census association via MalaCards
Search USP40 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for USP40

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with USP40: view

No data available for 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 YR … Lee-Chen GJ (Clinica chimica acta; international journal of clinical chemistry 2010) 3 23 41
  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 SJ … Chute CG (Mayo Clinic proceedings 2011) 3 41
  3. Genetic evidence for ubiquitin-specific proteases USP24 and USP40 as candidate genes for late-onset Parkinson disease. (PMID: 16917932) Li Y … Grupe A (Human mutation 2006) 3 41
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for USP40 Gene

Sources for USP40 Gene