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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 3.4.19.12 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. Diseases associated with USP40 include 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 for USP40 Gene

  • May be catalytically inactive.

Gene Wiki entry for USP40 Gene

Additional gene information 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

GeneHancer (GH) Regulatory Elements for USP40 Gene

Promoters and enhancers for USP40 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I233565 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 586.7 +0.4 423 2.1 PKNOX1 SMAD1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 USP40 SCARNA6 GIGYF2 ATG16L1 LOC100422710
GH02I233973 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 35.2 -409.0 -409002 5.2 PKNOX1 FOXA2 SIN3A YY1 GLIS2 ZNF143 FOS RXRA MXD4 MIER2 USP40 SCARNA6 TRPM8 ENSG00000237581 SPP2
GH02I233412 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 30.4 +145.0 145014 18.4 PKNOX1 CLOCK FOXA2 ARNT SIN3A FOS KLF13 REST ZNF592 SMARCA4 USP40 SAG ATG16L1 DGKD SCARNA6 SCARNA5 INPP5D LOC105373929 PIR59405 GC02M233380
GH02I233348 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.7 +212.4 212413 11.5 HDGF FOXA2 PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF2 DGKD ENSG00000259793 ATG16L1 USP40 SAG SCARNA5 GIGYF2 SCARNA6 INPP5D
GH02I233485 Enhancer 1.1 Ensembl ENCODE dbSUPER 27.1 +79.0 78992 4.4 JUN SIN3A GATA3 POLR2A FOSL2 FOS NFE2L2 TCF7L2 SMARCE1 CEBPB USP40 UGT1A4 PIR59405 LOC100422710
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around USP40 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the USP40 gene promoter:

Genomic Locations for USP40 Gene

Genomic Locations for USP40 Gene
chr2:233,475,519-233,566,787
(GRCh38/hg38)
Size:
91,269 bases
Orientation:
Minus strand
chr2:234,384,165-234,475,428
(GRCh37/hg19)

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=Translation N-terminally extended.; 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

Suggested Antigen Peptide Sequences for USP40 Gene

GenScript: Design optimal peptide antigens:

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 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

Phenotypes From GWAS Catalog 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

miRNA for USP40 Gene

miRTarBase miRNAs that target USP40

Clone 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

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

Subcellular locations from the

Human Protein Atlas (HPA)

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:

Clone 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: - -
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
ECgene alternative splicing isoforms for
USP40

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:

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)
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 33 34
  • 99.28 (n)
cow
(Bos Taurus)
Mammalia USP40 33 34
  • 86.96 (n)
mouse
(Mus musculus)
Mammalia Usp40 33 16 34
  • 83.56 (n)
rat
(Rattus norvegicus)
Mammalia Usp40 33
  • 83.16 (n)
dog
(Canis familiaris)
Mammalia -- 34
  • 81 (a)
OneToMany
-- 34
  • 80 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia USP40 34
  • 66 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia USP40 34
  • 59 (a)
OneToOne
chicken
(Gallus gallus)
Aves USP40 33 34
  • 68.58 (n)
lizard
(Anolis carolinensis)
Reptilia USP40 34
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp40 33
  • 58.52 (n)
zebrafish
(Danio rerio)
Actinopterygii usp40 33 34
  • 56.94 (n)
Dr.26632 33
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP15 34
  • 16 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 57 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.187 33
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

ENSEMBL:
Gene Tree for USP40 (if available)
TreeFam:
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 Variation AA Info Type
rs1000050197 -- 233,565,559(-) A/G 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant, upstream_transcript_variant
rs1000104114 -- 233,519,615(-) T/C coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1000209925 -- 233,477,119(-) A/C 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000211676 -- 233,479,354(-) A/G genic_downstream_transcript_variant, intron_variant
rs1000236570 -- 233,545,894(-) C/T genic_upstream_transcript_variant, 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)

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

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

Disorder Aliases PubMed IDs
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
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 22 44 58
  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 44 58
  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 44 58
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for USP40 Gene

Sources for USP40 Gene

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