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USP40 ubiquitin specific peptidase 40 [ Homo sapiens (human) ]

Gene ID: 55230, updated on 3-Apr-2024

Summary

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Official Symbol
USP40provided by HGNC
Official Full Name
ubiquitin specific peptidase 40provided by HGNC
Primary source
HGNC:HGNC:20069
See related
Ensembl:ENSG00000085982 MIM:610570; AllianceGenome:HGNC:20069
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 7.5), thyroid (RPKM 6.8) and 25 other tissues See more
Orthologs
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Genomic context

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See USP40 in Genome Data Viewer
Location:
2q37.1
Exon count:
44
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (233475526..233566782, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (233964044..234055315, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (234384172..234475428, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234227861-234228828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234228829-234229795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234234987-234235964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234237262-234238093 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:234238124-234238905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17342 Neighboring gene S-antigen visual arrestin Neighboring gene MPRA-validated peak4087 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17345 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:234307646-234308151 Neighboring gene diacylglycerol kinase delta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17347 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:234334881-234336080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234359341-234359904 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:234376565-234376780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:234382503-234383102 Neighboring gene PPFIA1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:234491694-234492284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17350 Neighboring gene UDP glucuronosyltransferase family 1 member A12, pseudogene Neighboring gene UDP glucuronosyltransferase family 1 member A11, pseudogene Neighboring gene UDP glucuronosyltransferase family 1 member A complex locus

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Association analysis of single-nucleotide polymorphisms of USP24 and USP40 with Parkinson's disease in the Han Chinese population. Zhao B, et al. Eur Neurol, 2012. PMID 22923019
  2. Genetic evidence for ubiquitin-specific proteases USP24 and USP40 as candidate genes for late-onset Parkinson disease. Li Y, et al. Hum Mutat, 2006 Oct. PMID 16917932
  3. Ubiquitin specific proteases USP24 and USP40 and ubiquitin thiolesterase UCHL1 polymorphisms have synergic effect on the risk of Parkinson's disease among Taiwanese. Wu YR, et al. Clin Chim Acta, 2010 Jul 4. PMID 20302855
  4. Glucocorticoid modulatory element-binding protein 1 (GMEB1) interacts with the de-ubiquitinase USP40 to stabilize CFLAR(L) and inhibit apoptosis in human non-small cell lung cancer cells. An W, et al. J Exp Clin Cancer Res, 2019 May 2. PMID 31046799, Free PMC Article
  5. RNA editing by adenosine deaminases that act on RNA. Bass BL. Annu Rev Biochem, 2002. PMID 12045112, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. USP40 promotes hepatocellular carcinoma cell proliferation, migration and stemness by deubiquitinating and stabilizing Claudin1.
    Title: USP40 promotes hepatocellular carcinoma cell proliferation, migration and stemness by deubiquitinating and stabilizing Claudin1.
  2. Our findings show the de-ubiquitinase USP40 regulates the ubiquitination and degradation of CFLARL; and GMEB1 acts as a bridge protein for USP40 and CFLARL. Mechanistically, we found GMEB1 inhibits the activation of CASP8 by modulating ubiquitination and degradation of CFLARL
    Title: Glucocorticoid modulatory element-binding protein 1 (GMEB1) interacts with the de-ubiquitinase USP40 to stabilize CFLAR(L) and inhibit apoptosis in human non-small cell lung cancer cells.
  3. present study is the first to report a lack of association between SNPs of USP40 and parkinson disease in Han Chinese patients. Other
    Title: Association analysis of single-nucleotide polymorphisms of USP24 and USP40 with Parkinson's disease in the Han Chinese population.
  4. USP24 alone plays a role in PD susceptibility among Taiwanese people >or=60 years of age, or acting synergistically with USP40 and UCHL1 in the total subjects.
    Title: Ubiquitin specific proteases USP24 and USP40 and ubiquitin thiolesterase UCHL1 polymorphisms have synergic effect on the risk of Parkinson's disease among Taiwanese.
  5. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Ubiquitin specific proteases USP24 and USP40 and ubiquitin thiolesterase UCHL1 polymorphisms have synergic effect on the risk of Parkinson's disease among Taiwanese.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic evidence for ubiquitin-specific proteases USP24 and USP40 as candidate genes for late-onset Parkinson disease.
  7. Da suggest that genetic variants in USP40 affect the risk for late-onset Parkinson disease (PD), which is consistent with the predicted role of the ubiquitination pathway in PD etiology.
    Title: Genetic evidence for ubiquitin-specific proteases USP24 and USP40 as candidate genes for late-onset Parkinson disease.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
EBI GWAS Catalog
Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10785, FLJ42100

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cysteine-type deubiquitinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ubiquitin carboxyl-terminal hydrolase 40
Names
deubiquitinating enzyme 40
ubiquitin specific protease 40
ubiquitin thioesterase 40
ubiquitin thiolesterase 40
ubiquitin-specific-processing protease 40
NP_001352408.1
NP_001369224.1
NP_001369225.1
NP_001369226.1
NP_001369227.1
NP_001369228.1
NP_001369229.1
NP_001369230.1
NP_001369231.1
NP_001369232.1
NP_060688.2
XP_011509699.1
XP_011509700.2
XP_011509701.1
XP_011509703.2
XP_016859916.1
XP_047300845.1
XP_047300846.1
XP_047300847.1
XP_047300848.1
XP_047300849.1
XP_054198743.1
XP_054198744.1
XP_054198745.1
XP_054198746.1
XP_054198747.1
XP_054198748.1
XP_054198749.1
XP_054198750.1
XP_054198751.1
XP_054198752.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001365479.2 → NP_001352408.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1), as well as variant 3, encodes isoform 1.
    Source sequence(s)
    AC019072, AC019221
    Consensus CDS
    CCDS92972.1
    UniProtKB/TrEMBL
    A0A7I2YQ75
    Related
    ENSP00000502952.1, ENST00000678225.2
    Conserved Domains (1) summary
    cd02659
    Location:39 → 344
    peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

  2. NM_001382295.1 → NP_001369224.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3), as well as variant 1, encodes isoform 1.
    Source sequence(s)
    AC019072, AC019221
    Consensus CDS
    CCDS92972.1
    UniProtKB/TrEMBL
    A0A7I2YQ75
    Conserved Domains (1) summary
    cd02659
    Location:39 → 344
    peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

  3. NM_001382296.1 → NP_001369225.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (3).
    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cd02659
    Location:39 → 344
    peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

  4. NM_001382297.1 → NP_001369226.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cd02659
    Location:39 → 344
    peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

  5. NM_001382298.1 → NP_001369227.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cl02553
    Location:39 → 392
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...

  6. NM_001382299.1 → NP_001369228.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cd02659
    Location:39 → 344
    peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

  7. NM_001382300.1 → NP_001369229.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cd02659
    Location:39 → 344
    peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

  8. NM_001382301.1 → NP_001369230.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cd02659
    Location:39 → 344
    peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

  9. NM_001382302.1 → NP_001369231.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC019221
    Related
    ENST00000483519.5

  10. NM_001382303.1 → NP_001369232.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC019072
    Consensus CDS
    CCDS92973.1
    UniProtKB/TrEMBL
    C9JK14
    Related
    ENSP00000394154.2, ENST00000443711.2
    Conserved Domains (1) summary
    cl02553
    Location:39 → 92
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...

  11. NM_018218.4 → NP_060688.2  ubiquitin carboxyl-terminal hydrolase 40 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Consensus CDS
    CCDS46547.2
    UniProtKB/Swiss-Prot
    Q6NX38, Q70EL0, Q9NVE5
    Related
    ENSP00000251722.6, ENST00000251722.10
    Conserved Domains (1) summary
    cd02659
    Location:39 → 344
    peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

RNA

  1. NR_168049.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221

  2. NR_168050.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221

  3. NR_168051.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221

  4. NR_168052.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221

  5. NR_168053.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221

  6. NR_168054.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221

  7. NR_168055.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC019221

  8. NR_168056.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC019221

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    233475526..233566782 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444889.1 → XP_047300845.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X4

  2. XM_011511399.3 → XP_011509701.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X3

    Conserved Domains (2) summary
    cl02553
    Location:39 → 392
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam00443
    Location:42 → 389
    UCH; Ubiquitin carboxyl-terminal hydrolase

  3. XM_011511397.3 → XP_011509699.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X1

    Conserved Domains (2) summary
    cd02659
    Location:39 → 344
    peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam13423
    Location:41 → 311
    UCH_1; Ubiquitin carboxyl-terminal hydrolase

  4. XM_047444891.1 → XP_047300847.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X6

  5. XM_047444890.1 → XP_047300846.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X5

  6. XM_017004427.2 → XP_016859916.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X8

    UniProtKB/TrEMBL
    B4DN96

  7. XM_047444893.1 → XP_047300849.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X10

  8. XM_011511398.4 → XP_011509700.2  ubiquitin carboxyl-terminal hydrolase 40 isoform X2

  9. XM_047444892.1 → XP_047300848.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X7

  10. XM_011511401.3 → XP_011509703.2  ubiquitin carboxyl-terminal hydrolase 40 isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    233964044..234055315 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342771.1 → XP_054198746.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X4

  2. XM_054342770.1 → XP_054198745.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X3

  3. XM_054342768.1 → XP_054198743.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X1

  4. XM_054342773.1 → XP_054198748.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X6

  5. XM_054342772.1 → XP_054198747.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X5

  6. XM_054342775.1 → XP_054198750.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X8

  7. XM_054342777.1 → XP_054198752.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X10

  8. XM_054342769.1 → XP_054198744.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X2

  9. XM_054342774.1 → XP_054198749.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X7

  10. XM_054342776.1 → XP_054198751.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X9

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NVE5.3 GenPept UniProtKB/Swiss-Prot:Q9NVE5

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