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

Gene ID: 55230, updated on 4-Jul-2021

Summary

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
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

See USP40 in Genome Data Viewer
Location:
2q37.1
Exon count:
44
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (233475521..233566789, complement)
105.20201022 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 S-antigen visual arrestin Neighboring gene diacylglycerol kinase delta Neighboring gene Sharpr-MPRA regulatory region 11245 Neighboring gene PPFIA1 pseudogene 1 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
GeneReviews: Not available
Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10785, FLJ42100

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables thiol-dependent deubiquitinase IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of protein stability IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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_006712675.1
XP_011509698.1
XP_011509699.1
XP_011509700.1
XP_011509701.1
XP_011509702.1
XP_011509703.1
XP_016859916.1
XP_016859917.1

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_001365479.2NP_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
    Related
    ENSP00000502952.1, ENST00000678225.1
    Conserved Domains (1) summary
    cd02659
    Location:39344
    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_001382295.1NP_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
    Conserved Domains (1) summary
    cd02659
    Location:39344
    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_001382296.1NP_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:39344
    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_001382297.1NP_001369226.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cd02659
    Location:39344
    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_001382298.1NP_001369227.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cl02553
    Location:39392
    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_001382299.1NP_001369228.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cd02659
    Location:39344
    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_001382300.1NP_001369229.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cd02659
    Location:39344
    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_001382301.1NP_001369230.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Conserved Domains (1) summary
    cd02659
    Location:39344
    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_001382302.1NP_001369231.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC019221
    Related
    ENST00000483519.5
  10. NM_001382303.1NP_001369232.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC019072
    Related
    ENSP00000394154.2, ENST00000443711.2
    Conserved Domains (1) summary
    cl02553
    Location:3992
    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_018218.4NP_060688.2  ubiquitin carboxyl-terminal hydrolase 40 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC019072, AC019221
    Consensus CDS
    CCDS46547.1
    Related
    ENSP00000251722.6, ENST00000251722.10
    Conserved Domains (1) summary
    cd02659
    Location:39344
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    233475521..233566789 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511399.2XP_011509701.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X6

    Conserved Domains (2) summary
    cl02553
    Location:39392
    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:42389
    UCH; Ubiquitin carboxyl-terminal hydrolase
  2. XM_011511397.2XP_011509699.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X3

    Conserved Domains (2) summary
    cd02659
    Location:39344
    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:41311
    UCH_1; Ubiquitin carboxyl-terminal hydrolase
  3. XM_006712612.3XP_006712675.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X2

    Conserved Domains (2) summary
    cd02659
    Location:51356
    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:53323
    UCH_1; Ubiquitin carboxyl-terminal hydrolase
  4. XM_011511396.2XP_011509698.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X1

    Conserved Domains (2) summary
    cd02659
    Location:51356
    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:53323
    UCH_1; Ubiquitin carboxyl-terminal hydrolase
  5. XM_017004428.1XP_016859917.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X10

  6. XM_011511400.2XP_011509702.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X7

    Conserved Domains (2) summary
    cl02553
    Location:1253
    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:1191
    UCH; Ubiquitin carboxyl-terminal hydrolase
  7. XM_017004427.1XP_016859916.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X8

  8. XM_011511398.3XP_011509700.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X5

    Conserved Domains (2) summary
    cd02659
    Location:51356
    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:53323
    UCH_1; Ubiquitin carboxyl-terminal hydrolase
  9. XM_011511401.2XP_011509703.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X9

    Conserved Domains (2) summary
    cd02659
    Location:51356
    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:53323
    UCH_1; Ubiquitin carboxyl-terminal hydrolase

RNA

  1. XR_001738820.1 RNA Sequence

  2. XR_001738819.1 RNA Sequence

  3. XR_001738818.1 RNA Sequence

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