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    Usp40 ubiquitin specific peptidase 40 [ Mus musculus (house mouse) ]

    Gene ID: 227334, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Usp40provided by MGI
    Official Full Name
    ubiquitin specific peptidase 40provided by MGI
    Primary source
    MGI:MGI:2443184
    See related
    Ensembl:ENSMUSG00000005501 AllianceGenome:MGI:2443184
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    C730029K03; B230215L03Rik
    Summary
    Predicted to enable cysteine-type endopeptidase activity and thiol-dependent deubiquitinase. Predicted to be involved in protein deubiquitination and regulation of protein stability. Predicted to be active in cytosol and nucleus. Orthologous to human USP40 (ubiquitin specific peptidase 40). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 6.6), CNS E11.5 (RPKM 4.8) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Usp40 in Genome Data Viewer
    Location:
    1 D; 1 44.45 cM
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (87872841..87936308, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (87945119..88008582, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_01624 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:89724892-89725168 Neighboring gene S-antigen, retina and pineal gland (arrestin) Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:89743594-89743830 Neighboring gene STARR-positive B cell enhancer ABC_E10019 Neighboring gene STARR-positive B cell enhancer mm9_chr1:89763253-89763553 Neighboring gene predicted gene, 19582 Neighboring gene diacylglycerol kinase, delta Neighboring gene STARR-seq mESC enhancer starr_01625 Neighboring gene UDP glycosyltransferase 1 family, polypeptide A10 pseudogene Neighboring gene karyopherin (importin) alpha 2 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. USP40 gene knockdown disrupts glomerular permeability in zebrafish. Takagi H, et al. Am J Physiol Renal Physiol, 2017 Apr 1. PMID 28148530
    2. Identification of differentially expressed genes in mouse spermatogenesis. Pang AL, et al. J Androl, 2003 Nov-Dec. PMID 14581517
    3. Identification by proximity labeling of novel lipidic and proteinaceous potential partners of the dopamine transporter. Piniella D, et al. Cell Mol Life Sci, 2021 Dec. PMID 34709416, Free PMC Article
    4. USP40 deubiquitinates HINT1 and stabilizes p53 in podocyte damage. Takahashi S, et al. Biochem Biophys Res Commun, 2022 Jul 23. PMID 35605301
    5. An Interaction Landscape of Ubiquitin Signaling. Zhang X, et al. Mol Cell, 2017 Mar 2. PMID 28190767

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The deubiquitinase USP40 preserves endothelial integrity by targeting the heat shock protein HSP90beta.
      Title: The deubiquitinase USP40 preserves endothelial integrity by targeting the heat shock protein HSP90β.
    2. USP40 deubiquitinates HINT1 and stabilizes p53 in podocyte damage.
      Title: USP40 deubiquitinates HINT1 and stabilizes p53 in podocyte damage.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein deubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within 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_001028463.1
    NP_001185502.1
    XP_006529540.1
    XP_036020425.1
    XP_036020426.1
    XP_036020427.1
    XP_036020429.1

    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_001033291.3 → NP_001028463.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 2

      See identical proteins and their annotated locations for NP_001028463.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame segment compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC087801, AC162281
      Consensus CDS
      CCDS15137.1
      UniProtKB/Swiss-Prot
      Q8BWR4
      Related
      ENSMUSP00000038533.5, ENSMUST00000040783.11
      Conserved Domains (2) summary
      cd02659
      Location:39 → 342
      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 ...
      pfam00443
      Location:42 → 340
      UCH; Ubiquitin carboxyl-terminal hydrolase

    2. NM_001198573.2 → NP_001185502.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 1

      See identical proteins and their annotated locations for NP_001185502.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC087801, AC162281
      Consensus CDS
      CCDS78645.1
      UniProtKB/Swiss-Prot
      Q08EB7, Q148V0, Q3TLV1, Q3TMN0, Q3V1R4, Q5EBN6, Q8BWR4
      Related
      ENSMUSP00000140107.2, ENSMUST00000187758.7
      Conserved Domains (2) summary
      cd02659
      Location:39 → 342
      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 ...
      pfam00443
      Location:42 → 340
      UCH; Ubiquitin carboxyl-terminal hydrolase

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000067.7 Reference GRCm39 C57BL/6J

      Range
      87872841..87936308 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006529477.5 → XP_006529540.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X1

      Conserved Domains (1) summary
      cd02659
      Location:39 → 342
      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. XM_036164533.1 → XP_036020426.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X2

      Conserved Domains (1) summary
      cl28922
      Location:30 → 95
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    3. XM_036164532.1 → XP_036020425.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X2

      Conserved Domains (1) summary
      cl28922
      Location:30 → 95
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    4. XM_036164534.1 → XP_036020427.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X3

    5. XM_036164536.1 → XP_036020429.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X4

    RNA

    1. XR_001784185.3 RNA Sequence

    2. XR_004942005.1 RNA Sequence

    3. XR_004942007.1 RNA Sequence

    4. XR_004942003.1 RNA Sequence

    5. XR_004942004.1 RNA Sequence

    6. XR_004942001.1 RNA Sequence

    7. XR_001784186.3 RNA Sequence

    8. XR_004942006.1 RNA Sequence

      Related
      ENSMUST00000188332.7
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BWR4.2 GenPept UniProtKB/Swiss-Prot:Q8BWR4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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