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Usp40 ubiquitin specific peptidase 40 [ Rattus norvegicus (Norway rat) ]

Gene ID: 316599, updated on 14-Nov-2024

Summary

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Symbol
Usp40provided by RGD
Full Name
ubiquitin specific peptidase 40provided by RGD
Primary source
RGD:1309613
See related
EnsemblRapid:ENSRNOG00000018395 AllianceGenome:RGD:1309613
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
LRRGT00071
Summary
Predicted to enable cysteine-type deubiquitinase activity. Predicted to be involved in regulation of protein stability. Predicted to be located in motile cilium. Predicted to be active in cytosol and nucleus. Orthologous to human USP40 (ubiquitin specific peptidase 40). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 216.1), Kidney (RPKM 130.8) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Usp40 in Genome Data Viewer
Location:
9q35
Exon count:
37
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (96055741..96126766, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (88607920..88678940, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (95072096..95143092, complement)

Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene S-antigen visual arrestin Neighboring gene diacylglycerol kinase, delta Neighboring gene UDP glucuronosyltransferase family 1 member A9 Neighboring gene UDP glycosyltransferase 1 family, pseudogene 1 Neighboring gene uncharacterized LOC108351970 Neighboring gene UDP glucuronosyltransferase family 1 member A8 Neighboring gene UDP glucuronosyltransferase 1 family, polypeptide A7C Neighboring gene UDP glucuronosyltransferase family 1 member A6

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. Quesada V, et al. Biochem Biophys Res Commun, 2004 Jan 30. PMID 14715245
  2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables cysteine-type deubiquitinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in protein deubiquitination IEA
Inferred from Electronic Annotation
more info
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of protein stability IBA
Inferred from Biological aspect of Ancestor
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
ubiquitin carboxyl-terminal hydrolase 40-like
ubiquitin specific protease 40
ubiquitin thioesterase 40
NP_001128357.1
XP_008765483.1
XP_038939653.1
XP_038939654.1
XP_038939655.1
XP_038939656.1
XP_038939657.1
XP_038939658.1
XP_038939660.1
XP_038939661.1
XP_038939662.1
XP_038939663.1
XP_063123363.1
XP_063123364.1
XP_063123365.1
XP_063123366.1

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_001134885.1 → NP_001128357.1  ubiquitin carboxyl-terminal hydrolase 40

    See identical proteins and their annotated locations for NP_001128357.1

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000009
    UniProtKB/TrEMBL
    A6JQE7, D3ZL95
    Related
    ENSRNOP00000060806.1, ENSRNOT00000064171.4
    Conserved Domains (1) summary
    cd02659
    Location:40 → 381
    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 ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086027.1 Reference GRCr8

    Range
    96055741..96126766 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039083726.2 → XP_038939654.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X1

    UniProtKB/TrEMBL
    A6JQE7, D3ZL95
    Conserved Domains (1) summary
    cd02659
    Location:40 → 381
    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_039083725.2 → XP_038939653.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X1

    UniProtKB/TrEMBL
    A6JQE7, D3ZL95
    Conserved Domains (1) summary
    cd02659
    Location:40 → 381
    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. XM_039083727.2 → XP_038939655.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X2

    UniProtKB/TrEMBL
    A6JQE7
    Conserved Domains (1) summary
    cl02553
    Location:40 → 318
    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 ...

  4. XM_039083728.2 → XP_038939656.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X5

    UniProtKB/TrEMBL
    A6JQF0
    Conserved Domains (2) summary
    cd02257
    Location:167 → 199
    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 ...
    cl02553
    Location:1 → 100
    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 ...

  5. XM_039083733.2 → XP_038939661.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X10

  6. XM_039083732.2 → XP_038939660.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X9

  7. XM_039083735.2 → XP_038939663.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X12

  8. XM_039083730.2 → XP_038939658.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X8

    UniProtKB/TrEMBL
    M0R5A3, Q6TUH3
    Conserved Domains (1) summary
    cl16912
    Location:1 → 202
    MDR; Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family

  9. XM_063267296.1 → XP_063123366.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X13

  10. XM_063267295.1 → XP_063123365.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X13

  11. XM_063267293.1 → XP_063123363.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X3

  12. XM_008767261.3 → XP_008765483.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X4

    UniProtKB/TrEMBL
    A6JQE7
    Conserved Domains (2) summary
    cd02659
    Location:40 → 381
    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 → 330
    UCH; Ubiquitin carboxyl-terminal hydrolase

  13. XM_063267294.1 → XP_063123364.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X7

  14. XM_039083729.2 → XP_038939657.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X6

    UniProtKB/TrEMBL
    A6JQG9
    Conserved Domains (1) summary
    cd02659
    Location:40 → 381
    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 ...

  15. XM_039083734.2 → XP_038939662.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X11

    UniProtKB/TrEMBL
    A6JQH0
    Conserved Domains (1) summary
    cd02659
    Location:40 → 381
    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. XR_001839663.3 RNA Sequence

  2. XR_005488916.2 RNA Sequence

  3. XR_005488917.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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