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

    Gene ID: 316599, updated on 2-May-2024

    Summary

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    Symbol
    Usp40provided by RGD
    Full Name
    ubiquitin specific peptidase 40provided by RGD
    Primary source
    RGD:1309613
    See related
    Ensembl: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 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
    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, polypeptide A9, pseudogene 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
    • 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 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
    		  
    located_in motile cilium IEA
    Inferred from Electronic Annotation
    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, ENSRNOT00000064171.3
      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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