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    Usp3 ubiquitin specific peptidase 3 [ Mus musculus (house mouse) ]

    Gene ID: 235441, updated on 12-Aug-2018

    Summary

    Official Symbol
    Usp3provided by MGI
    Official Full Name
    ubiquitin specific peptidase 3provided by MGI
    Primary source
    MGI:MGI:2152450
    See related
    Ensembl:ENSMUSG00000032376 Vega:OTTMUSG00000023730
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    AA409661; BC017156
    Summary
    The protein encoded by this gene is a chromatin-associated histone 2A and 2B deubiquitinating enzyme that negatively regulates the DNA damage response. Mice deficient for this enzyme have reduced hematopoietic stem cell reserves, demonstrating a requirement in hematopoietic stem cell homeostasis. In addition, knock down of protein levels results in spontaneous tumor development and shortened lifespan, consistent with a function in preserving chromosomal integrity. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]
    Expression
    Ubiquitous expression in thymus adult (RPKM 7.4), cerebellum adult (RPKM 5.9) and 28 other tissues See more
    Orthologs

    Genomic context

    See Usp3 in Genome Data Viewer
    Location:
    9; 9 C
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 9 NC_000075.6 (66514639..66593115, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (66365688..66440787, complement)

    Chromosome 9 - NC_000075.6Genomic Context describing neighboring genes Neighboring gene predicted gene, 23428 Neighboring gene HECT and RLD domain containing E3 ubiquitin protein ligase family member 1 Neighboring gene F-box and leucine-rich repeat protein 22 Neighboring gene carbonic anhydrase 12 Neighboring gene aph1 homolog B, gamma secretase subunit

    Genomic regions, transcripts, and products

    Expression

    • 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

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC28886

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    RNA polymerase II proximal promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    cysteine-type peptidase activity IEA
    Inferred from Electronic Annotation
    more info
     
    histone binding ISO
    Inferred from Sequence Orthology
    more info
     
    hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    peptidase activity IEA
    Inferred from Electronic Annotation
    more info
     
    promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    thiol-dependent ubiquitin-specific protease activity ISO
    Inferred from Sequence Orthology
    more info
     
    thiol-dependent ubiquitinyl hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    DNA repair ISO
    Inferred from Sequence Orthology
    more info
     
    cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to DNA damage stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    histone deubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    histone deubiquitination ISO
    Inferred from Sequence Orthology
    more info
     
    mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    protein deubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    proteolysis IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of protein stability ISO
    Inferred from Sequence Orthology
    more info
     
    ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    Flemming body ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytoplasmic ribonucleoprotein granule ISO
    Inferred from Sequence Orthology
    more info
     
    nuclear chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 3
    Names
    deubiquitinating enzyme 3
    ubiquitin specific protease 3
    ubiquitin thioesterase 3
    ubiquitin thiolesterase 3
    ubiquitin-specific-processing protease 3
    NP_001289045.1
    NP_001289051.1
    NP_659186.1
    XP_006511173.1
    XP_006511177.1
    XP_011241031.1
    XP_017168828.1
    XP_017168829.1
    XP_017168830.1

    NCBI Reference Sequences (RefSeq)

    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_001302116.1NP_001289045.1  ubiquitin carboxyl-terminal hydrolase 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC132087, AC166755, AK158516, AK161676, AW494393, BE947971, BF472523, BM206502, CK624803
      Consensus CDS
      CCDS81025.1
      UniProtKB/TrEMBL
      E9Q8W9, Q3TT00
      Related
      ENSMUSP00000096213.2, OTTMUSP00000028025, ENSMUST00000098613.8, OTTMUST00000057954
      Conserved Domains (3) summary
      cl02553
      Location:160471
      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:158470
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:29105
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
    2. NM_001302122.1NP_001289051.1  ubiquitin carboxyl-terminal hydrolase 3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences in the 5' UTR and coding region and uses a downstream start codon compared to variant 1. It encodes isoform 3, which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC132087, AC166755, AK158516, AW494393, BE947971, BF472523, BM206502, CK624803
      Conserved Domains (2) summary
      cd02257
      Location:7260
      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:2259
      UCH; Ubiquitin carboxyl-terminal hydrolase
    3. NM_144937.4NP_659186.1  ubiquitin carboxyl-terminal hydrolase 3 isoform 1

      See identical proteins and their annotated locations for NP_659186.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC132087, AC166755, AK031141, AK158516, AW494393, BE947971, BF472523, BM206502, CK624803
      Consensus CDS
      CCDS23305.1
      UniProtKB/Swiss-Prot
      Q91W36
      Related
      ENSMUSP00000122199.1, OTTMUSP00000028024, ENSMUST00000127569.7, OTTMUST00000057953
      Conserved Domains (2) summary
      pfam00443
      Location:159508
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:29105
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000075.6 Reference GRCm38.p4 C57BL/6J

      Range
      66514639..66593115 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011242729.2XP_011241031.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X3

      Conserved Domains (2) summary
      cl02553
      Location:1340
      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:1339
      UCH; Ubiquitin carboxyl-terminal hydrolase
    2. XM_006511110.3XP_006511173.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

      Conserved Domains (3) summary
      cl02553
      Location:246595
      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:244594
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:117191
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
    3. XM_017313339.1XP_017168828.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X2

      Conserved Domains (1) summary
      pfam00443
      Location:74423
      UCH; Ubiquitin carboxyl-terminal hydrolase
    4. XM_017313340.1XP_017168829.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X2

      Conserved Domains (1) summary
      pfam00443
      Location:74423
      UCH; Ubiquitin carboxyl-terminal hydrolase
    5. XM_017313341.1XP_017168830.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X2

      Conserved Domains (1) summary
      pfam00443
      Location:74423
      UCH; Ubiquitin carboxyl-terminal hydrolase
    6. XM_006511114.3XP_006511177.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X4

      Conserved Domains (2) summary
      cl02553
      Location:31308
      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:19307
      UCH; Ubiquitin carboxyl-terminal hydrolase
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