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

    Gene ID: 235441, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Usp3provided by MGI
    Official Full Name
    ubiquitin specific peptidase 3provided by MGI
    Primary source
    MGI:MGI:2152450
    See related
    Ensembl:ENSMUSG00000032376 AllianceGenome:MGI:2152450
    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
    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
    human all
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    Genomic context

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    Location:
    9 C; 9 35.96 cM
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (66421573..66501996, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (66514639..66593148, complement)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E6759 Neighboring gene STARR-positive B cell enhancer mm9_chr9:66213808-66214109 Neighboring gene predicted gene, 30447 Neighboring gene predicted gene, 50499 Neighboring gene predicted gene, 23428 Neighboring gene HECT and RLD domain containing E3 ubiquitin protein ligase family member 1 Neighboring gene STARR-positive B cell enhancer mm9_chr9:66312941-66313241 Neighboring gene STARR-positive B cell enhancer ABC_E3841 Neighboring gene STARR-positive B cell enhancer mm9_chr9:66351571-66351871 Neighboring gene F-box and leucine-rich repeat protein 22 Neighboring gene STARR-positive B cell enhancer mm9_chr9:66440763-66441064 Neighboring gene STARR-positive B cell enhancer mm9_chr9:66444915-66445215 Neighboring gene STARR-positive B cell enhancer ABC_E2900 Neighboring gene STARR-seq mESC enhancer starr_24480 Neighboring gene STARR-positive B cell enhancer ABC_E11413 Neighboring gene carbonic anhydrase 12 Neighboring gene STARR-positive B cell enhancer ABC_E8296 Neighboring gene aph1 homolog B, gamma secretase subunit

    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. Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells. Lancini C, et al. J Exp Med, 2014 Aug 25. PMID 25113974, Free PMC Article
    2. CRISPR/Cas9-based genome-wide screening of the deubiquitinase subfamily identifies USP3 as a protein stabilizer of REST blocking neuronal differentiation and promotes neuroblastoma tumorigenesis. Karapurkar JK, et al. J Exp Clin Cancer Res, 2023 May 12. PMID 37170124, Free PMC Article
    3. H2A-DUBbing the mammalian epigenome: expanding frontiers for histone H2A deubiquitinating enzymes in cell biology and physiology. Belle JI, et al. Int J Biochem Cell Biol, 2014 May. PMID 24647359
    4. USP16-mediated histone H2A lysine-119 deubiquitination during oocyte maturation is a prerequisite for zygotic genome activation. Rong Y, et al. Nucleic Acids Res, 2022 Jun 10. PMID 35640597, Free PMC Article
    5. Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection. Sousa-Nunes R, et al. Genome Res, 2003 Dec. PMID 14613977, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CRISPR/Cas9-based genome-wide screening of the deubiquitinase subfamily identifies USP3 as a protein stabilizer of REST blocking neuronal differentiation and promotes neuroblastoma tumorigenesis.
      Title: CRISPR/Cas9-based genome-wide screening of the deubiquitinase subfamily identifies USP3 as a protein stabilizer of REST blocking neuronal differentiation and promotes neuroblastoma tumorigenesis.
    2. USP3 deletion increased the levels of histone ubiquitination in adult tissues, reduced the hematopoietic stem cell reserves over time, and shortened animal life span.
      Title: Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC28886

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2A deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H2B deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA damage response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA repair-dependent chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cell cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein deubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Flemming body ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic ribonucleoprotein granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    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 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_011241031.1
    XP_017168828.1
    XP_036010799.1
    XP_036010800.1

    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_001302116.1 → NP_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
      ENSMUSP00000096213.3, ENSMUST00000098613.9
      Conserved Domains (3) summary
      cl02553
      Location:160 → 471
      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:158 → 470
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:29 → 105
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    2. NM_001302122.1 → NP_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:7 → 260
      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:2 → 259
      UCH; Ubiquitin carboxyl-terminal hydrolase

    3. NM_144937.4 → NP_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
      UniProtKB/TrEMBL
      Q3TT00
      Related
      ENSMUSP00000122199.2, ENSMUST00000127569.8
      Conserved Domains (2) summary
      pfam00443
      Location:159 → 508
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:29 → 105
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    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_000075.7 Reference GRCm39 C57BL/6J

      Range
      66421573..66501996 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011242729.4 → XP_011241031.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X4

      Conserved Domains (1) summary
      pfam00443
      Location:1 → 339
      UCH; Ubiquitin carboxyl-terminal hydrolase

    2. XM_036154907.1 → XP_036010800.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X5

      Conserved Domains (1) summary
      pfam00443
      Location:1 → 301
      UCH; Ubiquitin carboxyl-terminal hydrolase

    3. XM_036154906.1 → XP_036010799.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X2

      Conserved Domains (2) summary
      pfam00443
      Location:245 → 556
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:117 → 191
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    4. XM_006511110.5 → XP_006511173.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

      Conserved Domains (2) summary
      pfam00443
      Location:245 → 594
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:117 → 191
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    5. XM_017313339.3 → XP_017168828.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X3

      UniProtKB/TrEMBL
      G3UZF0
      Conserved Domains (1) summary
      pfam00443
      Location:74 → 423
      UCH; Ubiquitin carboxyl-terminal hydrolase

    RNA

    1. XR_004935410.1 RNA Sequence

    2. XR_004935409.1 RNA Sequence

    3. XR_004935413.1 RNA Sequence

    4. XR_004935415.1 RNA Sequence

    5. XR_004935408.1 RNA Sequence

    6. XR_004935406.1 RNA Sequence

    7. XR_004935411.1 RNA Sequence

    8. XR_004935412.1 RNA Sequence

    9. XR_004935414.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q91W36.1 GenPept UniProtKB/Swiss-Prot:Q91W36

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