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

Gene ID: 235441, updated on 2-Nov-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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See Usp3 in Genome Data Viewer
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 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 (27) 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 IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables cysteine-type deubiquitinase activity IEA
Inferred from Electronic Annotation
more info
  
enables cysteine-type deubiquitinase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H2A deubiquitinase 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 IEA
Inferred from Electronic Annotation
more info
  
enables histone H2B deubiquitinase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone binding IEA
Inferred from Electronic Annotation
more info
  
enables histone binding ISO
Inferred from Sequence Orthology
more info
  
enables promoter-specific chromatin binding 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
involved_in DNA repair 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 IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA repair-dependent chromatin remodeling ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of transcription by RNA polymerase II 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
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Flemming body IEA
Inferred from Electronic Annotation
more info
  
located_in Flemming body ISO
Inferred from Sequence Orthology
more info
  
located_in chromatin IEA
Inferred from Electronic Annotation
more info
  
located_in 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 IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic ribonucleoprotein granule ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
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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