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    Usp3 ubiquitin specific peptidase 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363084, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Usp3provided by RGD
    Official Full Name
    ubiquitin specific peptidase 3provided by RGD
    Primary source
    RGD:1308852
    See related
    Ensembl:ENSRNOG00000017714 AllianceGenome:RGD:1308852
    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
    Summary
    Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and promoter-specific chromatin binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nucleus. Orthologous to human USP3 (ubiquitin specific peptidase 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 215.7), Spleen (RPKM 116.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Usp3 in Genome Data Viewer
    Location:
    8q24
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (75973278..76049151, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (67078249..67154109, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (72207970..72284871, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene HECT and RLD domain containing E3 ubiquitin protein ligase family member 1 Neighboring gene uncharacterized LOC134480197 Neighboring gene F-box and leucine-rich repeat protein 22 Neighboring gene uncharacterized LOC120094375 Neighboring gene uncharacterized LOC134480068

    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. Identification of a short form of ubiquitin-specific protease 3 that is a repressor of rat glutathione S-transferase gene expression. Whalen R, et al. Biochem J, 2006 Mar 1. PMID 16279867, Free PMC Article
    2. 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
    3. Human USP3 is a chromatin modifier required for S phase progression and genome stability. Nicassio F, et al. Curr Biol, 2007 Nov 20. PMID 17980597
    4. Push back to respond better: regulatory inhibition of the DNA double-strand break response. Panier S, et al. Nat Rev Mol Cell Biol, 2013 Oct. PMID 24002223
    5. Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth. Mertz J, et al. Mol Cell Proteomics, 2015 Jul. PMID 25931508, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The study demonstrates that the short form of USP3 may be IL6DEX-NP and that it may play an important role in the negative regulation of proteins during the acute-phase response.
      Title: Identification of a short form of ubiquitin-specific protease 3 that is a repressor of rat glutathione S-transferase gene expression.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity ISO
    Inferred from Sequence Orthology
    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 promoter-specific chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    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
    		  
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    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 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
    ubiquitin specific protease 3
    ubiquitin thiolesterase 3
    NP_001020595.2
    XP_038937678.1
    XP_038937679.1
    XP_063121839.1

    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_001025424.2 → NP_001020595.2  ubiquitin carboxyl-terminal hydrolase 3

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      Q4JL29
      Related
      ENSRNOP00000084539.1, ENSRNOT00000094873.1
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086026.1 Reference GRCr8

      Range
      75973278..76049151 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039081751.2 → XP_038937679.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X2

      UniProtKB/TrEMBL
      Q4JL29
      Conserved Domains (2) summary
      pfam00443
      Location:129 → 478
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:2 → 75
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    2. XM_063265769.1 → XP_063121839.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A351

    3. XM_039081750.2 → XP_038937678.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A351, Q4JL29
      Related
      ENSRNOP00000086159.1
      Conserved Domains (2) summary
      pfam00443
      Location:145 → 494
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:17 → 91
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
    Nucleotide Protein Strain
    Heading Accession and Version

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