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    Usp4 ubiquitin specific peptidase 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 290864, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Usp4provided by RGD
    Official Full Name
    ubiquitin specific peptidase 4provided by RGD
    Primary source
    RGD:1587387
    See related
    EnsemblRapid:ENSRNOG00000054863 AllianceGenome:RGD:1587387
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable adenosine receptor binding activity; cysteine-type deubiquitinase activity; and identical protein binding activity. Predicted to be involved in several processes, including positive regulation of TORC1 signaling; protein localization to cell surface; and spliceosomal tri-snRNP complex assembly. Predicted to be located in cytosol and plasma membrane. Predicted to be active in nucleus. Orthologous to human USP4 (ubiquitin specific peptidase 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 197.7), Adrenal (RPKM 194.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Usp4 in Genome Data Viewer
    Location:
    8q32
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (117912576..117957934)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (109035402..109079382)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (117126692..117171012)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene ras homolog family member A Neighboring gene ribosomal protein S15a, pseudogene 7 Neighboring gene glutathione peroxidase 1 Neighboring gene similar to human chromosome 3 open reading frame 62 Neighboring gene interactor of HORMAD1 1 Neighboring gene uncharacterized LOC134480234

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Downregulation of USP4 Promotes Activation of Microglia and Subsequent Neuronal Inflammation in Rat Spinal Cord After Injury. Jiang X, et al. Neurochem Res, 2017 Nov. PMID 28755289
    2. Increased Expression of Ubiquitin-Specific Protease 4 Participates in Neuronal Apoptosis After Intracerebral Hemorrhage in Adult Rats. Liu C, et al. Cell Mol Neurobiol, 2017 Apr. PMID 27114249
    3. Oncogenic protein UnpEL/Usp4 deubiquitinates Ro52 by its isopeptidase activity. Wada K, et al. Biochem Biophys Res Commun, 2006 Jan 20. PMID 16316627
    4. Structural variability of the ubiquitin specific protease DUSP-UBL double domains. Elliott PR, et al. FEBS Lett, 2011 Nov 4. PMID 22001210
    5. The ubiquitin-specific protease Usp4 regulates the cell surface level of the A2A receptor. Milojevic T, et al. Mol Pharmacol, 2006 Apr. PMID 16339847

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. USP4 was expressed in microglia, but its expression decreased after spinal cord injury.
      Title: Downregulation of USP4 Promotes Activation of Microglia and Subsequent Neuronal Inflammation in Rat Spinal Cord After Injury.
    2. USP4 may be involved in neuronal apoptosis after intracerebral hemorrhage.
      Title: Increased Expression of Ubiquitin-Specific Protease 4 Participates in Neuronal Apoptosis After Intracerebral Hemorrhage in Adult Rats.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    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 adenosine receptor 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 cysteine-type deubiquitinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of protein ubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of protein ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of TORC1 signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of TORC1 signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein deubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein deubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein localization to cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to cell surface ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of protein stability ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of protein stability ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in spliceosomal tri-snRNP complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spliceosomal tri-snRNP complex assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 4
    Names
    deubiquitinating enzyme 4
    ubiquitin specific peptidase 4 (proto-oncogene)
    ubiquitin specific protease 4 (proto-oncogene)
    ubiquitin thioesterase 4
    ubiquitin-specific-processing protease 4
    NP_001128484.1
    XP_038936866.1
    XP_063121069.1
    XP_063121070.1
    XP_063121071.1
    XP_063121072.1

    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_001135012.3 → NP_001128484.1  ubiquitin carboxyl-terminal hydrolase 4

      See identical proteins and their annotated locations for NP_001128484.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/Swiss-Prot
      B2GUZ1
      Related
      ENSRNOP00000071463.1, ENSRNOT00000083046.3
      Conserved Domains (6) summary
      smart00695
      Location:27 → 125
      DUSP; Domain in ubiquitin-specific proteases
      COG5560
      Location:35 → 921
      UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
      cd02674
      Location:774 → 919
      Peptidase_C19R; 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 ...
      cl02553
      Location:302 → 486
      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 ...
      pfam14533
      Location:504 → 567
      USP7_C2; Ubiquitin-specific protease C-terminal
      pfam14836
      Location:139 → 226
      Ubiquitin_3; Ubiquitin-like domain

    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
      117912576..117957934
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063264999.1 → XP_063121069.1  ubiquitin carboxyl-terminal hydrolase 4 isoform X1

      UniProtKB/TrEMBL
      A6I350, M0R851
      Related
      ENSRNOP00000069514.1, ENSRNOT00000085609.3

    2. XM_063265000.1 → XP_063121070.1  ubiquitin carboxyl-terminal hydrolase 4 isoform X3

    3. XM_063265001.1 → XP_063121071.1  ubiquitin carboxyl-terminal hydrolase 4 isoform X4

    4. XM_063265002.1 → XP_063121072.1  ubiquitin carboxyl-terminal hydrolase 4 isoform X5

    5. XM_039080938.2 → XP_038936866.1  ubiquitin carboxyl-terminal hydrolase 4 isoform X2

      Conserved Domains (1) summary
      COG5560
      Location:1 → 575
      UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

    RNA

    1. XR_010053934.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_172071.1: Suppressed sequence

      Description
      NR_172071.1: This RefSeq was removed because currently there is insufficient support for the transcript.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B2GUZ1.1 GenPept UniProtKB/Swiss-Prot:B2GUZ1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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