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

Gene ID: 290864, updated on 13-Apr-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
Ensembl: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; identical protein binding activity; and thiol-dependent deubiquitinase. Predicted to be involved in several processes, including negative regulation of protein ubiquitination; 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, Apr 2022]
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

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. 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 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 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, ENSRNOT00000083046.2
    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

  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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