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

Summary

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, Nov 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

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_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

EC 3.4.19.12

XP_038936866.1

EC 3.4.19.12

XP_063121069.1

EC 3.4.19.12

XP_063121070.1

EC 3.4.19.12

XP_063121071.1

EC 3.4.19.12

XP_063121072.1

EC 3.4.19.12

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)

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

NC_086026.1 Reference GRCr8

Range

117912576..117957934

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A6I350, M0R851

Related

ENSRNOP00000069514.1, ENSRNOT00000085609.3
XM_063265000.1 → XP_063121070.1 ubiquitin carboxyl-terminal hydrolase 4 isoform X3
XM_063265001.1 → XP_063121071.1 ubiquitin carboxyl-terminal hydrolase 4 isoform X4
XM_063265002.1 → XP_063121072.1 ubiquitin carboxyl-terminal hydrolase 4 isoform X5
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

XR_010053934.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NR_172071.1: Suppressed sequence

Description

NR_172071.1: This RefSeq was removed because currently there is insufficient support for the transcript.