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USP4 ubiquitin specific peptidase 4 [ Homo sapiens (human) ]

Gene ID: 7375, updated on 3-May-2020

Summary

Official Symbol
USP4provided by HGNC
Official Full Name
ubiquitin specific peptidase 4provided by HGNC
Primary source
HGNC:HGNC:12627
See related
Ensembl:ENSG00000114316 MIM:603486
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UNP; Unph
Summary
The protein encoded by this gene is a protease that deubiquitinates target proteins such as ADORA2A and TRIM21. The encoded protein shuttles between the nucleus and cytoplasm and is involved in maintaining operational fidelity in the endoplasmic reticulum. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Expression
Ubiquitous expression in testis (RPKM 15.1), bone marrow (RPKM 14.6) and 25 other tissues See more
Orthologs

Genomic context

See USP4 in Genome Data Viewer
Location:
3p21.31
Exon count:
23
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (49277144..49340053, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (49314577..49377536, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene interactor of HORMAD1 1 Neighboring gene chromosome 3 open reading frame 62 Neighboring gene microRNA 4271 Neighboring gene Sjoegren syndrome nuclear autoantigen 1 homolog Neighboring gene GATA motif-containing MPRA enhancer 295 Neighboring gene glutathione peroxidase 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC149848, MGC149849

Gene Ontology Provided by GOA

Function Evidence Code Pubs
adenosine receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IDA
Inferred from Direct Assay
more info
PubMed 
thiol-dependent ubiquitinyl hydrolase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
negative regulation of protein ubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein deubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
 
protein localization to cell surface IDA
Inferred from Direct Assay
more info
PubMed 
regulation of protein stability IDA
Inferred from Direct Assay
more info
PubMed 
spliceosomal tri-snRNP complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
lysosome TAS
Traceable Author Statement
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
ubiquitin carboxyl-terminal hydrolase 4
Names
deubiquitinating enzyme 4
ubiquitin carboxyl-terminal esterase 4
ubiquitin specific peptidase 4 (proto-oncogene)
ubiquitin specific protease 4 (proto-oncogene)
ubiquitin thioesterase 4
ubiquitin thiolesterase 4
ubiquitin-specific processing protease 4
ubiquitous nuclear protein homolog
NP_001238806.1
NP_003354.2
NP_955475.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_030370.1 RefSeqGene

    Range
    5051..67960
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001251877.2NP_001238806.1  ubiquitin carboxyl-terminal hydrolase 4 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several exons and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR compared to variant 1. It encodes isoform c, which is shorter and has a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC121247, BC068017
    Consensus CDS
    CCDS58832.1
    UniProtKB/Swiss-Prot
    Q13107
    Related
    ENSP00000400623.1, ENST00000416417.5
    Conserved Domains (2) summary
    smart00695
    Location:27125
    DUSP; Domain in ubiquitin-specific proteases
    pfam14836
    Location:139226
    Ubiquitin_3; Ubiquitin-like domain
  2. NM_003363.4NP_003354.2  ubiquitin carboxyl-terminal hydrolase 4 isoform a

    See identical proteins and their annotated locations for NP_003354.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AI887410, BC125130, BC125131, DA267618, DB534804
    Consensus CDS
    CCDS2793.1
    UniProtKB/Swiss-Prot
    Q13107
    UniProtKB/TrEMBL
    A0A024R2T0, Q08AK7
    Related
    ENSP00000265560.4, ENST00000265560.9
    Conserved Domains (1) summary
    cl02553
    Location:35923
    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 ...
  3. NM_199443.3NP_955475.1  ubiquitin carboxyl-terminal hydrolase 4 isoform b

    See identical proteins and their annotated locations for NP_955475.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AF017306, AI887410, BC125130, BG717217, DA267618, DB534804
    Consensus CDS
    CCDS2794.1
    UniProtKB/Swiss-Prot
    Q13107
    UniProtKB/TrEMBL
    A0A024R2X6
    Related
    ENSP00000341028.4, ENST00000351842.8
    Conserved Domains (6) summary
    smart00695
    Location:27125
    DUSP; Domain in ubiquitin-specific proteases
    COG5560
    Location:35876
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cd02674
    Location:729874
    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:255439
    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:457520
    USP7_C2; Ubiquitin-specific protease C-terminal
    pfam14836
    Location:139226
    Ubiquitin_3; Ubiquitin-like domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    49277144..49340053 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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