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

    Gene ID: 7375, updated on 28-Oct-2024

    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; AllianceGenome:HGNC:12627
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See USP4 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (49277144..49340053, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (49305224..49369431, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (49314577..49377486, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene interactor of HORMAD1 1 Neighboring gene GCSH pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14359 Neighboring gene chromosome 3 open reading frame 62 Neighboring gene microRNA 4271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49353925-49354426 Neighboring gene Sjoegren syndrome nuclear autoantigen 1 homolog Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49354427-49354926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49377657-49378156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19864 Neighboring gene Sharpr-MPRA regulatory region 2568 Neighboring gene GATA motif-containing MPRA enhancer 295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19865 Neighboring gene H3K27ac hESC enhancers GRCh37_chr3:49395462-49396070 and GRCh37_chr3:49396071-49396679 Neighboring gene glutathione peroxidase 1 Neighboring gene ras homolog family member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49423846-49424400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49424401-49424954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49426165-49426934 Neighboring gene Sharpr-MPRA regulatory region 7935

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC149848, MGC149849

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables adenosine receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables cysteine-type deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cysteine-type deubiquitinase activity TAS
    Traceable Author Statement
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in lysosome TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in 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)

    NEW Try the new Transcript table

    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
      A8K6Y0, C9IY91, O43452, O43453, Q08AK8, Q13107
      UniProtKB/TrEMBL
      Q08AK7, Q53FJ3
      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/TrEMBL
      Q53H56
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      49305224..49369431 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)