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USP42 ubiquitin specific peptidase 42 [ Homo sapiens (human) ]

Gene ID: 84132, updated on 3-Apr-2024

Summary

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Official Symbol
USP42provided by HGNC
Official Full Name
ubiquitin specific peptidase 42provided by HGNC
Primary source
HGNC:HGNC:20068
See related
Ensembl:ENSG00000106346 AllianceGenome:HGNC:20068
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Enables thiol-dependent deubiquitinase. Involved in protein deubiquitination. Predicted to be located in nucleoplasm. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 9.2), bone marrow (RPKM 4.1) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
7p22.1
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (6081241..6161564)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (6197991..6280940)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (6144580..6201195)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 2 alpha kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17933 Neighboring gene RNA, 7SL, cytoplasmic 851, pseudogene Neighboring gene RNA, U6 small nuclear 218, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:6116071-6116985 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:6116986-6117899 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17934 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:6141129-6141352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6143513-6144112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17937 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:6189130-6190329 Neighboring gene cytohesin 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6262905-6263525 Neighboring gene Sharpr-MPRA regulatory region 15593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25620 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6310870-6311592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6311593-6312314 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6322371-6323253 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6323254-6324135 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6362882-6363382 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6387689-6388190 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6388191-6388690 Neighboring gene small integral membrane protein 10 like 3 Neighboring gene family with sequence similarity 220 member A

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. circUSP42 Is Downregulated in Triple-Negative Breast Cancer and Associated With Poor Prognosis. Yu J, et al. Technol Cancer Res Treat, 2020 Jan-Dec. PMID 32938310, Free PMC Article
  2. Overexpression and Biological Function of Ubiquitin-Specific Protease 42 in Gastric Cancer. Hou K, et al. PLoS One, 2016. PMID 27030989, Free PMC Article
  3. Ubiquitin-specific peptidase 42 (USP42) functions to deubiquitylate histones and regulate transcriptional activity. Hock AK, et al. J Biol Chem, 2014 Dec 12. PMID 25336640, Free PMC Article
  4. Whole transcriptome sequencing of a paediatric case of de novo acute myeloid leukaemia with del(5q) reveals RUNX1-USP42 and PRDM16-SKI fusion transcripts. Masetti R, et al. Br J Haematol, 2014 Aug. PMID 24673627
  5. Japanese Encephalitis Virus infection increases USP42 to stabilize TRIM21 and OAS1 for neuroinflammatory and anti-viral response in human microglia. Mishra R, et al. Virology, 2022 Aug. PMID 35779335

See all (38) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Investigating USP42 Mutation as Underlying Cause of Familial Non-Medullary Thyroid Carcinoma.
    Title: Investigating USP42 Mutation as Underlying Cause of Familial Non-Medullary Thyroid Carcinoma.
  2. [Ubiquitin-specific protease 42 regulates osteogenic differentiation of human adipose-derived stem cells].
    Title: [Ubiquitin-specific protease 42 regulates osteogenic differentiation of human adipose-derived stem cells].
  3. Japanese Encephalitis Virus infection increases USP42 to stabilize TRIM21 and OAS1 for neuroinflammatory and anti-viral response in human microglia.
    Title: Japanese Encephalitis Virus infection increases USP42 to stabilize TRIM21 and OAS1 for neuroinflammatory and anti-viral response in human microglia.
  4. circUSP42 Is Downregulated in Triple-Negative Breast Cancer and Associated With Poor Prognosis.
    Title: circUSP42 Is Downregulated in Triple-Negative Breast Cancer and Associated With Poor Prognosis.
  5. USP42 overexpression could be a potential prognostic marker for GC, regulate the survival and invasive properties of GC, and may represent a novel therapeutic molecular target for this tumor.
    Title: Overexpression and Biological Function of Ubiquitin-Specific Protease 42 in Gastric Cancer.
  6. a role for USP42 in regulating transcription by deubiquitylating histones
    Title: Ubiquitin-specific peptidase 42 (USP42) functions to deubiquitylate histones and regulate transcriptional activity.
  7. we report, for the first time, the identification of a RUNX1-USP42 fusion transcript detected at diagnosis in a child with AML and del(5).
    Title: Whole transcriptome sequencing of a paediatric case of de novo acute myeloid leukaemia with del(5q) reveals RUNX1-USP42 and PRDM16-SKI fusion transcripts.
  8. the function of USP42 is required to allow the rapid activation of p53-dependent transcription and a p53-dependent cell-cycle arrest in response to stress.
    Title: Regulation of p53 stability and function by the deubiquitinating enzyme USP42.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ12697, AC004895.4

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cysteine-type deubiquitinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ubiquitin carboxyl-terminal hydrolase 42
Names
deubiquitinating enzyme 42
ubiquitin specific protease 42
ubiquitin thioesterase 42
ubiquitin thiolesterase 42
ubiquitin-specific-processing protease 42
NP_001352693.1
NP_001376579.1
NP_115548.1
XP_005249940.1
XP_006715854.1
XP_011513875.1
XP_024302736.1
XP_024302737.1
XP_047276891.1
XP_047276892.1
XP_047276893.1
XP_047276894.1
XP_047276895.1
XP_047276896.1
XP_047276897.1
XP_047276898.1
XP_047276899.1
XP_047276900.1
XP_047276901.1
XP_054215173.1
XP_054215174.1
XP_054215175.1
XP_054215176.1
XP_054215177.1
XP_054215178.1
XP_054215179.1
XP_054215180.1
XP_054215181.1
XP_054215182.1
XP_054215183.1
XP_054215184.1
XP_054215185.1
XP_054215186.1
XP_054215187.1

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_001365764.1 → NP_001352693.1  ubiquitin carboxyl-terminal hydrolase 42 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC004895, AY618868, HY052239
    UniProtKB/Swiss-Prot
    A2RUE3, B5MDA5, Q0VIN8, Q3C166, Q6P9B4, Q9H9J4
    UniProtKB/TrEMBL
    A4D2N6
    Related
    ENST00000479544.6
    Conserved Domains (4) summary
    cd02661
    Location:110 → 410
    Peptidase_C19E; 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 ...
    cl26386
    Location:735 → 940
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
    cl26464
    Location:422 → 938
    Atrophin-1; Atrophin-1 family
    cl28310
    Location:846 → 1113
    Rho; Transcription termination factor Rho [Transcription]

  2. NM_001389650.1 → NP_001376579.1  ubiquitin carboxyl-terminal hydrolase 42 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC004895
    UniProtKB/TrEMBL
    A4D2N6
    Conserved Domains (4) summary
    PHA03247
    Location:422 → 938
    PHA03247; large tegument protein UL36; Provisional
    PRK07764
    Location:735 → 940
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:846 → 1113
    PRK12678; transcription termination factor Rho; Provisional
    cd02661
    Location:110 → 410
    Peptidase_C19E; 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 ...

  3. NM_032172.3 → NP_115548.1  ubiquitin carboxyl-terminal hydrolase 42 isoform 2

    See identical proteins and their annotated locations for NP_115548.1

    Status: VALIDATED

    Source sequence(s)
    AA936550, BC132862, BF725643, BM995466, DB457216
    Consensus CDS
    CCDS47535.1
    UniProtKB/TrEMBL
    A4D2N6
    Related
    ENSP00000301962.5, ENST00000306177.10
    Conserved Domains (4) summary
    cd02661
    Location:110 → 410
    Peptidase_C19E; 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 ...
    cl26386
    Location:735 → 940
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
    cl26464
    Location:422 → 938
    Atrophin-1; Atrophin-1 family
    cl28310
    Location:846 → 1113
    Rho; Transcription termination factor Rho [Transcription]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    6081241..6161564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420940.1 → XP_047276896.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  2. XM_047420938.1 → XP_047276894.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  3. XM_024446969.2 → XP_024302737.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

    UniProtKB/TrEMBL
    A4D2N6
    Conserved Domains (4) summary
    PHA03247
    Location:422 → 938
    PHA03247; large tegument protein UL36; Provisional
    PRK07764
    Location:735 → 940
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:846 → 1113
    PRK12678; transcription termination factor Rho; Provisional
    cd02661
    Location:110 → 410
    Peptidase_C19E; 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 ...

  4. XM_024446968.2 → XP_024302736.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

    UniProtKB/TrEMBL
    A4D2N6
    Conserved Domains (4) summary
    PHA03247
    Location:422 → 938
    PHA03247; large tegument protein UL36; Provisional
    PRK07764
    Location:735 → 940
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:846 → 1113
    PRK12678; transcription termination factor Rho; Provisional
    cd02661
    Location:110 → 410
    Peptidase_C19E; 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 ...

  5. XM_047420939.1 → XP_047276895.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  6. XM_011515573.2 → XP_011513875.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

    See identical proteins and their annotated locations for XP_011513875.1

    UniProtKB/TrEMBL
    A4D2N6
    Conserved Domains (4) summary
    PHA03247
    Location:422 → 938
    PHA03247; large tegument protein UL36; Provisional
    PRK07764
    Location:735 → 940
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:846 → 1113
    PRK12678; transcription termination factor Rho; Provisional
    cd02661
    Location:110 → 410
    Peptidase_C19E; 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 ...

  7. XM_047420942.1 → XP_047276898.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  8. XM_047420935.1 → XP_047276891.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  9. XM_047420936.1 → XP_047276892.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  10. XM_047420937.1 → XP_047276893.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  11. XM_006715791.2 → XP_006715854.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

    See identical proteins and their annotated locations for XP_006715854.1

    UniProtKB/TrEMBL
    A4D2N6
    Conserved Domains (4) summary
    PHA03247
    Location:422 → 938
    PHA03247; large tegument protein UL36; Provisional
    PRK07764
    Location:735 → 940
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:846 → 1113
    PRK12678; transcription termination factor Rho; Provisional
    cd02661
    Location:110 → 410
    Peptidase_C19E; 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 ...

  12. XM_005249883.6 → XP_005249940.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X4

    Conserved Domains (2) summary
    cd02661
    Location:110 → 410
    Peptidase_C19E; 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 ...
    pfam00443
    Location:111 → 409
    UCH; Ubiquitin carboxyl-terminal hydrolase

  13. XM_047420941.1 → XP_047276897.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  14. XM_047420943.1 → XP_047276899.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X2

  15. XM_047420944.1 → XP_047276900.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X3

    Related
    ENSP00000408217.2, ENST00000426246.2

  16. XM_047420945.1 → XP_047276901.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    6197991..6280940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054359207.1 → XP_054215182.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  2. XM_054359200.1 → XP_054215175.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  3. XM_054359204.1 → XP_054215179.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  4. XM_054359203.1 → XP_054215178.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  5. XM_054359206.1 → XP_054215181.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  6. XM_054359205.1 → XP_054215180.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  7. XM_054359202.1 → XP_054215177.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  8. XM_054359198.1 → XP_054215173.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  9. XM_054359199.1 → XP_054215174.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  10. XM_054359201.1 → XP_054215176.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  11. XM_054359212.1 → XP_054215187.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X4

  12. XM_054359208.1 → XP_054215183.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X1

  13. XM_054359209.1 → XP_054215184.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X2

  14. XM_054359210.1 → XP_054215185.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X3

  15. XM_054359211.1 → XP_054215186.1  ubiquitin carboxyl-terminal hydrolase 42 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H9J4.3 GenPept UniProtKB/Swiss-Prot:Q9H9J4

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