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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
    mouse all
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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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