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

Summary

Official Symbol: USP42provided by HGNC
Official Full Name: ubiquitin specific peptidase 42provided by HGNC
Primary source: HGNC:HGNC:20068
See related: Ensembl:ENSG00000106346 MIM:620946; 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 cysteine-type deubiquitinase activity. Predicted to be involved in protein deubiquitination and regulation of apoptotic process. Predicted to be located in nucleoplasm. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in testis (RPKM 9.2), bone marrow (RPKM 4.1) and 24 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 7p22.1

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (6081241..6161564)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (6197991..6280940)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (6144580..6201195)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
[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].
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.
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.
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.
a role for USP42 in regulating transcription by deubiquitylating histones
Title: Ubiquitin-specific peptidase 42 (USP42) functions to deubiquitylate histones and regulate transcriptional activity.
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.
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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

G38319 (e-PCR)
- UniSTS:66585

GDB:1318583 (e-PCR)
- UniSTS:63297

RH78626 (e-PCR)
- UniSTS:23154

RH103393 (e-PCR)
- UniSTS:97719

GDB:4585123 (e-PCR)
- UniSTS:50130

USP42 (e-PCR)
- UniSTS:519387

STS-W02789 (e-PCR)
- UniSTS:71165

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	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein deubiquitination	TAS Traceable Author Statement 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 regulation of protein stability	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

Go to the top of the page Help

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

EC 3.4.19.12

NP_001376579.1

EC 3.4.19.12

NP_115548.1

EC 3.4.19.12

XP_005249940.1

EC 3.4.19.12

XP_006715854.1

EC 3.4.19.12

XP_011513875.1

EC 3.4.19.12

XP_024302736.1

EC 3.4.19.12

XP_024302737.1

EC 3.4.19.12

XP_047276891.1

EC 3.4.19.12

XP_047276892.1

EC 3.4.19.12

XP_047276893.1

EC 3.4.19.12

XP_047276894.1

EC 3.4.19.12

XP_047276895.1

EC 3.4.19.12

XP_047276896.1

EC 3.4.19.12

XP_047276897.1

EC 3.4.19.12

XP_047276898.1

EC 3.4.19.12

XP_047276899.1

EC 3.4.19.12

XP_047276900.1

EC 3.4.19.12

XP_047276901.1

EC 3.4.19.12

XP_054215173.1

EC 3.4.19.12

XP_054215174.1

EC 3.4.19.12

XP_054215175.1

EC 3.4.19.12

XP_054215176.1

EC 3.4.19.12

XP_054215177.1

EC 3.4.19.12

XP_054215178.1

EC 3.4.19.12

XP_054215179.1

EC 3.4.19.12

XP_054215180.1

EC 3.4.19.12

XP_054215181.1

EC 3.4.19.12

XP_054215182.1

EC 3.4.19.12

XP_054215183.1

EC 3.4.19.12

XP_054215184.1

EC 3.4.19.12

XP_054215185.1

EC 3.4.19.12

XP_054215186.1

EC 3.4.19.12

XP_054215187.1

EC 3.4.19.12

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.

mRNA and Protein(s)

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]
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 ...
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

6081241..6161564

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047420940.1 → XP_047276896.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_047420938.1 → XP_047276894.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
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 ...
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 ...
XM_047420939.1 → XP_047276895.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
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 ...
XM_047420942.1 → XP_047276898.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_047420935.1 → XP_047276891.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_047420936.1 → XP_047276892.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_047420937.1 → XP_047276893.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
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 ...
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
XM_047420941.1 → XP_047276897.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_047420943.1 → XP_047276899.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X2
XM_047420944.1 → XP_047276900.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X3

Related

ENSP00000408217.2, ENST00000426246.2
XM_047420945.1 → XP_047276901.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

6197991..6280940

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054359207.1 → XP_054215182.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359200.1 → XP_054215175.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359204.1 → XP_054215179.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359203.1 → XP_054215178.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359206.1 → XP_054215181.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359205.1 → XP_054215180.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359202.1 → XP_054215177.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359198.1 → XP_054215173.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359199.1 → XP_054215174.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359201.1 → XP_054215176.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359212.1 → XP_054215187.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X4
XM_054359208.1 → XP_054215183.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X1
XM_054359209.1 → XP_054215184.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X2
XM_054359210.1 → XP_054215185.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X3
XM_054359211.1 → XP_054215186.1 ubiquitin carboxyl-terminal hydrolase 42 isoform X3