USP13 ubiquitin specific peptidase 13 [Homo sapiens (human)] - Gene

Summary

Official Symbol: USP13provided by HGNC
Official Full Name: ubiquitin specific peptidase 13provided by HGNC
Primary source: HGNC:HGNC:12611
See related: Ensembl:ENSG00000058056 MIM:603591; AllianceGenome:HGNC:12611
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
Also known as: ISOT3; IsoT-3
Summary: Enables several functions, including BAT3 complex binding activity; peptidase activity; and proteasome binding activity. Involved in several processes, including maintenance of unfolded protein; positive regulation of ERAD pathway; and regulation of autophagy. Acts upstream of or within protein deubiquitination and protein stabilization. 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 heart (RPKM 16.6), adrenal (RPKM 7.5) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q26.33

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (179653040..179789401)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (182456880..182592926)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (179370828..179507189)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Oncogenic KRAS effector USP13 promotes metastasis in non-small cell lung cancer through deubiquitinating beta-catenin.
Title: Oncogenic KRAS effector USP13 promotes metastasis in non-small cell lung cancer through deubiquitinating β-catenin.
USP13 drives lung squamous cell carcinoma by switching lung club cell lineage plasticity.
Title: USP13 drives lung squamous cell carcinoma by switching lung club cell lineage plasticity.
USP13 deubiquitinates p62/SQSTM1 to induce autophagy and Nrf2 release for activating antioxidant response genes.
Title: USP13 deubiquitinates p62/SQSTM1 to induce autophagy and Nrf2 release for activating antioxidant response genes.
Deubiquitinase USP13 regulates glycolytic reprogramming and progression in osteosarcoma by stabilizing METTL3/m[6]A/ATG5 axis.
Title: Deubiquitinase USP13 regulates glycolytic reprogramming and progression in osteosarcoma by stabilizing METTL3/m(6)A/ATG5 axis.
USP13 deubiquitinates and stabilizes cyclin D1 to promote gastric cancer cell cycle progression and cell proliferation.
Title: USP13 deubiquitinates and stabilizes cyclin D1 to promote gastric cancer cell cycle progression and cell proliferation.
USP13 promotes breast cancer metastasis through FBXL14-induced Twist1 ubiquitination.
Title: USP13 promotes breast cancer metastasis through FBXL14-induced Twist1 ubiquitination.
USP13 regulates HMGB1 stability and secretion through its deubiquitinase activity.
Title: USP13 regulates HMGB1 stability and secretion through its deubiquitinase activity.
ncRNA-mediated overexpression of ubiquitin-specific proteinase 13 contributes to the progression of prostate cancer via modulating AR signaling, DNA damage repair and immune infiltration.
Title: ncRNA-mediated overexpression of ubiquitin-specific proteinase 13 contributes to the progression of prostate cancer via modulating AR signaling, DNA damage repair and immune infiltration.
USP13 promotes deubiquitination of ZHX2 and tumorigenesis in kidney cancer.
Title: USP13 promotes deubiquitination of ZHX2 and tumorigenesis in kidney cancer.
USP13 genetics and expression in a family with thyroid cancer.
Title: USP13 genetics and expression in a family with thyroid cancer.

Submit: New GeneRIF Correction See all GeneRIFs (39)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S2768E (e-PCR)
- UniSTS:150810

SHGC-132346 (e-PCR)
- UniSTS:170785

D3S3565 (e-PCR), detects polymorphism
- UniSTS:73772

SHGC-132431 (e-PCR)
- UniSTS:173899

RH99087 (e-PCR)
- UniSTS:85603

RH93958 (e-PCR)
- UniSTS:88187

D3S3377 (e-PCR)
- UniSTS:67555

D3S4112 (e-PCR)
- UniSTS:35581

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables BAT3 complex binding	IDA Inferred from Direct Assay more info	PubMed
enables K48-linked deubiquitinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
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 cysteine-type endopeptidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables proteasome binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-folding chaperone binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin-like protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maintenance of unfolded protein	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in melanocyte differentiation	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein K29-linked deubiquitination	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within protein K6-linked deubiquitination	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within protein K63-linked deubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K63-linked deubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein deubiquitination	TAS Traceable Author Statement more info
acts_upstream_of_or_within protein stabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in protein stabilization	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within protein stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of autophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of protein stability	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement 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 13

Names: deubiquitinating enzyme 13; ubiquitin specific peptidase 13 (isopeptidase T-3); ubiquitin specific protease 13 (isopeptidase T-3); ubiquitin thioesterase 13; ubiquitin thiolesterase 13; ubiquitin-specific-processing protease 13

NP_003931.2

EC 3.4.19.12

XP_011511571.1

EC 3.4.19.12

XP_016862914.1

EC 3.4.19.12

XP_016862915.1

EC 3.4.19.12

XP_016862916.1

EC 3.4.19.12

XP_047305110.1

EC 3.4.19.12

XP_054204261.1

EC 3.4.19.12

XP_054204262.1

EC 3.4.19.12

XP_054204263.1

EC 3.4.19.12

XP_054204264.1

EC 3.4.19.12

XP_054204265.1

EC 3.4.19.12

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)

NM_003940.3 → NP_003931.2 ubiquitin carboxyl-terminal hydrolase 13

See identical proteins and their annotated locations for NP_003931.2

Status: VALIDATED

Source sequence(s)

AC007687, AC125604, BC016146

Consensus CDS

CCDS3235.1

UniProtKB/Swiss-Prot

A8K2S3, B4DYF3, D3DNS2, Q92995, Q96B25

UniProtKB/TrEMBL

A0A0A6YZ17, A0A7P0TAP9

Related

ENSP00000263966.3, ENST00000263966.8

Conserved Domains (5) summary

COG5207
Location:30 → 861

UBP14; Uncharacterized Zn-finger protein, UBP-type [General function prediction only]

cd02658
Location:337 → 859

Peptidase_C19B; 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 ...

cd14384
Location:652 → 700

UBA1_UBP13; UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13)

cd14386
Location:728 → 769

UBA2_UBP5; UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5)

pfam02148
Location:211 → 284

zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

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_000003.12 Reference GRCh38.p14 Primary Assembly

Range

179653040..179789401

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011513269.2 → XP_011511571.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X1

See identical proteins and their annotated locations for XP_011511571.1

UniProtKB/TrEMBL

A0A7P0TAP9

Conserved Domains (5) summary

COG5207
Location:30 → 852

UBP14; Uncharacterized Zn-finger protein, UBP-type [General function prediction only]

cd02658
Location:337 → 850

Peptidase_C19B; 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 ...

cd14384
Location:643 → 691

UBA1_UBP13; UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13)

cd14386
Location:719 → 760

UBA2_UBP5; UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5)

pfam02148
Location:211 → 284

zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
XM_017007426.2 → XP_016862915.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X3

UniProtKB/TrEMBL

A0A7P0TAP9
XM_047449154.1 → XP_047305110.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X4
XM_017007425.2 → XP_016862914.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X2

UniProtKB/TrEMBL

A0A7P0TAP9

Related

ENSP00000417146.1, ENST00000496897.5
XM_017007427.2 → XP_016862916.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X5

UniProtKB/TrEMBL

A0A7P0TAP9

Related

ENST00000679972.1

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

182456880..182592926

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054348286.1 → XP_054204261.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X1
XM_054348288.1 → XP_054204263.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X3
XM_054348289.1 → XP_054204264.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X4
XM_054348287.1 → XP_054204262.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X2
XM_054348290.1 → XP_054204265.1 ubiquitin carboxyl-terminal hydrolase 13 isoform X5