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

Gene ID: 8975, updated on 7-Apr-2024

Summary

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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; chaperone binding activity; and cysteine-type peptidase activity. Involved in several processes, including maintenance of unfolded protein involved in ERAD pathway; regulation of cellular catabolic process; and regulation of transcription, DNA-templated. 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, Apr 2022]
Expression
Broad expression in heart (RPKM 16.6), adrenal (RPKM 7.5) and 21 other tissues See more
Orthologs
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Genomic context

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See USP13 in Genome Data Viewer
Location:
3q26.33
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (179653040..179789401)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (182456880..182592926)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (179370828..179507189)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene NADH:ubiquinone oxidoreductase subunit B5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14922 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:179370658-179371301 Neighboring gene H3 histone pseudogene 13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:179446047-179446626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:179446627-179447205 Neighboring gene uncharacterized LOC124909464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20871 Neighboring gene peroxisomal biogenesis factor 5 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20872 Neighboring gene PEX5L antisense RNA 2

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. USP13 genetics and expression in a family with thyroid cancer. Maria AG, et al. Endocrine, 2022 Aug. PMID 35583846, Free PMC Article
  2. Molecular profiling of immune cell-enriched Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) interacting protein USP13. Biterge Süt B. Life Sci, 2020 Oct 1. PMID 32735883, Free PMC Article
  3. Ubiquitin Specific Protease 13 Regulates Tau Accumulation and Clearance in Models of Alzheimer's Disease. Liu X, et al. J Alzheimers Dis, 2019. PMID 31594232
  4. Amplification of USP13 drives non-small cell lung cancer progression mediated by AKT/MAPK signaling. Wu Y, et al. Biomed Pharmacother, 2019 Jun. PMID 30986623
  5. Identification of candidate substrates of ubiquitin-specific protease 13 using 2D-DIGE. Wang J, et al. Int J Mol Med, 2017 Jul. PMID 28498477, Free PMC Article

See all (101) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. USP13 promotes breast cancer metastasis through FBXL14-induced Twist1 ubiquitination.
    Title: USP13 promotes breast cancer metastasis through FBXL14-induced Twist1 ubiquitination.
  7. USP13 regulates HMGB1 stability and secretion through its deubiquitinase activity.
    Title: USP13 regulates HMGB1 stability and secretion through its deubiquitinase activity.
  8. 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.
  9. USP13 promotes deubiquitination of ZHX2 and tumorigenesis in kidney cancer.
    Title: USP13 promotes deubiquitination of ZHX2 and tumorigenesis in kidney cancer.
  10. 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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 IBA
Inferred from Biological aspect of Ancestor
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 
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
XP_011511571.1
XP_016862914.1
XP_016862915.1
XP_016862916.1
XP_047305110.1
XP_054204261.1
XP_054204262.1
XP_054204263.1
XP_054204264.1
XP_054204265.1

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_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_2023_10

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
    179653040..179789401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. XM_017007426.2 → XP_016862915.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X3

    UniProtKB/TrEMBL
    A0A7P0TAP9

  3. XM_047449154.1 → XP_047305110.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X4

  4. XM_017007425.2 → XP_016862914.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X2

    UniProtKB/TrEMBL
    A0A7P0TAP9
    Related
    ENSP00000417146.1, ENST00000496897.5

  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

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    182456880..182592926
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348286.1 → XP_054204261.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X1

  2. XM_054348288.1 → XP_054204263.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X3

  3. XM_054348289.1 → XP_054204264.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X4

  4. XM_054348287.1 → XP_054204262.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X2

  5. XM_054348290.1 → XP_054204265.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92995.2 GenPept UniProtKB/Swiss-Prot:Q92995

Gene LinkOut

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