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USP16 ubiquitin specific peptidase 16 [ Homo sapiens (human) ]

Gene ID: 10600, updated on 5-Mar-2024

Summary

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Official Symbol
USP16provided by HGNC
Official Full Name
ubiquitin specific peptidase 16provided by HGNC
Primary source
HGNC:HGNC:12614
See related
Ensembl:ENSG00000156256 MIM:604735; AllianceGenome:HGNC:12614
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UBPM; UBP-M
Summary
This gene encodes a deubiquitinating enzyme that is phosphorylated at the onset of mitosis and then dephosphorylated at the metaphase/anaphase transition. It can deubiquitinate H2A, one of two major ubiquitinated proteins of chromatin, in vitro and a mutant form of the protein was shown to block cell division. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 20.1), testis (RPKM 16.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
21q21.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (29024668..29054488)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (27388120..27417933)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (30396989..30426809)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18326 Neighboring gene ribosomal protein L23 pseudogene 2 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr21:30384585-30385165 Neighboring gene uncharacterized LOC124905005 Neighboring gene RWD domain containing 2B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18328 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:30416252-30416450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18330 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:30445041-30445952 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:30445953-30446864 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:30447741-30448940 Neighboring gene chaperonin containing TCP1 subunit 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18333 Neighboring gene MAP3K7 C-terminal like Neighboring gene Sharpr-MPRA regulatory region 4059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13237 Neighboring gene ribosomal protein L12 pseudogene 9

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. USP16 Regulates the Stability and Function of LDL receptor by Deubiquitination. Li Y, et al. Int Heart J, 2020. PMID 32999190
  2. Transcriptional activation of USP16 gene expression by NFκB signaling. Yang S, et al. Mol Brain, 2019 Dec 30. PMID 31888715, Free PMC Article
  3. USP16 Downregulation by Carboxyl-terminal Truncated HBx Promotes the Growth of Hepatocellular Carcinoma Cells. Qian Y, et al. Sci Rep, 2016 Sep 16. PMID 27633997, Free PMC Article
  4. USP16 regulates castration-resistant prostate cancer cell proliferation by deubiquitinating and stablizing c-Myc. Ge J, et al. J Exp Clin Cancer Res, 2021 Feb 5. PMID 33546726, Free PMC Article
  5. USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit. Montellese C, et al. Elife, 2020 Mar 4. PMID 32129764, Free PMC Article

See all (68) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LncRNA MNX1-AS1 sustains inactivation of Hippo pathway through a positive feedback loop with USP16/IGF2BP3 axis in gallbladder cancer.
    Title: LncRNA MNX1-AS1 sustains inactivation of Hippo pathway through a positive feedback loop with USP16/IGF2BP3 axis in gallbladder cancer.
  2. USP16 regulates castration-resistant prostate cancer cell proliferation by deubiquitinating and stablizing c-Myc.
    Title: USP16 regulates castration-resistant prostate cancer cell proliferation by deubiquitinating and stablizing c-Myc.
  3. USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit.
    Title: USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit.
  4. USP16 Regulates the Stability and Function of LDL receptor by Deubiquitination.
    Title: USP16 Regulates the Stability and Function of LDL receptor by Deubiquitination.
  5. USP16 gene expression is tightly regulated at transcription level.
    Title: Transcriptional activation of USP16 gene expression by NFκB signaling.
  6. data reveal the physiological function of CNA ubiquitination and its deubiquitinase USP16 in peripheral T cells.
    Title: USP16-mediated deubiquitination of calcineurin A controls peripheral T cell maintenance.
  7. USP16 was frequently downregulated.
    Title: USP16 Downregulation by Carboxyl-terminal Truncated HBx Promotes the Growth of Hepatocellular Carcinoma Cells.
  8. USP16 and TTC3 were dysregulated in all affected human cells and two mouse models of Down syndrome.
    Title: An Integrated Human/Murine Transcriptome and Pathway Approach To Identify Prenatal Treatments For Down Syndrome.
  9. The data unveil a unique mechanism by which Usp16 promotes the localization and maintenance of Plk1 on the kinetochores for proper chromosome alignment.
    Title: Usp16 regulates kinetochore localization of Plk1 to promote proper chromosome alignment in mitosis.
  10. Data show that histone H2A deubiquitinase USP16 interacts with E3 ubiquitin-protein ligase HERC2, negatively regulates DNA damage-induced ubiquitin foci formation, and is required for termination of the ubiquitin signal.
    Title: The histone H2A deubiquitinase USP16 interacts with HERC2 and fine-tunes cellular response to DNA damage.
Submit: New GeneRIF Correction See all GeneRIFs (15)

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 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 histone H2A deubiquitinase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H2A deubiquitinase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ribosomal small subunit binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription coactivator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in mitotic nuclear division IEA
Inferred from Electronic Annotation
more info
  
involved_in monoubiquitinated protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of ribosome biogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of translational elongation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein homotetramerization IPI
Inferred from Physical Interaction
more info
 PubMed 
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ubiquitin carboxyl-terminal hydrolase 16
Names
deubiquitinating enzyme 16
ubiquitin specific protease 16
ubiquitin thioesterase 16
ubiquitin thiolesterase 16
ubiquitin-processing protease UBP-M
ubiquitin-specific processing protease 16
NP_001001992.1
NP_001027582.1
NP_006438.1
XP_016883746.1
XP_016883747.1
XP_016883748.1
XP_054180287.1
XP_054180288.1
XP_054180289.1
XP_054189276.1
XP_054189277.1
XP_054189278.1

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_001001992.2 → NP_001001992.1  ubiquitin carboxyl-terminal hydrolase 16 isoform b

    See identical proteins and their annotated locations for NP_001001992.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AF113219, AF126736, CB960929
    Consensus CDS
    CCDS42912.1
    UniProtKB/Swiss-Prot
    Q9Y5T5
    Related
    ENSP00000382857.3, ENST00000399975.7
    Conserved Domains (2) summary
    cd02667
    Location:622 → 819
    Peptidase_C19K; 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 ...
    pfam02148
    Location:48 → 123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

  2. NM_001032410.2 → NP_001027582.1  ubiquitin carboxyl-terminal hydrolase 16 isoform a

    See identical proteins and their annotated locations for NP_001027582.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes an additional exon in the 5'UTR compared to variant 1. Variants 1 and 3 encode the same isoform (a).
    Source sequence(s)
    AF129075, AK025104, BQ637016
    Consensus CDS
    CCDS13583.1
    UniProtKB/Swiss-Prot
    A8MU43, B3KN13, B4DFV8, B4DY37, D3DSD9, Q53GP7, Q53HA0, Q5VKN8, Q8NEL3, Q9H3E6, Q9Y5T5
    Related
    ENSP00000334808.4, ENST00000334352.8
    Conserved Domains (2) summary
    cd02667
    Location:623 → 820
    Peptidase_C19K; 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 ...
    pfam02148
    Location:48 → 123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

  3. NM_006447.3 → NP_006438.1  ubiquitin carboxyl-terminal hydrolase 16 isoform a

    See identical proteins and their annotated locations for NP_006438.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF113219, AF126736, AK025104
    Consensus CDS
    CCDS13583.1
    UniProtKB/Swiss-Prot
    A8MU43, B3KN13, B4DFV8, B4DY37, D3DSD9, Q53GP7, Q53HA0, Q5VKN8, Q8NEL3, Q9H3E6, Q9Y5T5
    Related
    ENSP00000382858.2, ENST00000399976.7
    Conserved Domains (2) summary
    cd02667
    Location:623 → 820
    Peptidase_C19K; 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 ...
    pfam02148
    Location:48 → 123
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    29024668..29054488
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028258.2 → XP_016883747.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X2

    UniProtKB/Swiss-Prot
    Q9Y5T5
    Conserved Domains (2) summary
    cd02667
    Location:622 → 819
    Peptidase_C19K; 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 ...
    pfam02148
    Location:48 → 123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

  2. XM_017028257.2 → XP_016883746.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X1

    UniProtKB/Swiss-Prot
    A8MU43, B3KN13, B4DFV8, B4DY37, D3DSD9, Q53GP7, Q53HA0, Q5VKN8, Q8NEL3, Q9H3E6, Q9Y5T5
    Conserved Domains (2) summary
    cd02667
    Location:623 → 820
    Peptidase_C19K; 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 ...
    pfam02148
    Location:48 → 123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

  3. XM_017028259.2 → XP_016883748.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X2

    UniProtKB/Swiss-Prot
    Q9Y5T5
    Conserved Domains (2) summary
    cd02667
    Location:622 → 819
    Peptidase_C19K; 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 ...
    pfam02148
    Location:48 → 123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791813.1 Reference GRCh38.p14 PATCHES

    Range
    115402..145222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333302.1 → XP_054189277.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X2

  2. XM_054333301.1 → XP_054189276.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X1

    UniProtKB/Swiss-Prot
    A8MU43, B3KN13, B4DFV8, B4DY37, D3DSD9, Q53GP7, Q53HA0, Q5VKN8, Q8NEL3, Q9H3E6, Q9Y5T5

  3. XM_054333303.1 → XP_054189278.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    27388120..27417933
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324313.1 → XP_054180288.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X2

  2. XM_054324312.1 → XP_054180287.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X1

    UniProtKB/Swiss-Prot
    A8MU43, B3KN13, B4DFV8, B4DY37, D3DSD9, Q53GP7, Q53HA0, Q5VKN8, Q8NEL3, Q9H3E6, Q9Y5T5

  3. XM_054324314.1 → XP_054180289.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y5T5.1 GenPept UniProtKB/Swiss-Prot:Q9Y5T5

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