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

    Gene ID: 10600, updated on 3-Nov-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
    mouse all
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    Genomic context

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    See USP16 in Genome Data Viewer
    Location:
    21q21.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (29024668..29054488)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (27388120..27417933)
    RS_2024_09 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 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. O-GlcNAcylation stimulates the deubiquitination activity of USP16 and regulates cell cycle progression. Zhao J, et al. J Biol Chem, 2024 Apr. PMID 38462164, Free PMC Article
    2. USP16 Regulates the Stability and Function of LDL receptor by Deubiquitination. Li Y, et al. Int Heart J, 2020. PMID 32999190
    3. Transcriptional activation of USP16 gene expression by NFκB signaling. Yang S, et al. Mol Brain, 2019 Dec 30. PMID 31888715, Free PMC Article
    4. 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
    5. Usp16 contributes to somatic stem-cell defects in Down's syndrome. Adorno M, et al. Nature, 2013 Sep 19. PMID 24025767, Free PMC Article

    See all (77) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. O-GlcNAcylation stimulates the deubiquitination activity of USP16 and regulates cell cycle progression.
      Title: O-GlcNAcylation stimulates the deubiquitination activity of USP16 and regulates cell cycle progression.
    2. 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.
    3. 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.
    4. 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.
    5. USP16 Regulates the Stability and Function of LDL receptor by Deubiquitination.
      Title: USP16 Regulates the Stability and Function of LDL receptor by Deubiquitination.
    6. USP16 gene expression is tightly regulated at transcription level.
      Title: Transcriptional activation of USP16 gene expression by NFκB signaling.
    7. 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.
    8. USP16 was frequently downregulated.
      Title: USP16 Downregulation by Carboxyl-terminal Truncated HBx Promotes the Growth of Hepatocellular Carcinoma Cells.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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 protein binding IPI
    Inferred from Physical Interaction
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 deubiquitination TAS
    Traceable Author Statement
    more info
    		  
    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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    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)

    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_2024_08

    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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