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

Gene ID: 10600, updated on 5-Sep-2021

Summary

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
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

See USP16 in Genome Data Viewer
Location:
21q21.3
Exon count:
20
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (29024651..29054488)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (30396989..30426809)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ribosomal protein L23 pseudogene 2 Neighboring gene RWD domain containing 2B Neighboring gene chaperonin containing TCP1 subunit 8 Neighboring gene MAP3K7 C-terminal like Neighboring gene Sharpr-MPRA regulatory region 4059

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cysteine-type endopeptidase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables thiol-dependent deubiquitinase IDA
Inferred from Direct Assay
more info
PubMed 
enables thiol-dependent deubiquitinase TAS
Traceable Author Statement
more info
 
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 cell division IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to DNA damage stimulus IDA
Inferred from Direct Assay
more info
PubMed 
involved_in histone H2A K63-linked deubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in histone deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mitotic cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mitotic nuclear division IEA
Inferred from Electronic Annotation
more info
 
involved_in monoubiquitinated histone H2A deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 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
 
involved_in ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cytoplasm TAS
Traceable Author Statement
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

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_016883749.1
XP_016883750.1
XP_024307813.1

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_001001992.2NP_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:622819
    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:48123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  2. NM_001032410.2NP_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
    Q9Y5T5
    Related
    ENSP00000334808.4, ENST00000334352.8
    Conserved Domains (2) summary
    cd02667
    Location:623820
    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:48123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  3. NM_006447.3NP_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
    Q9Y5T5
    Related
    ENSP00000382858.2, ENST00000399976.7
    Conserved Domains (2) summary
    cd02667
    Location:623820
    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:48123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    29024651..29054488
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    Q9Y5T5
    Conserved Domains (2) summary
    cd02667
    Location:622819
    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:48123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  2. XM_017028261.2XP_016883750.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X3

    UniProtKB/Swiss-Prot
    Q9Y5T5
    Conserved Domains (2) summary
    cd02667
    Location:313510
    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 ...
    cl02553
    Location:4092
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
  3. XM_017028260.2XP_016883749.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X3

    UniProtKB/Swiss-Prot
    Q9Y5T5
    Conserved Domains (2) summary
    cd02667
    Location:313510
    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 ...
    cl02553
    Location:4092
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
  4. XM_024452045.1XP_024307813.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X3

    Conserved Domains (2) summary
    cd02667
    Location:313510
    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 ...
    cl02553
    Location:4092
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
  5. XM_017028257.1XP_016883746.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X1

    UniProtKB/Swiss-Prot
    Q9Y5T5
    Conserved Domains (2) summary
    cd02667
    Location:623820
    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:48123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  6. XM_017028259.1XP_016883748.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X2

    UniProtKB/Swiss-Prot
    Q9Y5T5
    Conserved Domains (2) summary
    cd02667
    Location:622819
    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:48123
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
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