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Aliases for USP16 Gene

Aliases for USP16 Gene

  • Ubiquitin Specific Peptidase 16 2 3 5
  • Ubiquitin-Processing Protease UBP-M 3 4
  • Ubiquitin Specific Protease 16 2 3
  • Deubiquitinating Enzyme 16 3 4
  • Ubiquitin Thioesterase 16 3 4
  • Ubiquitin-Specific Processing Protease 16 3
  • Ubiquitin-Specific-Processing Protease 16 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 16 3
  • Ubiquitin Thiolesterase 16 3
  • EC 3.4.19.12 4
  • EC 3.1.2.15 58
  • UBP-M 3
  • UBPM 3

External Ids for USP16 Gene

Previous GeneCards Identifiers for USP16 Gene

  • GC21P026975
  • GC21P029318
  • GC21P030396
  • GC21P015803

Summaries for USP16 Gene

Entrez Gene Summary for USP16 Gene

  • 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]

GeneCards Summary for USP16 Gene

USP16 (Ubiquitin Specific Peptidase 16) is a Protein Coding gene. Among its related pathways are Deubiquitination and Ubiquitin-Proteasome Dependent Proteolysis. GO annotations related to this gene include transcription coactivator activity and cysteine-type endopeptidase activity. An important paralog of this gene is USP45.

UniProtKB/Swiss-Prot for USP16 Gene

  • Specifically deubiquitinates Lys-120 of histone H2A (H2AK119Ub), a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Deubiquitination of histone H2A is a prerequisite for subsequent phosphorylation at Ser-11 of histone H3 (H3S10ph), and is required for chromosome segregation when cells enter into mitosis. In resting B- and T-lymphocytes, phosphorylation by AURKB leads to enhance its activity, thereby maintaining transcription in resting lymphocytes. Regulates Hox gene expression via histone H2A deubiquitination. Prefers nucleosomal substrates. Does not deubiquitinate histone H2B.

Gene Wiki entry for USP16 Gene

Additional gene information for USP16 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP16 Gene

Genomics for USP16 Gene

Regulatory Elements for USP16 Gene

Enhancers for USP16 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH21H029216 2 FANTOM5 Ensembl ENCODE dbSUPER 60.5 +195.3 195335 7 PKNOX1 FOXA2 FEZF1 ZNF2 ZNF302 FOS DEK SP3 REST ZNF662 LTN1 USP16 ENSG00000231125 RPL23P2 RPL12P9 BACH1 N6AMT1 HSPD1P7 ENSG00000259981 LINC00307
GH21H029298 1.4 ENCODE dbSUPER 42.1 +276.2 276230 5 HDGF ARNT ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF766 FOS SP3 ENSG00000231125 LTN1 RPL23P2 USP16 RPL12P9 GC21P029305 GC21P029306 LOC105369299
GH21H028991 1.2 ENCODE 35.7 -31.8 -31800 2 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 USP16 CCT8 LTN1 RWDD2B RPL23P2 N6AMT1 RPL12P9 ENSG00000231125 ENSG00000273254 MAP3K7CL
GH21H029341 1.3 Ensembl ENCODE dbSUPER 22 +318.3 318297 3 PKNOX1 ZSCAN4 BATF SCRT2 FOS ETV6 RUNX3 CREM IKZF2 CEBPB USP16 LTN1 CCT8 MAP3K7CL BACH1-IT1 GC21P029330 GC21P029329
GH21H029155 1.7 FANTOM5 Ensembl ENCODE dbSUPER 13.6 +131.1 131133 1 HDAC1 ATF1 EGR1 ZNF366 ZSCAN5C ATF7 CREM SP3 ZNF174 ZEB2 BACH1 ENSG00000231125 USP16 RPL23P2 LTN1 RPL12P9 CCT8 MAP3K7CL GC21M029140 ENSG00000201984
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USP16 on UCSC Golden Path with GeneCards custom track

Promoters for USP16 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000141143 283 1801 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766

Genomic Location for USP16 Gene

Chromosome:
21
Start:
29,024,617 bp from pter
End:
29,054,488 bp from pter
Size:
29,872 bases
Orientation:
Plus strand

Genomic View for USP16 Gene

Genes around USP16 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP16 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP16 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP16 Gene

Proteins for USP16 Gene

  • Protein details for USP16 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5T5-UBP16_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 16
    Protein Accession:
    Q9Y5T5
    Secondary Accessions:
    • A8MU43
    • B3KN13
    • B4DFV8
    • B4DY37
    • D3DSD9
    • Q53GP7
    • Q53HA0
    • Q5VKN8
    • Q8NEL3
    • Q9H3E6

    Protein attributes for USP16 Gene

    Size:
    823 amino acids
    Molecular mass:
    93570 Da
    Quaternary structure:
    • Homotetramer.
    Miscellaneous:
    • USP16 may contribute to somatic stem cell defects observed in Down syndrome. USP16 is triplicated in Down syndrome and its overexpression may contribute to proliferation defects in stem cells. Reduction of USP16 levels results in increased proliferation capacity of Down syndrome fibroblasts (PubMed:24025767).
    SequenceCaution:
    • Sequence=AAG39290.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAG51175.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for USP16 Gene

    Alternative splice isoforms for USP16 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP16 Gene

Selected DME Specific Peptides for USP16 Gene

Q9Y5T5:
  • LGQVVDYVRKQA
  • SQEQHALKHY
  • SKHLQKKAKK
  • VYEVVNEDP
  • HLSNLVLHGDIPQD
  • AKKQAKNQRRQQK
  • LVLSLDNWSVWCY
  • DANKLLCEVC
  • ALVNVEW
  • FLDLSLPV
  • PGPLTLAM
  • PSFVDRIFGGELTS
  • QQQDSQELL
  • IELENKKLEKESKNEQE
  • YTNAKKQML
  • PDEINIEI
  • VEHSGTMR
  • WLCLKCG
  • AYLLFYE
  • FSQVCKKA
  • NLGNTCF
  • ESFLDLS
  • KRFQQAGFNLRKVNKHIKFPEILDLAPFCTLKCKNVAEE

Post-translational modifications for USP16 Gene

  • Phosphorylated at the onset of mitosis and dephosphorylated during the metaphase/anaphase transition. Phosphorylation by AURKB enhances the deubiquitinase activity.
  • Ubiquitination at Lys293
  • Modification sites at PhosphoSitePlus

Domains & Families for USP16 Gene

Gene Families for USP16 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q9Y5T5

UniProtKB/Swiss-Prot:

UBP16_HUMAN :
  • The UBP-type zinc finger binds 3 zinc ions that form a pair of cross-braced ring fingers encapsulated within a third zinc finger in the primary structure. It recognizes the C-terminal tail of free ubiquitin.
  • Belongs to the peptidase C19 family. USP16 subfamily.
Domain:
  • The UBP-type zinc finger binds 3 zinc ions that form a pair of cross-braced ring fingers encapsulated within a third zinc finger in the primary structure. It recognizes the C-terminal tail of free ubiquitin.
Family:
  • Belongs to the peptidase C19 family. USP16 subfamily.
genes like me logo Genes that share domains with USP16: view

Function for USP16 Gene

Molecular function for USP16 Gene

GENATLAS Biochemistry:
ubiquitin specific protease 16,deubiquitin enzyme family
UniProtKB/Swiss-Prot CatalyticActivity:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
UniProtKB/Swiss-Prot Function:
Specifically deubiquitinates Lys-120 of histone H2A (H2AK119Ub), a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Deubiquitination of histone H2A is a prerequisite for subsequent phosphorylation at Ser-11 of histone H3 (H3S10ph), and is required for chromosome segregation when cells enter into mitosis. In resting B- and T-lymphocytes, phosphorylation by AURKB leads to enhance its activity, thereby maintaining transcription in resting lymphocytes. Regulates Hox gene expression via histone H2A deubiquitination. Prefers nucleosomal substrates. Does not deubiquitinate histone H2B.

Enzyme Numbers (IUBMB) for USP16 Gene

Phenotypes From GWAS Catalog for USP16 Gene

Gene Ontology (GO) - Molecular Function for USP16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IDA 17914355
GO:0004197 cysteine-type endopeptidase activity IMP 17914355
GO:0004843 thiol-dependent ubiquitin-specific protease activity TAS,IDA 17914355
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
genes like me logo Genes that share ontologies with USP16: view
genes like me logo Genes that share phenotypes with USP16: view

Animal Models for USP16 Gene

MGI Knock Outs for USP16:

Animal Model Products

  • Taconic Biosciences Mouse Models for USP16

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for USP16
  • Applied Biological Materials Clones for USP16
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for USP16 Gene

Localization for USP16 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP16 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USP16 gene
Compartment Confidence
nucleus 5
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for USP16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 17914355
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm TAS 10077596
genes like me logo Genes that share ontologies with USP16: view

Pathways & Interactions for USP16 Gene

genes like me logo Genes that share pathways with USP16: view

Pathways by source for USP16 Gene

SIGNOR curated interactions for USP16 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for USP16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle IDA 17914355
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter IEA,ISS --
GO:0006508 proteolysis IEA --
genes like me logo Genes that share ontologies with USP16: view

Drugs & Compounds for USP16 Gene

(1) Drugs for USP16 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
genes like me logo Genes that share compounds with USP16: view

Transcripts for USP16 Gene

Unigene Clusters for USP16 Gene

Ubiquitin specific peptidase 16:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for USP16
  • Applied Biological Materials Clones for USP16
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for USP16 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20a ·
SP1: - - - -
SP2: - - -
SP3: -
SP4: - -
SP5:
SP6:
SP7:

ExUns: 20b ^ 21
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for USP16 Gene

GeneLoc Exon Structure for
USP16
ECgene alternative splicing isoforms for
USP16

Expression for USP16 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for USP16 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for USP16 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (21.4), Placenta (11.3), Pancreas (8.8), Blymphocyte (6.4), and Testis (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for USP16 Gene



Protein tissue co-expression partners for USP16 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of USP16 Gene:

USP16

SOURCE GeneReport for Unigene cluster for USP16 Gene:

Hs.99819

mRNA Expression by UniProt/SwissProt for USP16 Gene:

Q9Y5T5-UBP16_HUMAN
Tissue specificity: Present in all the tissues examined including fetal brain, lung, liver, kidney, and adult heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas.

Evidence on tissue expression from TISSUES for USP16 Gene

  • Nervous system(4.8)
  • Liver(4.3)
  • Kidney(3.4)
genes like me logo Genes that share expression patterns with USP16: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP16 Gene

Orthologs for USP16 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for USP16 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia USP16 33 34
  • 99.43 (n)
dog
(Canis familiaris)
Mammalia USP16 33 34
  • 92.05 (n)
cow
(Bos Taurus)
Mammalia USP16 33 34
  • 90.59 (n)
rat
(Rattus norvegicus)
Mammalia Usp16 33
  • 85.61 (n)
mouse
(Mus musculus)
Mammalia Usp16 33 16 34
  • 84.94 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 71 (a)
OneToMany
-- 34
  • 68 (a)
OneToMany
chicken
(Gallus gallus)
Aves USP16 33 34
  • 70.2 (n)
lizard
(Anolis carolinensis)
Reptilia USP16 34
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp16 33
  • 62.22 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC68701 33
zebrafish
(Danio rerio)
Actinopterygii usp16 33 34
  • 56.85 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4165 34
  • 23 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cyk-3 34
  • 14 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP16 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
OneToOne
Species where no ortholog for USP16 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for USP16 Gene

ENSEMBL:
Gene Tree for USP16 (if available)
TreeFam:
Gene Tree for USP16 (if available)

Paralogs for USP16 Gene

Paralogs for USP16 Gene

(3) SIMAP similar genes for USP16 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with USP16: view

Variants for USP16 Gene

Sequence variations from dbSNP and Humsavar for USP16 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
rs1000051558 -- 29,048,325(+) TGATT(C/T)GCCCG intron-variant
rs1000059833 -- 29,046,013(+) GAGAT(A/G)GGTTT intron-variant
rs1000154633 -- 29,054,613(+) TTTTT(A/T)TTTTT downstream-variant-500B
rs1000179744 -- 29,049,304(+) AACTT(C/G)TAAAC intron-variant
rs1000208598 -- 29,042,067(+) TGGTG(A/C)ACTAA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for USP16 Gene

Variant ID Type Subtype PubMed ID
esv3893402 CNV gain 25118596

Variation tolerance for USP16 Gene

Residual Variation Intolerance Score: 37.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.75; 83.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USP16 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP16

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP16 Gene

Disorders for USP16 Gene

UniProtKB/Swiss-Prot

UBP16_HUMAN
  • Note=A chromosomal aberration involving USP16 is a cause of Chronic myelomonocytic leukemia. Inversion inv(21) (q21;q22) with RUNX1/AML1.

Relevant External Links for USP16

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP16

No disorders were found for USP16 Gene.

No data available for MalaCards and Genatlas for USP16 Gene

Publications for USP16 Gene

  1. Solution structure of the Ubp-M BUZ domain, a highly specific protein module that recognizes the C-terminal tail of free ubiquitin. (PMID: 17512543) Pai MT … Zhou P (Journal of molecular biology 2007) 3 4 22 60
  2. A mutant deubiquitinating enzyme (Ubp-M) associates with mitotic chromosomes and blocks cell division. (PMID: 10077596) Cai SY … Marchesi VT (Proceedings of the National Academy of Sciences of the United States of America 1999) 3 4 22 60
  3. Usp16 contributes to somatic stem-cell defects in Down's syndrome. (PMID: 24025767) Adorno M … Clarke MF (Nature 2013) 3 4 60
  4. Genome profiling of chronic myelomonocytic leukemia: frequent alterations of RAS and RUNX1 genes. (PMID: 18925961) Gelsi-Boyer V … Chaffanet M (BMC cancer 2008) 3 4 60
  5. Regulation of cell cycle progression and gene expression by H2A deubiquitination. (PMID: 17914355) Joo HY … Wang H (Nature 2007) 3 4 60

Products for USP16 Gene

  • Addgene plasmids for USP16

Sources for USP16 Gene

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