USP16 (ubiquitin specific peptidase 16)

Gene

• Entrez ID: 10600
• Gene name: Ubiquitin specific peptidase 16
• Gene symbol: USP16
• Synonyms (NCBI Gene): UBP-M, UBPM
• Chromosome: 21
• Chromosome location: 21q21.3
• 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 muta

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT049954	hsa-miR-30a-5p	CLASH	23622248
MIRT047199	hsa-miR-182-5p	CLASH	23622248
MIRT044492	hsa-miR-320a	CLASH	23622248
MIRT043256	hsa-miR-324-5p	CLASH	23622248
MIRT439338	hsa-miR-106b-5p	HITS-CLIP	22473208
MIRT439337	hsa-miR-20a-5p	HITS-CLIP	22473208
MIRT439338	hsa-miR-106b-5p	HITS-CLIP	22473208
MIRT726174	hsa-miR-17-5p	HITS-CLIP	22473208
MIRT726173	hsa-miR-20b-5p	HITS-CLIP	22473208
MIRT726172	hsa-miR-93-5p	HITS-CLIP	22473208
MIRT726171	hsa-miR-519d-3p	HITS-CLIP	22473208
MIRT439337	hsa-miR-20a-5p	HITS-CLIP	22473208
MIRT2694799	hsa-miR-204	CLIP-seq
MIRT2694800	hsa-miR-211	CLIP-seq
MIRT2694801	hsa-miR-3163	CLIP-seq
MIRT2694802	hsa-miR-331-5p	CLIP-seq
MIRT2694803	hsa-miR-338-5p	CLIP-seq
MIRT2694804	hsa-miR-4446-5p	CLIP-seq
MIRT2694805	hsa-miR-4678	CLIP-seq
MIRT2694806	hsa-miR-4755-5p	CLIP-seq
MIRT2694807	hsa-miR-548aa	CLIP-seq
MIRT2694808	hsa-miR-623	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000278	Process	Mitotic cell cycle	IEA
GO:0003713	Function	Transcription coactivator activity	IDA	17914355
GO:0003713	Function	Transcription coactivator activity	IEA
GO:0004197	Function	Cysteine-type endopeptidase activity	IEA
GO:0004197	Function	Cysteine-type endopeptidase activity	IMP	17914355
GO:0004197	Function	Cysteine-type endopeptidase activity	TAS	9827704
GO:0004843	Function	Cysteine-type deubiquitinase activity	IDA	17914355, 32129764
GO:0004843	Function	Cysteine-type deubiquitinase activity	IEA
GO:0004843	Function	Cysteine-type deubiquitinase activity	TAS	10077596
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005634	Component	Nucleus	IDA	17914355
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	32129764
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	TAS	10077596
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	ISS
GO:0006508	Process	Proteolysis	IEA
GO:0006974	Process	DNA damage response	IDA	20550933
GO:0008233	Function	Peptidase activity	IEA
GO:0008234	Function	Cysteine-type peptidase activity	IEA
GO:0008270	Function	Zinc ion binding	IDA	17512543
GO:0008270	Function	Zinc ion binding	IEA
GO:0010468	Process	Regulation of gene expression	IEA
GO:0016579	Process	Protein deubiquitination	IEA
GO:0016579	Process	Protein deubiquitination	TAS
GO:0016787	Function	Hydrolase activity	IEA
GO:0035520	Process	Monoubiquitinated protein deubiquitination	IDA	32129764
GO:0042393	Function	Histone binding	IDA	17914355
GO:0042393	Function	Histone binding	IEA
GO:0043024	Function	Ribosomal small subunit binding	IDA	32129764
GO:0043130	Function	Ubiquitin binding	IDA	17512543
GO:0043130	Function	Ubiquitin binding	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IBA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IMP	17914355
GO:0045901	Process	Positive regulation of translational elongation	IMP	20550933
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0051289	Process	Protein homotetramerization	IEA
GO:0051289	Process	Protein homotetramerization	IPI	17914355
GO:0051301	Process	Cell division	IEA
GO:0051726	Process	Regulation of cell cycle	IEA
GO:0090070	Process	Positive regulation of ribosome biogenesis	IDA	32129764
GO:0140014	Process	Mitotic nuclear division	IEA
GO:0140950	Function	Histone H2A deubiquitinase activity	IEA
GO:0140950	Function	Histone H2A deubiquitinase activity	IMP	20550933
GO:0140950	Function	Histone H2A deubiquitinase activity	ISS

Other IDs

• MIM: 604735
• HGNC: 12614
• e!Ensembl: ENSG00000156256

Protein

• UniProt ID: Q9Y5T5
• Protein name: Ubiquitin carboxyl-terminal hydrolase 16 (EC 3.4.19.12) (Deubiquitinating enzyme 16) (Ubiquitin thioesterase 16) (Ubiquitin-processing protease UBP-M) (Ubiquitin-specific-processing protease 16)
• Protein function: Specifically deubiquitinates 'Lys-120' of histone H2A (H2AK119Ub), a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator (PubMed:17914355). Deubiquitination of histone H2A is a prerequisite for subsequent phos
• PDB: 2I50, 8WG5
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02148	zf-UBP	48 → 128	Zn-finger in ubiquitin-hydrolases and other protein	Domain
  PF00443	UCH	196 → 819	Ubiquitin carboxyl-terminal hydrolase	Family

• Tissue specificity: 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. {ECO:0000269|PubMed:10077596}.
• Sequence:

  MGKKRTKGKTVPIDDSSETLEPVCRHIRKGLEQGNLKKALVNVEWNICQDCKTDNKVKDK
  AEEETEEKPSVWLCLKCGHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCD
  NEVQYCSSNQLGQVVDYVRKQASITTPKPAEKDNGNIELENKKLEKESKNEQEREKKENM
  AKENPPMNSPCQITVKGLSNLGNTCFFNAVMQNLSQTPVLRELLKEVKMSGTIVKIEPPD
  LALTEPLEINLEPPGPLTLAMSQFLNEMQETKKGVVTPKELFSQVCKKAVRFKGYQQQDS
  QELLRYLLDGMRAEEHQRVSKGILKAFGNSTEKLDEELKNKVKDYEKKKSMPSFVDRIFG
  GELTSMIMCDQCRTVSLVHESFLDLSLPVLDDQSGKKSVNDKNLKKTVEDEDQDSEEEKD
  NDSYIKERSDIPSGTSKHLQKKAKKQAKKQAKNQRRQQKIQGKVLHLNDICTIDHPEDSE
  YEAEMSLQGEVNIKSNHISQEGVMHKEYCVNQKDLNGQAKMIESVTDNQKSTEEVDMKNI
  NMDNDLEVLTSSPTRNLNGAYLTEGSNGEVDISNGFKNLNLNAALHPDEINIEILNDSHT
  PGTKVYEVVNEDPETAFCTLANREVFNTDECSIQHCLYQFTRNEKLRDANKLLCEVCTRR
  QCNGPKANIKGERKHVYTNAKKQMLISLAPPVLTLHLKRFQQAGFNLRKVNKHIKFPEIL
  DLAPFCTLKCKNVAEENTRVLYSLYGVVEHSGTMRSGHYTAYAKARTANSHLSNLVLHGD
  IPQDFEMESKGQWFHISDTHVQAVPTTKVLNSQAYLLFYERIL

• Sequence length: 823

Pathways

KEGG:

Polycomb repressive complex

Reactome:

Ub-specific processing proteases

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
OSTEOARTHRITIS, HIP	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, KNEE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations