USP16 Gene (Protein Coding)

Ubiquitin Specific Peptidase 16

GC21P029024
GIFtS:
41
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 isofor... See more...

Aliases for USP16 Gene

Aliases for USP16 Gene

  • Ubiquitin Specific Peptidase 16 2 3 5
  • Ubiquitin Carboxyl-Terminal Hydrolase 16 3 4
  • 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 Thiolesterase 16 3
  • EC 3.4.19.12 4
  • EC 3.1.2.15 51
  • UBP-M 3
  • USP16 5
  • Ubp-M 2
  • 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. Diseases associated with USP16 include Chronic Myelomonocytic Leukemia and Down Syndrome. Among its related pathways are Metabolism of proteins and Deubiquitination. Gene Ontology (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 Summary 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 , Rfam classification and piRNA Summary for USP16 Gene

Genomics for USP16 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for USP16 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP16 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP16

Top Transcription factor binding sites by QIAGEN in the USP16 gene promoter:
  • AML1a
  • AP-1
  • c-Fos
  • c-Jun
  • Chx10
  • FOXJ2 (long isoform)
  • GATA-1
  • ISGF-3
  • p53
  • RREB-1

Genomic Locations for USP16 Gene

Genomic Locations for USP16 Gene
chr21:29,024,617-29,054,488
(GRCh38/hg38)
Size:
29,872 bases
Orientation:
Plus strand
chr21:30,396,938-30,426,809
(GRCh37/hg19)
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 Structure • Gene Density

RefSeq DNA sequence for USP16 Gene

Proteins for USP16 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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.
    SequenceCaution:
    • Sequence=AAG39290.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAG51175.1; Type=Erroneous initiation; Evidence={ECO:0000305};
    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).

    Three dimensional structures from OCA and Proteopedia for USP16 Gene

    Alternative splice isoforms for USP16 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP16 Gene

Protein Expression for USP16 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

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

Other Protein References for USP16 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for USP16
  • Santa Cruz Biotechnology (SCBT) Antibodies for USP16

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

Protein Domains for USP16 Gene

InterPro:
Blocks:
  • Ubiquitin thiolesterase, family 2
  • Zn-finger in ubiquitin thiolesterase
ProtoNet:

Suggested Antigen Peptide Sequences for USP16 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57202, highly similar to Ubiquitin carboxyl-terminal hydrolase 16 (EC 3.1.2.15) (B4DUS4_HUMAN)
  • Ubiquitin-specific-processing protease 16 (UBP16_HUMAN)

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

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for USP16 Gene

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=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).; EC=3.4.19.12; Evidence={ECO:0000255|HAMAP-Rule:MF_03062, ECO:0000269|PubMed:17914355};.
GENATLAS Biochemistry:
ubiquitin specific protease 16,deubiquitin enzyme family

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 IEA,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:
  • Usp16 Usp16<tm1b(EUCOMM)Hmgu>

Animal Model Products

  • Taconic Biosciences Mouse Models for USP16

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP16

Clone Products

  • Addgene plasmids for USP16

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

Nucleus.

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
mitochondrion 1

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 IEA,IDA 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

1 BioSystems pathway for USP16 Gene
1 Qiagen pathway for USP16 Gene
  • Ubiquitin-Proteasome Dependent Proteolysis

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 IEA,IDA 17914355
GO:0006325 chromatin organization IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA,ISS --
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
genes like me logo Genes that share ontologies with USP16: view

Drugs & Compounds for USP16 Gene

Products:

  1. Drug

(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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for USP16 Gene

3 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP16

Clone Products

  • Addgene plasmids for USP16

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

Expression for USP16 Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for USP16 Gene
mRNA expression by GTEx for USP16 GenemRNA expression by BioGPS 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, MaxQB, and MOPED for USP16 Gene



Protein tissue co-expression partners for USP16 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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(4.4)
  • Kidney(3.6)
genes like me logo Genes that share expression patterns with USP16: view

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 30 31
  • 99.43 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia USP16 30 31
  • 92.05 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia USP16 30 31
  • 90.59 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Usp16 30
  • 85.61 (n)
Mouse
(Mus musculus)
 Mammalia Usp16 30 17 31
  • 84.94 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 71 (a)
 OneToMany
-- 31
  • 68 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves USP16 30 31
  • 70.2 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia USP16 31
  • 61 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia usp16 30
  • 62.22 (n)
African clawed frog
(Xenopus laevis)
 Amphibia MGC68701 30
Zebrafish
(Danio rerio)
 Actinopterygii usp16 30 31
  • 56.85 (n)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta CG4165 31
  • 23 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea cyk-3 31
  • 14 (a)
 OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes UBP16 33
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 35 (a)
 OneToOne
Species where no ortholog for USP16 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for USP16: view image

Paralogs for USP16 Gene

Paralogs for USP16 Gene

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

  • UBP16_HUMAN
  • B4DUS4_HUMAN
  • H9KVB6_HUMAN
genes like me logo Genes that share paralogs with USP16: view

Variants for USP16 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP16 Gene

SNP ID Clinical significance and condition Chr 21 pos Variation AA Info Type
721047 Benign: not provided 29,039,046(+) T/G SYNONYMOUS_VARIANT
769120 Benign: not provided 29,047,330(+) A/G INTRON_VARIANT
rs2274802 - p.Gln141His

Additional dbSNP identifiers (rs#s) for USP16 Gene

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)

Additional Variant Information for USP16 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for USP16 Gene

MalaCards: The human disease database

(2) MalaCards diseases for USP16 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
chronic myelomonocytic leukemia
  • leukemia, myelomonocytic, chronic
down syndrome
  • trisomy 21
- elite association - COSMIC cancer census association via MalaCards
Search USP16 in MalaCards View complete list of genes associated with diseases

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.

Additional Disease Information for USP16

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with USP16: view

No data available for 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 23
  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 23
  3. Usp16 contributes to somatic stem-cell defects in Down's syndrome. (PMID: 24025767) Adorno M … Clarke MF (Nature 2013) 3 4
  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
  5. Regulation of cell cycle progression and gene expression by H2A deubiquitination. (PMID: 17914355) Joo HY … Wang H (Nature 2007) 3 4

ExternalLinks

View latest publications for USP16 gene in Mastermind

Products for USP16 Gene

  • Addgene plasmids for USP16

Sources for USP16 Gene