Usp16 ubiquitin specific peptidase 16 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Usp16provided by MGI
Official Full Name: ubiquitin specific peptidase 16provided by MGI
Primary source: MGI:MGI:1921362
See related: Ensembl:ENSMUSG00000025616 AllianceGenome:MGI:1921362
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: UBPM; 1200004E02Rik; 2810483I07Rik; 6330514E22Rik
Summary: Enables histone H2A deubiquitinase activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be active in cytoplasm. Is expressed in several structures, including alimentary system; early embryo; genitourinary system; nervous system; and sensory organ. Orthologous to human USP16 (ubiquitin specific peptidase 16). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in testis adult (RPKM 10.7), CNS E11.5 (RPKM 8.0) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16 C3.3; 16 49.54 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (87251833..87280403)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (87454985..87483515)

Chromosome 16 - NC_000082.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

FGF18 alleviates hepatic ischemia-reperfusion injury via the USP16-mediated KEAP1/Nrf2 signaling pathway in male mice.
Title: FGF18 alleviates hepatic ischemia-reperfusion injury via the USP16-mediated KEAP1/Nrf2 signaling pathway in male mice.
Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer's model.
Title: Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer's model.
USP16-mediated histone H2A lysine-119 deubiquitination during oocyte maturation is a prerequisite for zygotic genome activation.
Title: USP16-mediated histone H2A lysine-119 deubiquitination during oocyte maturation is a prerequisite for zygotic genome activation.
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.
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.
these studies identified Usp16 as one of the histone H2A deubiquitinases, which coordinates with the H2A ubiquitin ligase PRC1 to regulate hematopoiesis, and revealed cell cycle regulation by Usp16 as key for HSC differentiation.
Title: The histone H2A deubiquitinase Usp16 regulates hematopoiesis and hematopoietic stem cell function.
study identifies Usp16 and H2A deubiquitination as critical regulators of ESC gene expression and differentiation
Title: The histone H2A deubiquitinase Usp16 regulates embryonic stem cell gene expression and lineage commitment.
results suggest that USP16 has an important role in antagonizing the self-renewal and/or senescence pathways in Down's syndrome and could serve as an attractive target to ameliorate some of the associated pathologies
Title: Usp16 contributes to somatic stem-cell defects in Down's syndrome.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (3) 1 citation
Transgenic (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Usp16 (e-PCR), detects polymorphism
- UniSTS:259670

Usp16 (e-PCR), detects polymorphism
- UniSTS:259169

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables cysteine-type deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables cysteine-type deubiquitinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables cysteine-type endopeptidase activity	ISO Inferred from Sequence Orthology more info
enables cysteine-type endopeptidase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H2A deubiquitinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H2A deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables histone H2A deubiquitinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribosomal small subunit binding	ISO Inferred from Sequence Orthology more info
enables ribosomal small subunit binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info
enables ubiquitin binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin binding	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA damage response	ISS Inferred from Sequence or Structural Similarity more info
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	ISO Inferred from Sequence Orthology more info
involved_in monoubiquitinated protein deubiquitination	ISS Inferred from Sequence or Structural Similarity more info
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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of ribosome biogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ribosome biogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of translational elongation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of translational elongation	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein homotetramerization	ISO Inferred from Sequence Orthology more info
involved_in protein homotetramerization	ISS Inferred from Sequence or Structural Similarity more info
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	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

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-specific-processing protease 16

NP_077220.2

EC 3.4.19.12

XP_006523163.1

EC 3.4.19.12

XP_006523164.1

EC 3.4.19.12

XP_006523165.1

EC 3.4.19.12

XP_036016050.1

EC 3.4.19.12

XP_036016051.1

EC 3.4.19.12

XP_036016052.1

EC 3.4.19.12

XP_036016053.1

EC 3.4.19.12

XP_036016054.1

EC 3.4.19.12

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)

NM_024258.2 → NP_077220.2 ubiquitin carboxyl-terminal hydrolase 16

See identical proteins and their annotated locations for NP_077220.2

Status: VALIDATED

Source sequence(s)

AC154631, AK160038, BE853521

Consensus CDS

CCDS28291.1

UniProtKB/Swiss-Prot

G5E860, Q99KM0, Q99LG0

UniProtKB/TrEMBL

D3YVU1

Related

ENSMUSP00000026710.6, ENSMUST00000026710.12

Conserved Domains (3) summary

COG5560
Location:135 → 823

UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

cd02667
Location:624 → 822

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 → 122

zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

87251833..87280403

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006523101.3 → XP_006523164.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X2

UniProtKB/TrEMBL

D3YVU1

Related

ENSMUSP00000114058.2, ENSMUST00000119504.8

Conserved Domains (3) summary

COG5207
Location:3 → 357

UBP14; Uncharacterized Zn-finger protein, UBP-type [General function prediction only]

cd02667
Location:623 → 821

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 → 122

zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
XM_006523102.5 → XP_006523165.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X3

Conserved Domains (2) summary

COG5560
Location:25 → 514

UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

cd02667
Location:315 → 513

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 ...
XM_036160159.1 → XP_036016052.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X4

Conserved Domains (2) summary

cd02667
Location:258 → 456

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:1 → 35

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 ...
XM_036160158.1 → XP_036016051.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X3

Conserved Domains (2) summary

COG5560
Location:25 → 514

UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

cd02667
Location:315 → 513

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 ...
XM_036160160.1 → XP_036016053.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X4

Conserved Domains (2) summary

cd02667
Location:258 → 456

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:1 → 35

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 ...
XM_006523100.3 → XP_006523163.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X1

See identical proteins and their annotated locations for XP_006523163.1

UniProtKB/Swiss-Prot

G5E860, Q99KM0, Q99LG0

UniProtKB/TrEMBL

D3YVU1

Conserved Domains (3) summary

COG5560
Location:135 → 823

UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

cd02667
Location:624 → 822

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 → 122

zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
XM_036160161.1 → XP_036016054.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X4

Conserved Domains (2) summary

cd02667
Location:258 → 456

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:1 → 35

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 ...
XM_036160157.1 → XP_036016050.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X3

Conserved Domains (2) summary

COG5560
Location:25 → 514

UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

cd02667
Location:315 → 513

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 ...