Usp16 ubiquitin specific peptidase 16 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Usp16provided by RGD
Official Full Name: ubiquitin specific peptidase 16provided by RGD
Primary source: RGD:1307192
See related: EnsemblRapid:ENSRNOG00000001598 AllianceGenome:RGD:1307192
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including peptidase activity; ribosomal small subunit binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including monoubiquitinated protein deubiquitination; positive regulation of macromolecule biosynthetic process; and positive regulation of ribosome biogenesis. Predicted to be located in nucleus. Predicted to be active in cytoplasm. Orthologous to human USP16 (ubiquitin specific peptidase 16). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 152.6), Testes (RPKM 136.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 11q11

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	11	NC_086029.1 (40166651..40196792)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	11	NC_051346.1 (26681359..26711313)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	11	NC_005110.4 (27101213..27130345)

Chromosome 11 - NC_086029.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Markers

RH130565 (e-PCR)
- UniSTS:213849

RH137401 (e-PCR)
- UniSTS:219489

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

AI072090 (e-PCR)
- UniSTS:244846

RH133685 (e-PCR)
- UniSTS:216968

Gene Ontology Provided by RGD

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	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 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 biological_process	ND No biological Data available more info
involved_in cell division	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	ISO Inferred from Sequence Orthology 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 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	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info

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_001093971.1

EC 3.4.19.12

XP_006248077.1

EC 3.4.19.12

XP_063126503.1

EC 3.4.19.12

XP_063126504.1

EC 3.4.19.12

XP_063126505.1

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_001100501.1 → NP_001093971.1 ubiquitin carboxyl-terminal hydrolase 16

Status: VALIDATED

Source sequence(s)

BC087705, BC112386, BI282215, BQ205918, CV112036

UniProtKB/Swiss-Prot

Q2KJ09

Conserved Domains (3) summary

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 ...

pfam00443
Location:633 → 821

UCH; Ubiquitin carboxyl-terminal hydrolase

pfam02148
Location:48 → 122

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086029.1 Reference GRCr8

Range

40166651..40196792

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063270433.1 → XP_063126503.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X1
XM_063270434.1 → XP_063126504.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X2
XM_006248015.4 → XP_006248077.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X3

See identical proteins and their annotated locations for XP_006248077.1

UniProtKB/Swiss-Prot

Q2KJ09

Related

ENSRNOP00000002173.6, ENSRNOT00000002173.8

Conserved Domains (3) summary

cd02667
Location:625 → 823

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 ...

pfam00443
Location:634 → 822

UCH; Ubiquitin carboxyl-terminal hydrolase

pfam02148
Location:48 → 122

zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
XM_063270435.1 → XP_063126505.1 ubiquitin carboxyl-terminal hydrolase 16 isoform X4