Usp28 ubiquitin specific peptidase 28 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Usp28provided by RGD
Official Full Name: ubiquitin specific peptidase 28provided by RGD
Primary source: RGD:1311555
See related: Ensembl:ENSRNOG00000007325 AllianceGenome:RGD:1311555
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable cysteine-type endopeptidase activity and thiol-dependent deubiquitinase. Predicted to be involved in several processes, including intracellular signal transduction; protein deubiquitination; and response to ionizing radiation. Predicted to be located in nuclear body. Predicted to be part of protein-containing complex. Predicted to be active in cytosol and nucleus. Orthologous to human USP28 (ubiquitin specific peptidase 28). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Heart (RPKM 245.7), Muscle (RPKM 159.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q23

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (58222258..58282711)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (49325766..49386229)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (53295188..53355572)

Chromosome 8 - NC_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

miR-92b-3p reverse the proliferaton of pulmonary artery smooth muscle cells under hypoxia condition. miR-92b-3p regulate the protein level of USP28.
Title: Reverse the down regulation of miR-92b-3p by hypoxia can suppress the proliferation of pulmonary artery smooth muscle cells by targeting USP28.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables cysteine-type deubiquitinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cysteine-type deubiquitinase activity	IEA Inferred from Electronic Annotation more info
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 deubiquitinase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage checkpoint signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in DNA damage checkpoint signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to UV	ISO Inferred from Sequence Orthology more info
involved_in intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	ISO Inferred from Sequence Orthology more info
involved_in intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein deubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in regulation of protein stability	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of protein stability	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein stability	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to ionizing radiation	ISO Inferred from Sequence Orthology more info
involved_in response to ionizing radiation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: ubiquitin carboxyl-terminal hydrolase 28

Names: deubiquitinating enzyme 28; ubiquitin specific protease 28; ubiquitin thioesterase 28; ubiquitin thiolesterase 28; ubiquitin-specific-processing protease 28

NP_001101614.1

EC 3.4.19.12

XP_006243068.1

EC 3.4.19.12

XP_006243069.1

EC 3.4.19.12

XP_006243070.1

EC 3.4.19.12

XP_006243071.1

EC 3.4.19.12

XP_006243072.1

EC 3.4.19.12

XP_006243073.1

EC 3.4.19.12

XP_006243074.1

EC 3.4.19.12

XP_038937372.1

EC 3.4.19.12

XP_038937373.1

EC 3.4.19.12

XP_063121511.1

EC 3.4.19.12

XP_063121512.1

EC 3.4.19.12

XP_063121513.1

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_001108144.1 → NP_001101614.1 ubiquitin carboxyl-terminal hydrolase 28

See identical proteins and their annotated locations for NP_001101614.1

Status: PROVISIONAL

Source sequence(s)

CH473975

UniProtKB/TrEMBL

A0A0H2UI12, A0A8I6AFT3

Conserved Domains (2) summary

cd02665
Location:163 → 650

Peptidase_C19I; 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 ...

cd14355
Location:23 → 64

UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins

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_086026.1 Reference GRCr8

Range

58222258..58282711

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006243011.5 → XP_006243073.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X6

UniProtKB/TrEMBL

A0A8I6AFT3

Related

ENSRNOP00000091262.1

Conserved Domains (4) summary

cd02665
Location:163 → 654

Peptidase_C19I; 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 ...

cd14355
Location:23 → 64

UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins

cl02553
Location:163 → 271

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 ...

pfam00443
Location:161 → 399

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_006243006.5 → XP_006243068.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X1

UniProtKB/TrEMBL

A0A140TAA0, A0A8I5ZWX4

Related

ENSRNOP00000083392.1

Conserved Domains (4) summary

cd02665
Location:163 → 654

Peptidase_C19I; 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 ...

cd14355
Location:23 → 64

UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins

cl02553
Location:163 → 271

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 ...

pfam00443
Location:161 → 399

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_006243008.5 → XP_006243070.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X3

See identical proteins and their annotated locations for XP_006243070.1

UniProtKB/Swiss-Prot

D2Y8W6, D3ZJ96

UniProtKB/TrEMBL

A0A8I6AFT3

Related

ENSRNOP00000060005.4

Conserved Domains (4) summary

cd02665
Location:163 → 654

Peptidase_C19I; 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 ...

cd14355
Location:23 → 64

UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins

cl02553
Location:163 → 271

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 ...

pfam00443
Location:161 → 399

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_006243009.5 → XP_006243071.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X4

UniProtKB/TrEMBL

A0A140TAA0

Conserved Domains (4) summary

cd02665
Location:163 → 594

Peptidase_C19I; 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 ...

cd14355
Location:23 → 64

UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins

cl02553
Location:163 → 271

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 ...

pfam00443
Location:161 → 593

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_063265441.1 → XP_063121511.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X8

UniProtKB/TrEMBL

A0A8I6A8Q3, A0A8I6AFT3
XM_006243007.5 → XP_006243069.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X2

UniProtKB/TrEMBL

A0A140TAA0

Conserved Domains (4) summary

cd02665
Location:163 → 653

Peptidase_C19I; 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 ...

cd14355
Location:23 → 64

UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins

cl02553
Location:163 → 271

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 ...

pfam00443
Location:161 → 398

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_006243010.5 → XP_006243072.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X5

UniProtKB/TrEMBL

A0A8I6AFT3

Conserved Domains (4) summary

cd02665
Location:163 → 653

Peptidase_C19I; 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 ...

cd14355
Location:23 → 64

UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins

cl02553
Location:163 → 271

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 ...

pfam00443
Location:161 → 398

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_006243012.5 → XP_006243074.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X7

UniProtKB/TrEMBL

A0A8I6AFT3

Conserved Domains (4) summary

cd02665
Location:163 → 653

Peptidase_C19I; 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 ...

cd14355
Location:23 → 64

UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins

cl02553
Location:163 → 271

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 ...

pfam00443
Location:161 → 398

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_063265442.1 → XP_063121512.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X9

UniProtKB/TrEMBL

A0A8I6AFT3
XM_039081444.2 → XP_038937372.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X10

Conserved Domains (3) summary

COG5207
Location:162 → 640

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

cd02665
Location:163 → 654

Peptidase_C19I; 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 ...

cd14355
Location:23 → 64

UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins
XM_039081445.2 → XP_038937373.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X11

Conserved Domains (3) summary

cl02553
Location:184 → 320

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 ...

cd20487
Location:530 → 809

USP28_C; carboxyl-terminal domain of ubiquitin-specific protease 28 (USP28)

pfam00443
Location:23 → 65

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_063265443.1 → XP_063121513.1 ubiquitin carboxyl-terminal hydrolase 28 isoform X12