Usp47 ubiquitin specific peptidase 47 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Usp47provided by RGD
Official Full Name: ubiquitin specific peptidase 47provided by RGD
Primary source: RGD:1310411
See related: Ensembl:ENSRNOG00000026754 AllianceGenome:RGD:1310411
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 WD40-repeat domain binding activity; cysteine-type endopeptidase activity; and thiol-dependent deubiquitinase. Predicted to be involved in several processes, including monoubiquitinated protein deubiquitination; negative regulation of G2/M transition of mitotic cell cycle; and negative regulation of nitrogen compound metabolic process. Predicted to act upstream of or within negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage. Predicted to be located in cytoplasm. Predicted to be part of SCF ubiquitin ligase complex. Predicted to be active in cytosol and nucleus. Orthologous to human USP47 (ubiquitin specific peptidase 47). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 466.1), Heart (RPKM 292.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q33

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (175586758..175669904)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (166152104..166235312)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (176854589..176937763)

Chromosome 1 - NC_086019.1 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?

Ubiquitin-specific protease 47 is associated with vascular calcification in chronic kidney disease by regulating osteogenic transdifferentiation of vascular smooth muscle cells.
Title: Ubiquitin-specific protease 47 is associated with vascular calcification in chronic kidney disease by regulating osteogenic transdifferentiation of vascular smooth muscle cells.
USP47 promotes apoptosis in rat myocardial cells after ischemia/reperfusion injury via NF-kappaB activation.
Title: USP47 promotes apoptosis in rat myocardial cells after ischemia/reperfusion injury via NF-κB activation.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH139146 (e-PCR)
- UniSTS:221232

RH129481 (e-PCR)
- UniSTS:212787

RH135216 (e-PCR)
- UniSTS:218493

RH139740 (e-PCR)
- UniSTS:221824

USP47__5050 (e-PCR)
- UniSTS:463342

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables WD40-repeat domain binding	ISO Inferred from Sequence Orthology more info
enables cysteine-type deubiquitinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cysteine-type deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables deubiquitinase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in base-excision repair	ISO Inferred from Sequence Orthology more info
involved_in cellular response to UV	ISO Inferred from Sequence Orthology more info
acts_upstream_of intrinsic apoptotic signaling pathway in response to DNA damage	ISO Inferred from Sequence Orthology more info
involved_in monoubiquitinated protein deubiquitination	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of G2/M transition of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell growth	ISO Inferred from Sequence Orthology 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 response to xenobiotic stimulus	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of SCF ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: ubiquitin carboxyl-terminal hydrolase 47

Names: ubiquitin specific protease 47

NP_001101012.2

EC 3.1.2.15

EC 3.4.19.12

XP_006230106.1

EC 3.1.2.15

EC 3.4.19.12

XP_006230107.1

EC 3.1.2.15

EC 3.4.19.12

XP_006230108.1

EC 3.1.2.15

EC 3.4.19.12

XP_038934018.1

EC 3.1.2.15

EC 3.4.19.12

XP_038934024.1

EC 3.1.2.15

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_001107542.2 → NP_001101012.2 ubiquitin carboxyl-terminal hydrolase 47

Status: VALIDATED

Source sequence(s)

BC166609, CA512624, CB325126, CF109520, CO571839, CV106232, EV771677

UniProtKB/TrEMBL

A0A8I6AAW7, F1MAA1

Related

ENSRNOP00000058846.1, ENSRNOT00000065712.3

Conserved Domains (2) summary

cd02659
Location:166 → 546

peptidase_C19C; 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:167 → 541

UCH; Ubiquitin carboxyl-terminal hydrolase

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_086019.1 Reference GRCr8

Range

175586758..175669904

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039078096.2 → XP_038934024.1 ubiquitin carboxyl-terminal hydrolase 47 isoform X5

UniProtKB/TrEMBL

A0A8I6AAW7

Conserved Domains (2) summary

cd02659
Location:50 → 450

peptidase_C19C; 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 ...

NF033609
Location:712 → 909

MSCRAMM_ClfA; MSCRAMM family adhesin clumping factor ClfA
XM_006230044.5 → XP_006230106.1 ubiquitin carboxyl-terminal hydrolase 47 isoform X1

UniProtKB/TrEMBL

A0A0G2JUX4, A0A8I6A571

Related

ENSRNOP00000069266.2

Conserved Domains (2) summary

cd02659
Location:186 → 586

peptidase_C19C; 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:187 → 581

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_006230046.5 → XP_006230108.1 ubiquitin carboxyl-terminal hydrolase 47 isoform X3

UniProtKB/TrEMBL

A0A8I6A571

Related

ENSRNOP00000088486.1

Conserved Domains (2) summary

cd02659
Location:186 → 566

peptidase_C19C; 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:187 → 561

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_006230045.4 → XP_006230107.1 ubiquitin carboxyl-terminal hydrolase 47 isoform X2

UniProtKB/TrEMBL

A0A8I6AAW7

Conserved Domains (2) summary

cd02659
Location:166 → 566

peptidase_C19C; 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:167 → 561

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_039078090.2 → XP_038934018.1 ubiquitin carboxyl-terminal hydrolase 47 isoform X4

UniProtKB/TrEMBL

A0A8I6AAW7

Conserved Domains (2) summary

cd02659
Location:98 → 498

peptidase_C19C; 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 ...

NF033609
Location:760 → 957

MSCRAMM_ClfA; MSCRAMM family adhesin clumping factor ClfA