Usp48 ubiquitin specific peptidase 48 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Usp48provided by RGD
Full Name: ubiquitin specific peptidase 48provided by RGD
Primary source: RGD:735213
See related: EnsemblRapid:ENSRNOG00000013602 AllianceGenome:RGD:735213
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
Also known as: Usp31; synUSP
Summary: Predicted to enable cysteine-type deubiquitinase activity. Predicted to be involved in regulation of protein stability. Located in postsynaptic membrane. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 85. Orthologous to human USP48 (ubiquitin specific peptidase 48). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 195.1), Spleen (RPKM 146.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (155083520..155151208)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (149800189..149867838)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (155935102..156002722)

Chromosome 5 - NC_086023.1 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?

mRNA for synUSP was localized to dendrites as well as somas of neuronal cells; both mRNA and protein were localized in the post-synaptic compartments, suggesting a regulatory mechanism for the ubiquitin-related system at the post-synaptic sites
Title: A novel ubiquitin-specific protease, synUSP, is localized at the post-synaptic density and post-synaptic lipid raft.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D5Got89 (e-PCR)
- UniSTS:116050

D5Kyo1 (e-PCR)
- UniSTS:518814

RH128097 (e-PCR)
- UniSTS:211405

AW533548 (e-PCR)
- UniSTS:245987

Usp48 (e-PCR), detects polymorphism
- UniSTS:527603

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 endopeptidase activity	IEA Inferred from Electronic Annotation more info
enables deubiquitinase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in protein deubiquitination	IEA Inferred from Electronic Annotation 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

Component	Evidence Code	Pubs
located_in cilium	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ubiquitin carboxyl-terminal hydrolase 48

Names: deubiquitinating enzyme 48; synaptic ubiquitin-specific protease; ubiquitin carboxyl-terminal hydrolase 48-like; ubiquitin specific protease 31; ubiquitin specific protease 48; ubiquitin thioesterase 48; ubiquitin thiolesterase 48; ubiquitin-specific-processing protease 48

NP_942080.2

EC 3.4.19.12

XP_006239296.1

EC 3.4.19.12

XP_006239297.1

EC 3.4.19.12

XP_006239298.1

EC 3.4.19.12

XP_006239299.1

EC 3.4.19.12

XP_038966349.1

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_198785.2 → NP_942080.2 ubiquitin carboxyl-terminal hydrolase 48

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

Q76LT8

Related

ENSRNOP00000030008.6, ENSRNOT00000031855.7

Conserved Domains (3) summary

cd02668
Location:90 → 419

Peptidase_C19L; 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 ...

cd01795
Location:940 → 1035

Ubl_USP48; ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and similar proteins

pfam06337
Location:484 → 554

DUSP; DUSP domain

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_086023.1 Reference GRCr8

Range

155083520..155151208

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006239234.5 → XP_006239296.1 ubiquitin carboxyl-terminal hydrolase 48 isoform X1

UniProtKB/Swiss-Prot

Q76LT8

UniProtKB/TrEMBL

A0A0G2JUQ8

Conserved Domains (4) summary

cd01795
Location:958 → 1064

USP48_C; USP ubiquitin-specific protease

cd02668
Location:118 → 447

Peptidase_C19L; 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:117 → 446

UCH; Ubiquitin carboxyl-terminal hydrolase

pfam06337
Location:512 → 582

DUSP; DUSP domain
XM_006239235.5 → XP_006239297.1 ubiquitin carboxyl-terminal hydrolase 48 isoform X2

UniProtKB/Swiss-Prot

Q76LT8

Conserved Domains (4) summary

cd01795
Location:957 → 1063

USP48_C; USP ubiquitin-specific protease

cd02668
Location:118 → 447

Peptidase_C19L; 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:117 → 446

UCH; Ubiquitin carboxyl-terminal hydrolase

pfam06337
Location:512 → 582

DUSP; DUSP domain
XM_006239236.5 → XP_006239298.1 ubiquitin carboxyl-terminal hydrolase 48 isoform X3

UniProtKB/Swiss-Prot

Q76LT8

Conserved Domains (4) summary

cd01795
Location:957 → 1063

USP48_C; USP ubiquitin-specific protease

cd02668
Location:118 → 446

Peptidase_C19L; 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:117 → 445

UCH; Ubiquitin carboxyl-terminal hydrolase

pfam06337
Location:511 → 581

DUSP; DUSP domain
XM_006239237.5 → XP_006239299.1 ubiquitin carboxyl-terminal hydrolase 48 isoform X4

UniProtKB/Swiss-Prot

Q76LT8

Related

ENSRNOP00000069188.3, ENSRNOT00000077933.3

Conserved Domains (4) summary

cd01795
Location:956 → 1062

USP48_C; USP ubiquitin-specific protease

cd02668
Location:118 → 446

Peptidase_C19L; 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:117 → 445

UCH; Ubiquitin carboxyl-terminal hydrolase

pfam06337
Location:511 → 581

DUSP; DUSP domain
XM_039110421.2 → XP_038966349.1 ubiquitin carboxyl-terminal hydrolase 48 isoform X5

Conserved Domains (1) summary

cd02668
Location:118 → 447

Peptidase_C19L; 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 ...