Usp39 ubiquitin specific peptidase 39 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Usp39provided by RGD
Official Full Name: ubiquitin specific peptidase 39provided by RGD
Primary source: RGD:1308103
See related: EnsemblRapid:ENSRNOG00000010930 AllianceGenome:RGD:1308103
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 zinc ion binding activity. Predicted to be involved in spliceosomal complex assembly. Predicted to be located in nucleoplasm. Predicted to be part of U4/U6 x U5 tri-snRNP complex. Orthologous to human USP39 (ubiquitin specific peptidase 39). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 95.5), Muscle (RPKM 83.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q32

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (105932140..105964551, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (104373948..104406359, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (100181408..100211425, complement)

Chromosome 4 - NC_086022.1 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: 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?

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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

D6Wsu157e (e-PCR), detects polymorphism
- UniSTS:142650

RH130860 (e-PCR)
- UniSTS:214144

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
NOT enables cysteine-type deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in protein deubiquitination	IEA Inferred from Electronic Annotation more info
involved_in spliceosomal complex assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in spliceosomal complex assembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of U4/U6 x U5 tri-snRNP complex	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
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of spliceosomal complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin carboxyl-terminal hydrolase 39

Names: U4/U6.U5 tri-snRNP-associated protein 2; ubiquitin specific protease 39

NP_001100067.1

EC 3.4.19.12

NP_001385670.1

EC 3.4.19.12

XP_063141848.1

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_001106597.2 → NP_001100067.1 ubiquitin carboxyl-terminal hydrolase 39 isoform 1

See identical proteins and their annotated locations for NP_001100067.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A6IAA2

Conserved Domains (4) summary

cd02669
Location:105 → 549

Peptidase_C19M; 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:223 → 548

UCH; Ubiquitin carboxyl-terminal hydrolase

pfam08648
Location:6 → 88

DUF1777; Protein of unknown function (DUF1777)

pfam12300
Location:3 → 93

DUF3628; Protein of unknown function (DUF3628)
NM_001398741.1 → NP_001385670.1 ubiquitin carboxyl-terminal hydrolase 39 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A0A9K3Y7X0, B2GV41, F7F1N8

Related

ENSRNOP00000015563.5, ENSRNOT00000015562.8

Conserved Domains (1) summary

cd02669
Location:105 → 552

Peptidase_C19M; 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 ...