Tbio EXOSC3 Exosome complex component RRP40

Protein Summary

Description

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5. This gene encodes a non-catalytic component of the human exosome, a complex with 3'-5' exoribonuclease activity that plays a role in numerous RNA processing and degradation activities. Related pseudogenes of this gene are found on chromosome 19 and 21. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2012]

Uniprot Accession IDs

• Q9NQT5
• A8K0K6
• Q5QP85
• Q9Y3A8

Gene Name

• EXOSC3

Ensembl ID

• ENST00000327304
• ENSP00000323046
• ENSG00000107371
• ENST00000396521
• ENSP00000379775
• ENST00000465229
• ENSP00000418422

Symbol

• RRP40
• p10
• PCH1B
• RRP40
• Rrp40p
• CGI-102
• hRrp-40
• bA3J10.7

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
biological process	0.94
interacting protein	0.87
transcription factor binding site profile	0.81
cellular component	0.76
histone modification site profile	0.75

Protein Classes

PANTHER Classes

Protein / Nucleic Acid Binding / Nuclease / Exoribonuclease / Exosome Complex Component Rrp40

Protein / Nucleic Acid Binding / Rna Binding Protein / Exoribonuclease / Exosome Complex Component Rrp40

Protein / Hydrolase / Esterase / Exosome Complex Component Rrp40

DTO Classes

Protein / Enzyme / Nuclease / Exoribonuclease / Exosome Complex Component Rrp40

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 37.17   (req: < 5)

Gene RIFs: 10   (req: <= 3)

Antibodies: 262   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 37.17   (req: >= 5)

Gene RIFs: 10   (req: > 3)

Antibodies: 262   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 16

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Expression Data (0 Tissues)

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No expression data found

Related Tools

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (222)

Explore Interacting Targets

1 – 10 of 222

• See Interactions on String-DB

C1D

Tbio

Novelty:  0.00997109

p_int:  1

Score:  0.999

Data Source:  BioPlex,STRINGDB

EXOSC1

Tbio

Novelty:  0.01386842

p_int:  0.999999941

p_ni:  5.9e-8

Score:  0.999

Data Source:  BioPlex,STRINGDB

DIS3L

Tbio

Family:  Enzyme

Novelty:  0.12886408

p_int:  0.999999795

p_ni:  2.05e-7

Score:  0.999

Data Source:  BioPlex,STRINGDB

EXOSC7

Tbio

Family:  Enzyme

Novelty:  0.07422851

p_int:  0.999999733

p_ni:  2.67e-7

Score:  0.999

Data Source:  BioPlex,STRINGDB

EXOSC8

Tbio

Family:  Enzyme

Novelty:  0.02013403

p_int:  0.999998193

p_ni:  0.000001807

Score:  0.999

Data Source:  BioPlex,STRINGDB

EXOSC10

Tbio

Novelty:  0.00335571

p_int:  0.99999136

p_ni:  0.00000864

Score:  0.999

Data Source:  BioPlex,STRINGDB

HBS1L

Tbio

Novelty:  0.00125579

p_int:  0.999987314

p_ni:  0.000012686

Score:  0.997

Data Source:  BioPlex,STRINGDB

MPHOSPH6

Tbio

Family:  Enzyme

Novelty:  0.24387167

p_int:  0.999970761

p_ni:  0.00002924

Score:  0.999

Data Source:  BioPlex,STRINGDB

RBM7

Tbio

Novelty:  0.07482689

p_int:  0.999782582

p_ni:  0.000217418

Score:  0.923

Data Source:  BioPlex,STRINGDB

EXOSC5

Tbio

Family:  Enzyme

Novelty:  0.03352493

p_int:  0.999147326

p_ni:  0.000852674

Score:  0.999

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (15)

Reactome (14)

KEGG (1)

ATF4 activates genes in response to endoplasmic reticulum stress (R-HSA-380994)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	ATF4 activates genes in response to endoplasmic reticulum stress	27 targets	R-HSA-380994
Reactome	Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA	17 targets	R-HSA-450385
Reactome	Deadenylation-dependent mRNA decay	53 targets	R-HSA-429914
Reactome	KSRP (KHSRP) binds and destabilizes mRNA	17 targets	R-HSA-450604
Reactome	Major pathway of rRNA processing in the nucleolus and cytosol	183 targets	R-HSA-6791226

Name	Explore in Pharos	Explore in Source
ATF4 activates genes in response to endoplasmic reticulum stress	27 targets	R-HSA-380994
Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA	17 targets	R-HSA-450385
Deadenylation-dependent mRNA decay	53 targets	R-HSA-429914
KSRP (KHSRP) binds and destabilizes mRNA	17 targets	R-HSA-450604
Major pathway of rRNA processing in the nucleolus and cytosol	183 targets	R-HSA-6791226

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (25)

Functions (2)

Components (9)

Processes (14)

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1 – 2 of 2

GO Term	Evidence	Assigned by
RNA binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
3'-5'-exoribonuclease activity	Non-traceable Author Statement (NAS)	UniProtKB

Disease Associations ()

No disease associations found

GWAS Traits (1)

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1 – 1 of 1

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
reticulocyte count	EFO_0007986	2	2	2		47.5

• Explore on Target Illumination GWAS Analytics (TIGA)

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
reticulocyte count	EFO_0007986	2		47.5

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Acetylation
Alternative splicing
Complete proteome
Cytoplasm
Direct protein sequencing
Disease mutation
Exosome
Isopeptide bond
Neurodegeneration

GWAS Trait Find Similar Targets

No Header	No Header
reticulocyte count

MGI Phenotype Find Similar Targets

No Header	No Header
cardiovascular system phenotype
mortality/aging

IDG Resources

No IDG generated resources found

Orthologs (16)

1 – 5 of 16

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	exosome component 3	VGNC:4687	465105
Macaque	exosome component 3		716347
Mouse	exosome component 3	MGI:1913612	66362
Rat	exosome component 3	RGD:1304739	313243
Dog	exosome component 3	VGNC:40524	481616

Species	Name	OMA	EggNOG	Inparanoid
Chimp	exosome component 3
Macaque	exosome component 3
Mouse	exosome component 3
Rat	exosome component 3
Dog	exosome component 3

Publication Statistics

PubMed Score 37.17

PubMed score by year

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PubTator Score 23.71

PubTator score by year

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Related Publications

Text Mined References (38)

GeneRif Annotations (10)

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PMID	Year	Title