Tbio PARN Poly(A)-specific ribonuclease PARN

Protein Summary

Description

3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization (PubMed:10882133, PubMed:11359775, PubMed:12748283, PubMed:15175153, PubMed:9736620). Also able to recognize and trim poly(A) tails of microRNAs such as MIR21 and H/ACA box snoRNAs (small nucleolar RNAs) leading to microRNAs degradation or snoRNA increased stability (PubMed:25049417, PubMed:22442037). The protein encoded by this gene is a 3'-exoribonuclease, with similarity to the RNase D family of 3'-exonucleases. It prefers poly(A) as the substrate, hence, efficiently degrades poly(A) tails of mRNAs. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs. This protein is also involved in silencing of certain maternal mRNAs during oocyte maturation and early embryonic development, as well as in nonsense-mediated decay (NMD) of mRNAs that contain premature stop codons. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

Uniprot Accession IDs

• O95453
• B2RCB3
• B4DDG8
• B4DSB0
• B4DWR4
• B4E1H6

Gene Name

• PARN

Ensembl ID

• ENST00000341484
• ENSP00000345456
• ENSG00000140694
• ENST00000420015
• ENSP00000410525
• ENST00000437198
• ENSP00000387911
• ENST00000539279
• ENSP00000444381
• ENST00000615183
• ENSP00000478668
• ENSG00000274829
• ENST00000618929
• ENSP00000484279
• ENST00000631868
• ENSP00000488554
• ENST00000634004
• ENSP00000487634

Symbol

• DAN
• DAN
• DKCB6
• PFBMFT4

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
molecular function	0.94
disease perturbation	0.93
virus perturbation	0.92
transcription factor binding site profile	0.85
co-expressed gene	0.76

Protein Classes

PANTHER Classes

Protein / Nucleic Acid Binding / Rna Binding Protein / Mrna Processing Factor / Mrna Polyadenylation Factor / Poly(a)-specific Ribonuclease Parn

DTO Classes

Protein / Nucleic Acid Binding / Rna Binding Protein / Mrna Processing Factor / Mrna Polyadenylation Factor / Poly(a)-specific Ribonuclease Parn

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: 136.06   (req: < 5)

Gene RIFs: 37   (req: <= 3)

Antibodies: 356   (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: 136.06   (req: >= 5)

Gene RIFs: 37   (req: > 3)

Antibodies: 356   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 23

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

Expression Data (0 Tissues)

tutorial

No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

Find Targets by Sequence

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Related Tools (4)

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 (138)

Explore Interacting Targets

1 – 10 of 138

• See Interactions on String-DB

B9D2

Tbio

Novelty:  0.11310836

p_int:  0.999998332

p_ni:  0.000001668

Data Source:  BioPlex

BYSL

Tbio

Novelty:  0.01919968

p_int:  0.999997793

p_ni:  0.000001602

p_wrong:  6.05e-7

Score:  0.642

Data Source:  BioPlex,STRINGDB

LGI2

Tbio

Novelty:  0.09195527

p_int:  0.999997287

p_ni:  0.000002713

Data Source:  BioPlex

RPS16

Tbio

Novelty:  0.00261983

p_int:  0.999987655

p_ni:  0.000012345

Data Source:  BioPlex

TEAD4

Tchem

Family:  TF

Novelty:  0.0114979

p_int:  0.996919166

p_ni:  0.003080758

p_wrong:  7.5e-8

Score:  0.193

Data Source:  BioPlex,STRINGDB

SRSF2

Tbio

Novelty:  0.00207072

p_int:  0.994430252

p_ni:  0.005569727

p_wrong:  2.1e-8

Data Source:  BioPlex

RPS13

Tbio

Novelty:  0.0019983

p_int:  0.982152739

p_ni:  0.017846996

p_wrong:  2.64e-7

Data Source:  BioPlex

TSR1

Tbio

Novelty:  0.01639069

p_int:  0.952161085

p_ni:  0.032138909

p_wrong:  0.015700006

Score:  0.765

Data Source:  BioPlex,STRINGDB

FGF12

Tbio

Novelty:  0.02094849

p_int:  0.938788375

p_ni:  0.060599191

p_wrong:  0.000612434

Data Source:  BioPlex

HIST1H1A

Tbio

Novelty:  0.00123818

p_int:  0.912048126

p_ni:  0.049570495

p_wrong:  0.038381378

Data Source:  BioPlex

Nearest Tclin Targets

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

Pathways (40)

Reactome (9)

KEGG (1)

WikiPathways (30)

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

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5

1 – 5 of 9

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	Deadenylation of mRNA	22 targets	R-HSA-429947
Reactome	Deadenylation-dependent mRNA decay	53 targets	R-HSA-429914
Reactome	KSRP (KHSRP) binds and destabilizes mRNA	17 targets	R-HSA-450604
Reactome	Metabolism of RNA	686 targets	R-HSA-8953854

Name	Explore in Pharos	Explore in Source
ATF4 activates genes in response to endoplasmic reticulum stress	27 targets	R-HSA-380994
Deadenylation of mRNA	22 targets	R-HSA-429947
Deadenylation-dependent mRNA decay	53 targets	R-HSA-429914
KSRP (KHSRP) binds and destabilizes mRNA	17 targets	R-HSA-450604
Metabolism of RNA	686 targets	R-HSA-8953854

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (27)

Functions (9)

Components (4)

Processes (14)

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1 – 9 of 9

GO Term	Evidence	Assigned by
poly(A)-specific ribonuclease activity	Inferred from Direct Assay (IDA)	UniProtKB
protein kinase binding	Inferred from Physical Interaction (IPI)	UniProtKB
cation binding	Inferred from Mutant Phenotype (IMP)	UniProtKB
RNA binding	Inferred from High Throughput Direct Assay (HDA)	UniProtKB
3'-5'-exoribonuclease activity	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
mRNA 3'-UTR binding	Traceable Author Statement (TAS)	ProtInc
nuclease activity	Traceable Author Statement (TAS)	ProtInc
telomerase RNA binding	Inferred by Curator (IC)	BHF-UCL
metal ion binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW

Disease Associations (null)

No disease associations found

GWAS Traits (4)

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5

1 – 4 of 4

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
self reported educational attainment	EFO_0004784	1	1	1		55.2
mathematical ability	EFO_0004875	1	1	1		52
brain aneurysm	EFO_0003870	1	1	0	2.2	38.8
diastolic blood pressure	EFO_0006336	1	1	1		5.2

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 4 of 4

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
self reported educational attainment	EFO_0004784	1		55.2
mathematical ability	EFO_0004875	1		52
brain aneurysm	EFO_0003870	0	2.2	38.8
diastolic blood pressure	EFO_0006336	1		5.2

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Acetylation
Alternative splicing
Complete proteome
Cytoplasm
Disease mutation
Dyskeratosis congenita
Exonuclease
Hydrolase
Magnesium

GWAS Trait Find Similar Targets

No Header	No Header
brain aneurysm
diastolic blood pressure
mathematical ability
self reported educational attainment

IDG Resources

No IDG generated resources found

Orthologs (12)

1 – 5 of 12

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	poly(A)-specific ribonuclease	VGNC:13784	453936
Macaque	poly(A)-specific ribonuclease		712984
Mouse	poly(A)-specific ribonuclease (deadenylation nuclease)	MGI:1921358	74108
Rat	poly(A)-specific ribonuclease	RGD:1565449	360464
Dog	poly(A)-specific ribonuclease	VGNC:53535	479839

Species	Name	OMA	EggNOG	Inparanoid
Chimp	poly(A)-specific ribonuclease
Macaque	poly(A)-specific ribonuclease
Mouse	poly(A)-specific ribonuclease (deadenylation nuclease)
Rat	poly(A)-specific ribonuclease
Dog	poly(A)-specific ribonuclease

Publication Statistics

PubMed Score 136.06

PubMed score by year

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PubTator Score 70.40

PubTator score by year

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Related Publications

Text Mined References (65)

GeneRif Annotations (37)

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PMID	Year	Title