Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F14%3A00075261" target="_blank" >RIV/00216224:14740/14:00075261 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00209775:_____/14:#0000283

Výsledek na webu

<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089570" target="_blank" >http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089570</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1371/journal.pone.0089570" target="_blank" >10.1371/journal.pone.0089570</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools

Popis výsledku v původním jazyce

Mutations in the first nucleotide of exons (E+1) mostly affect pre-mRNA splicing when found in AG-dependent 39 splice sites, whereas AG-independent splice sites are more resistant. The AG-dependency, however, may be difficult to assess just from primarysequence data as it depends on the quality of the polypyrimidine tract. For this reason, in silico prediction tools are commonly used to score 39 splice sites. In this study, we have assessed the ability of sequence features and in silico prediction tools to discriminate between the splicing-affecting and non-affecting E+1 variants. For this purpose, we newly tested 16 substitutions in vitro and derived other variants from literature. Surprisingly, we found that in the presence of the substituting nucleotide, the quality of the polypyrimidine tract alone was not conclusive about its splicing fate. Rather, it was the identity of the substituting nucleotide that markedly influenced it.

Název v anglickém jazyce

Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools

Popis výsledku anglicky

Mutations in the first nucleotide of exons (E+1) mostly affect pre-mRNA splicing when found in AG-dependent 39 splice sites, whereas AG-independent splice sites are more resistant. The AG-dependency, however, may be difficult to assess just from primarysequence data as it depends on the quality of the polypyrimidine tract. For this reason, in silico prediction tools are commonly used to score 39 splice sites. In this study, we have assessed the ability of sequence features and in silico prediction tools to discriminate between the splicing-affecting and non-affecting E+1 variants. For this purpose, we newly tested 16 substitutions in vitro and derived other variants from literature. Surprisingly, we found that in the presence of the substituting nucleotide, the quality of the polypyrimidine tract alone was not conclusive about its splicing fate. Rather, it was the identity of the substituting nucleotide that markedly influenced it.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

FH - Neurologie, neurochirurgie, neurovědy

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2014

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

PLoS One

ISSN

1932-6203

e-ISSN

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Svazek periodika

9

Číslo periodika v rámci svazku

2

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

13

Strana od-do

"nestránkováno"

Kód UT WoS článku

000331717900122

EID výsledku v databázi Scopus

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