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

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089570
Description	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 primary sequence 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. 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 primary sequence 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. (en)
Title	Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools (en)
skos:prefLabel	Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools (en)
skos:notation	RIV/00216224:14740/14:00075261!RIV15-MSM-14740___
http://linked.open...avai/riv/aktivita	P
http://linked.open...avai/riv/aktivity	P(ED1.1.00/02.0068), P(EE2.3.20.0045)
http://linked.open...iv/cisloPeriodika	2
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Grodecká, Lucie Freiberger, Tomáš Dušek, Ladislav
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	15727
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/14:00075261
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	POLYPYRIMIDINE TRACT RECOGNITION; HUMAN-DISEASE GENES; CONFORMATIONAL SELECTION; COMPUTATIONAL TOOLS; SEQUENCE MOTIFS; FACTOR U2AF(35); MSH2 MISSENSE; SITE; ENHANCERS; U2AF(65) (en)
http://linked.open.../riv/klicoveSlovo	SITE COMPUTATIONAL TOOLS CONFORMATIONAL SELECTION ENHANCERS FACTOR U2AF(35) HUMAN-DISEASE GENES MSH2 MISSENSE POLYPYRIMIDINE TRACT RECOGNITION SEQUENCE MOTIFS U2AF(65)
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[4960B180BCFB]
http://linked.open...i/riv/nazevZdroje	PLoS One
http://linked.open...in/vavai/riv/obor	FH
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	7 (xsd:int)
http://linked.open...vavai/riv/projekt	Central european institute of technology Support of Professional Growth and International Integration of Research Teams in the Filed of Molecular Medicine
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	9
http://linked.open...iv/tvurceVysledku	Dušek, Ladislav Freiberger, Tomáš Ravčuková, Barbora Buratti, Emanuele Grodecká, Lucie Baralle, Francisco E. Lockerová, Pavla
http://linked.open...ain/vavai/riv/wos	000331717900122
issn	1932-6203
number of pages	13 (xsd:int)
http://bibframe.org/vocab/doi	10.1371/journal.pone.0089570
http://localhost/t...ganizacniJednotka	14740

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