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Statements

Subject Item
n2:RIV%2F00216224%3A14740%2F14%3A00075261%21RIV15-MSM-14740___
rdf:type
skos:Concept n17:Vysledek
rdfs:seeAlso
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089570
dcterms: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.
dcterms: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
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
skos:notation
RIV/00216224:14740/14:00075261!RIV15-MSM-14740___
n4:aktivita
n16:P
n4:aktivity
P(ED1.1.00/02.0068), P(EE2.3.20.0045)
n4:cisloPeriodika
2
n4:dodaniDat
n9:2015
n4:domaciTvurceVysledku
n12:3898636 n12:4504135 n12:1271326
n4:druhVysledku
n15:J
n4:duvernostUdaju
n19:S
n4:entitaPredkladatele
n18:predkladatel
n4:idSjednocenehoVysledku
15727
n4:idVysledku
RIV/00216224:14740/14:00075261
n4:jazykVysledku
n14:eng
n4:klicovaSlova
POLYPYRIMIDINE TRACT RECOGNITION; HUMAN-DISEASE GENES; CONFORMATIONAL SELECTION; COMPUTATIONAL TOOLS; SEQUENCE MOTIFS; FACTOR U2AF(35); MSH2 MISSENSE; SITE; ENHANCERS; U2AF(65)
n4:klicoveSlovo
n5:U2AF%2865%29 n5:COMPUTATIONAL%20TOOLS n5:SITE n5:MSH2%20MISSENSE n5:CONFORMATIONAL%20SELECTION n5:POLYPYRIMIDINE%20TRACT%20RECOGNITION n5:ENHANCERS n5:HUMAN-DISEASE%20GENES n5:SEQUENCE%20MOTIFS n5:FACTOR%20U2AF%2835%29
n4:kodStatuVydavatele
GB - Spojené království Velké Británie a Severního Irska
n4:kontrolniKodProRIV
[4960B180BCFB]
n4:nazevZdroje
PLoS One
n4:obor
n7:FH
n4:pocetDomacichTvurcuVysledku
3
n4:pocetTvurcuVysledku
7
n4:projekt
n6:EE2.3.20.0045 n6:ED1.1.00%2F02.0068
n4:rokUplatneniVysledku
n9:2014
n4:svazekPeriodika
9
n4:tvurceVysledku
Freiberger, Tomáš Dušek, Ladislav Baralle, Francisco E. Ravčuková, Barbora Grodecká, Lucie Lockerová, Pavla Buratti, Emanuele
n4:wos
000331717900122
s:issn
1932-6203
s:numberOfPages
13
n10:doi
10.1371/journal.pone.0089570
n20:organizacniJednotka
14740