Despite a growing number of splicing mutations found in hereditary diseases, utilization of aberrant splice sites and their effects on gene expression remain challenging to predict. We compiled sequences of 346 aberrant 5'splice sites (5'ss) that were activated by mutations in 166 human disease genes. Mutations within the 5'ss consensus accounted for 254 cryptic 5'ss and mutations elsewhere activated 92 de novo 5'ss. Point mutations leading to cryptic 5'ss activation were most common in the first intron nucleotide, followed by the fifth nucleotide. Substitutions at position +5 were exclusively G>A transitions, which was largely attributable to high mutability rates of C/G>T/A. However, the frequency of point mutations at position +5 was significantly higher than that observed in the Human Gene Mutation Database, suggesting that alterations of this position are particularly prone to aberrant splicing, possibly due to a requirement for sequential interactions with U1 and U6 snRNAs. Cryptic 5'ss were best predicted by computational algorithms that accommodate nucleotide dependencies and not by weight-matrix models. Discrimination of intronic 5'ss from their authentic counterparts was less effective than for exonic sites, as the former were intrinsically stronger than the latter. Computational prediction of exonic de novo 5'ss was poor, suggesting that their activation critically depends on exonic splicing enhancers or silencers. The authentic counterparts of aberrant 5'ss were significantly weaker than the average human 5'ss. The development of an online database of aberrant 5'ss will be useful for studying basic mechanisms of splice-site selection, identifying splicing mutations and optimizing splice-site prediction algorithms.

译文

:尽管在遗传性疾病中发现了越来越多的剪接突变,但异常剪接位点的利用及其对基因表达的影响仍然难以预测。我们编辑了346个异常5'剪接位点(5个)的序列,这些序列被166个人类疾病基因的突变激活。 5位共识中的突变占254个隐性5位,而其他地方的突变则激活了92位从头5位。导致隐伏5激活的点突变最常见于第一个内含子核苷酸,其次是第五个核苷酸。位置5的替换仅是G> A转换,这主要归因于C / G> T / A的高变异率。但是,第5位的点突变频率显着高于人类基因突变数据库中观察到的频率,这表明该位置的改变特别容易出现异常剪接,这可能是由于需要与U1和U6 snRNA进行顺序相互作用所致。隐秘5最好通过适应核苷酸依赖性的计算算法进行预测,而不是通过权重矩阵模型进行预测。与前者相比,将内含子5与真正的异物区别开来的效果不佳,因为前者在本质上要强于后者。新外显子5's的计算预测很差,表明它们的激活关键取决于外显子剪接增强剂或沉默子。异常5的真实对应物显着弱于普通人类5的。异常5的在线数据库的开发将对研究剪接位点选择的基本机制,鉴定剪接突变和优化剪接位点预测算法非常有用。

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