An alternative-exon database and its statistical analysis
An alternative-exon database and its statistical analysis
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DOI：
10.1089/104454900750058107
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发表时间：
2000-12-01
影响因子：
3.1
通讯作者：
Zhang, MQ
中科院分区：
文献类型：
--
作者：
Stamm, S;Zhu, J;Zhang, MQ
我们从文献中编制了替代外显子的综合数据库，并对它们进行了统计分析。大多数替代外显子是盒式外显子，并且在两个以上组织中表达。据报道，在所有其表达对特定组织具有特异性的外显子中，大多数在大脑中表达。虽然组成型外显子的长度遵循正态分布，但替代外显子的分布偏向较小的外显子。此外，替代外显子剪接位点更多地偏离共有序列：它们的3'剪接位点的特征是多嘧啶序列中嘌呤含量较高，并且它们的5'剪接位点主要在+4和+5位置偏离共有序列。此外，对于在单个组织中表达的外显子，腺苷更频繁地使用在3'剪接位点的-3位置，除了已知的富含AC和富含嘌呤的外显子序列元件之外，使用吉布斯算法的序列比较鉴定了弱剪接位点包围的外显子和组织特异性外显子中的几个飞蛾，这些数据共同表明弱剪接位点、某些位置的非典型核苷酸使用和功能增强子的组合效应作为对替代外显子调控的重要贡献。
We compiled a comprehensive database of alternative exons from the literature and analyzed them statistically, Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. Whereas the length of constitutive exons follows a normal distribution, the distribution of alternative exons is skewed toward smaller ones. Furthermore, alternative-exon splice sites deviate more from the consensus: their 3' splice sites are characterized by a higher purine content in the polypyrimidine stretch, and their 5' splice sites deviate from the consensus sequence mostly at the +4 and +5 positions. Furthermore, for exons expressed in a single tissue, adenosine is more frequently used at the -3 position of the 3' splice site, In addition to the known AC-rich and purine-rich exonic sequence elements, sequence comparison using a Gibbs algorithm identified several moths in exons surrounded by weak splice sites and in tissue-specific exons, Together, these data indicate a combinatorial effect of weak splice sites, atypical nucleotide usage at certain positions, and functional enhancers as an important contribution to alternative-exon regulation.