Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.
Hum Mutat. 2009 Dec;30(12):E1010-20. doi: 10.1002/humu.21128.
Deep sequencing has shown that over 90% of human genes undergo alternative splicing. The splicing process requires exon-intron boundary recognition. SNPs located in the boundaries (splice sites) influence exon configuration. Also, splice site SNPs (ssSNPs) alter translation efficiency of the mRNA and lead to important changes in disease susceptibility. We developed the ssSNPTarget database to provide ssSNPs on human and mouse genes. It includes: 1) ssSNP distribution information in human and mouse genes; 2) effects of SNPs in splice sites: junction strength change, protein domain change, and alternative splicing events (exon skipping, 5'- or 3'-exon extension); 3) splice site conservation in eukaryotes; and 4) associated disease information derived from OMIM, GAD, and HGMD. ssSNPTarget contains 1,576 human ssSNPs associated with 1,193 genes and 538 mouse ssSNPs associated with 281 genes. Users can query ssSNPTarget with several types of search terms (gene symbol, SNP rs number, transcript ID, or genomic position), and the information can be accessed at http://variome.kobic.re.kr/ssSNPTarget/ or http://ssSNPTarget.org.
深度测序表明，超过 90%的人类基因经历可变剪接。剪接过程需要外显子-内含子边界识别。位于边界（剪接位点）的 SNP 影响外显子的构象。此外，剪接位点 SNP（ssSNP）改变 mRNA 的翻译效率，并导致疾病易感性的重要变化。我们开发了 ssSNPTarget 数据库，为人类和小鼠基因提供 ssSNPs。它包括：1）人类和小鼠基因中 ssSNP 的分布信息；2）SNP 在剪接位点的影响：连接强度变化、蛋白质结构域变化和可变剪接事件（外显子跳跃、5' 或 3' 外显子延伸）；3）真核生物剪接位点的保守性；4）来自 OMIM、GAD 和 HGMD 的相关疾病信息。ssSNPTarget 包含 1576 个与 1193 个基因相关的人类 ssSNP 和 538 个与 281 个基因相关的小鼠 ssSNP。用户可以使用几种类型的搜索词（基因符号、SNP rs 编号、转录本 ID 或基因组位置）查询 ssSNPTarget，信息可在 http://variome.kobic.re.kr/ssSNPTarget/ 或 http://ssSNPTarget.org 上访问。
