Information for the Coordinates of Exons (ICE): a human splice sites database
Information for the Coordinates of Exons (ICE): a human splice sites database
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DOI：
10.1016/j.ygeno.2004.05.007
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发表时间：
2004-10-01
期刊：
影响因子：
4.4
通讯作者：
Bajic, VB
中科院分区：
文献类型：
--
作者：
Chong, A;Zhang, GL;Bajic, VB
我们提出了一个全面的数据库，信息外显子的坐标（ICE），基因组剪接位点（SSs）的10,803个人类基因。ICE包含91846对供体-受体位点，由人类基因组序列上的“全长”人类mrna（包括转录变体）比对支持。ICE代表了迄今为止已知的最大的人类ss集合，并为分子生物学家和生物信息学家提供了重要的资源。用户可以可视化和提取供体-受体对SSs周围的基因组序列，也可以可视化单个基因的初级结构。我们在本文中列出了22个最常见的规范和非规范剪接位点。最具代表性的四种供体-受体配对（GT-AG、GC-AG、AT-AC和GT-GG）占我们数据集的99.16%。此外，我们计算了三种最常见的供体-受体对的SS矩阵模型。该数据库的重点是提供SS和周围序列信息，相关的SS和序列特征，以及与整个转录本结构的关系。它允许有针对性的搜索，并提供基因结构的证据。(C) 2004爱思唯尔公司版权所有。
We present a comprehensive database, Information for the Coordinates of Exons (ICE), of genomic splice sites (SSs) for 10,803 human genes. ICE contains 91,846 pairs of donor-acceptor sites, supported by the alignment of "full-length" human mRNAs (including transcript variants) on human genomic sequences. ICE represents the largest collection of human SSs known to date and provides a significant resource to both molecular biologists and bioinformaticians alike. A user can visualize and extract genomic sequences around SSs of the donor-acceptor pairs and can also visualize the primary structure of individual genes. We list in this article the 22 most frequently found canonical and noncanonical splice sites. The top four most represented donor-acceptor pairs (GT-AG, GC-AG, AT-AC, and GT-GG) accounted for 99.16% of our data set. In addition, we calculated the SS matrix models for the three most common donor-acceptor pairs. The database is focused on providing SSs and surrounding sequence information, associated SS and sequence characteristics, and relation to overall transcript structure. It allows targeted search and presents evidence for the gene structure. (C) 2004 Elsevier Inc. All rights reserved.