SpliceDB: database of canonical and non-canonical mammalian splice sites
SpliceDB: database of canonical and non-canonical mammalian splice sites
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DOI：
10.1093/nar/29.1.255
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发表时间：
2001-01-01
影响因子：
14.9
通讯作者：
Solovyev, VV
中科院分区：
文献类型：
--
作者：
Burset, M;Seledtsov, IA;Solovyev, VV
已开发了一个已知哺乳动物剪接位点序列的数据库(SpliceDB)。我们从以基因为中心的Infogene数据库的哺乳动物部分提取了43 337个剪接对，包括来自不完整或选择性剪接基因的位点。已知的EST序列支持其中的22815个。在丢弃具有假定错误和剪接连接位置不明确的序列之后，验证的数据集包括22 489个条目。其中98.71%含有典型的GT-AG连接(22199个条目)，0.56%具有非典型的GC-AG剪接位点对。其余的(0.73%)出现在许多小群体中(最大规模为0.05%)。我们特别研究了非典型剪接位点，它占GenBank注释剪接对的3.73%，EST比对使我们只能验证剪接位点的外显子部分。为了检查保守的二核苷酸序列，我们比较了人类非规范剪接位点的序列与高通量基因组测序计划(HTG)的序列，在171对人类非规范和EST支持的剪接对中，156对(91.23%)在人类HTG中有明显的匹配。经序列分析，可将其分类为：79个GC-AG对(其中1个是纠正为GC-AG的错误)，61个错误纠正为GT-AG典型对，6个AT-AC对(其中2个错误纠正为AT-AC)，1例来自不存在的内含子，7例在HTG中发现并保存在GenBank中，最后仅剩下2例支持的非典型剪接对。SpliceDB提供了有关典型和非典型位点的验证剪接位点序列的信息，并提供了支持证据。我们还建立了主要剪接组的权重矩阵，可以纳入到基因预测程序中。SpliceDB可以在桑格中心的计算基因组网络服务器上获得：http：//genomic.sanger.ac.uk/pldb/SpliceDB.html和http://www.softberry.com/spldb/SpliceDB.html.
A database (SpliceDB) of known mammalian splice site sequences has been developed. We extracted 43 337 splice pairs from mammalian divisions of the gene-centered Infogene database, including sites from incomplete or alternatively spliced genes. Known EST sequences supported 22 815 of them. After discarding sequences with putative errors and ambiguous location of splice junctions the verified dataset includes 22 489 entries. Of these, 98.71% contain canonical GT-AG junctions (22 199 entries) and 0.56% have non-canonical GC-AG splice site pairs. The remainder (0.73%) occurs in a lot of small groups (with a maximum size of 0.05%). We especially studied non-canonical splice sites, which comprise 3.73% of GenBank annotated splice pairs, EST alignments allowed us to verify only the exonic part of splice sites. To check the conservative dinucleotides we compared sequences of human non-canonical splice sites with sequences from the high throughput genome sequencing project (HTG), Out of 171 human non-canonical and EST-supported splice pairs, 156 (91.23%) had a clear match in the human HTG. They can be classified after sequence analysis as: 79 GC-AG pairs (of which one was an error that corrected to GC-AG), 61 errors corrected to GT-AG canonical pairs, six AT-AC pairs (of which two were errors corrected to AT-AC), one case was produced from a non-existent intron, seven cases were found in HTG that were deposited to GenBank and finally there were only two other cases left of supported non-canonical splice pairs. The information about verified splice site sequences for canonical and non-canonical sites is presented in SpliceDB with the supporting evidence. We also built weight matrices for the major splice groups, which can be incorporated into gene prediction programs. SpliceDB is available at the computational genomic Web sewer of the Sanger Centre: http:// genomic.sanger.ac.uk/spldb/SpliceDB.html and at http://www.softberry.com/spldb/SpliceDB.html.