SpliceDB: database of canonical and non-canonical mammalian splice sites

Abstract

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 server of the Sanger Centre: http://genomic.sanger.ac. uk/spldb/SpliceDB.html and at http://www.softberry. com/spldb/SpliceDB.html.

Figure 1

Examples of different situations in analysis of annotated splice junctions.

Figure 2

Consensus sequences and weight matrices for major groups of splice site pairs. Frequency matrices have only been calculated for major splice site groups (GT–AG and GC–AG). In the first row we indicated positions with respect to the splice cut point, which is always between –1 and 1. It should be taken into account that negative numbers in donor matrices correspond to exonic regions, but in acceptor matrices positive numbers correspond to exonic regions. In consensus sequences | means cut position (M: A or C, R: A or G, Y: C or T, S: C or G).

Figure 2

Consensus sequences and weight matrices for major groups of splice site pairs. Frequency matrices have only been calculated for major splice site groups (GT–AG and GC–AG). In the first row we indicated positions with respect to the splice cut point, which is always between –1 and 1. It should be taken into account that negative numbers in donor matrices correspond to exonic regions, but in acceptor matrices positive numbers correspond to exonic regions. In consensus sequences | means cut position (M: A or C, R: A or G, Y: C or T, S: C or G).