title: Analysis of canonical and non-canonical splice sites in mammalian genomes.
abstract: A set of 43 337 splice junction pairs was extracted from mammalian GenBank annotated genes. Expressed sequence tag (EST) sequences support 22 489 of them. Of these, 98.71% contain canonical dinucleotides GT and AG for donor and acceptor sites, respectively; 0.56% hold non-canonical GC-AG splice site pairs; and the remaining 0.73% occurs in a lot of small groups (with a maximum size of 0.05%). Studying these groups we observe that many of them contain splicing dinucleotides shifted from the annotated splice junction by one position. After close examination of such cases we present a new classification consisting of only eight observed types of splice site pairs (out of 256 a priori possible combinations). EST alignments allow us to verify the exonic part of the splice sites, but many non-canonical cases may be due to intron sequencing errors. This idea is given substantial support when we compare the sequences of human genes having non-canonical splice sites deposited in GenBank by high throughput genome sequencing projects (HTG). A high proportion (156 out of 171) of the human non-canonical and EST-supported splice site sequences had a clear match in the human HTG. They can be classified after corrections as: 79 GC-AG pairs (of which one was an error that corrected to GC-AG), 61 errors that were corrected to GT-AG canonical pairs, six AT-AC pairs (of which two were errors that corrected to AT-AC), one case was produced from non-existent intron, seven cases were found in HTG that were deposited to GenBank and finally there were only two cases left of supported non-canonical splice sites. If we assume that approximately the same situation is true for the whole set of annotated mammalian non-canonical splice sites, then the 99.24% of splice site pairs should be GT-AG, 0.69% GC-AG, 0.05% AT-AC and finally only 0.02% could consist of other types of non-canonical splice sites. We analyze several characteristics of EST-verified splice sites and build weight matrices for the major groups, which can be incorporated into gene prediction programs. We also present a set of EST-verified canonical splice sites larger by two orders of magnitude than the current one (22 199 entries versus approximately 600) and finally, a set of 290 EST-supported non-canonical splice sites. Both sets should be significant for future investigations of the splicing mechanism.
authors.affiliation: Informatic Division, The Sanger Centre, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: M
authors.initials: M
authors.lastname: Burset
authors.forename: I A
authors.initials: IA
authors.lastname: Seledtsov
authors.forename: V V
authors.initials: VV
authors.lastname: Solovyev
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D016384:Consensus Sequence / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D019992:Databases as Topic; D005091:Exons / Q000235:genetics; D020224:Expressed Sequence Tags; D016678:Genome; D006801:Humans; D007438:Introns / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics; D015203:Reproducibility of Results; D012984:Software
chemical_list: D022821:RNA Splice Sites