Analysis of canonical and non-canonical splice sites in mammalian genomes.

By M. Burset, I. Seledtsov, Victor V. Solovyev. Nucleic Acids Research, 2000

615 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/253f8decb5bd0429ad7ea1dc48677dfd8308c3fb

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Citations in the corpus

Current methods of gene prediction, their strengths and weaknesses. (2002, background): “Recently, mammalian annotated genes were controlled with EST matching sequences, producing new sets of ESTsupported non-canonical splice sites (125).”
Next-generation transcriptome assembly (2011, background): “Another advantage of de novo assembly is that it does not depend upon known canonical splice sites 60 or the prediction of novel splicing sites, as required by reference-based assemblers.”
GMAP: a genomic mapping and alignment program for mRNA and EST sequence (2005, background): “Existing cDNA–genomic mapping programs that use an oligomer index on a genomic scale begin by pre-loading the index into memory, which means that these programs not only have a long startup time, but also require computers with large amounts of dedicated RAM.”
Detection of splice junctions from paired-end RNA-seq data by SpliceMap (2010, background): “When the full reads are 50 nt in size, candidates of splicing point must meet two criteria: first, the alignment extension cannot be longer than 40 nt and the residual length has to be at least 10 nt; and second, the splicing point must be next to the canonical dinucleotides splicing signal GT and A”
A genomic view of alternative splicing (2002, background): “24% of introns have a GT-AG at their 5′ and 3′ ends, respectively), they can be used to verify candidate splice”
Gene prediction with a hidden Markov model and a new intron submodel (2003, positive): “dss model: We only consider canonical splice sites obeying the GT-AG rule as this rule accounts for about 99% of mammalian splice sites (Burset et al., 2000).”