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We found evidence of 18,322 alternative splicing events, and IR was the major splicing pattern detected (67.8 % of total events), while ES was rare (only 1.9%% of total events).
This indicated that the SPD1 was the major splicing pattern for the deletion allele of BrFLC2, while SPD2 and SPD3 were derived from SPD1.
In all three genomes, Class I patterns (linking two distinct exons) represent the major splicing pattern (chicken: 67%, human: 75%, mouse: 72%).
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TTS and TSS were the major splicing patterns detected in our study, which represented 86%% of the total splicing events; while MXE was a rare event which occurred in only 1.2%% of the total events (Fig. 4).
Four of these splice patterns, skipped exon, alternative 5′ and 3′splicing sites, and retained intron were the major splicing patterns found in our study, representing 96.5%% of the total AS events; mutually exclusive exon and complex were rare events and accounted for only 3.5%% of the AS events (Fig. 4).
Among 1637 genes with isoform expression changes, only 17 genes contain two or more isoforms showing opposite expression changes, which suggests that isoform switching is not likely to be a major contributor to splicing pattern changes in cancer progression.
Therefore, we classify ASEs into three major groups according to splicing pattern conservation (see Materials and Methods).
A major contribution to the success of splicing pattern predictions that generalize well comes from the richness of our feature set.
Snail1 also alters the splicing pattern of HNRNPH3, another protein involved in the splicing process [24].
Splicing pattern of GLI1 was the most variable.
The transgenic mice expressing this splicing reporter clearly showed the epithelial tissue-specific splicing pattern throughout their entire bodies.
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