Alternative splicing (AS) is an important post-transcriptional process and one of the most significant elements leading to increase protein functional complexity. In this study, we used the cross-species approach to comparatively analyze the conserved and non-conserved AS events in 15631, 13306 and 15549 orthologous gene pairs of human-mouse, human-rat and mouse-rat through a genome-wide analysis of expressed sequence tags. Our data revealed there are strong correlation and similar regulation between human and rodent orthologous AS genes. We detected 133 conserved exon-skipping events among 317 conserved AS events of human-mouse-rat. In comparison, the majority conserved AS events is major form and minority events revealed strongly species-specific. In addition, the majority of conserved AS events tend to occur within protein coding regions rather than within untranslated regions. Our result also implied that the vast majority of AS events are non-conserved with the other species and the majority events were observed in major form. Then we combined rodent-specific exon-skipping genes with GO classification. Overall, these genes are enriched for binding of molecular function, cellular and physiological process of biology process, cell and organelle of cellular component category. However, the regulation of biological process has lower conserved degree. At last, we identified 64 and 555 tissue-specific, 18 and 420 tumor-specific, 11 and 76 tissue-tumor-specific events in conserved and non-conserved exon-skipping events, respectively. The result indicated that non-conserved exon-skipping events have more strong correlation with tissue and tumor specificity.
