Understanding the mechanisms and regulatory consequences of AS will require experimental and computational analyses at many levels. At its core, AS involves the generation of alternative transcripts mediated by interactions between cis-regulatory elements in exons or introns and trans-acting splicing factors. The current study has integrated these three elements, inferring alternative transcripts from EST-genomic alignments, identifying candidate regulatory sequence motifs enriched in alternative exons from different tissues, and analyzing patterns of splicing-factor expression in different tissues. Our results emphasize differences in the frequencies of exon skipping versus alternative splice site usage in different tissues and highlight the liver, brain and testis as having particularly high levels of AS, supporting the idea that tissue-regulated AS plays important roles in the differentiation of these tissues. The high levels of alternative splice site usage in the liver may relate to the unusual patterns of splicing-factor expression observed in the adult liver, suggesting aspects of developmental regulation of AS at the tissue level. Obtaining a more comprehensive picture of AS will require the integration of additional types of data upstream and downstream of these
