Figure 2

Co-occurring motif pairs are found in intronic regions flanking exons. Shuffled intron control: we randomly exchanged the 50-nucleotide intronic region of an exon with that of another exon if the two shared the same GC content. Both upstream and downstream intronic regions underwent this GC-balanced intron pairing randomization. This control destroyed the original upstream and downstream intronic region pairings while preserving the sequences inside the 50-nucleotide region. Each large numeral is the average of ten shuffles while small numerals show the individual results. Pseudo exons: these are defined as deep intron sequences of 50 to 250 nucleotides bounded by sites resembling 3' and 5' splice site consensuses but with no evidence of ever being spliced. Upstream pseudo sites: we searched the upstream intronic region of constitutive exons and found sequences with better 3' splice site scores than those of the real 3' splice site of the exon, but with no evidence of ever being used. Downstream pseudo sites: analogous to upstream pseudo sites. Alternative exons include cassette exons and those using alternative 3' or 5' splice sites.