Figure 3

Classification of non-exonic regions. A hypothetical gene arrangement is shown. "5' intergenic": between exon1 and exon1 of two separate genes; "3' intergenic": between the last exon of both genes. "5'/3' intergenic": between first exon of one gene and last exon of the other gene; "intronic#": between any two exons of one gene; "other": all other possible combinations. In cases where the gene flanking a segment is known to exhibit alternative splicing, the segment was prefixed with 'alt_', i.e. 'alt_intronic#', 'alt_3'intergenic', etc. Two other categories, BEGIN and END, denote regions at the beginning or ending of the chromosome, in the case of C. elegans, or of the sequencing reads in the case of C. briggsae. There were two exceptions to the procedure. The first was due to the fact that the C. briggsae genome we used was an unassembled collection of 578 individual sequence reads. 112 of these reads had no exon annotations, and were ignored in this study. Of these 112, only two were greater than 10,000 bases long, with an average length of 3679.3 nucleotides. Secondly, there were 16 C. elegans and 35 C. briggsae exon annotations one nucleotide long. By visual inspection, we determined that for C. elegans these exons were in fact longer than one nucleotide, but noncoding: in all cases the single nucleotide is 'A' and when spliced forms a TGA stop codon. They were treated as non-existent for this study, which has very little effect on the procedure except that the last true intron of the gene will be considered its 3' region. For C. briggsae, they appear to be errors in the gene annotations and fall within introns. Thus, they were treated as part of the intron in which they occur.