Conservation of regulated PTCs and surrounding exons. (a) Mean per-position phastCon scores are shown, centered on the PTC, for upregulated junctions in liver and BMM. To visualize conservation around PTCs in comparison to normal exonic areas, phastCon scores from a random sample (n = 4,000) of BMM and liver-expressed exons were subtracted from either sample. For normal STOPs, phastCon-scores from random RefSeq exons (n = 4,000) were subtracted. Normal STOPs are based on all RefSeq transcript models. Ranges of scores do not extend into introns, and may be shorter than 100 bp for individual PTCs. For PTC+ junctions, a KO/WT fold change of 2 was required. BMM PTC+ positions: 884. Liver PTC+ positions: 3,091. Normal RefSeq STOP positions: 23,231. (b) Distribution of stop codons: for intronic, intergenic and exonic bins, all mm9 trinucleotides in all three reading frames were sampled. RefSeq STOPs represent normal stop codons for all 21,470 RefSeq transcript models (for genes with multiple models, the longest was used). For BMM (n = 497), PTC-inducing junctions were required to have a log2(KO/WT) fold change > 2, and a minimum of 5 reads for both genotypes summed. For liver (n = 670), PTC-inducing junctions were required to have a log2(KO/WT) fold change > 2, and a minimum of 10 reads for both genotypes summed. Fisher's exact test was used to test for significance.