Cytosine branchpoints and branchpoints lacking a −2 uracil display distinct properties. (A) Sequence motifs for C branchpoints (top) and branchpoints lacking a −2 U (bottom). (B) Conservation signatures for C and no −2 U branchpoints. (C) 3′SS nucleotide content for A and C branchpoints. C branchpoints have 1.43 times more C nucleotides in the −20 to −5 range than A branchpoints. (D) Both C and no −2 U branchpoints are found in shorter introns than expected. (E) Both groups have stronger than expected average 3′SS MaxEntScan scores and weaker than expected average 5′SS MaxEntScan scores (two-sided Wilcoxon rank sum test). (F) Both groups are enriched upstream of cassette exons and depleted in introns downstream from cassette exons (two-sided Fisher exact test).
