Examples of ambiguity in the identification or testing of splicing regulatory motifs. (1) Top: A functional SELEX selected sequence (Liu et al. 1998) that conferred responsiveness to SRp55. The match to the derived ESEfinder (Cartegni et al. 2003) SRp55 consensus sequence is underlined. The sequence also contains overlapping predicted PESE motifs (bold). Bottom: A functional SELEX selected sequence that conferred responsiveness to SRp40, with the SRp40 ESEfinder motif underlined. The sequence also contains a RESCUE-ESE (Fairbrother et al. 2002) motif (bold). These sequences are taken from those underlying ESEfinder (v.2; http://rulai.cshl.edu/tools/ESE2/) and were provided by Adrian Krainer (Cold Spring Harbor Laboratory). A similar analysis of all the sequences used by ESEfinder is presented in Supplemental Figure S1. (2) Testing of a predicted PESS by its insertion into a test exon (thbs4 exon 13) by Zhang and Chasin (2004). The bold sequence at the bottom was inserted into a BamHI site (arrowhead) in a test exon. Beyond the addition of the PESS, a fashex3 ESS (f-ESS) was disrupted (underlined in top sequence), a PESE was created (underlined in the bottom sequence), and two overlapping RESCUE-ESEs were created (R-ESEs, underlined in the bottom sequence). (3) Testing a predicted exonic splicing regulator (ESR, bold 6-mer at bottom) by substituting it for a 10-mer (bold at top) in a test exon (Goren et al. 2006). Besides the addition of the ESR, a PESE (underlined at top) was disrupted and an additional ESR (underlined at bottom) was created.
