iCLIP cDNA truncations identify RNA cross-link sites of Nova proteins with nucleotide resolution. (a) The occurrence of YCAY motifs around the CLIP cDNA deletions (FDR < 0.001). The black line shows the starting position of YCAY motifs on all cDNAs, whereas the light blue and yellow lines show the starting position on the plus or minus strand of the genome. The dashed line shows the background occurrence of YCAY motifs. (b) The occurrence of YCAY motifs starting closest to the iCLIP cDNA truncations (FDR < 0.05). The red line shows the starting position of YCAY motifs, and the green line shows the starting position of TTTCAY motifs. (c) Similar to (b), but the occurrence of YCAY motifs starting closest to redefined CLIP cDNA deletions, where the position of deletions mapping within TTT motifs is assigned to the middle of TTT. The red line shows the starting position of YCAY motifs, and the green line shows the starting position of TTTCAY motifs. (d) Occurrence of iCLIP cDNA truncations (black), deletions (blue) or truncations of cDNA with deletions (orange) around the re-defined CLIP deletion sites. The number of cDNAs was determined by considering the random barcode. iCLIP cDNA deletion sites were re-defined as described in Materials and methods.