Figure 5

Sequence motifs and stem-loop structures enriched in Tat-bound RNAs. A. Sequence motifs significantly enriched within the set of Tat-bound mRNAs generated by MEME-ChIP. The numbering of the motifs (0 to 3) is ordered by their significance, with the E-values shown to the right. The motifs are represented as logos with the height of the letter representing the probability of the base at that position multiplied by the total information content of the position. Motifs 0 and 2 were determined by MEME-ChIP to be statistically similar and are aligned. Motif 1 was judged by MEME-ChIP to be similar to that of the splicing factor TRA2 (aligned). B. The consensus structure of all sequences that match motifs 0 and 2, determined by LocARNA. The structure of TAR (from [30]) is shown for comparison.