Figure 3

Transcription termination elements overrepresented in Amphimedon queenslandica 3’ UTRs. A) Frequency per 20 bp bin (y-axis) of enriched motifs in mRNA 3’ ends signals 2,000 bp around the transcription termination site (TTS), including the consensus polyadenylation signal (PAS) AWUAAA (orange line). Motif numbers correspond to those in panel B and relate to the motif ranking found by MEME. The most prevalent position of novel motifs 1, 6 and 9 is highlighted in the grey shaded area (−60 to −100 bp relative to TTS). B) Sequence logo, number of occurrences and significance for four AT-rich motifs enriched before the canonical polyadenylation signal (PAS). The significance value is the e-value of the log likelihood ratio of each motif, while the number of sites per class shows the number of 3’ UTRs out of a total of 10,274 strict 3’ UTRs that had a particular motif. C) Cumulative frequency of the PAS consensus sequence (AWUAAA) 500 bp upstream (dashed grey line) or downstream (solid black line) of a set of strict transcription start sites (TSS) on scaffolds longer than 50 kb and not overlapping with other TSSs.