Figure 6

Predicted uORFs and translation. A) Example of a translated uORF that convincingly lies on the same transcript as the main CDS. A 5 aa uORF outlined in gold and delineated by the start codon (pink line) and a subsequent stop codon (black line) in the reading frame 2 is associated with the main CDS of Tb927.5.1020. It is translated in both stages (RRS = 23.5). We do not see a significant difference in TE of the main CDS between stages (slBF:PCF Δlog2 TE = -0.25). B) Candidate uORFs may not not lie on the same transcript as the CDS of Tb927.11.1850. Predicted uORFs are seen in all three reading frames downstream of the computationally predicted 5′ end of the mRNA defined by a peak in SL reads as described in Methods (black arrow). Two of these uORFs bear ribosome footprints with RRS scores >70 (gold arrows; ORFs are outlined on the map). The blue arrow marks a dip in the mRNA levels, followed by a second trans-splicing site just before the main CDS (red arrow). Thus, it is not convincing that most transcripts bearing the Tb927.11.1850 CDS also bear these putative uORFs. Data are shown for PCF3, although similar profiles were seen with slBF.