Fig. 2

Schematic representation of the algorithm to calculate uORF-mORF fusion ratios. For each original uORF-containing transcript sequence, RefSeq RNAs are selected that match an original uORF sequence, irrespective of the reading frame, and the original mORF sequence in the same reading frame as the largest ORF of the RefSeq RNA, using tBLASTx. The shaded regions in the open boxes represent the tBLASTx-matching regions. If the uORF-tBLASTx-matching region is within the largest ORF, the RefSeq RNA is considered a uORF-mORF fusion type. The number of this type of RefSeq RNA is defined as ‘X’. If the uORF-tBLASTx-matching region is not within the largest ORF, the RefSeq RNA is considered a uORF-mORF separate type. The number of this type of RefSeq RNA is defined as ‘Y’. For each of the original uORF-containing transcripts, the uORF-mORF fusion ratio is calculated as X / (X + Y)