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Figure 3 | Genome Biology

Figure 3

From: Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts

Figure 3

Presence of premature termination codons in spliceosomal introns, as a function of intron size (3n, 3n + 1, 3n + 2) and insertion frame (frame 0, 1 and 2) within the coding sequence. (a) A PTC is generated for all retained introns inserted in frame 2 and containing GTGAGT or GTAAGT as the 5'ss sequence, whatever their length; 209 introns are concerned, that is, 19.3% of all intron-containing genes. (b) PTCs (TAA) are also detected in the BP of 3n + 2 introns in frame 0, 3n + 1 introns in frame 1 or 3n introns in frame 2 if the S2 distance is indeed 1 bp. (c) The main 3'ss is CAG, but, in about 10.5% of the introns, TAG is also used. This sequence generates a PTC for 3n introns inserted in frame 0, 3n + 2 introns in frame 1 and 3n + 1 introns in frame 2. Overall, conserved intron motifs are present in about 50% of the PTC-containing introns.

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Genome Biology

ISSN: 1474-760X

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