Schematic representation of alternative transcripts from multi-intronic genes. Gene models include exons, represented by gray rectangles and introns, symbolized by thin black articulated lines. Vertical bars on each of the three phases (0, +1 and +2) represent an in-frame stop codon. The resulting mRNA variants are depicted as a concatenation of exons and the thick black vertical line represents the first in-frame codon of the transcript. The size of the putative proteins derived from each splicing variant is indicated on the right. All three genes generate at least three different splicing variants. (a) YALI0C23496g mRNAs are subject to intron retention (intron 1) or exon skipping (exon 2). The retention of intron 1 generates a PTC and a putative peptide of 11 amino acids. Exon 2 skipping generates a frameshift in exon 3 and in exon 4, which is slightly shortened (exon 4'), and generates a putative protein of 65 amino acids. (b) YALI0F26873g splicing variants display retained intron 1, alternative 3'ss (intron 2) usage or the skipping of exon 3. Both variants with a retained intron 1 generate a PTC in exon 2 and a putative truncated protein of 259 amino acids. (c) In YALI0F32043g mRNAs, the retention of intron 5 and the use of an alternative 3'ss do not generate a PTC or a frame shift in that intron 5 is a multiple of three (60 nucleotides) nucleotides long and the difference between E4 and E4' is also a multiple of three (15 nucleotides). Both variants generate a putative protein of about the same size as that generated by the fully spliced transcript. Considering the large size of exon 6, it is shown truncated with horizontal dashed lines.