Gene structures and alternative splicing of ten sample genes. Two splice variants (V1 and V2) are shown for each gene. Grey boxes are exons and the carets represent introns. Arrow heads indicate the position of primers used for amplification of the respective alternative splicing variant (V1 or V2); primers used for amplification of both splice variants in one reaction tube are shown in the depiction of V1 (Additional file 1: Table S3). Dashed lines indicate that a primer spans an exon-exon junction; the exact position of the exon-exon boundary within such a primer is given in Additional file 1: Table S3. Genes that undergo exon skipping are clpr2 (A), efg8 (B), hyd2 (C), lsg2 (D), mgmt (E), nrnp1 (F) and selEFf (G). cyn23 (H) has mutually exclusive exons, oee1 (I) shows intron retention and ppi1 (J) uses alternative 5′ splice sites. In the second splice variant (V2) of ppi1, 21 bp at the 5′ side of the intron are retained (black area).