Fig. 2

D6Ertd527e transcript variability. a Variability of exon–intron structure of D6Ertd527e transcripts in oocytes of five different rodent species. Shown are modified UCSC genome browser snapshots depicting distribution of RNA-seq reads, level of expression and exon–intron structures inferred from analysis of spliced individual sequence reads. Position of the MTD LTR insert is indicated by red rectangles. Blue rectangles depict regions containing expanded CAG repeats. Full display of repetitive sequences from Repeatmasker is available in Additional file 1: Fig. S2. Dashed lines indicate normalized expression level in CPMs. Rattus norvegicus analysis revealed a single spliced read from > 120 million mapped reads from four independent libraries. b Distribution of AGC codons in predicted D6Ertd527e transcripts in rodent species carrying the MTD LTR insertion. In case of Cricetulus griseus, we used the most abundant transcript isoform transcribed from a promoter upstream of the MTD insert. In case of Rattus norvegicus, where the locus seems silent, we show a hypothetical transcript spliced between the conserved splice sites (Fig. 1c) to demonstrate that the putative coding sequence starting from the AUG codon in MTD is soon terminated. CPAT score [37] was calculated for predicted coding sequences represented by the thicker part of a transcript scheme. The recommended cut-off for the mouse coding probability for the CPAT release 3.00 was 0.44 [37]