Figure 3

Alternative splicing of two genomic regions of transposable elements with contribution to T1 transcripts. The genomic regions are as defined in Figure 2A and Table 1. Sequence details are found in Additional file 1. (A) The L1-ERV segment is a composite of LINE1 (L1) (in grey) and ERV (in purple) sequences. The roofs above the TE sequences represent exons resulting from alternative splicing as demarcated by vertical dotted lines in the boxes representing TEs. Slanting dashed lines in black denote splicing events that generate the discerned exons. The dashed-dotted lines in red indicate two consecutive splicing events in this region that have led to the two TE-associated exons in the T1E16-B transcript. (B) The SINE1 (S1)-hAT sequence as defined in the text. There are two tandem copies of S1-hAT on chromosome 2 (in the Rn2_2148 supercontig [GenBank:NW_047626.2], RGSC ver3.4) and a single copy on chromosome 3 (Rn3_2179 supercontig, [GenBank:NW_047657.2]) of the rat genome; the nucleotide positions and the sizes of the respective sequence copies in these chromosomal segments are indicated. At the bottom, splicing events and the resulting exons are depicted using the same symbols as for (A) above. The scheme is not drawn to scale.