SVA and alternative splicing at the MAST2 locus. (A) The canonical SVA is displayed, consisting of some number of CCCTCT hexameric repeats followed by the Alu-like region, a variable number of tandem repeats, and then the SINE-R region, followed by a polyA signal with the entire SVA flanked by target-site duplications (black arrowheads). Two black arrows over the Alu-like region indicate sequence homology in the SVA to two ancestral Alu elements. (B) Shown is an ancestral CH1 MAST2 locus, sometime after the human–chimp split, containing a full-length SVA within intron 1 (top). An alternative splicing event into the Alu-like region (black line) likely occurred resulting in the original SVAF1 founder insertion (bottom) flanked by target-site duplications (black arrowheads) in the human genome. Note the loss of the entire CCCTCT hexamer and most of the Alu-like region after the alternative splicing event. The SVA splice site relative to SVARep is aligned to the known splice site sequence (middle).
