Fig. 3

AluS insertion polymorphism candidates. a Empty (pre-insertion) allele prior to AluS element insertion with the target site (TS) sequence noted. b Filled allele after a classical TPRT insertion. The ~300 bp long Alu element consists of two monomers separated by an A-rich region, and also contains a 3′ poly-A tail (An). The TS sequence is duplicated (TSD) and flanks the Alu insertion. c Of the 11 initial AluS insertion polymorphism candidates, ten were PCR validated to be polymorphic in the population. Of these, seven (70%) are full-length elements with 3′ poly-A tails, flanked by TSDs, and are thus classical TPRT insertion candidates. One AluS insertion polymorphism candidate (10%) is full-length and flanked by TSDs, but lacks a 3′ poly-A tail, and thus likely arose by a mechanism involving internal priming (IP). Two AluS insertion polymorphism candidates (20%) are both 5′ and 3′ truncated, lack flanking TSDs, and include non-Alu sequence (shown in purple), thus exhibiting features of non-classical Alu insertions (NCAI). d Characteristics of AluS insertion polymorphism candidates