Figure 3

Copy-specific amplification and TSD determination. Top: For a Xiao or un-rearranged DA locus, three sets of PCR experiments were performed to amplify the insertion (primers 1+2 & 3+4) and pre-insertion (1+4) junctions with the 12 primates. The 1+4 PCR product from humans' closest relatives was sequenced for TSD finding. Bottom: The images are the PCR products of the three junctions for chr2-71Mb Xiao. A-L represent primates as specified in Fig. 2, and M represents woolly monkey or Lagothrix lagotricha (LLA). The same 100 bp ladders were used as in Fig. 2. The reason that no products were amplified for the left insertion junction for the gibbon and for the right junction for the gorilla (lane F in the left- and D in the right top images) is likely due to variations between the human and the species involved (transposon insertions, sequence mutations, etc.). This is because the other insertion junction and the internal junction (Fig. 2) were amplified, and the pre-insertion junction was not amplified (the bottom image). The small bands in lanes H, I and J of the top right image are likely to be artifacts, because the pre-insertion junction was amplified for H and I. The pre-insertion junction for the siamang (HSY) was the last lane of the bottom image. The preinsertion site PCR product from the pigtail macaque was sequenced ("Cloned Seq") and compared to 500 bp sequences flanking each insertion junction (marked by a vertical pink bar) from the human genome, for TSD identification (CCATCA, underlined).