Figure 3

Alignments of 3' flanks of L1 family members. Two examples of parent-child pairs are shown. The TSDs of the L1-TDs are highlighted in blue, and the TSDs of other family members are highlighted in yellow. If L1s were 5' inversion events, the reverse complement of the 5' segment was used to view the alignment. The intensity of the background sequence shading is a function of the level of sequence conservation among all sequences. Numbers above the L1.3 consensus sequence indicate the sequence position. In calculating the percent identity, indels were counted as mismatches. In the case of family 12 depicted in (a), it appears that a cellular polyadenylation signal was used to generate a de novo poly(A) tail on the readthrough RNA. The polyadenylation signal is highlighted in pink. In the case of family 11 depicted in (b) no such signal is present; thus, this class of events may have arisen by an internal priming mechanism at an A-rich sequence.