Sequence and cross-mapping characteristics of the palindrome region. (A) An example of a Ji LTR showing the palindromes (red) and the conserved promoter (blue). Underlined are the fragments that form the long stem indicated by the arrows in Figure 4A. (B) Sequence logo of the 86,055 palindromes. (C) Length of indels identified during LTR pair alignment for Ji and Opie elements. The y-axis is cut off at 4000 so that the scale is appropriate for indels >1 nt. (D,E) Location of cross-mapping siRNAs between Ji and Opie LTRs (D) and all Sirevirus families (E) using Circos (Krzywinski et al. 2009). siRNAs that did not map to two or more elements within each family were removed. Ribbons connect windows (described in Fig. 2) to which each siRNA species mapped; red indicates an increased number of overlapping ribbons. Moving clockwise, the outer circle denotes the 5′ LTR, INT domain, and 3′ LTR. The black asterisk in E indicates the area near the envelope-like gene of Giepum that “cross-talks” with the palindrome region of Ji LTRs.
