Figure 4

TE-specific motifs are bound and conserved outside of TEs. We mapped 5,546 TE-specific motifs around the nonrepetitive transcriptome. (A) CLIP-Seq alignment coverage indicated that most motifs were bound; 87% of motif instances showed increased coverage at the motif versus the surrounding 200 nucleotides. (B) A motif discovered in PTB CLIP-Seq on antisense L1MB2 exemplified this, with coverage both in and out of L1MC4a. (C) PhyloP conservation scores indicated that many motifs were also conserved. The heatmap plots the median PhyloP score across all intronic motif instances. (D) At finer resolution, mutation rates differed by position within the motif, exemplified here by a PTB antisense L1MC4a motif.