C. Profiles of average RNAchIP signal as in Fig 2B over ±2kb centered on intragenic LINE, LTR, or SINE repeats annotated in Repeat masker database (n=34,000). All repeats are oriented in the same orientation (sense) relative to the overlapping annotated transcript, unless otherwise specified (antisense, shuffled), and as depicted by an oriented white box overlapping the transcript in 5' to 3' orientation (black line with arrowhead). D. Profiles of average RNAchIP signal, as in (C) centered on the 5 major families of intragenic SINE repeats. 