Figure 4. Control analyses of GRO-seq reads.

(A) Analysis of 36,905 exonic compositions regions (ECRs) obtained from [32]. ECRs were defined as exon-sized region within intronic or intergenic regions with sequence content similar to that of exons, flanked by regions with intronic sequence content. (B) Analysis of 49,276 pseudo-exons obtained from [30]. Pseudo-exons were defined as regions with a length distribution similar to that of exons flanked by relative strong splicing signals. (C) Sequence logos of all aligned GRO-seq reads, aligned by their 5′ end, as in Figure 1. (D) Positional nucleotide charts for GRO-seq reads, as in Figure 1. (E) Alignment of GRO-seq reads in the 200 nt surrounding transcription start and end sites (left and right panels, respectively). (F) Analysis as in Figure 1 following normalization of all read counts by the relative frequency of the nucleotide at the first position of each read.