Figure 4

Transcriptome-wide analysis of mRNAs reveals structural features of protein-coding and non-coding transcripts. (a) Meta-gene analysis across the last 50 nucleotides of the 5′ UTR, the first and last 100 nucleotides of the coding region, and the first 50 nucleotides of the 3′ UTR of approximately 9,500 mRNAs. (b) Average reactivity of the 5′ UTR, coding region, and 3′ UTR. (c) Average reactivity on the Kozak sequence (-6/+1 nucleotides around AUG), coding region, and stop codon (+3 nucleotides upstream). (d) Average reactivity for the first, second, and third base of each coding sequence codon, and for the first, second, and third base of the 5′ UTR and 3′ UTR, respectively, in the first and last 99 nucleotides of the coding region, last 48 nucleotides of the 5′ UTR, and first 48 nucleotides of the 3′ UTR. (e) Box-plot of base-normalized average CIRS-seq reactivities for protein-coding and non-coding RNAs, calculated on all transcript positions with sequencing depth >50 × .