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. 2013 Jul 1;140(13):2828–2834. doi: 10.1242/dev.098343

Fig. 2.

Fig. 2.

Ribosome profiles outline translated ORFs of coding genes. (A) Representative examples of ribosome-protected fragment (RPF) densities associated with protein-coding genes. Gene structures are depicted as thick bars for the coding sequence (CDS), thin bars for 5′ leaders and 3′ trailers, and dashed lines for introns. Note that the majority of RPFs map within the CDSs and are flanked by the annotated initiation (START, green) and termination codon (STOP, red). The bottom three panels show examples of uORF-containing genes. For these genes, RPF reads map to the CDSs and to short ORFs within the 5′ leaders. (B) RefSeq metagene analysis of relative phasing of ribosome P-sites (see Materials and methods). Relative phasing is defined as the number of RPFs at a given position divided by the mean of the number of RPFs at the four adjacent positions. i.e. relative phasing at position i=RPFs at position i/mean (RPFs at positions i-2, i-1, i+1 and i+2). As in previous studies (Ingolia et al., 2011), triplet phasing of ribosome profiles was observed.