Utilization of triplet periodicity for detecting translated reading frames. (A) A plot of the number of RPFs aligning to particular mRNA positions between the 30th and the 47th nucleotide downstream from the start codon aggregated over 6000 human RefSeq mRNAs. In each codon, subcodon position 2 is shown as a red bar, while subcodon positions 1 and 3 are shown as blue and green bars, respectively. (B) A schematic representation of the generation of a subcodon profile from the corresponding RPF profile. Each subcodon position (blue indicates 1; red, 2; green, 3) is shown on separated plots. (C) The absolute number of RPFs aligning to each subcodon position is shown for the coding region of human Antizyme 1 (OAZ1) mRNA. The location of the programmed ribosomal frameshift site is indicated by a broken black line. (D) The distribution of the number of RPFs aligning to different subcodon positions, upstream of the frameshift site (left) and downstream (right). It can be seen that the subcodon position with the lowest RPF count shifts from the second to the third upon ribosomal frameshifting.
