Table 1. Assessed X variables and their modes of measurement.
| Variable | Measurement | |
|---|---|---|
| Nucleotides in the mRNA channel | Stop codon (nt +1 to +3) in the A site | UAA, UAG, UGA |
| nt -1 to -15 and nt +4 to +9 | A, C, G, U | |
| Nascent peptide in the ribosome exit tunnel | P-site and E-site amino acids (aa 1–2 from PTC) | A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y |
| Amino acids in the upper tunnel (aa 3–9 from PTC) | Charge: fraction of +, 0,—residues Polarity: fraction of polar, nonpolar residues Aromaticity: fraction of aromatic residues Hydrophobicity: fraction of hydrophilic, neutral, hydrophobic, very hydrophobic residues Tendency to form α-helix (only for aa 20–30): fraction of residues involved in alpha helix formation, predicted by Jpred [47] |
|
| Amino acids at the constriction site (aa 10–12 from PTC) | ||
| Amino acids in the central tunnel (aa 13–19 from PTC) | ||
| Amino acids in the lower tunnel (aa 20–30 from PTC) | ||
| 3’-UTR secondary structure | Tendency for 3’-UTR sequence to form a secondary structure | The lowest minimum free energy (MFE) for a structure in 150 nt scanning window of entire 3’-UTR sequence, predicted by RNALFold function in ViennaRNA package [46] |
| Distance of structure from stop codon | Number of nt from stop codon to the base of the structure | |
| Proximity of PABP to stop codon | Distance of PABP (i.e., poly(A)-tail) to stop codon | 3’-UTR length (nt) |
| Negative controls | Randomly assigned factor (categorical) | A, C, G, U |
| Randomly assigned number (numeric) | 1–100 | |