Table 1.
Frequencies of base paired nucleotides at different codon sites in the human mRNAs and randomized sequences
| Sequences | Codon site 1 | Codon site 2 | Codon site 3 | |||
|---|---|---|---|---|---|---|
| Frequency | P-value | Frequency | P-value | Frequency | P-value | |
| Base paired G | ||||||
| Real mRNAs | 0.242 | 0.157 | 0.228 | |||
| Random CC | 0.239 | 0.097 | 0.151 | 10−8 | 0.202 | 10−38 |
| Random NS | 0.204 | 10−47 | 0.205 | 10−124 | 0.205 | 10−32 |
| Base paired C | ||||||
| Real mRNAs | 0.169 | 0.160 | 0.195 | |||
| Random CC | 0.157 | 10−22 | 0.163 | 0.12 | 0.156 | 10−93 |
| Random NS | 0.169 | 0.42 | 0.168 | 10−8 | 0.169 | 10−66 |
| Base paired U | ||||||
| Real mRNAs | 0.103 | 0.159 | 0.127 | |||
| Random CC | 0.114 | 10−51 | 0.155 | 10−3 | 0.148 | 10−54 |
| Random NS | 0.131 | 10−131 | 0.131 | 10−67 | 0.131 | 10−5 |
| Base paired A | ||||||
| Real mRNAs | 0.108 | 0.133 | 0.080 | |||
| Random CC | 0.100 | 10−19 | 0.129 | 0.0011 | 0.097 | 10−60 |
| Random NS | 0.103 | 10−10 | 0.103 | 10−65 | 0.102 | 10−77 |
| Nucleotides paired with codon site 1 | ||||||
| Real mRNAs | 0.290 | 0.354 | 0.358 | |||
| Random CSx4 | 0.297 | 10−8 | 0.350 | 10−6 | 0.353 | 10−3 |
| Random CCx4 | 0.315 | 10−119 | 0.335 | 10−71 | 0.352 | 10−5 |
| Random CC | 0.322 | 10−177 | 0.345 | 10−44 | 0.338 | 10−160 |
| Random NS | 0.328 | 10−210 | 0.336 | 10−162 | 0.335 | 10−202 |
| Random DCS | 0.287 | 10−5 | 0.352 | 10−2 | 0.361 | 10−10 |
| Random DNS | 0.328 | 10−103 | 0.335 | 10−95 | 0.337 | 10−80 |
| Nucleotides paired with codon site 2 | ||||||
| Real mRNAs | 0.344 | 0.293 | ||||
| Random CS×4 | 0.341 | 10−3 | 0.309 | 10−20 | ||
| Random CC×4 | 0.339 | 10−8 | 0.319 | 10−113 | ||
| Random CC | 0.327 | 10−63 | 0.322 | 10−250 | ||
| Random NS | 0.330 | 10−57 | 0.334 | 0 | ||
| Random DCS | 0.347 | 10−7 | 0.291 | 10−4 | ||
| Random DNS | 0.331 | 10−16 | 0.334 | 10−159 | ||
| Nucleotides paired with codon site 3 | ||||||
| Real mRNAs | 0.358 | |||||
| Random CS×4 | 0.352 | 10−12 | ||||
| Random CC×4 | 0.333 | 10−80 | ||||
| Random CC | 0.339 | 10−104 | ||||
| Random NS | 0.331 | 10−165 | ||||
| Random DCS | 0.356 | 10−3 | ||||
| Random DNS | 0.329 | 10−93 | ||||
Abbreviations: Real mRNAs, coding sequences of 19 317 native human mRNA; Random CC, mRNA sequences with randomly chosen synonymous codons; Random NS, sequences with randomly shuffled nucleotides and the same nucleotide composition as native mRNAs; Random CS×4, sequences with shuffled 4-fold degenerate synonymous codons; Random CC×4, sequences with randomly chosen 4-fold degenerate synonymous codons; Random DCS, dicodone shuffling that preserved dinucleotide frequencies, encoded amino acid sequence and codon usage of native mRNAs; Random DNS, random shuffling of all dinucleotides that retained nucleotide composition of native mRNAs. Start and stop codons were excluded from this analysis.