Table 1. The codon preferences for the sets of human cell cycle-regulated genes: B1, B2 and top-600 sets (Jensen et al, 2006).
| Aa | Codon 5′ → 3′ | Preferences human |
P-values human |
Anticodon 3′ → 5′ | Binding at third position | Affinity | Organisma |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B1 | B2 | Top-600 | B1 | B2 | Top-600 | S.p. | S.c. | A.t. | |||||
| P-values were calculated using bootstrapping procedure over 10 000 random samples. The binding affinity was found from the study of Watkins and SantaLucia (2005). Non-optimal codons characterized by low codon–anticodon affinities are presented in bold. Human cell cycle-regulated genes usually have high preferences for these codons. Most of the preferences in human are supported by that of Schizosaccharomyces pombe (S.p.), Saccharomyces cerevisiae (S.c.) or Arabidopsis thaliana (A.t.) for their corresponding sets of the cell cycle-regulated genes. | |||||||||||||
| aS.p. is Schizosaccharomyces pombe, S.c. is Saccharomyces cerevisiae, A.t. is Arabidopsis thaliana. | |||||||||||||
| Ala | GCA | 0.04 | 0.05 | 0.03 | 0.05 | 0.09 | 0.14 | CGI | I:A | Low | • | ||
| Ala | GCC | −0.1 | −0.07 | −0.04 | 0.0001 | 0.01 | 0.16 | CGI | I:C | High | • | ||
| Ala | GCG | −0.01 | −0.03 | −0.02 | 0.58 | 0.01 | 0.03 | CGC | C:G | High | • | • | • |
| Ala | GCT | 0.07 | 0.05 | 0.03 | 0.0001 | 0.0001 | 0.05 | CGI | I:T | Low | • | • | • |
| Arg | AGA | 0.07 | 0.05 | 0.04 | 0.02 | 0.14 | 0.13 | UCU | U:A | Low | • | ||
| Arg | AGG | −0.02 | −0.02 | −0.01 | 0.17 | 0.0001 | 0.02 | UCC | C:G | High | • | • | |
| Arg | CGA | 0 | 0.03 | 0.02 | 0.19 | 0.0001 | 0.0001 | GCI | I:A | Low | |||
| Arg | CGC | −0.01 | −0.04 | −0.03 | 0.75 | 0.09 | 0.06 | GCI | I:C | High | |||
| Arg | CGG | −0.06 | −0.04 | −0.03 | 0.0001 | 0.2 | 0.19 | GCC | C:G | High | • | • | • |
| Arg | CGT | 0.02 | 0.02 | 0.01 | 0.07 | 0.0001 | 0.04 | GCI | I:T | Low | • | • | |
| Asn | AAC | −0.13 | −0.11 | −0.08 | 0.0001 | 0.0001 | 0.0001 | UUG | G:C | High | • | ||
| Asn | AAT | 0.13 | 0.11 | 0.08 | 0.0001 | 0.0001 | 0.0001 | UUG | G:T | Low | • | ||
| Asp | GAC | −0.1 | −0.1 | −0.07 | 0.01 | 0.0001 | 0.01 | CUG | G:C | High | • | ||
| Asp | GAT | 0.1 | 0.1 | 0.07 | 0.01 | 0.0001 | 0.01 | CUG | G:T | Low | • | ||
| Cys | TGC | −0.15 | −0.12 | −0.04 | 0.0001 | 0.0001 | 0.37 | UCG | G:C | High | • | • | • |
| Cys | TGT | 0.15 | 0.12 | 0.04 | 0.0001 | 0.0001 | 0.37 | UCG | G:T | Low | • | • | • |
| Gln | CAA | 0.1 | 0.06 | 0.05 | 0.0001 | 0.42 | 0.09 | GUU | U:A | Low | |||
| Gln | CAG | −0.1 | −0.06 | −0.05 | 0.0001 | 0.43 | 0.1 | GUC | C:G | High | |||
| Glu | GAA | 0.13 | 0.1 | 0.08 | 0.0001 | 0.03 | 0.04 | CUU | U:A | Low | • | • | |
| Glu | GAG | −0.13 | −0.1 | −0.08 | 0.0001 | 0.04 | 0.04 | CUC | C:G | High | • | • | |
| Gly | GGA | 0.04 | 0.05 | 0.04 | 0.35 | 0.15 | 0.29 | CCU | U:A | Low | • | ||
| Gly | GGC | −0.04 | −0.06 | −0.04 | 0.17 | 0.01 | 0.21 | CCG | G:C | High | • | ||
| Gly | GGG | −0.05 | −0.03 | −0.03 | 0.02 | 0.09 | 0.0001 | CCC | C:G | High | • | ||
| Gly | GGT | 0.05 | 0.04 | 0.03 | 0.01 | 0.0001 | 0.0001 | CCG | G:T | Low | • | • | |
| His | CAC | −0.14 | −0.13 | −0.07 | 0.0001 | 0.0001 | 0.05 | GUG | G:C | High | • | • | |
| His | CAT | 0.14 | 0.13 | 0.07 | 0.0001 | 0.0001 | 0.05 | GUG | G:T | Low | • | • | |
| Ile | ATA | 0.05 | 0.05 | 0.04 | 0.03 | 0.12 | 0.08 | UAI | I:A | Low | |||
| Ile | ATC | −0.12 | −0.12 | −0.08 | 0.01 | 0.0001 | 0.02 | UAI | I:C | High | • | ||
| Ile | ATT | 0.07 | 0.07 | 0.04 | 0.02 | 0.0001 | 0.06 | UAI | I:T | Low | • | • | • |
| Leu | CTA | 0.02 | 0.01 | 0.01 | 0.0001 | 0.03 | 0.02 | GUI | I:A | Low | • | ||
| Leu | CTC | −0.05 | −0.04 | −0.03 | 0.0001 | 0.0001 | 0.0001 | GUI | I:C | High | • | • | |
| Leu | CTG | −0.1 | −0.08 | −0.06 | 0.0001 | 0.04 | 0.02 | GUC | C:G | High | |||
| Leu | CTT | 0.03 | 0.04 | 0.03 | 0.06 | 0.01 | 0.05 | GUI | I:T | Low | • | • | |
| Leu | TTA | 0.06 | 0.04 | 0.03 | 0.0001 | 0.03 | 0.0001 | AAU | U:A | Low | • | ||
| Leu | TTG | 0.04 | 0.03 | 0.02 | 0.0001 | 0.0001 | 0.0001 | AAC | C:G | High | • | • | |
| Lys | AAA | 0.04 | 0.09 | 0.06 | 0.43 | 0.01 | 0.11 | UUU | U:A | Low | |||
| Lys | AAG | −0.04 | −0.09 | −0.06 | 0.44 | 0.01 | 0.11 | UUC | C:G | High | |||
| Met | ATG | 0 | 0 | 0 | 1 | 1 | 1 | UAC | C:G | High | • | • | • |
| Phe | TTC | −0.13 | −0.1 | −0.07 | 0.0001 | 0.0001 | 0.0001 | AAG | G:C | High | • | ||
| Phe | TTT | 0.13 | 0.1 | 0.07 | 0.0001 | 0.0001 | 0.0001 | AAG | G:T | Low | • | ||
| Pro | CCA | 0.07 | 0.04 | 0.04 | 0.01 | 0.06 | 0.02 | GGI | I:A | Low | • | • | • |
| Pro | CCC | −0.1 | −0.06 | −0.06 | 0.0001 | 0.02 | 0.0001 | GGI | I:C | High | • | • | |
| Pro | CCG | −0.02 | −0.03 | −0.02 | 0.19 | 0.02 | 0.07 | GGC | C:G | High | • | • | • |
| Pro | CCT | 0.05 | 0.05 | 0.04 | 0.01 | 0.0001 | 0.0001 | GGI | I:T | Low | |||
| Ser | AGC | −0.05 | −0.05 | −0.03 | 0.0001 | 0.0001 | 0.02 | UCG | G:C | High | • | • | |
| Ser | AGT | 0.03 | 0.04 | 0.03 | 0.03 | 0.0001 | 0.0001 | UCG | G:T | Low | |||
| Ser | TCA | 0.03 | 0.03 | 0.02 | 0.1 | 0.02 | 0.34 | AGI | I:A | Low | • | ||
| Ser | TCC | −0.05 | −0.04 | −0.03 | 0.0001 | 0.0001 | 0.0001 | AGI | I:C | High | • | ||
| Ser | TCG | −0.02 | −0.02 | −0.02 | 0.0001 | 0.01 | 0.57 | AGC | C:G | High | • | • | |
| Ser | TCT | 0.06 | 0.04 | 0.03 | 0.0001 | 0.0001 | 0.01 | AGI | I:T | Low | • | • | • |
| Thr | ACA | 0.01 | 0.03 | 0.02 | 0.63 | 0.29 | 0.72 | UGI | I:A | Low | • | ||
| Thr | ACC | −0.05 | −0.07 | −0.05 | 0.09 | 0.0001 | 0.1 | UGI | I:C | High | • | ||
| Thr | ACG | −0.05 | −0.03 | −0.02 | 0.0001 | 0.0001 | 0.11 | UGC | C:G | High | • | • | • |
| Thr | ACT | 0.09 | 0.07 | 0.05 | 0.0001 | 0.0001 | 0.0001 | UGI | I:T | Low | • | • | • |
| Trp | TGG | 0 | 0 | 0 | 1 | 1 | 1 | ACC | G:C | High | • | • | • |
| Tyr | TAC | −0.08 | −0.1 | −0.06 | 0.03 | 0.0001 | 0.05 | AUG | G:C | High | • | ||
| Tyr | TAT | 0.08 | 0.1 | 0.06 | 0.04 | 0.0001 | 0.05 | AUG | G:T | Low | • | ||
| Val | GTA | 0.07 | 0.05 | 0.03 | 0.0001 | 0.0001 | 0.0001 | CUI | I:A | Low | |||
| Val | GTC | −0.05 | −0.05 | −0.03 | 0.0001 | 0.0001 | 0.0001 | CUI | I:C | High | • | ||
| Val | GTG | −0.09 | −0.06 | −0.05 | 0.01 | 0.15 | 0.03 | CUC | C:G | High | • | ||
| Val | GTT | 0.07 | 0.06 | 0.05 | 0.01 | 0.01 | 0.01 | CUI | I:T | Low | • | • | |