Table I.
Biased codon usage associated with VH 12-cRS at sites I and V
| VH cysteine codon usage | |||||
|---|---|---|---|---|---|
| TGT | TGC | Totals | |||
| Cys 23 | 129 (34%) | 253 | 382 | ||
| Cys 104 | 287 (98%) | 5 | 292 | ||
| VH valine codon usage | |||||
| GTG | GTC | GTA | GTT | Totals | |
| Val 2 | 131 (40%) | 148 | 10 | 37 | 326 |
| Val 13 | 292 (89%) | 3 | 26 | 7 | 328 |
| Val 19 | 183 (84%) | 24 | 9 | 2 | 218 |
| Val 42 | 173 (54%) | 42 | 28 | 75 | 318 |
| Val 80 | 0 (0%) | 0 | 139 | 2 | 141 |
VH cRSs are frequently conserved within degenerate codons; site V cRSs are associated with a conserved Cys104 residue (TGY codon); and a common site I cRS requires Val19 (GTN). The frequency of T and C nucleotides in the third position of cysteine codons (TGY) at VH gene segment codons 23 and 104 (top), and the frequency of nucleotides in valine codons (GTN) at VH gene segment codons 2, 13, 19, 42, and 80 (bottom) were compared. Numbers of relevant cysteine (TGY) or valine (GTN) codons in the mouse VH gene segments (n = 390) analyzed are shown, and frequencies of TGT (Cys) and GTG (Val) codons are in parentheses. Totals represent the numbers of VH gene segments containing a conserved residue.