Table 2.
RSCU values of highly expressed (HEG) and lowly expressed (LEG) housekeeping and tissue-specific genes in rice
| AA | Codons | RSCU (HEG) | RSCU (LEG) | tRNA copy number of Oryza sativa | AA | Codons | RSCU (HEG) | RSCU (LEG) | tRNA copy number of Oryza sativa |
|---|---|---|---|---|---|---|---|---|---|
| Phe | TTT | 0.78 (0.57) | 0.94 (0.72) | 0 | Ala | GCT | 1.12 (0.63) | 1.09 (0.76) | 25 |
| TTC* | 1.22 (1.43) | 1.06 (1.28) | 15 |  |
1.17 (1.43) | 1.13 (1.34) | 0 | ||
| Tyr | TAT | 0.81 (0.59) | 1 (0.76) | 0 | GCA | 0.82 (0.54) | 0.95 (0.72) | 11 | |
| TAC* | 1.19 (1.41) | 1 (1.24) | 16 | GCG | 0.88 (1.4) | 0.84 (1.17) | 13 | ||
| His | CAT | 0.96 (0.74) | 1.04 (0.91) | 0 | Gly | GGT | 1.01 (0.69) | 1.05 (0.73) | 0 |
| CAC* | 1.04 (1.26) | 0.96 (1.09) | 11 | GGC* | 1.3 (1.83) | 1.05 (1.63) | 24 | ||
| Asn | AAT | 0.88 (0.84) | 1.14 (0.89) | 0 | GGA | 0.86 (0.69) | 0.95 (0.78) | 13 | |
| AAC* | 1.12 (1.16) | 0.86 (1.11) | 14 | GGG | 0.82 (0.79) | 0.95 (0.86) | 8 | ||
| Asp | GAT | 1.05 (0.84) | 1.18 (0.92) | 0 | Leu | TTA | 0.37 (0.38) | 0.55 (0.41) | 7 |
| GAC* | 0.95 (1.16) | 0.82 (1.08) | 28 | TTG | 0.98 (0.88) | 1.22 (0.97) | 9 | ||
| Cys | TGT | 0.69 (0.39) | 0.98 (0.66) | 0 | CTT | 1.3 (0.75) | 1.28 (0.95) | 19 | |
| TGC* | 1.31 (1.61) | 1.02 (1.34) | 10 |  |
1.57 (1.94) | 1.34 (1.74) | 0 | ||
| Gln | CAAT | 0.7 (0.87) | 0.85 (0.78) | 16 | CTA | 0.41 (0.49) | 0.56 (0.51) | 8 | |
| CAG | 1.3 (1.13) | 1.15 (1.22) | 13 | CTG | 1.37 (1.56) | 1.05 (1.43) | 6 | ||
| Lys | AAA | 0.56 (0.55) | 0.79 (0.67) | 10 | Ser | TCT | 1.14 (0.73) | 1.21 (0.92) | 17 |
| AAG* | 1.44 (1.45) | 1.21 (1.33) | 22 | TCC | 1.2 (1.24) | 1.17 (1.23) | 0 | ||
| Glu | GAA | 0.7 (0.64) | 0.83 (0.7) | 15 | TCA | 1.06 (0.68) | 1.19 (0.94) | 10 | |
| GAG* | 1.3 (1.36) | 1.17 (1.3) | 29 | TCG | 0.76 (1.18) | 0.64 (0.94) | 7 | ||
| Val | GTT | 1.21 (0.7) | 1.26 (0.87) | 21 | AGT | 0.75 (0.84) | 0.84 (0.68) | 0 | |
 |
1.09 (1.24) | 0.92 (1.23) | 0 | AGC | 1.1 (1.34) | 0.95 (1.28) | 13 | ||
| GTA | 0.39 (0.32) | 0.56 (0.39) | 4 | Arg | CGTH | 0.8 (0.61) | 0.63 (0.56) | 16 | |
| GTG | 1.32 (1.74) | 1.27 (1.52) | 10 |  |
1.37 (1.71) | 1.26 (1.42) | 0 | ||
| Pro | CCT | 1.16 (0.68) | 1.14 (0.89) | 16 | CGA | 0.39 (0.34) | 0.48 (0.49) | 4 | |
 |
0.83 (0.98) | 0.86 (0.8) | 0 | CGG | 0.88 (1.05) | 0.94 (1.12) | 7 | ||
| CCA | 1.1 (0.78) | 1.16 (0.99) | 11 | AGA | 0.96 (0.65) | 1.19 (0.96) | 9 | ||
| CCG | 0.91 (1.56) | 0.83 (1.32) | 10 | AGG | 1.6 (1.63) | 1.51 (1.45) | 10 | ||
| Thr | ACT | 1.09 (0.79) | 1.12 (0.84) | 9 | Ile | ATT | 1.12 (0.76) | 1.24 (0.98) | 23 |
 |
1.26 (1.44) | 0.96 (1.23) | 0 |  |
1.32 (1.8) | 1 (1.39) | 0 | ||
| ACA | 1.05 (0.7) | 1.38 (0.96) | 8 | ATA | 0.56 (0.45) | 0.76 (0.63) | 6 | ||
| ACG | 0.61 (1.07) | 0.54 (0.98) | 0 |
RSCU values within parenthesis represent tissue-specific genes of rice, and the values outside represent housekeeping rice genes. Arrows indicate the correspondence between codon and their isoaccepting tRNA based on revised wobble rules. Codons marked with asterisk hold a perfect correspondence with most abundant tRNA gene copy number in both housekeeping and tissue-specific genes. Codons marked with superscript H shows higher preference in highly expressed housekeeping genes. Codons marked with superscript T shows higher preference in highly expressed tissue-specific genes.