Table 1.
The Detailed Information and Ka/Ks Analysis for 13 Annotated Genes.
| Gene order | Gene ID (TIGR) | Paralogs (identity and alignment length) | Annotation | Expression (no. of EST) | Ka | Ks | Ka/Ks (LRT p-value) |
| 1 | Os03g01380 | Os01g17360 (97.2%/2328) | TyGypsy retrotransposon | No (0) | NA | NA | NA |
| Os03g01390 | Os07g35630 (95.8%/988) | ||||||
| Os03g01400 | Os11g34420 (97.3%/1031) | ||||||
| 2 | Os03g01410 | Os01g72700 + de nova (93.8%/1190) | STK kinase | No (0) | 0.0250 | 0.1761 | 0.142/0.011 |
| 3 | Os03g01420# | Os03g01490 (100%/267) | Expression protein | FL-cDNA and EST transcript (65) | 0 | 0 | ∞ |
| 4 | Os03g01430 | Os03g01480 (100%/303) | Hypothetical protein | No (0) | 0 | 0 | ∞ |
| 5 | Os03g01436 | Os03g01470 (99.7%/1173) | Conserved hypothetical protein | FL-cDNA and EST transcript (1) (leaf of seedling 4 min gamma-irradiation, after 6 h) | NA | NA | NA |
| 6 | Os03g01442# | Os01g69904# (97.6%/2647) | Expression protein | FL-cDNA and EST transcript (12) | 0.0277 | 0.0003 | 99/0.13 |
| 7 | Os03g01450* | Os04g32150 (93.6%/643) + Os06g11900 (92.1%/478) | Hypothetical protein | EST transcript (3) (leaf of seedling 4 min gamma-irradiation, after 6 h) | NA | NA | NA |
| 8 | Os03g01460 | No close homology | Hypothetical protein | No (0) | NA | NA | NA |
| 9 | Os03g01470 | Os03g01436 | Expression protein | FL-cDNA and EST transcript (6) (shoot and callus) | NA | NA | NA |
| 10 | Os03g01480 | Os03g01430 | Hypothetical protein | No (0) | 0 | 0 | ∞ |
| 11 | Os03g01490*# | Os03g01420+ | Expression protein | FL-cDNA and EST transcript (46) | 0 | 0 | ∞ |
| 12 | Os03g01500* | Os12g24870 (94.0%/1050) | Hypothetical protein | EST transcript (2) | NA | NA | NA |
| 13 | Os03g01520*# | No close homology | Hypothetical protein | EST transcript (3)(2/2 callus) | NA | NA | NA |
Notes: * Denotes mis-annotated gene models described in the TIGR rice annotation database. # Denotes genes with multiple alternative splicing isoforms. The cDNA from each parental gene and young gene were aligned with BLASTN using a low complexity filter off. Identity and alignment length were calculated using the chained SearchIO module of BioPerl. NA stands for non-feasible substitution analysis due to retrotransposon, no candidate parental gene, or distinct gene structure.