Table 3.
Candidate SNPs and Indels identified in conserved regions as indicated by Pfam.
| Gene | Changea | Positionb | Indel length (aa) | Domain/family | Domain/family position |
|---|---|---|---|---|---|
| OsNCED1 | E/K | 448 | 63 | RPE (retinal pigment epithelial) membrane protein | 131–630 |
| G/R | 465 | ||||
| OsNCED2 | I/L | 188 | 0 | RPE membrane protein | 68–569 |
| V/A | 199 | ||||
| R/Q | 359 | ||||
| OsNCED3 | R/A | 238 | 43 | RPE membrane protein | 108–601 |
| A/G | 240 | ||||
| C/W | 241 | ||||
| G/R | 242 | ||||
| D/E | 245 | ||||
| N/Y | 254 | ||||
| L/F | 257 | ||||
| V/I | 258 | ||||
| D/G | 282 | ||||
| C/R | 492 | ||||
| OsNCED4 | P/S | 87 | 59 | RPE membrane protein | 76–575 |
| V/L | 109 | ||||
| G/A | 116 | ||||
| V/L | 125 | ||||
| A/T | 131 | ||||
| G/S | 549 | ||||
| OsNCED5 | A/V | 260 | 0 | RPE membrane protein | 110–606 |
| OsCYP707A5 | A/T | 237 | 59 | Cytochrome P450 | 40–432 |
| OsCYP707A6 | NA | NA | 4 | Cytochrome P450 | 52–489 |
| OsCYP707A7 | N/H | 69 | 0 | Cytochrome P450 | 45–474 |
| OsGA20ox1 | NA | NA | 0 | 2OG-Fe(II) oxygenase superfamily | 208–307 |
| OsGA20ox2 | NA | NA | 0 | 2OG-Fe(II) oxygenase superfamily | 225–324 |
| OsGA20ox3 | NA | NA | 9 | 2OG-Fe(II) oxygenase superfamily | 199–304 |
| S/V | 304 | ||||
| C/S | 312 | ||||
| S/A | 313 | ||||
| I/T | 315 | ||||
| OsGA20ox4 | R/L | 316 | 49 | 2OG-Fe(II) oxygenase superfamily | 234–369 |
| L/V | 318 | ||||
| L/F | 320 | ||||
| T/R | 321 | ||||
| T/Q | 331 | ||||
| Q/S | 347 | ||||
| OsGA3ox1 | NA | NA | 0 | 2OG-Fe(II) oxygenase superfamily | 226–327 |
| OsGA3ox2 | NA | NA | 0 | 2OG-Fe(II) oxygenase superfamily | 212–304 |
| OsGA2ox1 | NA | NA | 0 | 2OG-Fe(II) oxygenase superfamily | 190–321 |
| OsGA2ox2 | NA | NA | 0 | 2OG-Fe(II) oxygenase superfamily | 179–287 |
| OsGA2ox3 | NA | NA | 0 | 2OG-Fe(II) oxygenase superfamily | 174–278 |
| OsGA2ox4 | 25 | / | 113 | 2OG-Fe(II) oxygenase superfamily | 113–177 |
| OsGA2ox5 | F/P | 206 | 0 | 2OG-Fe(II) oxygenase superfamily | 179–292 |
| G/R | 207 | ||||
| OsGPCR | 18 | / | 47 | Lanthionine synthetase C-like protein | 120–461 |
| OsGID1 | 24 | / | 172 | alpha/beta hydrolase fold | 116–330 |
aAmino acid changes in functional regions are indicated as well as Indels numbers.
bThe position of amino acid changes in functional regions. NA stands for no change. Positions of three proteins, OsGA2ox4, OsGPCR, and OsGID1 were not listed due to a high number of changes.
/ represents that there are too many SNPs to list in the Table.