Table 2.
NdhB C-to-U editing events by PREP and SNP approach using reads derived from sRNA-seq.
| Organism | Codon change | Nucleotide position | AA change | AA position | Total coverage | Edited coverage | % Editing | SNP P-value | PREP score |
|---|---|---|---|---|---|---|---|---|---|
| Arabidopsis | TCA–TTA | 149 | S–L | 50 | 40 | 32 | 80 | 4.8E-108 | 1 |
| (1,539: 870)* | CCA–CTA | 467 | P–L | 156 | 40 | 28 | 75 | 8.5E-109 | 1 |
| CAT–TAT | 586 | H–Y | 196 | 1 | 0 | no editing | - | 1 | |
| TCA–TTA | 611 | S–L | 204 | 5 | 0 | no editing | - | 0.8 | |
| TCT–TTT | 746 | S–F | 249 | 12 | 5 | 41.7 | 5.3E-109 | 1 | |
| TCA–TTA | 830 | S–L | 277 | 20 | 9 | 45 | 8.4E-29 | 1 | |
| TCA–TTA | 836 | S–L | 279 | 21 | 10 | 47.6 | 1.1E-23 | 1 | |
| GCC–GTC | 842 | T–I | 281 | 19 | 2 | 10.5 | 1.3E-8 | nd | |
| CAT–TAT | 1,255 | H–Y | 419 | 47 | 47 | 100 | nd | 1 | |
| CCA–CTA | 1,481 | P–L | 494 | 34 | 14 | 41.2 | 5.5E-40 | 1 | |
| Soybean | CCT–CTT | 74 | P–L | 25 | 4 | 0 | no editing | nd | 1 |
| (1,533: 543)* | TCA–TTA | 149 | S–L | 50 | 35 | 10 | 28 | 3.3E-11 | 1 |
| ACG–ATG | 542 | T–M | 181 | 1 | 1 | 100 | nd | 1 | |
| CAT–TAT | 586 | H–Y | 196 | 11 | 2 | 18.2 | 0.0000038 | 1 | |
| TCA–TTA | 611 | S–L | 204 | 14 | 0 | no editing | nd | 0.8 | |
| CCA–CTA | 737 | P–L | 246 | 2 | 2 | 100 | nd | 1 | |
| TCT–TTT | 746 | S–F | 249 | 12 | 4 | 33.3 | 2.0E-14 | 1 | |
| TCA–TTA | 830 | S–L | 277 | 12 | 5 | 41.7 | 3E-17 | 1 | |
| TCA–TTA | 836 | S–L | 279 | 11 | 5 | 45.5 | 2.6E-15 | 1 | |
| TCA–TTA | 1,112 | S–L | 371 | 22 | 5 | 22.7 | 4.3E-17 | 1 | |
| CAT–TAT | 1,255 | H–Y | 419 | 1 | 0 | no editing | nd | 1 | |
| CCT–CTT | 1,391 | P–L | 464 | 9 | 2 | 22.7 | 0.0000036 | ||
| CCC–TCC | 1,414 | P–S | 472 | 10 | 0 | no editing | nd | 1 | |
| CCA–CTA | 1,481 | P–L | 494 | 13 | 8 | 64.3 | 1.3E-31 | 1 | |
| Rice | AGC–AGT | 258 | S–S | 86 | 8 | 2 | 25 | 1.6E-8 | nd |
| (1,533: 619)* | CCA–CTA | 467 | P–L | 156 | 14 | 9 | 64.3 | 1.30E-31 | 1 |
| CAT–TAT | 586 | H–Y | 196 | 5 | 3 | 60 | 4.00E-12 | 1 | |
| TCA–TTA | 611 | S–L | 204 | 2 | 1 | 50 | nd | 0.8 | |
| TCC–TTC | 704 | S–F | 235 | 16 | 3 | 18.8 | 7.10E-08 | 1 | |
| CCA–CTA | 737 | P–L | 246 | 0 | 0 | nd | nd | 1 | |
| TCA–TTA | 830 | S–L | 277 | 3 | 1 | 33 | nd | 1 | |
| TCA–TTA | 836 | S–L | 279 | 4 | 1 | 25 | nd | 1 | |
| CTC–TTC | 850 | L–F | 284 | 2 | 0 | no editing | nd | 0.6 | |
| ACT–ATT | 1,454 | T–I | 485 | 30 | 0 | no editing | nd | 0.6 | |
| CCA–CTA | 1,481 | P–L | 494 | 6 | 5 | 83 | 8.0E-17 | 1 |
*
Coding sequence length and coverage values.
“Nucleotide position”: position in base pair is from the A of the initiator codon.
“Total Coverage”: total mapped reads in respective nucleotide position.
“Edited Coverage”: number of reads shown T, instead C.
“% Editing”: percentage of RNA editing using the edited reads divided by total mapped reads.
“PREP score”: confidence value of prediction according PREP.
“nd”: no defined.