Skip to main content

Table 3 RNA editing sites and amino acid changes

From: Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses

Gene Subunit Genome Position Gene Position Nucleotide Change Codon Change Edit Position within Codon Amino Acid Change Sequencing Depth Editing Efficiency
matK exon 2963 710 G > A UCU > UUU 2 S > F 37 70
matK exon 3518 155 G > A UCU > UUU 2 S > F 38 84
rps16 exon 5795 212 G > A UCA > UUA 2 S > L 179 82
rps16 intron 6389 G > A 47 81
atpA exon 12,099 914 G > A UCA > UUA 2 S > L 120 98
atpA exon 12,222 791 G > A CCG > CUG 2 P > L 189 98
atpF exon 14,294 92 G > A CCA > CUA 2 P > L 199 81
IGR-1 IGR 16,247 G > A 229 97
rps2 exon 17,781 248 G > A UCA > UUA 2 S > L 85 95
rpoC2 exon 18,698 3761 G > A UCA > UUA 2 S > L 41 98
rpoC2 exon 20,661 1798 G > T GGU > AGU 1 G > S 33 18
rpoC2 exon 20,763 1696 G > C CUC > GUC 1 L > V 34 12
rpoC1 exon 24,185 488 G > A UCA > UUA 2 S > L 79 80
rpoC1 exon 25,453 41 G > A UCA > UUA 2 S > L 20 65
rpoB exon 26,307 2426 G > A UCA > UUA 2 S > L 11 100
rpoB exon 26,733 2000 G > A UCU > UUU 2 S > F 15 93
rpoB exon 27,555 1178 G > A UCG > UUG 2 S > L 12 67
rpoB exon 28,167 566 G > A UCG > UUG 2 S > L 6 17
rpoB exon 28,182 551 G > A UCA > UUA 2 S > L 9 44
rpoB exon 28,395 338 G > A UCU > UUU 2 S > F 22 86
IGR − 2 IGR 35,186 A > C 23 17
psbZ exon 39,947 50 C > U UCA > UUA 2 S > L 176 26
rps14 exon 41,250 149 G > A CCA > CUA 2 P > L 210 90
rps14 exon 41,319 80 G > A CCC > CUC 2 P > L 240 88
psaA exon 44,617 1395 G > A CCC > CCU 3 P > P 95 37
IGR-3 IGR 51,329 C > U 614 17
ndhK exon 54,554 65 G > A UCA > UUA 2 S > L 826 89
ndhC exon 54,719 323 G > A ACU > AUU 2 T > I 816 96
IGR-4 IGR 59,062 G > A 349 28
accD exon 62,731 815 C > U UCG > UUG 2 S > L 65 92
accD exon 63,322 1406 C > U CCA > CUA 2 P > L 302 82
psaI exon 64,351 88 C > U CAU > UAU 1 H > Y 89 84
cemA exon 66,260 492 C > U UUC > UUU 3 F > F 84 49
IGR-5 IGR 67,928 C > U 31 13
psbF exon 69,182 77 G > A UCU > UUU 2 S > F 26 96
psbF 5’UTR 69,260 -2 G > A 39 62
psbE exon 69,306 214 G > A CCU > UCU 1 P > S 46 96
petL exon 70,671 5 C > U CCU > CUU 2 P > L 28 46
IGR-6 IGR 71,784 C > U 1163 99
clpP exon 74,986 559 G > A CAU > UAU 1 H > Y 33 97
psbN exon 79,461 29 G > A UCU > UUU 2 S > F 70 30
petB intron 80,119 C > T 56 18
petB exon 81,188 418 C > U CGG > UGG 1 R > W 206 94
petB exon 81,381 611 C > U CCA > CUA 2 P > L 207 94
rpoA exon 83,130 830 G > A UCA > UUA 2 S > L 144 70
rpoA exon 83,760 200 G > A UCU > UUU 2 S > F 76 83
rps11 exon 84,338 108 G > A UUC > UUU 3 F > F 357 55
rpl23 exon 91,217 89 G > A UCA > UUA 2 S > L 25 84
rpl23 exon 91,235 71 G > A UCU > UUU 2 S > F 31 97
ycf2 exon 98,495 6863 A > G UAA > UGA 2 *>* 6 50
ndhB exon 99,901 1487 G > A CCA > CUA 2 P > L 20 80
ndhB exon 99,955 1433 G > A UCA > UUA 2 S > L 15 40
ndhB exon 100,133 1255 G > A CAU > UAU 1 H > Y 17 100
ndhB exon 100,276 1112 G > A UCA > UUA 2 S > L 25 88
ndhB exon 100,558 830 G > A UCA > UUA 2 S > L 10 70
ndhB exon 101,328 746 G > A UCU > UUU 2 S > F 9 22
ndhB exon 101,337 737 G > A CCA > CUA 2 P > L 11 64
ndhB exon 101,488 586 G > A CAU > UAU 1 H > Y 11 82
ndhB exon 101,607 467 G > A CCA > CUA 2 P > L 23 91
ndhB exon 101,925 149 G > A UCA > UUA 2 S > L 23 91
rps12 intron 103,149 G > A 87 67
rps12 intron 103,290 G > A 115 85
IGR-7 IGR 104,462 G > A 629 30
rrn16S exon 106,489 577 G > A/U/C 1404 49
rrn16S exon 107,021 45 U > A/G 1112 41
rrn23S exon 111,418 881 U > A/G/C 3163 73
ndhF exon 116,076 1734 C > U AUG > AUA 3 M > I 23 26
ndhF exon 117,520 290 G > A UCA > UUA 2 S > L 21 38
ndhD exon 121,618 1298 G > A UCA > UUA 2 S > L 52 92
ndhD exon 122,029 887 G > A CCC > CUC 2 P > L 12 58
ndhD exon 122,242 674 G > A UCA > UUA 2 S > L 40 85
ndhD exon 122,317 599 G > A UCA > UUA 2 S > L 46 76
ndhD exon 122,533 383 G > A UCA > UUA 2 S > L 28 75
ndhD exon 122,914 2 G > A ACG > AUG 2 T > M 33 64
ndhE exon 123,626 233 G > A CCA > CUA 2 P > L 110 9
ndhA exon 125,765 961 G > A CCU > UCU 1 P > S 334 94
ndhA exon 127,589 341 G > A UCA > UUA 2 S > L 99 79
ndhH exon 128,810 303 G > A AUC > AUU 3 I > I 44 25
ycf1 exon 131,464 4236 G > A CGC > CGU 3 R > R 160 19
ycf1 exon 133,945 1755 G > A UUC > UUU 3 F > F 250 17
  1. Editing efficiency is counted by edited reads divided by total mapped reads at the same site
  2. If the sequencing depth of an editing site is less than 30, the edit rate may have a great error
  3. The editing sites in the IR region are calculated only once
  4. IGR Intergenic region
  5. UTR untranslated region, it belongs to exon
  6. *: Stop codon