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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
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BMC Genomics

ISSN: 1471-2164

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