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Table 1 Statistics describing the base composition of ORF2 in nLTR-RT

From: Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons

Clades

Organisms

N

%AT

%GC

%A

GC1

GC2

GC3

PolyA

Nc

CAI

eCAI

RCDI

eRCDI

L1

Mammals

14

62.3 ± 1.3

37.7 ± 1.3

41.5 ± 1.6

39.5 ± 1.2

32.9 ± 1.0

40.7 ± 2.2

13.5 ± 3.5

45.3

0.74

0.77

1.41

1.54

 

Lizard

12

66.8 ± 1.1

33.2 ± 1.1

42.9 ± 1.6

37.2 ± 1.4

29.4 ± 0.8

33.2 ± 2.4

23.0 ± 6.5

44.8

0.72

0.75

1.65

1.71

 

Frog

35

56.4 ± 3.1

43.6 ± 3.1

33.4 ± 3.0

47.4 ± 3.3

38.3 ± 2.2

42.8 ± 4.5

6.3 ± 3.5

50.9

0.79

0.84

1.25

1.31

 

Fish

18

63.7 ± 2.1

36.3 ± 2.1

33.2 ± 3.4

39.6 ± 2.4

30.6 ± 2.2

32.1 ± 2.8

11.7 ± 7.4

43.1

0.72

0.75

1.71

1.92

Tx1

frog

2

57.7 ± 9.0

42.3 ± 9.0

28.8 ± 5.3

48.0 ± 9.2

35.7 ± 7.2

43.1 ± 10.6

6.0 ± 5.7

50.3

0.84

0.84

1.20

1.38

 

fish

11

61.4 ± 9.6

38.6 ± 9.6

33.1 ± 7.8

44.6 ± 7.3

33.7 ± 6.6

37.5 ± 15.5

9.7 ± 7.6

46.1

0.71

0.73

1.55

1.71

CR1

Lizard

1

53.8

46.2

33.8

50.2

37.8

50.7

2.0

52.4

0.78

0.78

1.15

1.38

 

Frog

3

58.2 ± 1.0

41.8 ± 1.0

30.4 ± 0.0

46.1 ± 1.3

36.0 ± 1.3

42.6 ± 0.6

5.0 ± 1.0

50.1

0.85

0.85

1.17

1.86

Daphne

Fish

4

66.8 ± 3.0

33.2 ± 3.0

39.1 ± 1.4

36.9 ± 2.6

28.9 ± 2.2

33.8 ± 4.7

10.0 ± 2.9

46.8

0.61

0.64

1.70

2.00

Crack

Fish

4

64.7 ± 4.0

35.3 ± 4.0

33.6 ± 1.7

39.3 ± 2.2

35.3 ± 4.3

31.3 ± 5.9

7.0 ± 2.9

46.5

0.67

0.68

1.70

2.00

L2

Lizard

17

45.1 ± 1.2

54.9 ± 1.2

20.5 ± 1.2

59.1 ± 1.0

46.1 ± 0.8

59.4 ± 2.9

0.9 ± 0.7

54.7

0.77

0.78

1.11

1.37

 

Frog

2

52.0 ± 0.9

48.0 ± 0.9

21.5 ± 2.0

49.7 ± 0.8

46.1 ± 0.2

48.4 ± 1.6

2.5 ± 0.7

49.9

0.79

0.81

1.31

1.44

 

Fish

19

57.7 ± 4.4

42.3 ± 4.4

26.8 ± 3.7

45.6 ± 3.8

38.5 ± 4.0

40.4 ± 6.6

3.1 ± 2.7

51.7

0.74

0.77

1.31

1.49

Rex1

Frog

3

51.1 ± 1.2

48.9 ± 1.2

27.1 ± 0.5

48.7 ± 1.6

43.6 ± 0.5

55.0 ± 1.4

1.3 ± 0.6

54.6

0.84

0.83

1.09

1.93

 

Fish

12

47.7 ± 4.9

52.3 ± 4.9

25.9 ± 2.7

47.6 ± 2.9

42.5 ± 2.8

47.7 ± 10.1

1.7 ± 2.8

52.6

0.77

0.79

1.19

1.48

I

Lizard

1

54.6

43.4

31.9

50.2

42.3

43.7

4

53.2

0.76

0.76

1.20

1.48

 

Fish

6

65.7 ± 1.5

34.3 ± 1.5

39.2 ± 2.2

41.0 ± 1.6

33.4 ± 0.8

28.4 ± 2.7

15.8 ± 6.2

42.4

0.72

0.74

1.67

1.80

R4

Lizard

1

57.3

43.7

38.2

47.5

34.3

46.4

2

51.1

0.79

0.77

1.17

1.44

 

Fish

1

47.5

52.5

31.6

51.3

43.2

63.1

1

49.5

0.70

0.73

1.27

1.40

RTE

Lizard

1

50.0

50.0

31.2

54.3

41.2

54.5

0

53.3

0.79

0.79

1.12

1.36

 

Fish

5

45.4 ± 6.1

54.6 ± 6.1

23.7 ± 5.3

57.1 ± 5.3

46.4 ± 6.4

60.4 ± 7.3

0.4 ± 0.5

50.7

0.72

0.74

1.27

1.45

Penelope

Lizard

7

62.7 ± 3.4

37.3 ± 3.4

35.5 ± 1.1

40.5 ± 4.0

34.8 ± 0.9

36.5 ± 5.7

5.4 ± 2.6

49.0

0.75

0.75

1.40

1.61

 

Frog

11

56.4 ± 2.9

43.4 ± 2.9

30.2 ± 2.5

46.0 ± 2.0

39.7 ± 2.3

44.1 ± 5.0

1.5 ± 1.3

52.7

0.84

0.84

1.15

1.39

 

Fish

3

55.2 ± 1.5

44.8 ± 1.5

31.7 ± 1.0

46.4 ± 3.7

37.1 ± 1.0

50.7 ± 0.2

5.0 ± 5.0

54.1

0.68

0.69

1.24

1.62

  1. N = number of consensus sequences; %AT, %GC and %A = % of nucleotides on the positive strand;GC1, GC2 and GC3 = % of GC at the 1st, 2nd and 3rd positions of codons; polyA Average number of potential poly-adenylation signals; Nc = effective number of codons; CAI Codon Adaptation Index, eCAI Exepected CAI, RCDI Realtive Codon Deoptimization Index, eRCDI Expected RCDI
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Mobile DNA

ISSN: 1759-8753