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Table 2 Examples of gene families that are known to be associated with traits in rice and their TEs insertions numbers

From: Domestication of rice has reduced the occurrence of transposable elements within gene coding regions

PFAMa

 

Cultivated rice

Wild rice

 

O.sat

O.ind

O.gla

O.ruf

O.niv

O.bar

PF08323

Glycosyl Transferaes family 5

13b

8c

21d

9

8

16

9

11

17

12

15

19

14

15

15

17

12

17

PF00646

F-box protein

56

21

51

56

29

48

33

4

22

26

153

26

23

113

24

27

106

17

PF03254

Xyloglucan fucosyltransferase

21

6

17

15

12

19

18

7

15

5

43

3

3

41

2

1

46

1

PF00194

Carbonic anhydrase

4

2

1

0

1

1

2

1

2

6

19

2

4

33

3

2

15

3

PF04616

Glycoside Hydrolase family 43

2

1

3

6

5

4

4

1

2

4

7

2

4

7

2

7

6

3

PF01486

MADS-box family

0

0

1

1

0

1

0

0

1

2

4

1

2

4

1

2

4

1

PF01734

patatin protein family

3

5

9

9

5

8

4

3

6

7

21

4

9

34

3

5

12

3

PF03083

Flavin-containing monooxygenase

2

3

1

3

1

2

2

1

2

2

11

0

3

7

0

5

8

1

PF00743

Flavin-containing monooxygenase

10

2

3

8

1

3

1

1

0

4

18

1

4

14

1

3

12

0

PF05691

Glycoside hydrolase family 36

7

2

9

11

2

9

7

2

9

7

4

9

9

6

7

7

3

9

PF00141

Haem peroxidase

1

0

1

4

0

1

0

0

1

2

5

1

4

5

3

3

5

2

  1. aThe PFAM is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models
  2. TEs insertions numbers in
  3. b2kb upstream
  4. cgene regions and
  5. d2kb downstream of a gene
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BMC Genomics

ISSN: 1471-2164

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