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Table 2 Regions with extreme TE density in the D. melanogaster Release 4 genome sequence

From: Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome

HDR

Chromosome

Start

End

No. of families

No. of TEs

No. nested

Duplicated TEs

Collinear

Genes

1

X

19,744,508

19,790,060

7

22

0

+

+

2 (8)

2

X

20,958,143

20,988,686

13

18

2

+

+

1

3*

X

21,332,555

21,366,773

13

14

13

-

+

0

4†

X

21,434,542

21,663,556

42

104

39

+

+

6

5

X

21,726,082

21,780,371

10

12

4

-

+

5

6

X

21,883,728

21,974,732

16

21

0

-

+

0

7

X

22,085,438

22,224,390

19

38

12

+

Base

9

8

2L

20,100,865

20,210,447

27

61

18

+

+

1

9‡§

2L

21,312,749

21,403,782

20

29

6

+

+

7 (3)

10‡§

2L

21,527,053

21,725,165

36

55

17

-

+

10 (1)

11

2L

22,064,386

22,407,834

61

157

52

+

Base

19 (1)

12*

2R

387

1,185,590

103

571

156

+

Base

45

13§

2R

1,744,145

2,011,104

42

92

46

+

-

2

14

3L

22,910,473

23,771,865

91

411

128

+

Base

17

15

3R

310,015

436,430

22

37

8

-

+

9

16*

3R

8,294,200

8,327,684

5

38

33

+

+

1

17

3R

27,888,358

27,905,053

2

20

12

+

Tip

1

18

4

1

46,860

12

14

4

-

Base

2 (2)

19

4

201,177

269,428

10

16

9

-

+

6

20

4

303,028

348,412

7

10

2

-

+

4

21

4

433,967

496,527

10

20

7

+

+

4

22

4

926,385

997,041

12

18

3

-

+

5

23

4

1,163,173

1,281,586

18

44

13

-

Tip

9

  1. HDRs were defined as having >10 non-INE-1 TEs in a 50 Kb window. Numbers of distinct families, numbers of TEs, number of TEs involved in nests, and the presence of duplicated TEs all exclude INE-1. A plus indicates that unique sequences flanking a HDR are in the collinear orientation in the D. yakuba genome. Orthologous regions could not be obtained for both flanking regions for HDRs at the tip or base of chromosome arms. Numbers of genes include coding and non-coding genes, with numbers of pseudogenes indicated in parentheses. *Likely to be fixed in D. melanogaster. †Physical gap present in HDR. ‡HDRs 9 and 10 flank the Histone gene cluster and likely represent a single HDR. §'Weak points' in polytene chromosomes.