Table 1

An overview of the numbers of transposable elements in the euchromatic genome of D. melanogaster
Class
 Arm
 Total transposable element sequence (in bp)
 % of arm
 Total number of transposable elements
 Number full length
 % Full length
 Number of transposable elements perMb in genome
 Number of transposable elements perMb in proximal 2 Mb
All families
 X
 828,370
 3.80
 276
 83
 30.43
 12.67
 50

2L
 878,471
 3.95
 305
 100
 32.79
 13.73
 58.5

2R
 870,914
 4.29
 313
 84
 26.84
 15.42
 89

3L
 938,947
 4.02
 288
 100
 34.72
 12.33
 66.5

3R
 866,971
 3.11
 288
 102
 35.76
 10.33
 24.5

4
 127,874
 10.33
 102
 9
 8.82
 82.40
 -

Total
 4,511,547
1,572
 478



Average
3.86

30.53
 13.46
 57.70


















LTR
 X
 628,924
 2.89
 134
 54
 41.04
 6.15
 19.00

2L
 603,536
 2.72
 127
 67
 52.76
 5.72
 20.00

2R
 573,034
 2.82
 140
 54
 38.57
 6.90
 30.50

3L
 618,441
 2.65
 117
 58
 49.57
 5.01
 24.00

3R
 621,272
 2.23
 154
 67
 44.16
 5.52
 7.50

4
 44,121
 3.56
 10
 4
 40.00
 8.08
 -

Total
 3,089,328
682
 304



Average
2.65

44.87
 5.84
 20.20


















LINE-like
 X
 136,348
 0.63
 71
 18
 25.35
 3.26
 14.50

2L
 185,499
 0.83
 98
 20
 20.41
 4.41
 18.50

2R
 225,984
 1.11
 109
 18
 16.51
 5.37
 37.50

3L
 251,077
 1.08
 106
 27
 25.47
 4.54
 24.00

3R
 176,355
 0.63
 70
 19
 27.14
 2.51
 4.50

4
 37,399
 3.02
 32
 1
 3.12
 25.85
 -

Total
 1,012,662
486
 103



Average
0.87

21.19
 4.16
 19.80


















TIR
 X
 45,324
 0.21
 59
 7
 11.86
 2.71
 14.50

2L
 82,761
 0.37
 76
 11
 14.47
 3.42
 18.00

2R
 69,291
 0.34
 62
 11
 17.74
 3.05
 20.50

3L
 52,743
 0.23
 57
 12
 21.05
 2.44
 16.50

3R
 63,359
 0.23
 60
 14
 23.33
 2.15
 12.50

4
 44,195
 3.57
 58
 3
 5.17
 46.85
 -

Total
 357,673
372
 58



Average
0.31

15.59
 3.19
 16.40


















FB
 X
 17,774
 0.08
 12
 4
 33.33
 0.55
 2.00

2L
 6,675
 0.03
 4
 2
 50.00
 0.18
 2.00

2R
 2,605
 0.01
 2
 1
 50.00
 0.1
 0.50

3L
 16,686
 0.07
 8
 3
 37.50
 0.34
 2.00

3R
 5,985
 0.02
 4
 2
 50.00
 0.14
 0.00

4
 2,159
 0.17
 2
 1
 50.00
 1.62
 -

Total
 51,884
32
 13



Average
0.04

40.62
 0.27
 1.30

For each class, the total numbers of each family of element, together with the numbers (and percentage of elements) that are full length is given for each chromosome arm. Column 3 gives the total base pairs contained within transposable elements, column 4 the percentage of each chromosome arm composed of transposable element sequences, column 8 the number of elements perMb, and column 9 the numbers of elements within the most proximal 2 Mb of each of the five major chromosome arms. Differences in density and amount of transposable element sequence were tested by binning major chromosomal arms into 50-kb windows and testing significance by Mann-Whitney U tests. The only significant difference (p < 0.05) observed, either including or excluding the proximal 2 Mb, was an increase in density and amount of sequence on the X chromosome relative to 3R.

Kaminker et al. Genome Biology 2002 3:research0084.1   doi:10.1186/gb-2002-3-12-research0084

Open Data