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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
9ठ2L 21,312,749 21,403,782 20 29 6 + + 7 (3)
10ठ2L 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.