Table 2 |
|||||||||||||
|
The transposable elements of D. melanogaster |
|||||||||||||
|
Class |
Family |
Canonical length |
X |
2L |
2R |
3L |
3R |
4 |
Total number |
Number full length |
Number partial |
Number in proximal 2 Mb |
Average pairwise distance |
|
|
|||||||||||||
|
LTR |
17.6 |
7439 |
2 |
0 |
3 |
5 |
2 |
0 |
12 |
7 |
5 |
4 |
0.006 |
|
1731 |
4648 |
1 |
0 |
0 |
0 |
1 |
0 |
2 |
1 |
1 |
1 |
0.000 |
|
|
297 |
6995 |
22 |
12 |
6 |
7 |
10 |
0 |
57 |
18 |
39 |
12 |
0.032 |
|
|
3S18 |
6126 |
4 |
0 |
1 |
1 |
0 |
0 |
6 |
4 |
2 |
3 |
0.075 |
|
|
412 |
7566 |
8 |
0 |
7 |
11 |
5 |
0 |
31 |
24 |
7 |
6 |
0.024 |
|
|
accord |
7404 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
- |
|
|
aurora |
4263 |
0 |
0 |
2 |
1 |
0 |
0 |
3 |
1 |
2 |
3 |
0.074 |
|
|
blastopia |
5034 |
5 |
2 |
7 |
1 |
2 |
0 |
17 |
13 |
4 |
4 |
0.016 |
|
|
blood |
7410 |
1 |
11 |
2 |
3 |
5 |
0 |
22 |
22 |
0 |
6 |
0.001 |
|
|
Burdock |
6411 |
2 |
4 |
4 |
0 |
3 |
0 |
13 |
7 |
6 |
4 |
0.002 |
|
|
Circe |
6356 |
0 |
0 |
2 |
0 |
0 |
0 |
2 |
0 |
2 |
2 |
0.057 |
|
|
copia |
5143 |
4 |
13 |
4 |
5 |
4 |
0 |
30 |
26 |
4 |
3 |
0.002 |
|
|
diver |
6112 |
1 |
1 |
3 |
1 |
3 |
0 |
9 |
9 |
0 |
1 |
0.002 |
|
|
diver2 |
4917 |
0 |
4 |
3 |
2 |
0 |
0 |
9 |
0 |
9 |
9 |
0.032 |
|
|
Dm88 |
4558 |
0 |
0 |
2 |
0 |
30 |
0 |
32 |
0 |
32 |
2 |
0.015 |
|
|
frogger |
2483 |
0 |
1 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
1 |
- |
|
|
GATE |
8507 |
1 |
0 |
16 |
0 |
0 |
3 |
20 |
0 |
20 |
17 |
0.077 |
|
|
gtwin |
7411 |
2 |
2 |
0 |
2 |
0 |
0 |
6 |
2 |
4 |
3 |
0.038 |
|
|
gypsy |
7469 |
0 |
1 |
1 |
0 |
0 |
0 |
2 |
1 |
1 |
1 |
0.000 |
|
|
gypsy2 |
6841 |
1 |
0 |
0 |
2 |
0 |
0 |
3 |
1 |
2 |
2 |
0.067 |
|
|
gypsy3 |
6973 |
0 |
0 |
2 |
0 |
0 |
0 |
2 |
1 |
1 |
2 |
0.038 |
|
|
gypsy4 |
6852 |
0 |
1 |
0 |
0 |
1 |
0 |
2 |
1 |
1 |
2 |
0.041 |
|
|
gypsy5 |
7369 |
1 |
0 |
0 |
1 |
0 |
0 |
2 |
1 |
1 |
0 |
0.005 |
|
|
gypsy6 |
7826 |
0 |
1 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
- |
|
|
HMS-Beagle |
7062 |
4 |
5 |
1 |
0 |
3 |
0 |
13 |
9 |
4 |
3 |
0.054 |
|
|
Idefix |
7411 |
1 |
2 |
0 |
3 |
1 |
0 |
7 |
2 |
5 |
5 |
0.022 |
|
|
invader1 |
4032 |
0 |
0 |
4 |
3 |
18 |
1 |
26 |
1 |
25 |
7 |
0.023 |
|
|
invader2 |
5124 |
1 |
4 |
3 |
2 |
0 |
0 |
10 |
3 |
7 |
10 |
0.053 |
|
|
invader3 |
5484 |
2 |
5 |
2 |
2 |
5 |
0 |
16 |
3 |
13 |
5 |
0.044 |
|
|
invader4 |
3105 |
0 |
4 |
2 |
1 |
1 |
1 |
9 |
2 |
7 |
2 |
0.068 |
|
|
invader5 |
4038 |
1 |
4 |
0 |
1 |
0 |
0 |
6 |
0 |
6 |
6 |
0.068 |
|
|
McClintock |
6450 |
0 |
0 |
0 |
1 |
0 |
1 |
2 |
2 |
0 |
1 |
0.002 |
|
|
mdg1 |
7480 |
5 |
2 |
9 |
6 |
3 |
0 |
25 |
13 |
12 |
2 |
0.012 |
|
|
mdg3 |
5519 |
3 |
5 |
2 |
2 |
4 |
0 |
16 |
8 |
8 |
8 |
0.009 |
|
|
micropia |
5457 |
1 |
0 |
0 |
0 |
4 |
0 |
5 |
2 |
3 |
1 |
0.010 |
|
|
opus |
7521 |
3 |
6 |
6 |
6 |
3 |
0 |
24 |
16 |
8 |
5 |
0.003 |
|
|
qbert |
7650 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
1 |
- |
|
|
Quasimodo |
7387 |
2 |
7 |
0 |
4 |
1 |
0 |
14 |
5 |
9 |
5 |
0.016 |
|
|
roo |
9092 |
35 |
22 |
31 |
31 |
27 |
0 |
146 |
58 |
88 |
22 |
0.012 |
|
|
rooA |
7621 |
1 |
0 |
0 |
1 |
1 |
2 |
5 |
0 |
5 |
3 |
0.045 |
|
|
rover |
7318 |
3 |
0 |
1 |
0 |
2 |
0 |
6 |
3 |
3 |
3 |
0.035 |
|
|
springer |
7546 |
2 |
1 |
4 |
1 |
3 |
0 |
11 |
5 |
6 |
5 |
0.061 |
|
|
Stalker |
7256 |
3 |
1 |
0 |
5 |
3 |
0 |
12 |
3 |
9 |
7 |
0.014 |
|
|
Stalker2 |
8119 |
4 |
0 |
5 |
2 |
1 |
1 |
13 |
4 |
9 |
6 |
0.015 |
|
|
Stalker4 |
7379 |
1 |
0 |
0 |
0 |
1 |
0 |
2 |
2 |
0 |
0 |
0.001 |
|
|
Tabor |
7345 |
1 |
2 |
0 |
0 |
0 |
0 |
3 |
2 |
1 |
0 |
0.001 |
|
|
Tirant |
8526 |
4 |
3 |
3 |
4 |
5 |
1 |
20 |
15 |
5 |
5 |
0.001 |
|
|
Transpac |
5249 |
2 |
1 |
0 |
0 |
2 |
0 |
5 |
5 |
0 |
0 |
0.000 |
|
|
ZAM |
8435 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
- |
|
|
LINE-like |
baggins |
5453 |
1 |
2 |
10 |
0 |
0 |
1 |
14 |
0 |
14 |
12 |
0.076 |
|
BS |
5142 |
2 |
6 |
6 |
7 |
8 |
0 |
29 |
6 |
23 |
6 |
0.028 |
|
|
Cr1a |
4470 |
1 |
5 |
17 |
21 |
2 |
10 |
56 |
1 |
55 |
42 |
NC |
|
|
Doc |
4725 |
5 |
16 |
5 |
19 |
10 |
0 |
55 |
30 |
25 |
7 |
0.006 |
|
|
Doc2 |
4789 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
- |
|
|
Doc3 |
4740 |
0 |
1 |
6 |
1 |
0 |
1 |
9 |
0 |
9 |
8 |
0.065 |
|
|
F |
4708 |
2 |
7 |
10 |
10 |
11 |
2 |
42 |
16 |
26 |
11 |
0.019 |
|
|
G |
4346 |
1 |
2 |
0 |
0 |
0 |
0 |
3 |
0 |
3 |
1 |
0.059 |
|
|
G2 |
3102 |
1 |
9 |
1 |
2 |
1 |
0 |
14 |
2 |
12 |
2 |
0.036 |
|
|
G3 |
4605 |
1 |
1 |
2 |
0 |
0 |
0 |
4 |
0 |
4 |
3 |
0.029 |
|
|
G4 |
3856 |
0 |
5 |
0 |
2 |
3 |
1 |
11 |
0 |
11 |
6 |
0.100 |
|
|
G5 |
4856 |
0 |
5 |
0 |
1 |
2 |
1 |
9 |
0 |
9 |
6 |
0.063 |
|
|
G6 |
2042 |
1 |
1 |
0 |
1 |
0 |
0 |
3 |
1 |
2 |
3 |
0.006 |
|
|
Helena |
1317 |
2 |
1 |
1 |
1 |
2 |
0 |
7 |
0 |
7 |
5 |
0.097 |
|
|
HeT-A |
6083 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
0 |
3 |
0 |
0.018 |
|
|
I |
5371 |
7 |
5 |
6 |
3 |
5 |
2 |
28 |
8 |
20 |
9 |
0.037 |
|
|
Ivk |
5402 |
3 |
3 |
0 |
1 |
0 |
0 |
7 |
2 |
5 |
4 |
0.070 |
|
|
jockey |
5020 |
16 |
9 |
15 |
13 |
14 |
2 |
69 |
12 |
57 |
4 |
0.003 |
|
|
jockey2 |
3428 |
4 |
2 |
0 |
0 |
1 |
3 |
10 |
0 |
10 |
5 |
0.112 |
|
|
Juan |
4236 |
4 |
1 |
1 |
1 |
2 |
0 |
9 |
6 |
3 |
3 |
0.001 |
|
|
R1 |
5356 |
2 |
1 |
2 |
2 |
0 |
3 |
10 |
2 |
8 |
7 |
0.049 |
|
|
R2 |
3607 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
- |
|
|
Rt1a |
5108 |
0 |
0 |
6 |
5 |
2 |
0 |
13 |
5 |
8 |
6 |
0.053 |
|
|
Rt1b |
5183 |
4 |
6 |
14 |
7 |
5 |
1 |
37 |
5 |
32 |
22 |
0.095 |
|
|
Rt1c |
5443 |
11 |
2 |
2 |
1 |
0 |
1 |
17 |
1 |
16 |
14 |
0.177 |
|
|
TART |
10654 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
1 |
0 |
- |
|
|
X |
4740 |
3 |
8 |
4 |
8 |
2 |
0 |
25 |
6 |
19 |
12 |
0.049 |
|
|
TIR |
1360 |
1177 |
10 |
18 |
16 |
20 |
11 |
30 |
105 |
10 |
95 |
48 |
0.087 |
|
Bari1 |
1728 |
0 |
1 |
1 |
0 |
2 |
1 |
5 |
5 |
0 |
0 |
0.002 |
|
|
Bari2 |
1064 |
0 |
2 |
0 |
0 |
1 |
1 |
4 |
1 |
3 |
3 |
0.043 |
|
|
HB |
1653 |
5 |
7 |
6 |
3 |
7 |
4 |
32 |
5 |
27 |
21 |
0.114 |
|
|
H |
2959 |
5 |
11 |
2 |
1 |
5 |
0 |
24 |
1 |
23 |
3 |
0.069 |
|
|
hopper |
1435 |
5 |
2 |
3 |
2 |
3 |
0 |
15 |
11 |
4 |
6 |
0.048 |
|
|
hopper2 |
1680 |
0 |
3 |
0 |
2 |
0 |
0 |
5 |
1 |
4 |
0 |
0.042 |
|
|
looper1 |
1881 |
1 |
0 |
0 |
0 |
2 |
0 |
3 |
0 |
3 |
2 |
0.048 |
|
|
mariner2 |
912 |
5 |
5 |
2 |
2 |
0 |
3 |
17 |
4 |
13 |
13 |
0.144 |
|
|
NOF |
4347 |
2 |
0 |
2 |
2 |
1 |
0 |
7 |
0 |
7 |
4 |
0.013 |
|
|
P |
2907 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
- |
|
|
pogo |
2121 |
9 |
12 |
5 |
7 |
11 |
0 |
44 |
5 |
39 |
5 |
0.020 |
|
|
S |
1736 |
9 |
4 |
11 |
11 |
12 |
4 |
51 |
14 |
37 |
27 |
0.079 |
|
|
S2 |
1735 |
1 |
3 |
3 |
3 |
2 |
1 |
13 |
0 |
13 |
8 |
0.268 |
|
|
Tc1 |
1666 |
2 |
1 |
4 |
1 |
2 |
11 |
21 |
1 |
20 |
7 |
0.085 |
|
|
transib1 |
2167 |
0 |
0 |
2 |
0 |
0 |
0 |
2 |
0 |
2 |
2 |
0.000 |
|
|
transib2 |
2844 |
3 |
5 |
2 |
2 |
0 |
0 |
12 |
0 |
12 |
6 |
0.082 |
|
|
transib3 |
2883 |
0 |
1 |
1 |
1 |
1 |
3 |
7 |
0 |
7 |
4 |
0.088 |
|
|
transib4 |
2656 |
2 |
1 |
2 |
0 |
0 |
0 |
5 |
1 |
4 |
4 |
0.152 |
|
|
FB |
FB |
1492 |
12 |
4 |
2 |
8 |
4 |
2 |
32 |
13 |
19 |
13 |
0.066 |
|
|
|||||||||||||
|
The canonical length of each element (in bp) is shown in column 3, the total numbers of each family on each chromosome arm in columns 4-9, the grand totals for each family in column 10, and the numbers that are full length, partial and in the most proximal 2 Mb of the major chromosome arms, in columns 11-13. Partial elements are defined as those whose length is less than 97% of the canonical element. The average pairwise distance within each family is shown in column 14. The Cr1a family could not be reliably aligned and therefore average pairwise distance was not computed (NC). |
|||||||||||||
|
Kaminker et al. Genome Biology 2002 3:research0084.1-0084.20 doi:10.1186/gb-2002-3-12-research0084 |
|||||||||||||
