Table 4 |
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|
Numbers and frequencies of association between LTR retrotransposons and putative genes for all known copia and some gypsy representative families in the rice (Nipponbare) genome |
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|
LTR Retrotransposon Families |
Full-length |
Solo LTRs |
Fragment |
Subtotal |
Percentages of Association Cases in Total Retroelements |
|
|
|||||
|
Osr1 |
0 |
0 |
3 |
3 |
3/18 = 16.67% |
|
Osr2 |
0 |
0 |
0 |
0 |
0 |
|
Osr3 |
0 |
0 |
2 |
2 |
2/3 = 66.67% |
|
Osr4 |
0 |
0 |
0 |
0 |
0 |
|
Osr5 |
0 |
0 |
0 |
0 |
0 |
|
Osr6 |
0 |
0 |
0 |
0 |
0 |
|
Osr7 |
0 |
0 |
0 |
0 |
0 |
|
Osr8 |
1 |
0 |
8 |
9 |
10/59 = 16.95% |
|
Osr9a |
0 |
0 |
0 |
0 |
0 |
|
Osr10 |
0 |
1 |
2 |
3 |
3/30 = 10% |
|
Osr11a |
0 |
0 |
0 |
0 |
0 |
|
Osr12 |
0 |
0 |
0 |
0 |
0 |
|
Osr13 |
1 |
3 |
2 |
6 |
6/35 = 17.14% |
|
Osr14 |
0 |
0 |
0 |
0 |
0 |
|
Osr15 |
0 |
0 |
5 |
5 |
5/18 = 27.58% |
|
Osr16 |
1 |
0 |
0 |
1 |
1/4 = 25.00% |
|
Osr17 |
2 |
0 |
1 |
3 |
3/13 = 23.08% |
|
Osr18a |
0 |
0 |
0 |
0 |
0 |
|
Osr19 |
0 |
0 |
0 |
0 |
0 |
|
Osr20 |
0 |
0 |
0 |
0 |
0 |
|
Osr21a |
0 |
0 |
0 |
0 |
0 |
|
Osr22 |
0 |
0 |
0 |
0 |
0 |
|
Osr23 |
0 |
0 |
0 |
0 |
0 |
|
Subtotal for Copia |
5 |
4 |
23 |
32 |
32/230 = 14.04% |
|
Osr31 |
1 |
0 |
0 |
1 |
1/7 = 14.29% |
|
Osr34 |
7 |
8 |
57 |
72 |
72/257 = 28.24% |
|
Osr36 |
1 |
0 |
0 |
1 |
1/2 = 50.00% |
|
Osr43 |
1 |
0 |
3 |
4 |
4/8 = 50.00% |
|
Osr44 |
0 |
0 |
1 |
1 |
1/7 = 14.29% |
|
Subtotal for Gypsy |
10 |
8 |
61 |
79 |
79/280 = 28.42% |
|
|
|||||
|
Overall |
15 |
12 |
84 |
111 |
111/510 = 21.94% |
|
|
|||||
|
a. No full-length element was identified for this family in the GenBank database of O. sativa. Location given is for an example RT in the database |
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|
Gao et al. BMC Genomics 2004 5:18 doi:10.1186/1471-2164-5-18 |
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