Table 4 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
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% |