Table 1.
Open reading frames (ORFs) predicted by GENSCAN in the 649 kb region around S4-RNase
| ORFs | Homologous protein | Species | Amino acid identity | Score (bits) | E-valuea | Accession no. | |
| ORF1 | None | ||||||
| ORF2 | Transposon protein | Oryza sativa | 64/122 (52%) | 134 | 9e-30 | DP000011 | |
| ORF3 | (SFBB4-u4) | PpSFBB9-γ | Pyrus pyrifolia | 291/378 (76%) | 566 | 4e-159 | AB297939 |
| ORF4 | Putative retroelement pol polyprotein | Arabidopsis thaliana | 24/36 (66%) | 50.8 | 4e-05 | AC006920 | |
| ORF5 | GAG-POL precursor | Vitis vinifera | 34/124 (27%) | 61.2 | 3e-08 | AB111100 | |
| ORF6 | None | ||||||
| ORF7 | Retrotransposon protein | Oryza sativa | 45/107 (42%) | 79.7 | 9e-14 | DP000009 | |
| ORF8 | Retrotransposon protein | Oryza sativa | 45/158 (28%) | 82.4 | 1e-14 | DP000009 | |
| ORF9 | (SFBB4-u3) | MdSFBB9-β | Malus×domestica | 350/390 (89%) | 726 | 0.0 | AB270792 |
| ORF10 | Retrotransposon protein | Oryza sativa | 31/78 (39%) | 54.3 | 6e-08 | DP000011 | |
| ORF11 | None | ||||||
| ORF12 | Retrotransposon protein | Oryza sativa | 36/82 (43%) | 81.6 | 6e-14 | DP000009 | |
| ORF13 | Hypothetical protein | Vitis vinifera | 59/181 (32%) | 71.6 | 3e-11 | AM472051 | |
| ORF14 | Zinc knuckle family protein | Oryza sativa | 60/182 (32%) | 100 | 4e-19 | DP000010 | |
| ORF15 | (SFBB4-u2) | MdSFBB9-α | Malus×domestica | 300/315 (95%) | 590 | 4e-166 | AB270792 |
| ORF16 | Retrotransposon protein | Oryza sativa | 71/165 (43%) | 124 | 7e-27 | DP000009 | |
| ORF17 | None | ||||||
| ORF18 | Predicted protein | Populus trichocarpa | 44/134 (32%) | 69.7 | 2e-10 | DS017968 | |
| ORF19 | None | ||||||
| ORF20 | Retrotransposon protein | Oryza sativa | 31/81 (38%) | 60.1 | 1e-09 | DP000086 | |
| ORF21 | Hypothetical protein | Vitis vinifera | 43/132 (32%) | 70.5 | 1e-10 | AM426737 | |
| ORF22 | Retrotransposon protein | Beta vulgaris | 61/173 (35%) | 82.0 | 3e-13 | EF101866 | |
| ORF23 | Retrotransposon gag protein | Asparagus officinalis | 418/767 (54%) | 772 | 0.0 | AC183435 | |
| ORF24 | Retrotransposon gag protein | Oryza sativa | 487/1032 (47%) | 921 | 0.0 | AC120534 | |
| ORF25 | (SFBB4-u1) | MdSFBB3-β | Malus×domestica | 306/394 (77%) | 628 | 4e-178 | AB270796 |
| ORF26 | Hypothetical protein | Vitis vinifera | 28/42 (66%) | 64.3 | 4e-08 | AM455744 | |
| ORF27 | None | ||||||
| ORF28 | Reverse transcriptase | Vigna radiata | 23/37 (62%) | 48.5 | 2e-04 | AY684634 | |
| ORF29 | Retrotransposon protein | Oryza sativa | 521/962 (54%) | 1028 | 0.0 | DP000011 | |
| ORF30 | Retrotransposon gag protein | Asparagus officinalis | 48/129 (37%) | 91.3 | 2e-16 | AC183436 | |
| ORF31 | Retrotransposon gag protein | Asparagus officinalis | 827/1636 (50%) | 1568 | 0.0 | AC183435 | |
| ORF32 | Integrase | Populus trichocarpa | 48/149 (32%) | 84.0 | 3e-14 | DQ536160 | |
| ORF33 | Predicted protein | Populus trichocarpa | 34/92 (36%) | 62.4 | 3e-08 | EQ134071 | |
| ORF34 | None | ||||||
| ORF35 | Retrotransposon gag protein | Asparagus officinalis | 95/194 (48%) | 172 | 4e-41 | AC183435 | |
| ORF36 | Retrotransposon gag protein | Asparagus officinalis | 117/405 (28%) | 141 | 2e-31 | AC183435 | |
| ORF37 | None | ||||||
| ORF38 | None | ||||||
| ORF39 | None | ||||||
| ORF40 | Transposon protein Pong subclass | Zea mays | 31/120 (25%) | 60.1 | 3e-07 | EU964924 | |
| ORF41 | Transposon protein Pong subclass | Zea mays | 185/380 (48%) | 355 | 8e-96 | EU962682 | |
| ORF42 | (S4-RNase) | S4-RNase | Pyrus pyrifolia | 49/50 (98%) | 115 | 2e-24 | AB014072 |
| ORF43 | Zinc finger | Medicago truncatula | 23/63 (36%) | 47.8 | 6e-04 | AC148290 | |
| ORF44 | None | ||||||
| ORF45 | Retrotransposon gag protein | Asparagus officinalis | 65/291 (22%) | 59.7 | 5e-07 | AC183435 | |
| ORF46 | Retroelement pol polyprotein-like | Arabidopsis thaliana | 667/1331 (50%) | 1272 | 0.0 | AB024037 | |
| ORF47 | Retrotransposon gag protein | Asparagus officinalis | 793/1644 (48%) | 1496 | 0.0 | AC183435 | |
| ORF48 | Retrotransposon protein | Oryza sativa | 352/728 (48%) | 673 | 0.0 | DP000011 | |
| ORF49 | None | ||||||
| ORF50 | Chromosome-associated kinesin KIF4A | Ricinus communis | 37/96 (38%) | 60.5 | 2e-07 | EQ974117 | |
| ORF51 | None | ||||||
| ORF52 | None | ||||||
| ORF53 | Retrotransposon protein | Beta vulgaris | 101/201 (50%) | 191 | 7e-46 | EF101866 | |
| ORF54 | (SFBB4-d1) | S4F-box0 | Pyrus pyrifolia | 400/400 (100%) | 834 | 0.0 | AB308360 |
| ORF55 | None | ||||||
| ORF56 | Hypothetical protein | Vitis vinifera | 45/154 (29%) | 72.0 | 2e-11 | AM429787 | |
| ORF57 | Hypothetical protein | Vitis vinifera | 50/135 (37%) | 81.3 | 2e-13 | AM467140 | |
| ORF58 | RNase H family protein | Asparagus officinalis | 35/63 (55%) | 78.6 | 2e-18 | AC183436 | |
| ORF59 | Retrotransposon protein | Oryza sativa | 67/121 (55%) | 137 | 1e-30 | DP000009 | |
| ORF60 | Retrotransposon protein | Oryza sativa | 127/297 (42%) | 234 | 2e-59 | DP000009 | |
| ORF61 | Retrotransposon gag protein | Asparagus officinalis | 37/129 (28%) | 74.7 | 1e-11 | AC183435 | |
| ORF62 | Unknown protein | Arabidopsis thaliana | 51/74 (68%) | 102 | 6e-20 | AK117191 | |
| ORF63 | Retrotransposon gag protein | Asparagus officinalis | 119/299 (39%) | 195 | 3e-47 | AC183435 | |
| ORF64 | None | ||||||
| ORF65 | Retrotransposon protein | Beta vulgaris | 35/44 (79%) | 76.3 | 2e-18 | EF101866 | |
| ORF66 | Hypothetical protein | Vitis vinifera | 39/110 (35%) | 55.1 | 5e-06 | AM489256 | |
| ORF67 | RNase H family protein | Asparagus officinalis | 58/121 (47%) | 115 | 2e-24 | AC183436 | |
| ORF68 | Retrotransposon gag protein | Asparagus officinalis | 229/692 (33%) | 341 | 2e-91 | AC183435 | |
| ORF69 | Hypothetical protein | Vitis vinifera | 68/227 (29%) | 84.7 | 3e-14 | AM451669 | |
| ORF70 | None | ||||||
| ORF71 | None | ||||||
| ORF72 | Retrotransposon gag protein | Asparagus officinalis | 714/1299 (54%) | 1440 | 0.0 | AC183435 | |
| ORF73 | Retrotransposon gag protein | Asparagus officinalis | 401/608 (65%) | 821 | 0.0 | AC183435 | |
| ORF74 | None | ||||||
| ORF75 | Integrase | Populus trichocarpa | 212/535 (39%) | 357 | 2e-96 | DQ536178 | |
| ORF76 | Retrotransposon gag protein | Asparagus officinalis | 167/506 (33%) | 223 | 1e-55 | AC183435 | |
| ORF77 | None | ||||||
| ORF78 | None | ||||||
| ORF79 | (SFBB4-d2) | MdSFBB3-β | Malus×domestica | 293/393 (74%) | 561 | 4e-158 | AB270796 |
| ORF80 | Retrotransposon protein | Oryza sativa | 175/487 (35%) | 225 | 9e-57 | DP000009 | |
| ORF81 | None | ||||||
| ORF82 | None | ||||||
| ORF83 | Hypothetical protein | Vitis vinifera | 27/46 (58%) | 56.2 | 1e-06 | AM482339 | |
| ORF84 | None | ||||||
| ORF85 | Retrotransposon protein | Oryza sativa | 242/432 (56%) | 471 | 4e-130 | DP000009 | |
| ORF86 | None | ||||||
| ORF87 | None | ||||||
| ORF88 | None | ||||||
| ORF89 | None |
a Significant similarity corresponds to an E-value <e −4.