Table 1 RISCI annotates the transposon locus in the main genome or the orthologous locus in the comparative genome into several classes based on specific alignment signatures.
Data set | Â | L1HS (Full length) | L1HS (Truncated) | AluYa5 (all) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
Reference genome - Reference human genome | Â | Comparative genomes | Comparative genomes | Comparative genomes | ||||||
Class | RISCI annotation | Chimp | Celera | HuRef | Chimp | Celera | HuRef | Chimp | Celera | HuRef |
Shared ancestry | OCCUPIED | 1 | 217 | 171 | 274 | 1227 | 1174 | 314 | 3529 | 3334 |
Post insertion changes | C_DISRUPTED_M_INTER_RMD | 1 | 7 | 43 | 16 | 8 | 11 | 5 | 9 | 6 |
| Â | C_INTER_RMD_M_DISRUPTED | 4 | 12 | 11 | 32 | 13 | 21 | 90 | 22 | 74 |
| Â | M_INTRA_RMD | 0 | 0 | 0 | 32 | 7 | 36 | 0 | 0 | 0 |
| Â | C_INTRA_RMD | 0 | 15 | 24 | 10 | 3 | 12 | 0 | 0 | 0 |
Orthologous locus empty | CAN | 170 | 27 | 25 | 426 | 62 | 76 | 3132 | 326 | 420 |
| Â | PAC | 68 | 9 | 10 | 109 | 16 | 22 | 54 | 2 | 4 |
| Â | PTS | 32 | 3 | 3 | 78 | 12 | 14 | 23 | 2 | 4 |
INDELS | INDEL_CAN | 3 | 2 | 7 | 43 | 4 | 6 | 164 | 34 | 79 |
| Â | INDEL_PAC | 6 | 1 | 1 | 14 | 1 | 2 | 7 | 1 | 0 |
| Â | INDEL_PTS | 9 | 5 | 5 | 28 | 6 | 3 | 96 | 24 | 53 |
Others | TWIN PRIMING | 0 | 0 | 0 | 142 | 17 | 24 | 0 | 0 | 0 |
Others | FRAGMENTED | 0 | 0 | 0 | 14 | 1 | 1 | 6 | 1 | 1 |
NMF | NMF | 8 | 4 | 2 | 203 | 44 | 19 | 165 | 106 | 81 |
Total | Â | 302 | 302 | 302 | 1421 | 1421 | 1421 | 4056 | 4056 | 4056 |