Table 3.
Coding potential and functional domain predicted for the HML7 proviral loci.
| gag | pro | pol | env | Translation | GC% | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HML7 Locus |
Shift | Stop | MA | CA | NC | NC ZnF |
Shift | Stop | PR | dUTPase | Shift | Stop | RT | RH | IN ZnB |
IN core | Shift | Stop | SU gp | TM hr | gag/pro Shift | pro/pol Shift |
|
| 1q43 | 6 | 7 | x | x | 1 | 1 | x | x | 39.6 | ||||||||||||||
| 2q11.2 | x | 3 | 1 | x | x | x | x | 5 | 5 | x | x | 40.6 | |||||||||||
| 2q31.1 | x | x | x | x | 38.8 | ||||||||||||||||||
| 3q11.2 | x | 6 | 2 | x | x | 41.1 | |||||||||||||||||
| 3q23 | x | x | 41.9 | ||||||||||||||||||||
| 3q26.1 | 39.0 | ||||||||||||||||||||||
| 4q25 | 6 | 8 | 1 | 5 | x | x | 39.2 | ||||||||||||||||
| 4q32.1 | x | x | x | 40.6 | |||||||||||||||||||
| 5p13.2 | x | 4 | 5 | x | x | x | 1 | 1 | x | x | 40.3 | ||||||||||||
| 5q22.3 | x | 8 | 4 | x | x | x | x | 9 | 1 | x | 40.2 | ||||||||||||
| 6p12.3 | x | 0 | 6 | x | x | x | 8 | 1 | 40.0 | ||||||||||||||
| 6q22.31 | x | 4 | 8 | x | x | x | x | 4 | 4 | x | x | 40.1 | |||||||||||
| 7q21.12 | 43.0 | ||||||||||||||||||||||
| 7q36.2 | 43.4 | ||||||||||||||||||||||
| 11p12 | x | x | x | x | x | 40.1 | |||||||||||||||||
| 11q14.3 | x | 1 | 1 | x | x | x | 1 | 5 | x | 40.3 | |||||||||||||
| 12q12 | x | 3 | 7 | x | x | x | x | 2 | 2 | x | x | 39.3 | |||||||||||
| 15q24.3 | x | x | 38.8 | ||||||||||||||||||||
| 19q13.2 | x | 40.3 | |||||||||||||||||||||
| Xq11.1 | 1 | 11 | x | x | x | xx | 2 | 4 | x | x | 8 | 4 | x | x | x | x | 4 | 5 | x | x | 0 | −1 | 40.0 |
| Xq22.3 | 39.7 | ||||||||||||||||||||||
| Yq11.221 | 3 | 7 | x | x | x | xx | 0 | 3 | x | x | 3 | 7 | x | x | x | x | 6 | 5 | x | x | 0 | −1 | 39.6 |
| Yp11.2 | 0 | 3 | x | x | x | xx | 2 | 2 | x | x | 11 | 8 | x | x | x | 7 | 7 | x | x | 0 | 0 | 40.0 | |
The table reports the presence of the different retroviral open reading frames and the occurrence of internal stop codonsand frameshifts in the 14 most intact HML7 loci, as identified by RetroTector software (locus name in bold). For each HML7 provirus, the presence of functional domains and taxonomical signatures was also predicted and is indicated with the symbol “x.” Abbreviations not explained in the main text: ZnF = Zinc finger motif, ZnB = Zinc-binding domain, gp = glycoprotein, hr = heptad repeats, GC% = percentage of GC nucleotides.