TABLE 1.
Profile of nine perissodactyl ERV lineages in the domestic horse genome
| Lineage or genus | Clade | Prototype | Prototype reference(s) |
ERV lineagea | PBSb | RepBase LTR subgroup(s)b | Copy no. |
|||
|---|---|---|---|---|---|---|---|---|---|---|
| RTc | Provirusd | env+ proviruse | Solo LTRf | |||||||
| Rho | I | HERV.R(b) | 3 | Rho.1 | Arg(CCG) | 1-2, 1-3, 15, 45, 72A, 72B, 8B, 8E, 8F | 151 | 20 | 6 | 4,057 |
| Zeta | I | HERV.W | 70 | Zeta.1 | Leu(TAA) | 1, 14, 1420 | 37 | 13 | 5 | 3,862 |
| Theta | I | HERV.L(b) | 71–73 | Theta.1 | ND | 1-4, 27_FC | 251 | 11 | 2 | 351 |
| I | Theta.2 | ND | 1-4B, 1-6, 13A, 19, 23B, 6, 6B, MER34A_CF, MER34A1 |
67 | 9 | 6 | 8,675 | |||
| Betaretrovirus | II | MMTV | Beta.1 | Lys(TTT) | [4] | 10 | 3* | 3* | 350 | |
| Kappa | II | HERV.K(HML2) | 33 | Kappa.1 | Lys(CTT) | 2-2 | 5 | 4 | 4 | 79 |
| II | Kappa.2 | Lys(CTT) | This study | 3 | 1 | 1 | 35 | |||
| U1 | II | NA | U1 | Trp(CCA) | 2-1 | 45 | 32 | 32 | 705 | |
| U2 | III | NA | U2 | ND | ND | 54 | NA | NA | NA | |
| Lambda | III | HERV.L | 28 | Lambda | ND | None identified | 691 | NA | 0 | NA |
| Sigma | III | HERV.S | 3 | Sigma | Ser(AGA) Ser(CGA) | 3-1C, 74 | 67 | 1 | 0 | 296 |
| Total | 1,381 | 92 | 57 | 18,410 | ||||||
a
ERV lineages demarcated in Fig. 1.
b
PBS, primer binding site. ND, not detected.
c
Number of RT loci.
d
Only loci that contained RT plus at least two retroviral coding domains represented in PFAM (64) and that were flanked by paired LTRs of >100 bp in length were counted as proviruses. NA, not available.
e
Number of proviruses for which we detected the presence of env genes (intact or fragmentary).
f
Number of solo LTRs.