Table 3. Putative HERVs mined from the NCBI reference genome using the burn-associated HERVs as a probe.
Among the putative HERVs mined from this study, only the ones which retain at least one 500 amino acid coding potential for gag, pol, or env polypeptides are listed.
| HERV locus | Contig | Chr | +/− | Chr location | Size | gag | pol | env | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
|
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| from | to | start | end | size (a.a.) | start | end | size (a.a.) | start | end | size (a.a.) | ||||||
|
| ||||||||||||||||
| Pt 1 | 01-H-6A-02_2D01 (HERV-H/env62)* | NT_005403.17 | 2 | − | 166564060 | 166572708 | 8649 | 1227 | 1874 | 215 | (−) | 6255 | 8009 | 584 | ||
|
| ||||||||||||||||
| Pt 1 and Pt 2 | 12-K2-2A-04_1D02 | NT_032977.9 | 1 | + | 75842771 | 75849143 | 6373 | (−) | (−) | 3685 | 5451 | 588 | ||||
| 12-K2-2A-04_1D01 (HERV-K50A) | NT_004487.19 | 1 | − | 155596457 | 155605636 | 9180 | 1112 | 1648 | 178 | 4131 | 6434 | 767 | 6492 | 8231 | 579 | |
| 12-K2-2A-04_3D01 | NT_005612.16 | 3 | − | 112693124 | 112702282 | 9159 | 1104 | 3188 | 694 | 3870 | 6014 | 714 | 6478 | 7728 | 416 | |
| 12-K2-2A-04_3D02 (HERV-K50B) | NT_005612.16 | 3 | − | 185230336 | 185239436 | 9101 | 1032 | 3038 | 668 | 3800 | 6709 | 969 | (−) | |||
| 12-K2-2A-04_5D01 (JN675037.1)* | NT_023133.13 | 5 | − | 156084717 | 156093896 | 9180 | 1112 | 3112 | 666 | 3879 | 6923 | 1014 | (−) | |||
| 12-K2-2A-04_6D01 (HERV-K109) | NT_007299.13 | 6 | − | 78426663 | 78436083 | 9421 | 1104 | 3104 | 666** | 3871 | 4455 | 195 | 6412 | 8508 | 698 | |
| 12-K2-2A-04_7D01 (HML-2.HOM)* | NT_007819.17 | 7 | − | 4622057 | 4631528 | 9472 | 1865 | 2401 | 178 | 4632 | 7502 | 956 | 7204 | 9303 | 699 | |
| 12-K2-2A-04_7D02 (HML-2.HOM)* | NT_007819.17 | 7 | − | 4630560 | 4640030 | 9471 | 1111 | 2205 | 364 | 3877 | 6747 | 956 | 7203 | 9302 | 699 | |
| 12-K2-2A-04_8D01 (HERV-K115) | NT_023736.17 | 8 | − | 7355397 | 7364859 | 9463 | 1104 | 3047 | 647** | 3870 | 6740 | 956 | 6442 | 8541 | 699 | |
| 12-K2-2A-04_11D01 (JN675064.1)* | NT_033899.8 | 11 | + | 101565794 | 101575259 | 9466 | 926 | 1648 | 240 | 3879 | 6743 | 954 | 7198 | 9183 | 661 | |
| 12-K2-2A-04_12D01 (JN675068.1)* | NT_029419.12 | 12 | − | 58721242 | 58730698 | 9457 | 1113 | 3113 | 666 | (−) | 6440 | 8536 | 698 | |||
| 12-K2-2A-04_22D01 (JN675087.1)* | NT_011519.10 | 22 | + | 18926187 | 18935361 | 9175 | 1112 | 3112 | 666 | (−) | 6491 | 8248 | 585 | |||
| 12-K2-4A-01_3D01 (JN675021.1)* | NT_005612.16 | 3 | + | 101360737 | 101369859 | 9123 | 1113 | 3116 | 667 | (−) | (−) | |||||
| 12-R-3A-05_7D01 (ERV3-1) | NT_007933.15 | 7 | − | 64450702 | 64460320 | 9619 | (−) | (−) | 7893 | 9707 | 604 | |||||
| 12-W-5A-01_7D01 (ERVW-1) | NT_007933.15 | 7 | − | 92097285 | 92107506 | 10222 | (−) | 4564 | 4974 | 136 | 7812 | 9428 | 538 | |||
|
| ||||||||||||||||
| Pt 2 | 02-E-7A-01-17D01 (AB062274.1)* | NT_010799.15 | 17 | − | 26557545 | 26566365 | 8821 | 1462 | 2655 | 397 | 2689 | 4371 | 560 | 6264 | 6923 | 219 |
| 02-K2-7A-09-1D01 (JN675013.1)* | NT_004487.19 | 1 | + | 160660575 | 160669807 | 9233 | 1113 | 1874 | 253 | 4188 | 5777 | 529 | 6544 | 8226 | 560 | |
Pt (patient); Chr (chromosome); +/− (strand orientation); underline (putative full coding potential);
*
HERV references with an incomplete match to the corresponding putative HERV loci identified in this study;
**
two gag polypeptides which were subjected to functional analysis.