TABLE 1.
Set of 110 CKS17d-positive sequences from GenBank release 115
| IDa | CKS17db | RTc | LTRd | Family or viruse |
|---|---|---|---|---|
| AB019437 | 44076 (+) | + | + | HERV-R |
| AB019440 | 34816 (+) | + | + | HERV-T∗ |
| AC000047 | 30757 (+) | + | HERV-FRD | |
| AC000378 | 94638 (+) | + | + | HERV-F(XA) |
| AC002346 | 84258 (+) | + | + | HERV-W |
| AC002386 | 73583 (−) | + | ERV9 | |
| AC002992 | 17206 (+) | + | RRHERV-I | |
| AC003087 | 46235 (+) | + | + | ERV9 |
| AC003093 | 25376 (−) | + | HERV-E | |
| AC004006 | 9034 (+) | + | ERV9 | |
| AC004253 | 9911 (+) | + | + | ERV9 |
| AC004534 | 81583 (−) | ERV9 | ||
| AC004772 | 83200 (+) | + | HERV-E | |
| AC004869 | 99245 (+) | + | HERV-FRD | |
| AC004924 | 89383 (+) | + | HERV-E | |
| AC005036 | 171165 (+) | HERV-H | ||
| AC005183 | 27600 (+) | + | ERV9 | |
| AC005386 | 178754 (+) | + | + | HERV-H |
| AC005817 | 97156 (−) | + | MuERV-UI∗ | |
| AC005942 | 22750 (+) | + | + | HERV-F(XA) |
| AC006017 | 142708 (−) | + | ERV9 | |
| AC006485 | 14188 (+) | + | RRHERV-I | |
| AC006539 | 12323 (−) | + | HERV-U3∗ | |
| AC006989 | 4728 (−) | RRHERV-I | ||
| AC006999 | 71755 (−) | + | ERV9 | |
| AC007204 | 10189 (−) | + | HERV-U3∗ | |
| AC007244 | 137080 (+) | ERV9 | ||
| AC007275 | 129167 (−) | + | HERV-T∗ | |
| AC007353 | 129702 (+) | + | + | HERV-T∗ |
| AC007458 | 8944 (−) | ENV-U4∗ | ||
| AC007526 | 97589 (+) | + | + | ERV9 |
| AC007779 | 89968 (+) | + | HERV-F(XA) | |
| AC007876 | 114202 (−) | + | + | HERV-H |
| AC007939 | 26365 (−) | + | HERV-HS49C23 | |
| AC008573 | 51728 (−) | HERV-U3∗ | ||
| AC008752 | 33833 (−) | + | HERV-H | |
| AC008981 | 26664 (−) | HERV-R | ||
| AC009271 | 92913 (+) | + | + | HERV-E |
| AC009276 | 33461 (−) | HERV-T∗ | ||
| AC009831 | 67534 (+) | HERV-H | ||
| AC009946 | 93859 (−) | + | HERV-W | |
| AC010104 | 60731 (−) | + | ERV9 | |
| AC010131 | 67248 (−) | + | ERV9 | |
| AC010141 | 120496 (−) | HERV-E | ||
| AC010152 | 57664 (−) | + | HERV-F | |
| AC010340 | 69706 (−) | + | HERV-F | |
| AC011447 | 133957 (−) | + | + | HERV-H |
| AC011607 | 170698 (+) | HERV-U2∗ | ||
| AC011778 | 104300 (−) | + | + | ERV9 |
| AC012062 | 13750 (+) | + | HERV-H | |
| AC012089 | 136656 (−) | + | HERV-H | |
| AC012147 | 174249 (+) | + | + | Type C |
| AC012408 | 156301 (+) | + | + | ERV9 |
| AC012593 | 152461 (+) | + | HERV-H | |
| AC013243 | 33932 (−) | + | + | ERV9 |
| AC013294 | 33838 (+) | + | HERV-HS49C23 | |
| AC013406 | 20757 (−) | + | + | ERV9 |
| AC013592 | 101976 (−) | + | HERV-H | |
| AC013759 | 144260 (+) | + | + | HERV-W |
| AC016677 | 152001 (−) | + | + | ERV9 |
| AC016699 | 53279 (−) | ERV9 | ||
| AC016769 | 8915 (+) | ERV9 | ||
| AC017005 | 45085 (+) | + | HERV-T∗ | |
| AC017104 | 72857 (−) | + | HERV-E | |
| AC018389 | 141038 (+) | + | HERV-R(b) | |
| AC018640 | 113549 (−) | + | HERV-E | |
| AC018747 | 40719 (−) | HERV-HS49C23 | ||
| AC018966 | 21146 (+) | + | HERV-E | |
| AC019157 | 137529 (+) | + | HERV-E | |
| AC019191 | 9682 (−) | HERV-W | ||
| AC020617 | 76159 (+) | HERV-F(c)∗ | ||
| AF010170 | 7946 (+) | + | + | Type C |
| AF064861 | 85519 (+) | + | HERV-U2∗ | |
| AF072711 | 11331 (−) | + | HERV-R | |
| AF151794 | 7502 (+) | + | + | Type C |
| AF196779 | 74784 (−) | + | HERV-E | |
| AL133258 | 47537 (+) | + | HERV-T∗ | |
| AL135922 | 2076 (−) | + | ERV9 | |
| AP000037 | 85657 (+) | + | HERV-E | |
| AP000645 | 20257 (+) | + | HERV-S | |
| AP000793 | 24743 (−) | ERV9 | ||
| BEVEVCG | 7552 (+) | + | + | BaEV |
| CGU09104 | 7879 (+) | + | + | Type C |
| FCVF6A | 7520 (+) | + | mRNA | Type C |
| HS142F18 | 82679 (+) | + | + | HERV-E |
| HS162C6 | 63858 (−) | + | + | ERV9 |
| HS215K18 | 30913 (−) | + | HERV-E | |
| HS295C6 | 22922 (+) | HERV-E | ||
| HS30P20 | 50221 (+) | + | HERV-F | |
| HS413H6 | 111259 (−) | HERV-F | ||
| HS57A13 | 50357 (−) | + | HERV-F(b) | |
| HS611N7 | 102072 (+) | + | HERV-W | |
| HSAC000064 | 37016 (+) | + | HERV-W | |
| HSDJ306F2 | 20288 (−) | ERV9 | ||
| HSDJ319M7 | 93125 (−) | + | + | HERV-H |
| HSDJ62D2 | 147474 (−) | HERV-FRD | ||
| HSERV9 | 2938 (+) | + | mRNA | ERV9 |
| HSJ612B15 | 7532 (+) | + | ERV9 | |
| HSU95626 | 65824 (−) | + | + | HERV-H |
| HUAC004382 | 171855 (−) | + | + | ERV9 |
| HUMER41 | 7853 (+) | + | + | HERV-E |
| HUMERGPE | 7476 (+) | + | HERV-E | |
| HUMERV | 2932 (+) | + | mRNA | ERV9 |
| HUMERVA34A | 2329 (+) | HERV-R | ||
| HUMRGH2 | 7659 (+) | + | HERV-H | |
| HUMRTVE | 3986 (+) | HERV-E | ||
| MMHC438N12 | 122487 (−) | + | Type C | |
| PEN133818 | 7683 (+) | + | + | Type C |
| RVRD114EV | 1927 (+) | RD114 | ||
| SIVMPCG | 7613 (+) | + | + | MPMV |
ID, Identifier.
Position and orientation (sense, +; antisense, −) of the CKS17d motif in the sequence, according to GenBank release 115 for the high-throughput-genomic sequences (and still unfinished in release 120) or to the definitive positions.
+, positive for the RT7 consensus motif.
+, positive for a proviral structure (two-LTR screen); mRNA, sequence corresponds to the RNA retroviral genome and not to the provirus.
Infectious retrovirus or endogenous retrovirus family (45), including families newly described in this paper (∗). ERVs are grouped in families designated by a letter corresponding to the amino acid whose tRNA is used as a primer for reverse transcription by annealing to the PBS. Families devoid of a PBS (in the CKS17d-positive sequences or in homologous ones found by BLAST searches) were thus designated U for unknown, followed by a number. In the ENV-U4 human family, only env sequences were found.