Table 4.
List of 39 canonical HERV clades found in GRCh37/hg19
| Tax-order | HERV clade | Nr of HERV sequencesa | Repbase identifiersb | Previously estimated nr of copiesc | |
|---|---|---|---|---|---|
| Canonical | Non-canonical | ||||
| Class I, Gamma-like | |||||
| 10100 | Supergroup MLLV* | ||||
| 10110 | HERVT | 21 | 12 | HERVS71/LTR6 | 80 |
| 10200 | Supergroup HERVERI | ||||
| 10210 | HERVE | 41 | 107 | HERVE/LTR2 | 250 |
| 10230 | HERV3 | 20 | 37 | HERV3/LTR4 | 100 |
| 10240 | HERV1 | 2 | 11 | HERV1 | NA |
| 10250 | HERVI | 3 | 13 | HERVI/LTR10 | 250 (together w. HERVIP) |
| 10300 | Supergroup HERVW9 | ||||
| 10310 | HERVW | 40 | 86 | HERV17/LTR17 | 40 |
| 10320 | HERV9 | 114 | 171 | HERV9/LTR12 | 300 |
| 10400 | Supergroup HERVIPADP | ||||
| 10410 | HERVIP | 67 | 72 | HERVIP10F/LTR10F | 250 (together with HERVI) |
| 10420 | HERVADP | 16 | 8 | HERVP71A_1/LTR71 | 40 |
| 10600 | Supergroup HERVHF | ||||
| 10610 | HERVH | 531 | 500 | HERVH/LTR7 | 1000 |
| 10620 | HERVH48 | 16 | 8 | HERVH48I/MER48 | 60 |
| 10630 | HERVFA | 8 | 7 | HERVFH19/LTR19 | 45 |
| 10640 | HERVFB | 8 | 14 | HERVFH21/LTR21A | 30 |
| 10650 | HERVFC | 2 | 3 | HERV46I/LTR46 | 6d |
| 10660 | LTR46 | 8 | 2 | LTR46-in/LTR46 | NA |
| 10700 | Supergroup HERVFRDlike | ||||
| 10710 | HERVFRD | 1 | 10 | ERV3-1-i/LTR58 MER50 |
NA |
| 10720 | PRIMA41 | 3 | 17 | PRIMA41/MER41 | 40 |
| 10740 | HERV1_artiodact | 2 | 7 | NA | NA |
| 10750 | PABL | 2 | 8 | PABL_BI/PABL_A, PABL_B | 8 |
| 10760 | HERV4 | 8 | 23 | NA | NA |
| 10800 | Supergroup HEPSI | ||||
| 10820 | HEPSI2 | 2 | 4 | NA | NA |
| 10830 | HEPSI3 | 1 | 5 | NA | NA |
| 10852 | MER65 | 1 | 1 | MER65/MER65C | NA |
| 10882 | PRIMA4 | 3 | 4 | PRIMA4 | NA |
| 10900 | Supergroup HUERSP | ||||
| 10910 | HUERSP1 | 1 | 3 | HUERSP1/LTR8 | 200 (together with other HUERSP) |
| 10920 | HUERSP2 | 10 | 12 | HUERSP2/LTR1_LTR28 | See above |
| 10930 | HUERSP3 | 16 | 40 | HUERSP3/LTR9 | See above |
| Class II Beta-like | |||||
| Supergroup HML | |||||
| 20010 | HML1 | 9 | 45 | HERVK14I/LTR14 | 70 |
| 20020 | HML2 | 19 | 70 | HERVK/LTR5 | 91e |
| 20030 | HML3 | 31 | 151 | HERVK9I/MER9 | 150 |
| 20040 | HML4 | 7 | 5 | HERVK13I/LTR13 | 10 |
| 20050 | HML5 | 27 | 69 | HERVK22/LTR22 | 100 |
| 20060 | HML6 | 17 | 48 | HERVK31/LTR3 | 50 |
| 20070 | HML7 | 9 | 5 | HERVK11DI/MER11D | 20 |
| 20080 | HML8 | 34 | 24 | HERVK11I/MER11A | 60 |
| 20090 | HML9 | 10 | 9 | HERVK(14C)/LTR14C | 25 |
| 20100 | HML10 | 2 | 7 | HERVKC4/LTR14 | 10 |
| Class III Spuma-like | |||||
| Supergroup HSERVIII | |||||
| 30100 | HERVL | 86 | 75 | HERVL (HERVL/MLT2) | 200 |
| 30200 | HERVS | 16 | 4 | HERVS (HERV18/LTR18) | 50 |
Only groups and supergroups with at least one canonical chain are included. Additional file 6: List S6 is more comprehensive
aNumber of canonical and non-canonical HERV sequences identified in this study (see details in the main text)
bsee Bannert and Kurth [8] and Mager and Medstrand [56]
csee Mager and Medstrand [56]
dsee Bénit et al. [97]
esee Subramanian et al. [98]