TABLE 3.
Location and classification of the HGMP-derived and prototype HERVs used in the present phylogenetic analyses
| Family and accession no.a | Chromosome locationb | Positionc (orientationd) |
|---|---|---|
| HERV.L family | ||
| HERV.L | (X89211) | |
| AL008713 | X | 22260 (+) |
| AL031119 | 6q24 | 95570 (−) |
| *AC004614 | 7p21-p22 | 51860 (−) |
| *AL021706 | Xq21.1-21.3 | 61100 (−) |
| *AC005261 | 19q13.4 | 26030 (−) |
| *AB000880 | 6p21.3 | 5580 (−) |
| *AC004544 | 4 | 60000 (+) |
| *Z98043 | 1q24 | 23600 (−) |
| *AC002449 | Xq23 | 117070 (−) |
| *AC002467 | 7q31 | 51010 (+) |
| *AC004225 | 5p | 32060 (−) |
| *AC004075 | X | 96290 (+) |
| *AF003528 | Xq13 | 60780 (+) |
| *AC003973 | 19 | 31200 (+) |
| *D86999 | 22q11.2 | 29120 (−) |
| *D86998 | 22q11.2 | 32700 (+) |
| *AC004045 (a) | 4q25 | 68940 (−) |
| *Z95124 | Xq21 | 43550 (+) |
| *Z70039 | X | 4831 (+) |
| *AC003975 | 7q31.3 | 15580 (−) |
| *AC002487 | 7q31 | 44600 (+) |
| *Z95331 | 22q11.2 | 6520 (−) |
| *AC004389 | X | 30390 (+) |
| *Z72519 | X | 31010 (−) |
| *Z69923 | 4p16.3 | 14690 (+) |
| *Z80771 | X | 75100 (+) |
| *AF070718 | 8q21 | 46200 (−) |
| *AF003529 | Xq26 | 122070 (+) |
| *AC004397 | 7q31.3 | 11500 (+) |
| *AC004541 | 7q11.2-21.1 | 43280 (+) |
| *AC003003 | 16p11.2-12 | 93430 (−) |
| *Z83841 | X | 57284 (+) |
| *AC004006 | 7q21-q22 | 100000 (+) |
| *AC002302 | 16p12.2-12 | 242050 (+) |
| *AJ006997 (b) | 21 | 27700 (+) |
| *Z84720 | X | 89900 (−) |
| *AL031054 | Xq27.2 | 137160 (+) |
| *AL023279 | Xq27.2 | 88420 (−) |
| *AC005530 | 6p21 | 43200 (−) |
| *AJ006997 (a) | 21 | 82360 (−) |
| *Z97054 | Xp11.2 | 83980 (−) |
| HERV.S family | ||
| AC004385 | X | 57520 (+) |
| AL009047 | X | 124667 (−) |
| AC002523 | Xq28 | 71140 (+) |
| Z68758 | 22q11.2-qter | 1146 (−) |
| AL009051 | 1q23-24 | 54501 (+) |
| HERV.E family | ||
| HERV.E | (M10976) | |
| AL023280 | Xq21.3-22.3 | 101960 (−) |
| AC000385 (a) | 11 | 153050 (−) |
| *AC000385 (b) | 11 | 132070 (−) |
| *AC002094 | 17 | 165330 (+) |
| *Z98257 | 1p35-36.2 | 11720 (+) |
| *AC004054 | 4q21 | 26830 (−) |
| RRHERV.I family, | ||
| AC002992 (b) | Y | 12550 (+) |
| HERV.R family, | ||
| AC004609 | 19p13.1 | 33950 (−) |
| HERV.S71 family, | ||
| AC002992 (a) | Y | 53730 (−) |
| HERV.ADP family | ||
| HERV.ADP | (L14752) | |
| AC004595 | 7p15.3-p21 | 96174 (−) |
| AL023579 | 6q26-27 | 42430 (−) |
| AC005741 | 5 | 67158 (−) |
| HERV.H family | ||
| HERV.H | (K01891) | |
| AC002384 | 7q22 | 51020 (+) |
| U95626 | 3 | 78690 (−) |
| *AC004456 (a) | 7q31 | 114150 (−) |
| *AC004456 (b) | 7q31 | 5660 (−) |
| *AF026251 | NDe | ND |
| *AL009031 | 6p22.3-24.1 | 138520 (+) |
| *AC002326 | 6 | 148750 (+) |
| *AF011889 | Xq28 | 85570 (+) |
| *AC004025 | Xp22 | 104670 (−) |
| *AC002066 | 7q31 | 36130 (−) |
| *AC004072 | X | 117925 (+) |
| *AF070717 | 8q21 | 16160 (−) |
| *AP000014 | 21q22.2 | 38340 (−) |
| *Z92543 | 6q22 | 30575 (+) |
| *AC003009 | 16p13.2-3 | 108950 (+) |
| *AC002530 | 7p15-p21 | 3475 (+) |
| *AC005276 | 7q31.3 | 3590 (+) |
| *AC000114 | Xq23 | 34280 (+) |
| *AC003091 | 7p21 | 116510 (+) |
| *Z71183 | 22q11.2 | 17985 (+) |
| *AL021327 | 6q21 | 28840 (+) |
| *Z76735 | X | 83560 (−) |
| *AC003078 | 7q21-q22 | 6200 (+) |
| *Z82210 | X | 19480 (−) |
| *AC004706 | 17 | 109705 (−) |
| *AC002526 | Xq23 | 70080 (−) |
| *U80460 | Xq13 | 65800 (+) |
| *AL021940 | 1q24 | 14875 (+) |
| *AC000064 (a) | 7q21-22 | 24110 (+) |
| *AC005145 | Xp22-166-169 | 75610 (−) |
| *AC005410 | 17 | 16905 (+) |
| *AC005549 | 17 | 130120 (−) |
| *AL031256 | 20q12 | 40955 (+) |
| *AC005392 | 19q13.2 | 174160 (−) |
| *AL023877 | Xp23-24 | 97410 (−) |
| *AF068862 | 8q21 | 75430 (−) |
| *Z99495 | 6p24 | 70115 (−) |
| *AC004514 | 16q21-22 | 41510 (−) |
| *AC005576 | 5q | 11040 (−) |
| *AC005386 | 10q25 | 175240 (+) |
| *AC002984 | 19q13.1 | 23490 (−) |
| HERV.F family, Z94277 | Xp11.3-Xp11.4 | 101180 (+) |
| HERV.F (type b) family | ||
| Z83745 (b) | X | 60210 (+) |
| AC002416 | X | 111780 (+) |
| HERV.XA family, AC000378 | 11 | 92770 (+) |
| HERV.I family | ||
| HERV.I | (M92067) | |
| AC004682 | 16q22.2 | 167493 (−) |
| AC004210 | 6p21 | 11996 (+) |
| *AL021878 | 22q13.1-13.2 | 29650 (−) |
| *AC004074 | X | 90318 (+) |
| *AC003100 (a) | 4q25 | 75436 (+) |
| *AC000394 | 9q34 | 19247 (−) |
| HERV.Z69907 family | ||
| Z69907 | 22q11.2 | 27132 (+) |
| AC004474 | Y | 106160 (+) |
| HERV.R (type b) family, | ||
| AC004045 (b) | 4q25 | 79040 (+) |
| ERV-9 family | ||
| ERV-9 | (X57147) | |
| AC004534 | 7q21-22 | 76280 (−) |
| Z84475 | 6q21 | 31440 (−) |
| *AC003087 | 7p15 | 43870 (+) |
| *AC004617 | Y | 168320 (−) |
| *Z99496 (a) | 6q22.1 | 2400 (−) |
| HERV.W family | ||
| HERV.W | (AF009668) | |
| AF045450 | 21q22.3 | 30400 (−) |
| AC000064 (b) | 7q21-22 | 33230 (+) |
| *U85196 | ND | 11680 (+) |
| *AC005187 | 4q25 | 108400 (+) |
| *AL023581 | 6 | 82630 (−) |
| *Z83850 | Xq22 | 92240 (+) |
| *AL022067 | 6 | 138140 (+) |
| HERV.P family | ||
| Z98255 | Xq11.2-13.3 | 148180 (+) |
| AC002069 | 7q21 | 42530 (+) |
| AL008987 | Xq21 | 47420 (−) |
| AC003969 | 11p14.3 | 116980 (−) |
| Z99496 (b) | 6q22.1 | 39850 (−) |
| HERV.HS49C23 family | ||
| AC002319 | 9q34 | 6388 (+) |
| AL023753 | 1p36.11 | 16270 (−) |
| HS49C23 | X | 62990 (+) |
| Z78021 | X | 28920 (−) |
| AL008706 | Xq27-28 | 10120 (−) |
| HERV-FRD family | ||
| HERV.FRD | (U27240) | |
| AC004022 | 7q21-22 | 91820 (+) |
| HERV.K family | ||
| HERV.K | (M14123) | |
| U91321 | 16p13.1 | 112740 (−) |
| Z70280 | X | 36610 (+) |
| AL022154 | Xq21.1-2 | 44890 (+) |
| Z83745 (a) | X | 44960 (−) |
| AC002464 | ND | 53850 (−) |
| AC003686 | 12q13.1 | 31140 (−) |
| Z99129 | 6q22 | 107600 (−) |
| AC003100 (b) | 4q25 | 23420 (+) |
| AC005318 | 15q26.1 | 16400 (+) |
| AL031601 | 10 | 264070 (+) |
| AL031393 | Xp11.3 | 9370 (−) |
| HERV-HML5 family | ||
| Z95437 | 6p21.3 | 8930 (−) |
| AC004536 | 7q31 | 36540 (+) |
| U69569 | Xq28 | 6380 (−) |
| HERV-HML6 family | ||
| HERV.HML6 | (HSU60269) | |
| Z84814 | 6p21.3 | 59370 (+) |
| AC005946 | 19q13.4 | 17800 (−) |
| AC003029 | 12q24 | 30850 (−) |
a
Asterisks indicate sequences that were excluded from maximum-parsimony analyses to reduce computation times (i.e., the sequence was only used in the neighbor-joining analyses).
b
Accession numbers (rather than locations) are given for prototype HERVs (in parentheses).
c
Approximate position of LPQG motif (or equivalent) in domain 4 of the RT protein.
d
Orientation with respect to the cosmid sequence.
e
ND, no data.