Table 2.
(top) primers for HERVs, (middle) primers for gag genes, and (bottom) primers for inflammatory mediators
| HERV family | Primer name | Sequence | Reference | |
|---|---|---|---|---|
| HERV | E | HERV-E(F) HERV-E(R) |
CACTTCTCCTGTTGTCCTT TACAACTCTAAGGGGTCT |
M10976 and AB062274 |
| FRD | HERV-Frd(F) HERV-Frd(R) |
CAGG/TCTCCCAAC/TAGATAGA AGAGCAGGAG/ATGAAAGGAA |
AC004022 | |
| H | HERV-H(F) HERV-H(R) |
CTGATGAC/TATTCCACCA AGACCACCAAACAGGC/GTT |
D11078, AJ289709, AJ289711, M18048 | |
| L | HERV-L(F) HERV-L(R) |
GATTGG/TATG/TGAAGGATGC CTGAGTCTGAGTCCCAAAGC |
X89211 | |
| R | HERV-R(F) HERV-R(R) |
AGGAAAAACAAGTAAAGGG CCGTGACAGGTTTTACAA |
M12410 | |
| K1 | HERV-K(HML1)(F) HERV-K(HML1)(R) |
CTGCTCTCCATTATCTCAAGT AAGGAATGAGAAAAGACAGT |
Repbase version 8.2.0 consensus sequences | |
| K2 | HERV-K(HML2)(F) HERV-K(HML2)(R) |
GTCATCACCACTCCCTAATCT GGAAAAGAAAAAGACACAGAG |
AF074086, AF164609, AF164610 | |
| K4 | HERV-K(HML4)(F) HERV-K(HML4)(R) |
TGTGGGCGAAGGATTACC AATGTCCCTTCAGCACCT |
AF020092 | |
| K5 | HERV-K(HML5)(F) HERV-K(HML5)(R) |
GCAGAGGGCAAGGAGTAG GCGATGGATGAAAGGAGTA |
Repbase version 8.2.0 consensus sequences | |
| K6 | HERV-K(HML6)(F) HERV-K(HML6)(R) |
CAGAATGTGGGCAAACTC TGAACAAAGGAGGACGAA |
AF079797 | |
| W | HERV-W(F) HERV-W(R) |
AGAGCACAGCAGGAGGGA GGGGTCCTTGCTCACAGA |
AY101582, AY101583, AY101584 AY101585 | |
| RRI | RRHERV-I(F) RRHERV-I(R) |
TATCTCTCCCTTTCCCAG AGGAATCAGAGAGACCA/GG/ATG |
M64936 | |
| HERV | Region | Primer name | Sequence | Reference |
|---|---|---|---|---|
| HERV-K109 (AF164615.1) | LTR-gag | 6D01_LTR-1A 3D02_Sgag-2A |
CAGTCTCAGGTGTTTGGATCTTCCAC CGCGgcggccgcCTACTGCTGCACTGCCGCTTGT |
NT_007299.13 (16546496-16555953) |
| gag | 3D02_Sgag-1A 3D02_Sgag-2A |
CGCGgcggccgcATGGGGCAAACTAAAAGTAAAG CGCGgcggccgcCTACTGCTGCACTGCCGCTTGT |
||
| HERV-K115 (AY037929.1) | LTR-gag | 8D01_LTR-1A 3D02_Lgag-2A |
TGATCAATATAAAAGGTGTAGGGGTGG CGCGgcggccgcGCTTATTCCCTGAAACACTTGGGAC |
NT_023736.17 (7345381-7354859) |
| gag | 3D02_Lgag-1B 3D02_Lgag-2A |
CGCGgcggccgcGCTAGGGTGATAATGGGGCAAAC CGCGgcggccgcGCTTATTCCCTGAAACACTTGGGAC |
| Cytokines | Primer name | Sequence | Reference |
|---|---|---|---|
| Ptgs2 | COX2_1B COX2_2A |
ACACAGTGCACTACATCCTGAC ATCATCTCTACCTGAGTGTC |
NM_011198.3 |
| ICAM1 | ICAM1_ 1A ICAM1_ 2A |
AGCTGTTTGAGCTGAGCGAGA CTGTCGAACTCCTCAGTCA |
NM_010493.2 |
| Il1b | Il1b_ 1A Il1b_ 2A |
GACAGTGATGAGAATGACCTG GAACTCTGCAGACTCAAACTCCA |
NM_008361.3 |
| Il6 | Il6_1E Il6_2G |
GCCTTCCCTACTTCACAAGTCC CACTAGGTTTGCCGAGTAGATCTC |
NM_031168.1 |
| Nos2 | Nos2_1B Nos2_2B |
ACAAGCTGCATGTGACATCGA CAGAGCCTGAAGTCATGTTTGC |
NM_010927.3 |
| Tnf | Tnf_1A Tnf_2A |
GCATGATCCGCGACGTGGAA AGATCCATGCCGTTGGCCAG |
NM_013693.2 |
| b-actin | b-actin-1A b-actin-2A |
CCAACTGGGACGTGGAA GTAGATGGGCACAGTGTGGG |
NM_007393.3 NM_001101.3 |
bold font (degenerate nucleotides); italic font (NotI restriction enzyme site)