Table 2.
Primers used for assay design.
| Target | LTR status | Polarity | Sequence | Position | Target | Polarity | Sequence | Position |
|---|---|---|---|---|---|---|---|---|
| Intronic HERV-W proviral element (3' region) | Gene harboring provirus | |||||||
| Sense | ||||||||
| CD72 intron 1 | 3' | F | TGTCTCCAATTTTAACCCTATTTGC | chr9:35629741 | CD72 exon 1~2 | F | CTCTAGCTGATCGACTCACAAATACC | AK311283 |
| R | TTCCCCAGCCAGCATGTAA | chr9:35629792 | R | TGAACATTCTCGTAGGTGATTTCC | ||||
| TBX18 intron 7 | 5'&3' | F | CCATTCCATGTTCCTCATTAAATCT | chr6:85477157 | TBX18 exon 7~8 | F | CCCAAGCAAGAATACAGGGACTT | BC040697 |
| R | AGGCAATCTTACCACCCAGAAG | chr6:85477208 | R | GGTTTCCCTTGAGACCAAATTG | ||||
| Antisense | ||||||||
| ACOX3 intron 1 | 5'&3' | F | AGACGCTTGGAGCAGTTTCTG | chr4:8480630 | ACOX3 exon 1~2 | F | CTGTGGAGTGTGTGGGCTCTT | AK225080 |
| R | TCGGAGGACTTTACACATTGAACTAG | chr4:8480744 | R | CAGAGCTGTGTCGCCTCCTT | ||||
| KYNU intron 2 | 5'&3' | F | AGTGGGAATACTGACGCTCTTACC | chr2:143372701 | KYNU exon 2~3 | F | ACAGGATCTGCCTCCAGTTGA | U57721 |
| R | GCCAAGAACCCAAGGTCAGA | chr2:143372792 | R | TGGCCCACTTATCTAGTTCTTCTTC | ||||
| THEM2 intron 1 | 5' | F | TGAGATACCAGAGATCACCAAACTCTT | chr6:24787905 | THEM2 exon 1~2 | F | GGGAGGTGATAAAGGCCATGA | BC000894 |
| R | TGAAGTTTTATAAGGGTTAGGACAATCTT | chr6:24788017 | R | GGAGCAGCAGAGACAAGAGTAATCT | ||||
| ZNF678 intron 1 | 5'&3' | F | GGAAATGAACATAGTCTTACTGTCAGGTA | chr1:225878139 | ZNF678 exon 1~2 | F | TGCAGGTACTGGGAGTTACATAGC | BC042500 |
| R | CATAGAGTCCAGAAATGTGTCTATCCA | chr1:225878254 | R | TGCCAGTAGTCCCGTTTTCC | ||||
| ANO3 intron 14 | 3' | F | AAAGGATTGTGTAAGAGAAGCTGATAAGA | chr11:26568090 | ANO3 exon 14~15 | F | TTGTTCGATAATGGAGGGACAGT | BC172396 |
| R | GCAGAGATGTTATCCCTGTTGGT | chr11:26568167 | R | CGATAAGGTCCCAAGTATAGGTCAGT | ||||
| Intronic HERV-W proviral element (5' region) | ||||||||
| CD72 intron 1 | F | GCAGAGGTCTACTCACACCATAGC | chr9:35633414 | |||||
| R | GGCAATCAGGAGGCCTAAA | chr9:35633462 | ||||||
| TBX18 intron 7 | F | GGGCTACAGTGATCCATTTATAAGG | chr6:85488459 | |||||
| R | AAACTTTATCCAAACATTCCCTATGTTAG | chr6:85488532 | ||||||
| ANO3 intron 14 | F | TCTCCTTCACCACGAGAGTTTG | chr11:26576040 | |||||
| R | TGCTACTCGTCCAGAGCTTACAGA | chr11:26576091 | ||||||
| Intronic HERV-W pseudoelement (3' region) | Gene harboring pseudoelement | |||||||
| Sense | ||||||||
| SLC16A10 intron 1 | F | TGGCAGTGCTCGTTGAATGT | chr6:111566680 | SLC16A10 exon 1~2 | F | GGCTCCAAAGACGATGACAAG | BC034031 | |
| R | ACATAAGCCCCAAAACTGTCAGA | chr6:111566728 | R | AAATCATCCCCATGGAGAGAGA | ||||
| AK024261 intron 1 | F | GGCCCACCTCCAGCAAA | chr2:218160716 | AK024261 exon 1~2 | F | CAGCAGATGATGGTGATGGAA | AK024261 | |
| R | TGGGTGTGATCAGGTCATGGT | chr2:218160778 | R | CATCCCTCGGACTCAGTTTCTC | ||||
| Antisense | ||||||||
| FOXP2 intron 3 | F | CAAGAGGACATCTCTAAATCAAAGACTGT | chr7:113805180 | FOXP2 exon 3~4 | F | GCGAGGTTAATTCGAAAGTCTTGTGGAA | AF454830 | |
| R | GAGCATGCCAGGCAAAGC | chr7:113805235 | R | TTGCTTATTGTCTCTGTCGCAGAT | ||||
| APG5 intron 6 | F | TCAAATCACACAATGCTCCAATG | chr6:106791850 | APG5 exon 6~7 | F | ATCCCCTTTAGAATATATCAGACAACGA | BC093011 | |
| R | TTAGCAGTTGCATATGAGATCTTTCA | chr6:106791905 | R | CCTAGTGTGTGCAACTGTCCATCT | ||||
| KIAA0423 intron7 | F | GACATGAATATTTTTTGTGGACATAACTC | chr14:44557550 | KIAA0423 exon 7~8 | F | CCAACAAGACTTTCTTCTGCAAAG | AB007883 | |
| R | GCCAAACAGAACAGTACTAAACTATATTATAGACT | chr14:44557636 | R | TTTGCTGTGGATTTGATGATGAC | ||||
| NRCAM intron 2 | F | AAGTCTGGGTTCCAGGTTCATC | chr7:107772873 | NRCAM exon 2~3 | F | GCTGGTCTTAGCTGTTGGCATT | BC115736 | |
| R | CTGAGGAACCTTTCTGAGTTGAGTAA | chr7:107772929 | R | CGTCTTCTTAGCATTGCTCTTCAG | ||||
| ZMAT3 intron 2 | F | GGATTCCCAGGTACGGTGAAA | chr3:180258291 | ZMAT3 exon 2~3 | F | CTCTGCAATGTCACCTTGAACTCT | BC002896 | |
| R | CCTAGAAAGCTACTTCCGCTTCAG | chr3:180258381 | R | GCTGCATAGTAATTTCGGAGTTTCT | ||||
| Intronic HERV-W pseudoelement (5' region) | ||||||||
| SLC16A10 intron 1 | F | CAAGAGGACATCTCTAAATCAAAGACTGT | chr6:111558508 | |||||
| R | GAGCATGCCAGGCAAAGC | chr6:111558555 | ||||||
| FOXP2 intron 3 | F | TCAAATCACACAATGCTCCAATG | chr7:113813845 | |||||
| R | TTAGCAGTTGCATATGAGATCTTTCA | chr7:113813901 | ||||||
| NRCAM intron 2 | F | GACATGAATATTTTTTGTGGACATAACTC | chr7:107763923 | |||||
| R | GCCAAACAGAACAGTACTAAACTATATTATAGACT | chr7:107763973 | ||||||
| Intronic solitary LTR | Gene harboring solitary LTR | |||||||
| Sense | ||||||||
| ZNF 277 intron 1 | F | AGAACCCAGGTCAGAAAACAAGAG | chr7:111648615 | ZNF277 exon 1~2 | F | GGCTGTCGCCCGAATG | AF209198 | |
| R | CAGTCCCTGGTGCCAAGAAG | chr7:111648735 | R | ACAATCCTTACTGTCCCCATAACC | ||||
| WDR72 intron 14 | F | AAACACTATCTGATTGCCTGACAGA | chr15:51704774 | WDR72 exon 14~15 | F | CCAGCTTGGGCCATTACCTT | BX53788 | |
| R | CCAGGACCTTGTCTATGATGCA | chr15:51704828 | R | GCAAAATTTGGCATCAGTAACCT | ||||
| chrXq13.1 | F | CAGGTCCATTTAAAGCCCAAGT | chrX:71350691 | PIN4 exon 3~4 | F | CAGGTCCATTTAAAGCCCAAGT | AK12760 | |
| R | CCTGAAAGTGAAGCCAAAAGGA | chrX:71350741 | R | CCTGAAAGTGAAGCCAAAAGGA | ||||
| chrXq26.2 | F | TGGGAGAAGCAATGTCCAATT | chrX:131380909 | MBNL3 exon 1~2 | F | TGGCCTGTTTTGATTCTCTAAAGG | AB077698 | |
| R | TTTGTCAAGTCATGGCCGTTT | chrX:131380961 | R | AGTGTGGAGGAGGGTGAAGGT | ||||
| Antisense | ||||||||
| C9orf85 intron 2 | F | ACCCACCAATTCCGGATACA | chr9:73769452 | C9orf85 exon 2~3 | F | GAGTGGCGTGTAAAATACAGCAAA | BC052375 | |
| R | TGGCCCAAGATTTCATTCCT | chr9:73769523 | R | CATGGCCTGCACATTATGTGA | ||||
| UBD exon 1~2 | F | GATGGCTCCCAATGCTTCCT | AF123050 | |||||
| R | TGGCATCAAAGGTCATTAAATCC | |||||||
| chr6p22.1 | F | GCCAGATAACCAGCTTCTCTTCA | chr6:29635237 | GABBR1 exon 18~19 | F | GGAGTCGAGTGCATTTGCTTTAT | BC051463 | |
| R | GAGAAGAGGCTGGCATTGACA | chr6:29635286 | R | TGGCATCAAAGGTCATTAAATCC | ||||
| chrXq13.1 | ERCC6L exon 1~2 | F | GGAAGCCGAGGCCTTGAG | BC111486 | ||||
| R | TTAGTTGCTTCTTTGGCCTCTTTC | |||||||
| chrXq26.2 | AK095439 exon 2~3 | F | ACTTCATTGAATGTCTTAGACGGAAA | AK09543 | ||||
| R | TCACATATGCAGTTATCAAAAGAGCTT | |||||||
| Intergenic HERV-W proviral element and adjacent genes | Intergenic HERV-W pseudoelement and adjacent genes | |||||||
| LRIG3 (5') | F | TCGAGTAATTCTTTCATGGGTACCT | AY505340 | COBLL1 (5') | F | CAGAGTTTGCTGACTGCAATCC | BC071588 | |
| R | ATCTGATGGCTGTCCAAAGCTT | R | GACCTTCCATTCACAGATATTGTATTTG | |||||
| pro chr12q14,1 | F | TGGTCAAGAGGAGTCCAGAGTTT | chr12:57530852 | pse chr2q24,3 | F | ACCTACACCAATTCAGCTGTTAAGG | chr2:165222305 | |
| R | GCCCACCAATGCAATGCT | chr12:57530902 | R | CCACAATGCTCCGAGTTCACT | chr2:165222360 | |||
| AK093124 (3') | F | TGTCCCTTGCTACATACCTGCTT | GRB14 (3') | F | TGTGCTGCAGACAGGCGAAAA | |||
| R | TGCACTCAGATAAAGTGTCAATAAGAAG | AK093124 | R | CAGATGTAAATGGAGAACAGCATAGC | BC053559 | |||
| GSTA4 | N/A | GRK7 (5') | F | TGCAGGCTCTTCTTGGCTAAG | AF439409 | |||
| R | GTTTCCTGGGATCATCAGAATTTT | |||||||
| pro chr6p12,1 | F | GACCTTTTTCCTGGGCATCA | chr6:52887125 | pse chr3q23 | F | GGGTCCAAGGCTGCTCCTA | chr3:143023903 | |
| R | GGGTAGGTGAACATGCCAGAA | chr6:52887169 | R | GGTAAGCCTCCTGCACTCTGA | chr3:143023960 | |||
| GSTA3 (3') | F | GCGGAGACCGGCTAGACTTT | ATP1B3 | N/A | ||||
| R | CCGTCCATTGAAGTAGTGAAGCT | BC020619 | ||||||
| AKR1B10 (5') | F | TGCTGAGGAGATGGCAACCAT | B C008837 | CLSTN3 (5') | F | GGGATGACTCAGCTCTCACCAT | BC039075 | |
| R | TCCAAATGAGAGGATTGCAACAC | R | TCACACAGGACTGCCGATTC | |||||
| pro chr7q33 | F | TGGAAGAAACAAATTGCCTGATC | chr7:133929406 | pse chr12p13.31 | F | CAGAAAGGTTTTGCCTAGTAGTGTTG | chr12:7230506 | |
| R | AAATGCCCTTAGGCCAGATAGAT | chr7:133929455 | R | TGTGCTGTACTTCTGCTTTTTAGAAAT | chr12:7230605 | |||
| BPGM (3') | F | GGTGGCCCCTTTGCAGAT | PEX5 (3') | F | ATGCAGCAGATTGAGCAGTCA | |||
| R | TGGACATACTGATGGCTGAACTTC | BC01705 | R | CAGTTCTCAGACAAGGCCAAGTC | AK301700 | |||
| TMEM26 (5') | F | TGCCATCCTTGTTATATGGACTTG | CR749606 | INTS7 (5') | F | CACTGCAGAGTAAATCTGGACAAGA | BC020523 | |
| R | CAGGGCACACAACGTTCTGT | R | TCAACCCTTTGCTCCATCTCA | |||||
| pro chr10q21.2 | F | TGAAACGTGTCATGTATCATCTCAA | chr10:62462501 | pse chr1q32.3 | F | TCTGATGAACTCTGAATAAACTCTTTCT | chr1:210095554 | |
| R | GGTAACACCCGGCCATTTT | chr10:62462549 | R | G | chr1:210095648 | |||
| RHOBTB1 (3') | F | CCGCGGGAGCTTCCA | LPGAT1 (3') | F | GATTGCATGCCCTAATTATGGAA | |||
| R | CCATTTTCATAACTTAGTCAAGAATGCT | BC093035 | R | CCCTGAGAGATCACCGAGAAAG | BC034621 | |||
| LRRK2 (5') | F | GGTACACAAAAGCAGAAAGAGATACAA | chr7:133929455 | RNGTT (5') | F | GCCACGGAGCTTCTTCCA | BC019954 | |
| R | TTTGCACTTCATGTGGAAGATTG | R | CAAAAGTTTTCCTAATGCCTACAACA | |||||
| pro chr12q12 | F | GGGAGCAGATGAGGAGCAAA | chr12:39072588 | pse chr6q15 | F | CATCTCCTTGGTGACAGGGTTT | chr6:89180050 | |
| R | GGTGGACCTGGAAAATGGAA | chr12:39072637 | R | TGGTCACTTGATTTATAAGAAACGTGTT | chr6:89180152 | |||
| CR749517 (3') | F | TTTGACTTACTCGTTCACTGTGATCA | CNR1 (3') | F | CCACATAGGACTGGTTTTCAATTG | |||
| R | TGTGGCTGCTGTGCTGAAA | CR749517 | R | ATGCCTCCACCAGTGATTGC | AK313908 | |||
| GGCCATCTAGGATCGACTTCAT | ||||||||
Target, primer sequences and position of sequences used for assay design. The same orientation of HERV-W element or solitary LTR and genes harboring such elements is indicated by sense, whereas opposite orientation is indicated by anti-sense. For simplicity, intergenic HERV-W elements transcribed in the same orientation as their adjacent genes were selected. Genes located upstream and downstream of intergenic elements are labeled 5' and 3', respectively.