Table 2.
Overview of oligonucleotides used for Q-PCR analysis and deletion-specific breakpoint PCR
| Location | Taqman oligonucleotides | cDNA numbering 5′–3′ |
|---|---|---|
| Promoter | ggctcagcgtggttgtgact | c.−415 − 516 |
| tctttggcgctttcattcagt | c.−415 − 458 | |
| cctcapgtcacgcagc | c.−415 − 495 | |
| Exon 2 | tttctagggtgaggatggttctaca | c.−332 |
| agggcgcacctttcaactaag | c.−271 | |
| agclaclcgpagtt | c.−306 | |
| Intron 3 | tgtcttactgttccctaggccttt | c.−124 + 398 |
| cccaacatcaatccacattcac | c.−124 + 462 | |
| cttaaapglapaapctg | c.−124 + 423 | |
| Exon 4 | cgtgggctgtcctgtgaaa | c.378 |
| agcgtacaactccaggaaattttt | c.442 | |
| tacegltpapatltgg | c.398 | |
| Exon 5 | ggagaaacaatagaatctggaacagtt | c.721 |
| ccacaccaacaaaatatcctaagct | c.802 | |
| tgtgatpttttglcapgaa | c.754 | |
| Exon 6 | ggcaactgggatggaagatt | c.820 |
| ttgtactttcaacacacgcaaaact | c.883 | |
| atgpaptpceglttt | c.842 | |
| Exon 7 | ctcaaatccactgtgggtgatatc | c.914 − 42 |
| tccaacacgacacttaggagtca | c.922 + 26 | |
| tttttpctgalacalagc | c.914 − 17 | |
| Exon 8 | agagtgtgacgcaggaaagga | c.923 |
| tgtccccaacacctcttgaca | c.985 | |
| cctcclaaalttpcctt | c.946 | |
| Intron 9 | tgtgcagtgaaggtgcatga | c.1138 + 537 |
| cccctaagaccctgagaaaaatc | c.1138 + 602 | |
| ctgtpapaatalaclaaag | c.1138 + 559 | |
| Exon 10 | tggccacagtccactttctct | c.1299 |
| cgggtgcagtgtttagctctt | c.1360 | |
| tcapcclagtltptaatg | c.1321 | |
| Exon 11 | gctgtacggatggaaccttca | c.1535 |
| cacaaacagcgccttcttca | c.1602 | |
| tcggtatttlalctgtgcc | c.1563 | |
| Exon 12 | cttggagataatgattgggaagaag | c.1749 |
| gaataaggttgagtctaagtaacaagaattgt | c.1824 | |
| aagglatclagpgtc | c.1775 | |
| Exon 13 | tcttttgcagcttatttgcttttagt | c.1827 − 10 |
| catcgttcttttctttgggtctaagt | c.1888 | |
| ctgttltpgacaltgtg | c.1844 | |
| Intron 14 | aaagattcaccacctgactttgaat | c.2042 − 399 |
| ttcctgcaagcctctgaacatt | c.2042 − 326 | |
| tgtlapcaglataltgta | c.2042 − 373 | |
| Intron 15 | agcgccttcattttagaaatgaa | c.2109 − 456 |
| tgctggatgtgacagaccctta | c.2109 − 390 | |
| agttlgazctapaapgtc | c.2109 − 432 | |
| Intron 16 | tcaagattattgaactctgtgacctctag | c.2242 − 243 |
| caagtcttcaagtggctcatgatc | c.2242 − 173 | |
| tgctpgtgtpcccc | c.2242 − 213 | |
| Exon 18 | ctcacatttcagctcccagaca | c.2351 − 12 |
| gcattctctacactcatacattgcaa | c.2406 | |
| tgccgpatatgtpgagg | c.2362 | |
| Exon 19 | cccagtgtcacttcccaaaga | c.2508 |
| aagggatgcagccgtgtct | c.2566 | |
| ttacclgactpggactg | c.2530 | |
| Exon 20 | aagatgtctctggaagacctgcat | c.2749 |
| ttcgtgcacagccttgga | c.2809 | |
| ccttpgactccapgaga | c.2774 |
| Primers for deletion PCR | ||
|---|---|---|
| c.2686+60_*3340del5362 | ||
| Forward | cccagtgtcacttcccaaaga | c.2508 |
| Reversed | tcgtccctactctgccactt | c.*3563 |
| Internal | cctcaagccccttaaacctc | c.2686 + 715 |
cDNA numbering is according to reference sequence NM_015247_2. In the oligonucleotides used in the Taqman assay, the following abbreviations are used for the LNA incorporations: E, A-LNA; L, C-LNA; P, G-LNA and Z, T-LNA