Primer sequences and restriction enzymes used to screen the selected SNPs
| SNP | Position on chr. 11 (Mb) | Primer sequences | Restriction enzyme | Frequency in controls | |
|---|---|---|---|---|---|
| Single nucleotide polymorphisms selected for genotyping of the RAPSN N88K founder allele. Information about the position of the SNP on chromosome 11 and the flanking sequences for PCR primer design and selection of an appropriate restriction enzyme have been retrieved from the NCBI SNP database (accessed December 2003). The last column represents the frequency of the polymorphisms in a group of 40 European control alleles. | |||||
| 1 | rs1446331 A/G | 44.745543 | 5′- TCCATCCACCCAGTCATTTTC -3′ | RsaI | 40.0% A |
| 5′- GAGAAATGGATGGATGGGTAGTGTA -3′ | |||||
| 2 | rs728516 C/T | 45.565115 | 5′- GGCTCCAGAAACTCCACCCTG -3′ | MseI | 70.0% T |
| 5′- CTTCCTGAGTCGTTTTGGCTC -3′ | |||||
| 3 | rs7476 A/C | 46.307143 | 5′- CACTGTACAGAGACCAAGAAC -3′ | HinfI | 62.5% A |
| 5′- ATGTGCTGAGCTGATGAAGAG -3′ | |||||
| 4 | rs3136516 A/G | 46.725065 | 5′- CCTGTGAAGGTGACAGTGGGG -3′ | EcoNI | 52.5% A |
| 5′- TCAATGACCTTCTGTATCCAC -3′ | |||||
| 5 | rs2279438 T/A | 47.168484 | 5′- CTACTTGTCTAGGGGAGGAGCCGA -3′ | Bsp143I | 82.5% A |
| 5′- TCCTCCACCCGCTGTACCGTG -3′ | |||||
| 6 | rs2278890 C/T | 47.363911 | 5′- GGTTTCCTCCCTGGAACTCCTG -3′ | AvaI | 37.5% T |
| 5′- CTCTCTACCACCGCCTTCAC -3′ | |||||
| 7 | rs2293577 T/C | 47.401511 | 5′- GCGCCTGTCCCCAGCCATGC -3′ | HpaII | 65.0% T |
| 5′- GTCCCAGCAGGGCAAGGCCTC -3′ | |||||
| 8 | rs4282946 C/T | 47.420511 | 5′- GGCGCAGTGATATGCCAACAG -3′ | MseI | 72.5% T |
| 5′- GAGCCCATCCAAGCTGGCTCC -3′ | |||||
| 9 | 1143C/T | RAPSN exon 7 | 5′- AAGTGGCTGAGACCGGAGCCTA -3′ | Sequencing | 72.5% C |
| 5′- TTAAGCCAGCTGGGCCCTAGAGT -3′ | |||||
| 10 | IVS3–11C/delC | RAPSN intron 3 | 5′- GCAGAGGAGTTGGCCTGAGCCACAGG -3′ | StuI | 72.5% delC |
| 5′- TGCATCCCGGTGACCTCACCTC -3′ | |||||
| 11 | 456 C/T | RAPSN exon 2 | 5′- GAGAGCTTCGAGAAGGCCCTGCGGTA -3′ | RsaI | 72.5% C |
| 5′- GCCACAGGGTGTGTGCCTCA -3′ | |||||
| 12 | −365 G/A | RAPSN promoter | 5′- TGAGTGACCCACGGTGCTCAG -3′ | MnlI | 92.5% G |
| 5′- AGGCCTTGGGCTAGAGGTGCTC -3′ | |||||
| 13 | rs2242081 T/C | 47.464576 | 5′- TATCAGAGAACAGCCTCAGTC -3′ | RsaI | 37.5% C |
| 5′- CCAATGGGAGGTAAGTGTTTC -3′ | |||||
| 14 | rs2280231 C/T | 47.564747 | 5′- ACCCGCCTGGTTCTTCAGCGTC -3′ | Eco47I | 25.0% T |
| 5′- AGGAGGGAACGCAGGTGAGAAAG -3′ | |||||
| 15 | rs3817334 C/T | 47.615302 | 5′- ACTATTCATAACTGTAAGCAGG -3′ | TaiI | 45.0% T |
| 5′- CCATTCTTGCTTTGTAATTTTTCAC -3′ | |||||
| 16 | rs9909 C/G | 47.764084 | 5′- CTTCATTGGTCAGATTTAGAAGC -3′ | Bst1107I | 57.5% C |
| 5′- AAGTATATAATGTAAATATGGTATTG -3′ | |||||
| 17 | rs2270994 A/G | 48.122178 | 5′- GAGACAGTTAGAGTGGCTGTTC -3′ | MnlI | 52.5% G |
| 5′- GGCACCTTATATAACATCACC -3′ | |||||
| 18 | rs2299650 G/T | 49.138316 | 5′- ACAAATGAAAGTAATGTGATG -3′ | SduI | 60.0% G |
| 5′- TGCTATCAGAAAAGCATGGAG -3′ | |||||
| 19 | rs1880438 C/T | 49.335007 | 5′- TCCTTCACTAACTGAAGGTGAG -3′ | SfaNI | 77.5% C |
| 5′- TACGTATCTCTGATTCAGTACG -3′ | |||||
| 20 | rs1916207 C/T | 50.500285 | 5′- GTGTAACTCTGAGAGACTAATG -3′ | HinfI | 32.5% C |
| 5′- GGGGTTTGGAAACACTGTTGTGG -3′ | |||||
| 21 | rs507015 G/A | 51.454648 | 5′- ACAGCCACTGGATGAAATGTTC -3′ | HpaII | 62.5% A |
| 5′- TTTTGTATCCAAGGTCTTCC -3′ | |||||