Table 2 Oligonucleotide sequences used for EMSA. For every SNP, 4 oligonucleotides (2 complimentary pairs) were synthesized, one pair for each allele. One oligonucleotide sequence from each pair had additional GG dinucleotide overhangs at the 5'end for fill-in labeling reaction. Care was taken to make sure that the additional GG-dinucleotide did not influence the predicted TF binding capability. The complementary sequences lacked the GG pairs. Only the allelic sequence predicted to bind most stably was chosen for the fill-in labeling reaction (marked *) while the gel shift assays were carried out using competitor with a perfect match versus a competitor with the allelic mismatch. The polymorphic site is underlined. Column 'Ratio' shows the difference in competition between the labeled and non-labeled oligomers at 25-fold excess, by dividing Allele2 (x25) values by Allele1 (x25).
From: Identification of functional SNPs in the 5-prime flanking sequences of human genes
Gene name and rs ID | Sequence | Allele 1(competitor oligo is a perfect match) | Allele 2 (competitor oligo has a mismatch) | Ratio | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
x5 | x10 | x15 | x20 | x25 | x5 | x10 | x15 | x20 | x25 | |||
Serotonin receptor (5-HT-1A) rs968554 ENST00000323865 | GGAAAAGAATCCA C TTGGGCCAATG * GGAAAAGAATCCA G TTGGGCCAATG | 1.29 | - | 1.27 | 1.23 | 1.00 | 1.16 | - | 1.12 | 1.13 | 0.96 | 0.96 |
Dopamine receptor DRD1 rs267412 ENST00000329144 | GGAATGTAAA CCC AACACAAAAG * GGAATGTAAG CCC AACACAAAAG | 0.72 | - | - | 0.54 | 0.56 | 0.98 | - | 1.06 | 1.03 | 1.12 | 2.05 |
Dopamine receptor DRD1 rs267413 ENST00000329144 | GGTATAAAAGTCA GTGAATACAG * GGTATAAAAGTCT GTGAATACAG | 0.96 | - | 0.81 | 0.74 | 0.81 | 0.97 | - | 0.98 | 0.97 | 1.01 | 1.24 |
Muscarinic acetylcholine receptor M1 rs509813 ENST00000306960 | GGCTTGGGCTCCT CCCC CCAGCCAAC * GGCTTGGGCTCCT CCCG CCAGCCAAC | 0.21 | 0.11 | 0.08 | 0.05 | 0.09 | 0.70 | 0.60 | 0.46 | 0.46 | 0.37 | 4.11 |
Follicle stimulating hormone receptor. rs2882225 ENST00000304421 | GGCAAGGGAGCTG TTTTTTTT GGCAAGGGAGCTT TTTTTTTT * | 1.10 | 1.00 | 0.86 | 0.71 | 0.75 | 1.96 | 1.73 | 1.67 | 1.36 | 1.35 | 1.80 |
Adenosine-A3 receptor. rs1538251 ENST00000241356 | GGTGGCCACCAGA GGGC AGCACG * GGTGGCCACCAGA GGGA AGCACG | 1.08 | 1.11 | 0.95 | 0.89 | 0.76 | 1.49 | 1.41 | 1.44 | 1.51 | 1.40 | 1.84 |
Bradykinin receptor B2 rs1800508 ENST00000306005 | GGGAAGTGCC CAG GAGGC * GGGAAGTGCT CAG GAGGC | 1.67 | 1.28 | 1.17 | 1.16 | 1.20 | 1.10 | 1.06 | 1.11 | 1.27 | 1.33 | 1.03 |
Bradykinin receptor B2 rs945032 ENST00000306005 | GGTTCCTGGGTG C GGG * GGTTCCTGGGTA C GGG | 0.88 | 0.72 | 0.72 | 0.62 | 0.55 | 1.15 | 1.22 | 1.29 | 1.22 | 1.27 | 2.30 |
Bradykinin receptor B2 rs1799722 ENST00000306005 | GGCTGGGTAG TGA TGTCATCAGC GGCTGGGTAA TGA TGTCATCAGC * | 0.36 | 0.21 | 0.16 | 0.12 | 0.12 | 0.50 | 0.29 | 0.22 | 0.20 | 0.20 | 1.66 |
Calcitonin receptor precursor rs2528521 ENST00000316576, ENST00000248548 | GGCTGTCCCCGGA GTGG CGGCT GGCTGTCCCCGGA GTGA CGGCT * | 0.54 | 0.36 | 0.25 | 0.22 | 0.21 | 0.90 | 0.83 | 0.73 | 0.60 | 0.55 | 2.62 |