Table 1. Primer sequences for COBRA.
| Forward and reverse primer sequences | Product length (bp) |
Annealing (°C) |
Restriction enzyme |
Bovine features of the sequences including the target CpG | Accession No., location | Target ID of array | |
| CpG1 | 5'GTTTTATTTTATTTTGTTTTTTTT3' | 181 | 50 | TaqaI | mitochondrial glutamate carrier 1 isoform | AC_000186.1, 50835888 | cg27100471 |
| 5'ACCATTCTACTAATTCTACAACCT3' | |||||||
| CpG2 | 5'GGGTTTTAGGTAGATTAATTAGGTT3' | 112 | 54 | AciI | ubiquitin-conjugating enzyme E2 D2, CXXC-type zinc finger protein 5 isoform | AC_000162.1, 52499000 | cg26301389 |
| 5'CTCTAAAACACAAACCCCAAAAC3' | |||||||
| CpG3 | 5'GGGATTTGGTTAATATGATAGGTTT3' | 294 | 54 | TaqaI | leucine-rich repeat and fibronectin typ-III domain-containing protein 3 precursor | AC_000175.1, 46821245 | cg15658249 |
| 5'CCTCCCAAAACAACTACTCCA3' | |||||||
| CpG4 | 5'TGTTATTTGTTGGTTAGAGGGTGTAT3' | 203 | 52 | BstUI | myosin-9 | AC_000162.1, 75099407 | cg01816775 |
| 5'ATAATAATACCAAACCTCTCCTCCC3' | |||||||
| CpG5 | 5'GTTGGTGGAGGATAGTAGGGTTA3' | 191 | 52 | BstUI | Transmembrane protein 125 | AC_000160.1, 103338929 | cg14088090 |
| 5'CCAAATCAACCATATCTAAAAAAAA3' |