Table 2.
RD3 primers used for amplification of canine cDNA (A), for rcd2 mutation screening (B), and to develop hybridization probes (C). Primers RD3NH3F1 and RD3NH3R1 were designed for amplification of deaminated DNA.
| Primer | Sequence (5’ to 3’) | Source | Location | CanFam2.0 |
|---|---|---|---|---|
| A. Primers used to amplify canine RD3 cDNA | ||||
| 36R1A | gtggatcttggcacagacgtcctct | Canine | Canine exon 3 | 12,835,497–521 |
| 36F9 | cgcagtaacgcgctcaggaaggtct | Canine | Canine exon 3 | 12,835,601–625 |
| 36F18 | ccaggctggatccctccggtca | Canine | Canine exon 1 | 12,847,140–161 |
| 36R16 | agtcatctgaaggcactccagacct | Canine | Canine exon 6 | 12,820,212–236 |
| 36JR2 | gcagcgactacgcctccaggaacaat | Canine | 3’UTR v2 | 12,832,366–391 |
| 36e2R2 | cgctccacgtcctcggagatggt | Human | Human exon2 | |
| 36F2 | gtgctggagacgctcatgatgga | Canine | Canine exon 3 | 12,835,669–691 |
| 36R1 | gatcttggcacagacgtcctcta | Canine | Canine exon 3 | 12,835,500–522 |
| 36e2F3og | cggctcttccgctcggtgct | Canine | Canine exon 4 | Missing in CanFam2.0 |
| 36e2ogR16 | ggcgcccggaattcgggcatg | Human | Human exon 2 | |
| 36e2ogR13 | cggctttgggcgcccggaattc | Human | Human exon 2 | |
| 36BACR2 | ggaaggcccgctccctcccgtg | Canine | 3’UTR v3 | Missing in CanFam2.0 |
| 36JR3 | ctgaatctccagagccgcgacacc | Canine | Canine exon 4 | Missing in CanFam2.0 |
| 36e2F7og | ctcgcccttcgccggccacatc | Canine | Canine exon 4 | Missing in CanFam2.0 |
| 36e2F30 | ccccggccctggagcctgcg | Canine | Canine exon 4 | Missing in CanFam2.0 |
| 36e2R30 | gcaggctccaggtgcgcagc | Canine | Canine exon 4 | Missing in CanFam2.0 |
| 36e2R31 | cggaactcgggcaggctccaggtg | Canine | Canine exon 4 | Missing in CanFam2.0 |
| 36e2R32 | cctgcggcgcccggaactcg | Canine | Canine exon 4 | Missing in CanFam2.0 |
| B. Primers used to screen the rcd2 mutation | ||||
| RD3NH3F1 | tgagtgtgagtttgaggtgtatgagg | Canine | Canine exon 4 | Missing in CanFam2.0 |
| RD3NH3R1 | cacacacaaaacccacaaaaatcc | Canine | Canine exon 4 | Missing in CanFam2.0 |
| C. Primers used to produce PCR probes for BAC DNA hybridization | ||||
| RD3F2 | gtggtgtccatcctctgctggt | Canine | Canine exon 5 | 12,832,565–586 |
| RD3R2 | ccctacaggcttcgctgtcctt | Canine | Intronic sequence | 12,832,000–021 |
| RD3F4 | tgcaagagcccatagaacacca | Canine | Intronic sequence | 12,835,201–222 |
| RD3R4 | gtaaagggatgcagatccaccg | Canine | Intronic sequence | 12,834,685–706 |
| 36e2F1c | gttccggcagctgctggccga | Canine | Canine exon 4 | Missing in CanFam2.0 |
| 36e2ogR16 | ggcgcccggaattcgggcatg | Human | Human exon 2 | |