Table 1.
PCR primers and conditions for CoBRA analysis
| IAP | Clade | Position | Forward primer | Reverse primer | Nearest gene | Distance | Cycles | Temperature (°C) |
|---|---|---|---|---|---|---|---|---|
| CabpIAP |
1 (red) |
chr2:154179911-154180159 |
ATTATTTTTTGATTGGTTGTAGTTTATGG |
CACCAACATACAATTAACA |
Cdk5rap1 |
intron |
39 |
47 |
| iap31 |
1 (red) |
chr1:89356306-89357454 |
TAAGAAGTAAGAGAGAGAAGTAA |
CCAAACAAATCCAAAAACCTAA |
- |
- |
45 |
52 |
| iap44 |
1 (red) |
chr10:77413077-77414228 |
GGTTAGGAAGAATATAATAATTAG |
CTAAAAATAAAACCCAAAAACCC |
Trpm2 |
Intron |
45 |
52 |
| iap51 |
1 (red) |
chr12:53835543-53836696 |
GGGAAAAATAGAGTATAAGTAG |
TCTAACAACTACCCACAAAAAAT |
Akap6 |
Intron |
40 |
52 |
| iap77 |
1 (red) |
chr17:64098002-64099153 |
AAGTAAGAGAGAGAGAAAAT |
TATAACCCCCAAATAACTAACAT |
- |
- |
45 |
52 |
| iap90 |
1 (red) |
chr18:47812857-47814008 |
GGGAAAAATAGAGTATAAGY |
CACTAAAAACAACAATCTAACAAC |
Gm5095 |
Intron |
43 |
52 |
| iap110 |
1 (red) |
chr2:72112889-72114056 |
AAGTAAGAGAGAGTAAGAAGTAA |
CATATACAACACTTAAAACAAAACC |
Rapgef4 |
18 kb upstream |
45 |
52 |
| iap176 |
2 (green) |
chr1:127212941-127214106 |
TTTATATTTTTGGGAGTTAGG |
AACACTCTTCTACAATAACATCT |
- |
- |
40 |
52 |
| iap182 |
2 (green) |
chr1:26288894-26290059 |
TGTTTATATTTTTGGGAGTTAG |
AACCTACTTCATCTTAAAAC |
- |
- |
45 |
52 |
| iap186 |
2 (green) |
chr10:24567718-24568883 |
GTATTATTTTTTGATTGGTTGTAG |
AAACCCACTAATTCTTCCTAT |
Enpp3 |
12 kb upstream |
40 |
52 |
| iap195 |
2 (green) |
chr12:25079835-25080998 |
TTGTTTATATTTTTGGGAGT |
CACCTTATATTCTCCAAAAAAAC |
- |
- |
40 |
52 |
| iap236 |
2 (green) |
chr4:155057154-155058318 |
GTATTATTTTTTGATTGGTTGTAG |
AATTTTTTTCCCCTTCAATC |
Mib2 |
15 kb upstream |
45 |
52 |
| iap268 |
2 (green) |
chr9:123106561-123107725 |
TTTATATTTTTGGGAGTTAGG |
ACACCTAACATCATCTAAAT |
Cdcp1 |
Intron |
45 |
52 |
| iap281y |
2 (green) |
chrY:2136760-2137925 |
GGTTAGGAAGAATATTATAGA |
TACACCAAAAACAAACCAAA |
Rbmy1a1 |
8 kb downstream |
45 |
52 |
| iap506 |
3 (black) |
chr12:74416066-74417247 |
AGTAAGAAGTAAGAGAGTAAGAA |
CTACACCCCAAAAATAATAAAAAC |
Slc38a6 |
Intron |
45 |
52 |
| iap655 |
3 (black) |
chr15:11992027-11993248 |
AGAGAAAAGTAAGAGAGAGAAAA |
AAAACAAAAAAAACTACACCC |
- |
- |
45 |
52 |
| iap1112 |
3 (black) |
chr6:101092968-101094168 |
TAAGAGAGAGAGAAAAGTAAGAGA |
CCACCAAAATAAAAACTCAAAAC |
Pdzrn3 |
6 kb downstream |
43 |
52 |
| iap1248 |
3 (black) |
chr8:63849572-63850723 |
TTTTTAGGAGTTAGAGTGTA |
CTCCTTTCTAATTTTATTCTCCA |
Sh3rf1 |
Intron |
45 |
53 |
| iap1252 |
3 (black) |
chr8:47435363-47436559 |
AGAAAAAGTAAGAGAGAGAGAAA |
AACCCTAAAATTCCTCAAAAAAC |
Helt |
56 kb upstream |
40 |
54 |
| iap1259 |
3 (black) |
chr8:8319882-8321071 |
AAGAAGTAAGAGAGTAAGAAGTAA |
ACAAAAAATCAACTAAACTCTAC |
- |
- |
45 |
53 |
| iap1334 | 3 (black) | chr9:121236806-121238001 | AAGTAAGAGAGAGAGAAAAGTAA | RACTACTACTAAAAACCCACAA | Trak1 | Intron | 40 | 54 |