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 |