Table 6 Functional annotation of SNP identified in the 14 positional candidate genes, from sequencing data of 28 parental chickens of the Embrapa F2 Chicken Resource Population
Genetic variants annotation | Positional candidate genes | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PTPN11 | RB1 | TNFSF11 | ITGB4 | SLC6A4 | GTF2F2 | SPERT | KCTD4 | HTR2A | PCDH7 | LCORL | LDB2 | NR4A2 | GPD2 | |
3′ UTR1 | – | 20 | – | – | – | 10 | – | 6 | – | – | 5 | 3 | 14 | – |
5′ UTR2 | 1 | 2 | – | – | – | 1 | – | – | – | – | – | – | 1 | – |
Downstream | 57 | 94 | 104 | 127 | 70 | 129 | 54 | 80 | 60 | 16 | 127 | 80 | 83 | 88 |
Intron | 290 | 1431 | 332 | 436 | 150 | 1849 | 13 | – | 404 | 1789 | 811 | 3138 | 14 | 490 |
Non-synonymous | – | 2 | 3 | 9 | 4 | – | – | – | – | 1 | – | – | 7 | – |
Splice region (synonymous) | – | – | – | 3 | 2 | – | – | – | – | – | – | – | 1 | – |
Splice region (intron) | 2 | 3 | – | 8 | – | – | – | – | – | – | – | – | – | – |
Synonymous | 5 | 15 | 4 | 49 | 11 | 2 | 2 | 1 | 3 | 7 | – | 1 | 16 | 8 |
Upstream | 97 | 101 | 90 | 296 | 89 | 90 | 66 | 106 | 64 | 12 | 52 | 42 | 60 | 35 |
Total | 452 | 1668 | 533 | 928 | 326 | 2081 | 135 | 193 | 531 | 1825 | 995 | 3264 | 196 | 621 |