Table 3.
Polymorphism | Location in gene | Predicted TF | WKY ConSite score | SHR ConSite score |
−1694 Ins/Del | Promoter | Hand1 (MA0092, +) | 5.828 | 6.090 |
Pbx1 (MA0070, −) | 8.101 | 7.716 | ||
A-1616T | Promoter | Irf1 (MA0050, −) | 7.822 | n/a |
Sox17 (MA0078, +) | 7.255 | n/a | ||
−753 Ins/Del | Promoter | Foxd3 (MA0041, −) | 9.407 | 8.520 |
C-177T | Promoter | E2f1 (MA0024, −) | 6.381 | n/a |
Brachyury (MA0009, −) | 7.749 | 12.466 | ||
C-59T | Promoter | Foxi1 (MA0042, +) | n/a | 8.300 |
Mycn (MA0104, −) | 4.675 | n/a | ||
Rreb1 (MA0073, −) | 8.543 | 9.205 | ||
Polymorphism | Location in gene | Predicted microRNA | WKY free energy | SHR free energy |
G + 174T | 3′UTR | rno-miR-22 | −22.9 kcal/mol | −23.71 kcal/mol |
rno-miR-320 | n/a | −22.6 kcal/mol |
The ConSite algorithm predicted differential binding (indicated by difference in score) of 10 transcription factors to regions within the Chga promoter containing the five polymorphisms discovered through resequencing. Transcription factor JASPAR accession number and DNA strand binding orientation (+ or −) are listed in parentheses following the transcription factor symbol. The MicroInspector tool predicted differential stability of hybridization (indicated by difference in free energy) between two microRNAs and the region of the Chga mRNA 3′-UTR containing the G + 174T polymorphism. A lower free energy indicates a more stable interaction between microRNA and mRNA.
TF, transcription factor; n/a, not applicable (no binding or hybridization was predicted).