Table 3.

Computational prediction of transcription factor and microRNA binding to polymorphic regions within the Chga locus

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).