With the iodinated TxR agonist [125I]BOP, TxA2 binding sites were detected throughout the kidney.
Overlapping σ-factor binding sites were detected frequently in Escherichia coli: e.g. 38 genes were assigned to 4 different sigma factors and 2 genes were even assigned to 6 sigma factors (Cho et al. 2014).
Potential binding sites were detected with the grid-based cavity prediction algorithm.
ISRE (IFN-stimulated response element), GAS (gamma-activated sequence), and hepatocyte nuclear factors HNF1 and HNF3 [34] binding sites were detected with CONSITE (http://asp.ii.uib.no:8090/cgi-bin/CONSITE/consite/ 8090/cgi-bin/CONSITE/consite/ally.
Although no transcription factor binding sites were detected around SNP-638 by this program, it should be noted that SNP-638 had the same statistical association as SNP-358.
55 different TFs binding sites were detected with high confidence, of which the most frequently found were those for CRP, Fis, PhoB, RhaS, PurR and FNR (Table S4 and Figure S6), of which, CRP, Fis and FNR are general TFs that regulate many genes in E. coli (Table S5).
This is a phenomenon arising from the integration of cavity detection into the workflow and represents a case where two overlapping binding sites are detected (depicted in red and yellow).
To test the MAR potential of this newly identified fragment, the core sequence of this fragment with predicted SATB1 binding sites was detected for the SATB1 binding capacity by EMSA.
Moreover, no binding of these two proteins in the Xenopus haemoglobin promoter which lacks Pax2 and Sox2 binding sites was detected, confirming the specificity of Pax2 and Sox2 binding to the endogenous Xenopus HCNR 81675 (Figure 6B and quantitative PCR results shown in Figure 6C).
