Fig. 3

Predicted miRNA target sites in the mouse Pax6 3’UTR. a Strategy for miRNA target site selection. A total of 6665 unique hits were identified within 876 bp of the Pax6 3’UTR using the miRNA target site prediction tool PITA. A unique hit encapsulates a single predicted MRE-miRNA interaction. Exclusion of predicted hits containing a single mismatch between the miRNA seed and the target site in the mRNA, and predicted 6mer target sites containing a G:U wobble base pair between the miRNA and the target reduced the number of hits to 449 and then 190, respectively. Requiring a high degree of conservation between orthologous mammalian Pax6 3’UTRs (≥85%), and requiring that targeting miRNAs also be present in humans reduced the number of predicted hits to 62 and 55, respectively. Since some miRNAs share common MREs, 42 unique MREs were identified (b) Schematic of the mouse Pax6 3’UTR showing locations and target site types for the 42 unique MREs. These MREs are predicted to be targeted by 47 different miRNAs. Some miRNAs are predicted to target multiple sites within the Pax6 3’UTR