Appendix 8 of Eiberg, Mol Vis 2019; 25:1-11.
Results of miRNA target prediction. The genomic region around the RP1-140A9.1 SNP (chr1: 1,891,852 G/C, hg38) showing the following tracks from top to bottom: “miRNA target predictions by TargetScan” shows miRNA target (miRT) sites as predicted by TargetScan . Note that TargetScan requires an exact complement match to the seed sequence (only the seed sequence is marked). The set of miRNAs is limited to those were the mutation is predicted to create or destroy a binding site by either TargetScan or miRanda. For the predictions that overlap the mutation position, it is indicated whether the binding site is specific to wild-type “(WT)” or mutant “(MUT)”. Additional target sites for those miRNAs predicted along the transcript are also shown. Different miRNAs are highlighted with individual colors and labeled with miRT-XXX which refers to predicted target site for hsa-miR-XXX. “miRNA target predictions by miRanda” same details as above but for miRanda  predictions. “Repeat region” displays the location of the self-complementary “CAGCTG” repeats in the lncRNA transcript. The repeats that are common in wild-type and mutant sequence are shown in dark blue; the new repeat formed by the mutation is highlighted in light blue color. “Mutation” indicates the position of the G to C mutation in the lncRNA gene.“Ensembl Gene Predictions” shows Gencode v24, transcript of RP1-140A9.1. “cDNA_1: Found in B-lymphocyte cDNA in this study (Figure 2 lane 1), cDNA_2: Found in universal RNA, fetal eye and lens cDNA in this study /Figure 2 lane 3,4 and 5). 1. TargetScan software for prediction of microRNA targets: http://www.targetscan.org/ 2. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol 2003; 5:R1.1-R14. To access the data, click or select the words “Appendix 8.”