since you're interested in isoform level, you could download the predicted miRNA binding sites and look for the ones that specifically overlap with your transcript coordinates. also notice that TargetScan and microT are focused on the 3'UTR of genes, while microT-CDS is analyzing the whole coding sequence.
Finding Mirna Binding Site In Transcriptome Of An Organisim
1 answer
you can try TargetScan http://www.targetscan.org/vert_50/, microT http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microtv4/index or microT-CDS http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index. In all cases you can download the predicted miRNA sites or submit your gene list query.
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