suppose we have a gene A which produces 4 diffrent isoforms. if a specific miRNA target gene A, which means that it's target all 4 isoforms of it ?
A miRNA targets a seed region in gene's 3' UTR. So if all 4 isoforms share the same UTR, it targets all of them, otherwise it depends on individual 3' UTR composition of isoforms.
@Mikhail, thanks. now the question is that whether all isoforms of a single gene have identical 3' UTR ?
Well if you ask about a concrete gene, you can manually look for it in a genome browser (http://genome.ucsc.edu/). If you have a bulk list of genes, then the task is quite hard. You need to download gene tracks with coordinates (Tables -> RefGene track at http://genome.ucsc.edu/), and see if the cdsEnd, the number and coordinates of 3' UTR exons are the same between isoforms. Some of the exons will be wholly or part of 3' UTR (span the region from cdsEnd to transcriptEnd), and they all need to be compared.
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