Question: If Mirna Target A Gene, It Target It'S All Isoforms ?
0
gravatar for jack
5.3 years ago by
jack420
jack420 wrote:

Hi all,

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 ?

genomic mira • 1.5k views
ADD COMMENTlink modified 5.3 years ago by mikhail.shugay3.3k • written 5.3 years ago by jack420
2
gravatar for mikhail.shugay
5.3 years ago by
mikhail.shugay3.3k
Czech Republic, Brno, CEITEC
mikhail.shugay3.3k wrote:

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.

ADD COMMENTlink written 5.3 years ago by mikhail.shugay3.3k

@Mikhail, thanks. now the question is that whether all isoforms of a single gene have identical 3' UTR ?

ADD REPLYlink written 5.3 years ago by jack420
2

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.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by mikhail.shugay3.3k
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