I am in the process of choosing several model test mRNAs for further study. This is being done based on simple analysis of some deep sequencing data and by bioinformatics using a few simple criteria. One of the desired features is no alternative splicing in the 5' UTR. What is the best place to check (computationally) if alternatively spliced transcripts with different 5' UTRs are known? I have been pulling records from RefSeq using the gene product annotation, then manually checking the 5' UTR.
Dear George,
in general Ensembl will give you an idea of all the possible alternative splicing events for a given transcript. However, let me give you a word of warning: if you want to be absolutely sure that in your gene(s) of interest you have no alternative splicing at the 5'UTR level you should really perform an experimental validation in the cell lines/tissues of interest using 5'RACE techniques, etc.. all database annotations, especially at the 5'UTR and 3'UTR gene levels, are still full of mistakes (this will improve over time, of course, but at the moment I would not assume any prediction that wasn't backed up by some experimental data). Hope this helps,
Emanuele
Thanks.... I understand the importance of doing my own 5' RACE and defiantly intend to do this. But if a given transcript already as annotated isoforms differing in the 5' UTR I can cross those off the list right off the bat.
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