There are many way arrange exon in the alternative slicing, so how to identify what exon and exon's order in the mature mRNA ???
Hi,
There are many ways of identifying alternative splicing events, either by whole-transcriptome analysis or gene specific assays.
For global analysis, you can use either microarrays or RNA-seq, but you need someone to analyze the data and that is not trivial.
For gene specific assays, first check the exon/intron structure of the region of interest and identify known splicing events. Remember that many splicing events are tissue-specific or developmental stage specific, so you will always need to validate their expression in your conditions of interest. To visualize a splicing event, you can use PCR primers to amplify either several splicing events at the same time, or isoform specific primers. If you want quantitative data you will have to use either radioactive PCR, or Q-PCR. Also remember to sequence the PCR bands of interest to insure of the sequence.Alternatively you can also perform Northern Blots.
Hope it helps
Good luck,
Best
Thank prof. Olga,
It is very happy day to receive your answer this morning. It help me so much.
Because I want to obserb the differences between mature mRNA of usual and unusual cell so I think that PCR is the best way (according to your answer I can see that PCR technique might give me the results of exon's order). Therefore, I will try to learn how to design primers for identifying exon's order. If you have more experiment about my problem, please give some advice.
thanks and best regards.
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