I performed an RT-PCR on my gene of interest hoping to see which isoforms are present on the mRNA level. Literature suggested there should be 4. To my surprise, i see lots (too many to count) of transcripts of various sizes. I isolated about 50, sequenced them, and aligned them to the original gene cDNA. Majority of the transcripts I isolated have chunks of sequence missing at seemingly random places, with random chunks of exons would be missing here and there. some has majority of exons missing.
I am wondering if transcription often produce these aberrant transcripts or is something unique going on here?
Hi
the main point is to know wether you used total RNA or polyA+ RNA. Since in total RNA you'll get mature and non-mature templates, it's not surprising. on the other hand, in regards to a previous work where I sequenced a targeted gene after 3'RACE-PCR (full length sequencing), it's not surprising to find new exons and transcripts. you just need to count each molecules and see if it has sense in your study to go further.
best new year
fred
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