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Detection of intron in pre-mRNA

Detection of intron in pre-mRNA - Real-Time PCR and Quantitative PCR Forum

Detection of intron in pre-mRNA - Real-Time PCR and Quantitative PCR Forum


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Old 08-25-2009, 12:55 AM
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Default Detection of intron in pre-mRNA



Hi all,

I'm trying to design specific qRT-PCR probes for the 2 splice variants of my gene-of-interest. This is what they look like:

Variant 1: Exon1-Exon2-Exon3

Variant 2: Exon1-(Exon2, slightly longer)

Basically, the coding region of Exon2 from Variant 2 contains a tiny piece of intron from Variant 1. I designed a probe for Variant 1 across the border of Exon2 and Exon3, so that should be fine. However, my question is, even if I design a probe against the tiny bit of Exon2 that's unique for Variant 2, wouldn't it still pick up signal from the pre-mRNA of Variant 1, which will still have that piece of intron before splicing?

Please advise! I appreciate any comment on this. Thanks much!!

Konnicska
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detection , intron , premrna , probe design , qrt-pcr


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