RNA binding motif
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7.2 years ago

I am scanning an RNA binding motif which is CTCC and I am scanning it in the corresponding genomic sequence of the exonic positions, my question is that when scanning the corresponding genomic sequence, do I scan it as GAGG for forward stranded sequences and as GGAG for reverse, is that correct?

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7.2 years ago
Girolamo ▴ 140

The CTCC motif is the specific fingerprint of a certain RNA binding protein. Hence, you should always search for CTCC independently of the strand.

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7.2 years ago

Yes but if I have the corresponding genomic sequence do I scan for it's complement?

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