RNA binding motif

Question

[Aishwarya Kulkarni]

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?

Answer 1

[Girolamo]

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

Answer 2

[Aishwarya Kulkarni]

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