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Characterizing Signals in Alternatively Spliced Exons through Pre-mRNA Conformation

This study investigates the splice signals distinguishing alternatively spliced exons from constitutively spliced ones, focusing on exon skipping. We hypothesize that exon skipping occurs due to a specific 3-D conformation of pre-mRNA that obscures the splice sites of the flanking introns. Previous research indicates the splice signal in RNA sequences is weak, leading us to explore stronger signals in pre-mRNA structures. We utilize tools like BLAST, BLAT, and RNAfold to analyze intron/exon data and assess folding energy and stacking counts.

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Characterizing Signals in Alternatively Spliced Exons through Pre-mRNA Conformation

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  1. Splice Signal in Alternatively Spliced Exons by George Su (gpsu@ucsd.edu) Advisor: Vineet Bafna (vbafna@cs.ucsd.edu) Shaojie Zhang (shzhang@cs.ucsd.edu) Question: Is there a signal that characterizes alternatively spliced exons from constitutively spliced exons? We focus on exon-skipping. Alternative splicing variants Exon skipping Previous work have shown that the splice signal in the RNA sequence is very weak. Therefore a much stronger signal must be found in the pre-mRNA 3-D conformation. Introns flanking alternatively spliced exons are more conserved. Hypothesis: Exon-skipping occurs when the pre-mRNA folds in such a way such that the two flanking introns comes together, and thus obscuring the flanking splice sites. The spliceosome than splices out the exon. Available intron/exon sequence data: Tools: BLAST, BLAT, RNAfold(mFold), QRNA, etc. Result of attempt through folding energy Results of attempt through stack counting

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