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Splice Signal in Alternatively Spliced Exons

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.

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Splice Signal in Alternatively Spliced Exons

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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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