Splice Signal in Alternatively Spliced Exonsby George Su (gpsu@ucsd.edu) Advisor: Vineet Bafna (vbafna@cs.ucsd.edu)Shaojie Zhang (shzhang@cs.ucsd.edu)

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.

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.

Question:

Is there a signal that characterizes alternatively spliced exons from constitutively spliced exons?

We focus on exon-skipping.

Introns flanking alternatively spliced exons are more conserved.

Alternative splicing variants Exon skipping

Results of attempt through stack countingResult of attempt through folding energy

Human Mouse

Alternatively spliced 1966 1540

Constitutively spliced 243 241

Tools:

BLAST, BLAT, RNAfold(mFold), QRNA, etc.

Available intron/exon sequence data: