In your quest to understand gene regulation instem cells you sequenced a cDNA library from mouse ES cells and found anapparent splice variant of an important transcription factor. When you showthis interesting finding to your P.I. he dismisses it as garbage because thesplice sites looks so odd. Since you feel like you are onto somethinginteresting, you decide to take another look at the splice variant and itsalignment to the genome.

alignment: Alignment_genomic_mRNA.gif

context image: Genomic_context.gif

Can you find what is the problem with the alignment?

Tips:   Splicing_Introduction.pdf 

-- RickardSandberg - 14 May 2008