Exercise 3 - Gene Prediction through mRNA Evidence
Often genes are predicted solely by the existene of mRNA fragments that are related back
to their genomic origins. These type of gene prediction is based on alignments of mRNA
fragments with genomic DNA utilizing programs designed to detect stretches of sequence
similarity and dissimilarity (as opposed to software that is designed to
detect single-nucleotide differences between sequences).
Determine the exact locations of exons and introns as well as the extension of the gene in the
1,500-nucleotide sequence by examining
this RNA evidence.
Utilize this SIM4 program
that allows the pairwise alignment of cDNA and genomic sequence for this task; you may have to download a viewer
in order to be able to view the results on your computer.
(Also, make sure that you align T's with T's and save your results in a word processor, as entire web pages,
and/or as screen shots.)
(Should you experience problems with the program, see
input,
graphical output).
Answer the following questions utilizing your notes and appropriate tools from :
What characteristics does this gene have? (Length, exons, introns, splice sites, promoter, etc.)?
What do the mRNA and amino acid sequences of the gene and its product look like?
Compare your results with those of your predictions in Exercise 1 and Exercise 2.
