This website was produced as an assignment for Genetics 677 at UW-Madison Spring 2009
In order to search for any DNA motifs present in the Htt sequence, I used the Motif Search program and the MEME program (MEME). The results are described below for each.
I used the full DNA sequence of human huntingtin for this program. Initially, with the cutoff score set at 85, I did not retrieve any motifs. I reran the program with the cutoff score set at 100 and still did not retrieve any results. I switched to using the mRNA with the two cutoff settings. I found 189 motifs at a cutoff of 85, and at a cutoff 100 found 10 motifs. These 10 motifs follow.
Because of the size of the gene (17.5 kb) exceeded the maximum sequence size, I had to use the shorter mRNA sequence for the analysis. The program identified 3 motifs, with the first one appearing the most highly conserved, with a pattern of [AT]GC[AT]GCAGCAGCAG[CG]. The full MEME results follow this paragraph. While I was impressed with the graphical nature of the program, I am not sure I gained a good understanding of the actual motifs, at least so far as how they might indicate a certain function of the protein. Click on the images to the right to enlarge the images.
Created by Eric Nickels firstname.lastname@example.org 3/13/2009 Genetics 677 Webpage