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.
MotifSearch
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.
Motif Name
Description
HSF
heat shock factor (Drosophila)
HSF
heat shock factor (yeast)
CRE-BP1/c-Jun
CRE-binding protein 1/c-Jun heterodimer
GCR1
GCR1
ADR1
alcohol dehydrogenase gene
regulator 1
CdxA
CdxA
CF1
chorion factor 1
SRY
sex-determining region Y gene product
AML-1
arunt-factor AML-1
CF1
chorion factor 1
MEME
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.
