This web page was produced as an assignment for Gen677 at UW-Madison Spring 2010
Motifs
A motif is a DNA sequence or a protein sequence that is found widespread and is believed to have a biological significance. These motifs provide insight on the structure and the function of the transcribed protein in the organism.
Through the use of Motif Finder, the ABL1 DNA sequence was determined to have 14 different motifs. There are as followed:
Through the use of Motif Finder, the ABL1 DNA sequence was determined to have 14 different motifs. There are as followed:
- IGF_Binding
- Integrin_Beta
- CTCK_1
- Anaphylatoxin_1
- I_Conotoxin
- 4FE4S_Ferredoxin
- Agouti_1
- Thiolase_3
- Tubulin
- Hydrophobin
- VWFC_1
- 2FE2S_FER_1
- Defensin
Motifs were also found using MEME. Due to the length of the DNA sequence, the sequence to be divided into four sections. Below are a few examples of motifs found by MEME.
Analysis
The Motif Finder (1) found 14 different motifs in the DNA sequence for the ABL1 gene while MEME (2) found a total of 12 motifs. Motifs such as the IGF-Binding, Integrin Beta, and CTCK 1 motifs are signatures found in proteins that play roles in cell-to-cell adhesion and in growth factors. The Tublin motif plays a role in microtubules and the EGF-1 motif is a signature in proteins known to activate tyrosine kinase which is the type of protein ABL1 transcribes. The ABL1 gene also transcribes a protein that regulates the cell cycle and apoptosis is it is not a surprise that many of these motifs are found in the gene or that there are motifs related to the immune response.
References
1. Motif Finder http://motif.genome.jp/
2. MEME http://meme.sdsc.edu/meme4_6_0/intro.html
3. Prosite http://ca.expasy.org/prosite/
2. MEME http://meme.sdsc.edu/meme4_6_0/intro.html
3. Prosite http://ca.expasy.org/prosite/
