This web page was produced as an assignment for Genetics 677, an undergraduate course at UW‐Madison.
DNA Motifs
DNA motifs are sequence patterns with biological significance. For instance, the DNA sequence that ultimately produces a particular protein domain or is necessary for some sort of biological interaction between proteins and DNA or proteins and other proteins. At the DNA level, these likely include transcription factors and cofactors.
MotifFinder DNA sequence analysis
Click the image to go to the MOTIF Search page [1]
MotifFinder [1] is a tool that locates amino acid or nucleotide motifs and domains. Below is the motif list generated for a seach of the human ABC1
DNA and mRNA sequences:
DNA
1. EGF_1 (EGF-like domain signature 1IGF_BINDING: Insulin-like growth factor binding proteins signature)
2. IGF_BINDING (Insulin-like growth factor binding proteins signature)
3. INTEGRIN_BETA (Integrins beta chain cysteine-rich domain signature)
4. CTCK_1 (C-terminal cystine knot signature)
5. ANAPHYLATOXIN_1 (Anaphylatoxin domain signature)
6. L_CONOTOXIN (I-superfamily conotoxin signature)
7. 4FE4S_FERREDOXIN (Fe-4S ferredoxins, iron-sulfur binding region signature)
8. THIOLASE_3 (Thiolases active site)
9. TUBULIN (Tubulin subunits alpha, beta, and gamma signature)
10. HYDROPHOBIN (Fungal hydrophobins signature)
11. VWFC_1 (VWFC domain signature)
12. 2FE2S_FER_1 (Fe-2S ferredoxins, iron-sulfur binding region signature)
13. DEFENSIN (Mammalian defensins signature)
2. IGF_BINDING (Insulin-like growth factor binding proteins signature)
3. INTEGRIN_BETA (Integrins beta chain cysteine-rich domain signature)
4. CTCK_1 (C-terminal cystine knot signature)
5. ANAPHYLATOXIN_1 (Anaphylatoxin domain signature)
6. L_CONOTOXIN (I-superfamily conotoxin signature)
7. 4FE4S_FERREDOXIN (Fe-4S ferredoxins, iron-sulfur binding region signature)
8. THIOLASE_3 (Thiolases active site)
9. TUBULIN (Tubulin subunits alpha, beta, and gamma signature)
10. HYDROPHOBIN (Fungal hydrophobins signature)
11. VWFC_1 (VWFC domain signature)
12. 2FE2S_FER_1 (Fe-2S ferredoxins, iron-sulfur binding region signature)
13. DEFENSIN (Mammalian defensins signature)
mRNA
1. EGF_1
2. INTEGRIN_BETA
3. ANAPHYLATOXIN_1
4. L_CONOTOXIN
5. 4FE4S_FERREDOXIN
6. THIOLASE_3
7. VWFC_1
8. 2FE2S_FER_1
2. INTEGRIN_BETA
3. ANAPHYLATOXIN_1
4. L_CONOTOXIN
5. 4FE4S_FERREDOXIN
6. THIOLASE_3
7. VWFC_1
8. 2FE2S_FER_1
Summary of motif results:
The coding regions of human ABC1 showed a total of 13 motifs in the untranscribed DNA and 8 motifs after post-transcriptional processing, which include:
- Membrane protein binding sites
- Cofactor (Fe, S) binding sites
- Transcription factor binding sites
Sources:
1. http://www.genome.jp/tools/motif/
1. http://www.genome.jp/tools/motif/
