This webpage was produced as an assignment for Genetics 677, an undergraduate course at the University of Wisconsin - Madison.
 

DNA Motifs

A motif is a string of nucleotides in a DNA sequence which is repeated , or conserved in all sequences in a multiple alignment at a particular position . Motifs may correspond to structural or functional elements within the sequence they characterize.

MOTIF

No motifs were found using MOTIF (1), because the nucleotide sequence is so large. Therefore, I used the intron-free CFTR mRNA sequence. Using mRNA, many motifs were found, depending upon the cut-off value used.

Cut-off value: 85
Number of found motifs: 161

Cut-off value: 95
Number of found motifs: 28

Cut-off value: 97
Number of found motifs: 15

Cut-off value: 100
Number of found motifs: 11
 
MOTIF returned 11 motifs, at a cut-off value of 100, of the mRNA of CFTR:

 Motif Name          Sequence          Number          Function

1. HSF                    AGAAN                 2               Heat Shock Factor
2. ADR1                 NGGRGK               1               Alcohol Dehydrogenase Gene Regulator 1
3. CdxA                 MTTTATR              2              May be part of network regulating gastrulation
4. NIT2                  TATCTM                1              Activation of nitrogen-regulated genes
5. SRY                    AAACWAM            1               Sex-determining region Y gene product
6. STRE                  TMAGGGGN           1              Stress response element
7. AML-1a             TGTGGT                 1              Runt-factor AML-1
8.GAmyb               YAACSGMC            1              GA-regulated myb gene from barley
9. GATA-1             NCWGATACA         1              GATA-binding factor 1 

MEME

MEME (2) only allows nucleotide sequences of 60,000 base pairs or less.  The CFTR sequence was too large for the search engine and the mRNA sequence was used instead. Three motifs were found in the sequence.
Motif 1
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Motif 2
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Motif 3
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Analysis

Using MOTIF, only 11 motifs were identified at the 100 cut-off value, indicating that these motifs are truly found within the CFTR mRNA. MOTIF clearly states the names and sequences of motifs, while MEME gives a more aesthetic view of each motif sequence found. However, MEME did not give the name of the sequence or its function.
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References

1.  MOTIF. March 8, 2010. http://motif.genome.jp/

2.  MEME. March 11, 2010. http://meme.sdsc.edu/meme4/intro.html

3. NCBI: Entrez Nucleotide. "CFTR mRNA Sequence". March, 11, 2010.                                                                  http://www.ncbi.nlm.nih.gov/nuccore/NM_000492?report=fasta&log$=seqview

 
 
 
 

Alexandra Reynolds
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