DNA Motifs in Filaggrin

Using the FASTA for the filaggrin gene, I searched for DNA motifs in the gene.

Results using MotifFinder
Number of found motifs: 153
View results in the file below.

Download to view Motics found: number_of_found_motifs.doc
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The first 3 motifs found using MEME:

MOTIF 1 width = 41 sites = 5 llr = 263 E-value = 1.5e-032

gi|60097901|ref|NM_002016.1| + 9506 4.87e-25
GGCAGTCAGG ATCCAGAAGTGCAAGCAGAACAACACGTAATGAGGAACAAT CAGGAGACAG gi|60097901|ref|NM_002016.1| + 8534 4.87e-25
GGCAGTCAGG ATCCAGAAGTGCAAGCAGAACAACACGTAATGAGGAACAAT CAGGAGACGG gi|60097901|ref|NM_002016.1| + 11450 5.82e-24
GGCAGTCAGG ATCCAGAAGTGCAAGCAGAGAAACACGTAATGAGGAACAGT CAGGAGACGG gi|60097901|ref|NM_002016.1| + 7562 1.02e-23
GGCACTCAGG ATCCAGAAGTGCAAGCAGACAAACTCGTAACGATGAACAAT CAGGAGACGG gi|60097901|ref|NM_002016.1| + 10478 1.16e-23
GGCAGTCAGG ATCCAGAAGTGCCAGCAGACAAACTCGTAATGACGAACAAT CAGGAGATGG

 MOTIF 2 width = 41 sites = 5 llr = 273 E-value = 3.0e-036

gi|60097901|ref|NM_002016.1| + 11023 1.96e-25
AGTGGTAGTC AGGCCAGTGACAGTGAGGGACATTCAGAAGACTCAGACACA CAGTCAGTGT gi|60097901|ref|NM_002016.1| + 7135 1.96e-25
AGTGGTAGTC AGGCCAGTGACAGTGAGGGACATTCAGAAGACTCAGACACA CAGTCAGTGT gi|60097901|ref|NM_002016.1| + 6163 1.96e-25
AGTGGTAGTC AGGCCAGTGACAGTGAGGGACATTCAGAAGACTCAGACACA CAGTCAGTGT gi|60097901|ref|NM_002016.1| + 10051 1.19e-24
AGTGGTAGTC AGGCCAGTGATAGTGAGGGACATTCAGAAGAGTCAGACACA CAGTCAGTGT gi|60097901|ref|NM_002016.1| + 5188 2.98e-24
AGTGGTAGCC AGGCCAGTGACAGCGAGGGACACTCAGAAGAGTCAGACACA CAGTCAGTGT

MOTIF 3 width = 29 sites = 5 llr = 191 E-value = 4.5e-019

gi|60097901|ref|NM_002016.1| + 4514 5.54e-18
GTGGACACCC GGGGTCAAGCAGAGGAGGAAGGCAGGGAT CCTACCACGA
gi|60097901|ref|NM_002016.1| + 1595 5.54e-18
GTGGACACCC GGGGTCAAGCAGAGGAGGAAGGCAGGGAT CCCACCACGA
gi|60097901|ref|NM_002016.1| + 3542 1.11e-17
GTGCACACCC GGGGTCAAGGAGAGGAGGAAGGCAGGGAT CCCACCATGA
gi|60097901|ref|NM_002016.1| + 5486 2.05e-17
GTGGACACCC AGGGTCAAGCAGAGGAGGAAGGCAGGGAT CCCACTATGA
gi|60097901|ref|NM_002016.1| + 11321 3.00e-17
GTGGACACCC GGGGTCAAGGAGAGGAGGAAGACAGGGAT CCTACCACGA

References
1. MotifFinder: http://motif.genome.jp/
2. MEME:  http://meme.sdsc.edu/meme4/intro.html

Dalia Saleh
saleh [ @ ] wisc.edu
last updated 2/9/10
gen677.weebly.com