how to find p53 bibding site in my target gene promoter - (Dec/06/2007 )

Hi,
I am trying to look up whether there is a p53 binding site in the promoter area of my target gene in mouse. It was reported that there is p53 site (gggcgtgcgctcccgacatgccc) in the promter of this gene in human. I try find this same sequence in the mouse promter by BLAST, but I failed. Is there a better way to do it? What is the minimal sequence for p53 binding. In addition, I also want to find out whether there is CpG island in this promoter
The sequence of the mouse promoter is as below:
ggattaaaacaaaaacacattcataaacataactgggcttttagagaaactcaaattctcactacagggaagagtcctat
ctgaaccgggccatgagagaggagaggaagagatgagagagggaagaggaccaagagagaagtggaaagtttcagaccaag
ggagcaagctgtagaaatggctggtctatacagggaagagaagctcaaacgctggactggtgaggtttaggataggggcag
ggtgagaagagctggggggagccacaggaattgatacttgatccatgtttcttcgggacgtgacaaaacccctcttgttcc
agctgcctatgtggtatgatctgttcttcctcacaatctgtgaggtggcctggagctcattggaggcccactggcaggaag
cctactgagatttattgaaaaggaaaccgaattatcagggcactcgtttgcaacgccaacctgggctgtgttcggggcatg
cccagcctgctgtctgcagtgtgaagctctttagaagccactgcaaccacaggccgcccgacaggaacagagacactgaaa
acgggcccgcagcaaggcaggctcagcagccaacagtcacacccaggaagcagtatttttcttctgctcctggactctctt
gcggtgtatggctgcttccctttggtctgagccaggccgatggtctcagaaatagacacccattgactttcttttccagcg
ctgggacatacagaccccgcctccatcccagggtgtctataggaaggatggcggctgctgcagggaggagggtctcctgtc
ttcctaagggcgcccctccaccagcctgtgggtgggtccgaggcacttccattccgatatctagctggccaaatcctgcaa
accttgaggcaggaagaacctgcagagcacatgggacttgcagcggacatgctttaaagaggtgccccaggcccgtccacc
gccctcggccaccctccgtgtcctctggggagcagctgcggaagattcgagtcagaatagcaagaaggaaccgcagcagaa
ggtacaactcccagcatgccctgcgcccgccacgcccacaaggccaggcgcagatgggcgtggggcgggactttcccggct
cgcctcgcgccgtccactcccagaaggcagcgggcgagggcgtggggccggggctctcccggcatgctctgcggcgcgcct
ccgcccgcgcgatttgaatcctgcgtttgagtcgtcttggcggaggttgtggtgacgccatcatgggagctccggcgctgc
cccag

Thanks for help

What you want to use is a search algorithm that looks for binding sites based on a matrix
Free access websites are:

www.genomatix.com
genomatix is nice, good matirx curated excellent search algorithms all free but you have to pay to see the consensus sequence and matrix they actually use (still get a good idea of the matrix at www.gene-regulation.com - Transfac database
http://www.chick.manchester.ac.uk/SiteSeer/ )
siteseer uses Transfac database for searching your input sequence access to all information/uses is free www.gene-regulation.com

Hi,beccaf22,

Thanks for yor suggestion.

if you use BLAT (genome.ucsc.edu) to compare your sequence to the mouse genome, you can add the track for CpG islands in the browser.

Apparently, there is a CpG island which overlaps with the 3' end of your promoter.

Hi, Have a look through this site;

http://www.oxfordjournals.org/nar/database/a

it contains a list published annually of the bioinformatics sites on the web. I can suggest "Mapper" for your query, you need to register, but this is free if you are in a uni/academic institution.