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Help with estrogen receptor 1 promoter search - (Jan/13/2008 )

Hi everyone. I am trying to determine where the promoter is for the estrogen receptor 1 gene in mouse. My problem is that I can locate it in NCBI (at least I think I did) but I am at a lost as to where to go from there.

This is what I am doing:
1. I search for the nucleotide Esr1.
2. From the CoreNucleotide records of 435 I choose the one for mus musculus - NM 007956
This is the link that I get when I search for Esr1 --> http://www.ncbi.nlm.nih.gov/entrez/viewer....mp;id=145966838

After that, I am completely lost! Can anyone guide me through this process? Yes, I have read ALL of the posts on how to search for the promoter but I just cannot replicate what they say I need to do.

Thanks a bunch!

-briannesilverdragon-

mouse ESR1 gene may have an alternative promoter usage.

the following sequence is immediate upstream the refseq you gave and should contain the promoter

CODE
CTTGGCCTATGTGATTATTCCTTCTATAAATGAGTTTTATCAAGTTTAACGTTCGCTAAT
TTGAAATAAAACATTTCAGATCACAACTAAAATACATCCTACACTATGTAGTTTGGGGGA
GTTAAATTCAGACACATTTGTGTATTTGAATTGTTTTGGGGCCAAACTCACCAGGGTATA
GAAAACTGAAGACAATCAAGACAACTTATTATAAAGAATGTGTAGATCAGTCATGAGACA
TTTGGTATCTTTTCTCCTCTCAGCCAATTCTGAGATGCTTTTCTTACCCAGCATGCACTA
ATGTTCATGTATAGGGATCGAGACAGTGGCCAGAGTCTTTTTTGGTCTTTTGCCTGATAC
CATTCTTACTTCCACAGAAGCATTCTTTCTCAGATTTATAGAATAGGGAAAAAAGAAAAA
AAGAAAAACTAAGACATTAAAACAACAACCCAGCATTTAAAACACATGTTACATAGAACA
CAACAGATTTTATGAGCTATTAAAATTCCAAAAGGTCTGAAAAAATTAGAGGTCTGTGGA
TCAGAGGTAATGTGTTTGCTTAGCACATCAAAGTTTTGGGTTTATCCCTAGTACCAAAAA
GGAAAATAAATTTAAAATGCTTTTTATCTCATATTATTGCTTCAGCGTGTTTGTCTCTGA
GTTAAAAAAAAAAAAGAAAGAATAACAAACAAAATAAGTTTTTAAAAAGCCAGTCATGTT
GGCTTACGCCTGTAAGTTTAGCACTTGGAAGACCGAGGCAGGGGGAATCCTGAGAGTTTA
AGGCCAGTCTGAAATGCAGAGTGAGACCTTGTCTCAACAAAACAAAACACCAGATTAAAG
CCCCAAAGCAAACAGGACTTGTAAATCACGGCAGGAAATGCCAAGCAGTTTATAGAAGGC
TCATACACCTGAAGGCTTTCAGAGTCAGCTCAGGCTAAGCTGTTCAGGTTTCCAAAATCA
GGAACCCCATTCATTAATCAGTGACAAGAACTGCTGAGCCACGGACTTAGCTGGTTGAGT
CAATGAGTGAAAGAGAAACTCTGAGAAGCGCTCACATTAGAAACACCCTTATGCCCCTTC
TTAGCTAGTTTTCAGCGAGGAAAATCTGTGTGCAGAAAGAACGCTCCCTTATTTTATTTT
TTCCAAGTCAACATGTTCGTCTAGACTTCGAGCTTTATTGCAAGGAAAGAGAAAGTGGGT
TGGATCACTTTTTTTTTTTTTTTTCAGCCAGAGGCTTGTCCTTCTGCAAACATCTATCTG
TAGGCAAACGCTGAGAAAGTTGGAAGCAGACCTGGCTGGAGAGAGAGAGGAAGGCCACCC
CCTCCCCTATTATCCGGAGCAGAGTTTCCAATCCCAGTCAAGTGGTGGTGCTAGCTCTTT
GCTTCTGAGTCTCTGCATTTCCTAATTTCATGGTCATAACAGCCTCGGAACGGATTCTAC
CAAAACCGAAAAC


Run promoter prediction using the above sequence and obtain the following result
Start End Score Promoter Sequence
691 741 1.00 AAAATAAGTTTTTAAAAAGCCAGTCATGTTGGCTTACGCCTGTAAGTTTA
852 902 0.97 ACAGGACTTGTAAATCACGGCAGGAAATGCCAAGCAGTTTATAGAAGGCT
881 931 0.99 CCAAGCAGTTTATAGAAGGCTCATACACCTGAAGGCTTTCAGAGTCAGCT

-pcrman-

Thanks for the help pcrman...but how did you locate the sequence immediately upstream? Do I need to locate the gene on the respective chromosome and work my way from there? Or do I align the my gene with the chromosome and go back about 1-2kb? I am sorry for all the questions, but this is very confusing to me...

-briannesilverdragon-

[attachment=4065:ESR1.gif]
In the above graph, the 5' flanking sequence is the sequence aligned to the genomic sequence and is upstream the esr1 gene (exon1). As you can see, there is an isoform of esr1 gene (annotated as mouse mRNA) whose first exon extends further into the 5' flanking sequence. So there are likely two promoters for esr1 gene. The first or the main promoter should reside immediately upstream the first exon of esr1, the 2nd one is upstream the first exon of "mouse mRNA". The two promoters should be within the sequence I gave in my first post.

-pcrman-

QUOTE (pcrman @ Jan 14 2008, 01:17 AM)
[attachment=4065:ESR1.gif]
In the above graph, the 5' flanking sequence is the sequence aligned to the genomic sequence and is upstream the esr1 gene (exon1). As you can see, there is an isoform of esr1 gene (annotated as mouse mRNA) whose first exon extends further into the 5' flanking sequence. So there are likely two promoters for esr1 gene. The first or the main promoter should reside immediately upstream the first exon of esr1, the 2nd one is upstream the first exon of "mouse mRNA". The two promoters should be within the sequence I gave in my first post.


Thank you very much for explaining this to me!

-briannesilverdragon-