writing DNA

[Mega]

Hallo guys,

I'm desperately looking for some good websites which explain how DNA is written (by nature or by human).


For example:

[.....]  that promoter activity of a 257 nucleotide fragment (-257 to the transcription initiation site) and a 241 nucleotide fragment (-241 to the transcription initiation site) were 5-fold and 2-fold stronger than that of the full-length CLCuMV C1 promoter respectively.

(5') TCATGATTACGGGAGCGTAAAATACAAATTAAATCCCGTATTAACTCGTACCCAAGCGTA
TCCGGTGAATAATCCTGCGACAAAAGTTGCAAATATTTCACAGAAAGCATACACCGAAAC
CCGTGAACCGTATCAGGGAATTCGTTTAATAGTGGATCCCACATGTTTGAATTTGAAACT
TAGTGCGCAAGTACTTATAGTGTGCGGGAGCGTTATTTAGCTTTGAGGGAGCAATCTCGT
AAATCGGGGGCCCACAAAAAAAAAAGCGCGGCCATCCGGTAATATTATACGGATGGCCGC
TTTTTGGAGCGTGAGGATTTTGAAATGATTTCTCAAATTACGATAATGCCATTTGGGGTA
CACCTATATATTGCACCCCGTTACACCGATTGCCAGAGAATTAGAGTGTACACCGATTGC
CACCATG (3')

Is the red string the core promotor I'm looking for?? Or is it  the underlined 257 bp fragment?? Where do you start counting (the TIS must be at the 3' end, I think?? ) 

thx

[Nathan McCorkle]

http://en.wikipedia.org/wiki/Directionality_(molecular_biology)

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--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics