RSA

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NOTE: - when using rsa tools, the reference position depends on whether you are searching for upstream or downstream regions.

For upstream:

  • position 0 is the first nucleotide of the start codon

For downstream:

  • position 0 is the last nucleotide of the stop codon (last nucleotide in the ORF)

start codons - ATG stop codons - TAA, TAG or TGA

TRANSFAC database - transcription factor database where all all regulatory elements are between -1 & -800 relative to start codon.

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