Frequently Asked Questions
test sequence (TRH-R1)
TSS:
Insert the position of the transcription start side (TSS) (optional).
ATG:
Add the position of start ATG (optional).
Ex.1 and Ex.2: Enter the position of the first and/or the second Exon (optional).
direction
The algorithms search for the consensus sequence of thyroid hormone binding sides in promoter regions (A/G G G T C/G/A A). You can look for a single, double or triple TREs. TREs could be orientated as a direct repeat (DR), as an inverted palindrome (IP) or as an inverted repeat (IR). Select the wanted orientation and the length of the spacer between different parts of the multiple-TREs.
---> -/-> <--- <-/- all 0 1 2 3 4 5 6 7 8 9 ---> -/-> <--- <-/- all off 0 1 2 3 4 5 6 7 8 9 ---> -/-> <--- <-/- all off
Another option is to search for the optimal constitutions for TREs. If you prefer this option select TRE: IR0 + DR4 + IP6. In this case all other settings will be unimportant.
or TRE: IRO + DR4 + IP6 ------------------
There are TREs known, that don’t contain the exact consensus sequence of TREs. The lower the percentage the higher is the tolerance for variance.
100 % 83 % 67 % 100 % 83 % 67 % 100 % 83 % 67 %
score
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