Table 2. List of predicted binding sites and mutagenesis strategy.
Sequences of 21 bp fragments including the underlined binding sites are shown. The critical invariant bases are in bold. For sites on the reverse strand (-), the reserve strand sequence is shown. For deletions, all 21bps are deleted. Mutated bases are shown as lower-case letters. * indicates that the binding site is predicted by the FIMO pipeline.
| Site Name | Strand | Original Sequence | Mutate to | Constructs (Size in bp) |
|---|---|---|---|---|
| 220-Ey-Site1 | + | TAATTCCGTTTAAATGATTTC | Deleted | 220-Ey-1d (199 bp) |
| 220-Ey-Site2* | - | TTTTCACGGCTCAGTGGCCTT | TTTTCACGGCTatGTGGCCTT | 220-Ey-2m (220 bp) |
| 220-SuH-Site1* | + | GGTGAGCGATAGTTTTCACAT | GGTGAGCGActaggagacgAT | 220-SuH-1d has the first site deleted. 220-SuH-1–4 m (220 bp) has all four sites mutated. 220-SuH-1m4m (220 bp) has site 1 and site 4 mutated. |
| 220-SuH-Site2 | + | TTTGAGCTTTGCACGTAATCA | TTTGAGCTTaGactGTAATCA | |
| 220-SuH-Site3 | - | AAATTCATTTCCACTTGATTA | AAATcCAcTTCCACTTGATTA | |
| 220-SuH-Site4 | - | CTGATATTTTTCACGGCTCAG | CTGActcgcTTtACGGCTCAG | |
| 220-Scro-Site1 | + | CACGTAATCAAGTGGAAATGA | CACGTAATCgtGTGGAAATGA | 220-Scro-1m (220 bp) |
| 220-Slp1-Site1 | + | TTCACATGTTTTGTTCGAGCA | TTCACATGTaccaagCGAGCA | 220-Slp1-1m2m has both sites mutated (220 bp) |
| 220-Slp1-Site2 | - | CTCTTGTGTTGGTCAAATTCA | CTCTTGgagTcGatcAATTCA | |
| 850-Ey-Site1* | + | TTGTGCCCTGTGTGTGTGAAA | aTGTGgCtTGTGTGTGTGAAA | 850-Ey-1m2d3d has site 1 mutated, and sites 2 and 3 deleted (808 bp). |
| 850-Ey-Site2 | + | TGATTCCAATTGACTGATTTC | Deleted | |
| 850-Ey-Site3 | - | ATGTGAGCCACTTGTGTGGCA | Deleted | |
| 850-SuH-Site1 | - | TTTTTGTTTCACACACACAGG | TaTcTGTcgCACACACACAGG | 850-SuH-1m2m3m6m has sites 1, 2, 3 and 6 mutated (850 bp). 850-SuH-1–6 m has sites 1–6 mutated (850 bp). |
| 850-SuH-Site2 | - | CGTCTGTTTCCCAACACCGTA | CGTCTGTaTCCgtACACCGTA | |
| 850-SuH-Site3* | - | TCCAAAGTTCCCACAGTGCGC | TCCAAAGaTCCgACAGTGCGC | |
| 850-SuH-Site4 | + | GCATTTTTAACAACTTTAAGC | GCATTTcTAAgtACTTTAAGC | |
| 850-SuH-Site5 | + | GTCGACCTTGTCAAGTACCTT | GTCGACCaTGTCAAGTACCTT | |
| 850-SuH-Site6 | - | AGCAGCGTTTTCTCAACTTTG | AGCAGCGTTaTCTgAACTTTG | |
| 850-Scro-Site1* | + | TTGATGTTAAGTGTCTGCCAC | Deleted | 850-Scro-1-7d has all 7 sites deleted (724 bp) |
| 850-Scro-Site2 | - | CATAGTGTCCTAAATGCTGTT | Deleted | |
| 850-Scro-Site3 | + | CAAGCCAAAACTAATGGGTAT | Deleted | |
| 850-Scro-Site4,5 | - | TCGTTAAAGG GGTTAAATAGG | Deleted | |
| 850-Scro-Site6* | + | TTGTCAAGTACCTTGTTAGCT | Deleted | |
| 850-Scro-Site7 | + | CGTTTAATTGACAATTGAACC | Deleted | |
| 850-Slp1-Site1* | + | TGACTTTGTTTTTGCTACTCA | Deleted | 850-Slp1-1d (829 bp) |