Table 1.
Base Frequency Matrix as a Function of Nucleotide Position.
The tri-nucleotide spacer sequence is conserved at ERα-bound ERE sequences. Base frequency matrix as a function of nucleotide position for 646 ERE sequences. Transcription Element Search Software (TESS) was used to analyze 1017 ERα-bound loci at two different stringencies of detection. High stringency (0–10% deviation from the consensus ERE sequence) and low stringency (10–20% deviation from the consensus ERE) results are shown in Table 1A and 1B, respectively. These data are pooled (Table 1C) to reveal a total of 646 ERE sequences residing within 509 receptor-bound loci. The distribution of ERE sequences within repetitive elements is indicated for each stringency. The tri-nucleotide spacer sequences are non-randomly distributed at all stringencies of detection (see main text) even when repetitive element EREs are excluded from the analysis (see Table S4).
| A. Stringency 0–10%, 162 total EREs, 26 (17%) of EREs in repetitive elements. | |||||||||||||||
| Position | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 |
| %A | 77.4% | 3.0% | 0.6% | 2.4% | 0.6% | 94.5% | 14.0% | 28.7% | 14.6% | 1.8% | 1.8% | 87.8% | 3.0% | 4.9% | 6.1% |
| %C | 3.0% | 0.0% | 1.8% | 2.4% | 94.5% | 1.2% | 43.3% | 17.1% | 24.4% | 0.0% | 1.2% | 7.3% | 93.9% | 91.5% | 13.4% |
| %G | 15.2% | 90.9% | 97.0% | 7.3% | 1.8% | 1.8% | 25.0% | 22.6% | 49.4% | 0.6% | 94.5% | 2.4% | 0.0% | 0.0% | 3.7% |
| %T | 4.3% | 6.1% | 0.6% | 87.8% | 3.0% | 2.4% | 17.7% | 31.7% | 11.6% | 97.6% | 2.4% | 2.4% | 3.0% | 3.7% | 76.8% |
| B. Stringency 10–20%, 484 total EREs, 169 (36%) of EREs in repetitive elements. | |||||||||||||||
| Position | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 |
| %A | 76.6% | 8.7% | 5.4% | 5.8% | 2.1% | 75.9% | 12.9% | 36.7% | 11.8% | 5.0% | 12.9% | 82.6% | 3.9% | 6.6% | 6.4% |
| %C | 3.1% | 1.2% | 11.4% | 6.2% | 74.9% | 3.9% | 57.1% | 13.7% | 17.8% | 9.1% | 4.8% | 9.8% | 75.7% | 86.1% | 20.1% |
| %G | 16.2% | 81.5% | 78.8% | 7.1% | 3.9% | 15.6% | 17.6% | 18.0% | 58.3% | 4.1% | 80.1% | 3.1% | 17.2% | 1.2% | 3.5% |
| %T | 4.1% | 8.5% | 4.4% | 80.9% | 19.1% | 4.6% | 12.4% | 31.5% | 12.0% | 81.7% | 2.3% | 4.6% | 3.1% | 6.0% | 69.9% |
| C. Stringency 0–20%, 646 total EREs, 195 (30%) of EREs in repetitive elements. | |||||||||||||||
| Position | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 |
| %A | 76.8% | 7.3% | 4.2% | 5.0% | 1.7% | 80.7% | 13.2% | 34.7% | 12.5% | 4.2% | 10.1% | 83.9% | 3.7% | 6.2% | 6.3% |
| %C | 3.1% | 0.9% | 9.0% | 5.3% | 79.9% | 3.3% | 53.6% | 14.6% | 19.5% | 6.8% | 3.9% | 9.1% | 80.3% | 87.5% | 18.4% |
| %G | 15.9% | 83.9% | 83.4% | 7.1% | 3.4% | 12.1% | 19.5% | 19.2% | 56.0% | 3.3% | 83.7% | 2.9% | 12.8% | 0.9% | 3.6% |
| %T | 4.2% | 7.9% | 3.4% | 82.7% | 15.0% | 4.0% | 13.8% | 31.6% | 11.9% | 85.8% | 2.3% | 4.0% | 3.1% | 5.4% | 71.7% |