Table 1. Genes (Transcripts) Selected for Electrophoretic Mobility Shift Assay (EMSA).
| Gene Description | Predictions | EMSA Results | ||||||
| Gene Symbol | FlyBase ID | RepresentativeTranscript | NRE_PAT Match | NRE_M8 (cutoff = 7.5, max = 10.97) | NRE_M10 (cutoff = 10, max = 15.21) | Probe Position in 3UTR | Percent Binding | Binding Sites |
| Ace | FBgn0000024 | CG17907-RA | 9.119 (751), 8.875 (814)a, 9.798 (1265)o, 9.119 (1351) | 14.78 (814)a, 10.34 (1229)a | 722–1095 | 33 | 1 | |
| AP-1gamma | FBgn0030089 | CG9113-RA | 122–141 (GTTGT..9..ATTGTA)n | 10.97 (122)n, 8.873 (136)n, 8.349 (240)n | 85–191 | 21.8 | 1 | |
| Csp | FBgn0004179 | CG6395-RA | 7.666 (109)a, 8.872 (1050), 7.666 (1242)a, 9.795 (1303), 9.119 (1519)a, 7.666 (1561), 7.666 (1909) | 13.95 (87), 10.13 (1537)a | 1218–1545 | 57.2 | 2 | |
| dlg1 | FBgn0001624 | CG1725-RA | 1491–1534 (GTTGT..33..ATTGTA)a | 9.8 (367)a, 10.97 (1491)a, 8.872 (1529)a | 12.57 (367)a | 1485–1539 | 56.9 | 1 |
| dlg1 | FBgn0001624 | CG1725-RC | 8.59 (277), 8.59 (783), 10.04 (793) | 744–829 | 0 | 0 | ||
| EP2237 | FBgn0043364 | CG4427-RA | 401–443 (GTTGT..32..ATTGTA) | 9.12 (390)a | 10.40 (318) | 340–514 | 20.5 | 1 |
| Gad1 | FBgn0004516 | CG14994-RA | 8.872 (730), 8.595 (950) | 704–973 | 35.9 | 2 | ||
| mam | FBgn0002643 | CG8118-RA | 716–735 (GTTGT..9..ATTGTA)n | 9.795 (7)n, 9.8 (716)n, 8.875 (1037)n | 10.40 (1037)n | 642–1110 | 73.8 | 2 |
| shn | FBgn0003396 | CG7734-RA | 8.872 (480), 7.666 (835), 7.72 (913)a, 8.875 (983)a, 8.873 (1105)a | 10.78 (895)a, 14.78 (983)a | 809–1013 | 59 | 2 | |
Gene symbols, FlyBase IDs, and transcript IDs are from the Berkeley Drosophila Genome Project (BDGP) Release 3.1 annotation. Pattern-match predictions are represented as: start-end coordinates (matched sequence). The number between the dots represents the length of the sequence between the two boxes. Matrix predictions are represented as: score(coordinate). The coordinate corresponds to the first position in the matrix. The probe positions are shown as a coordinate range. All coordinates are referred to the stop codon (the first nucleotide of the stop codon as coordinate 1).
Superscripts in the predictions represent the conservation between D. melanogaster and D. pseudoobscura.
The predicted site is aligned with a predicted site in D. pseudoobscura.
The predicted site overlaps with a predicted site in D. pseudoobscura.
Corresponding 3′UTR sequence in D. pseudoobscura is not available. The predicted sites in boldface are covered by the tested RNA probes.