Table 2 List of the significant blocks detected in the hoxb2 dataset
From: A novel approach to identifying regulatory motifs in distantly related genomes
| Block | Consensus sequence and possible binding sites |
|---|---|
| Hoxb2 1.1 (-) | AATTCTTTGATGCAATCGGAGGGAGCTGTCAGGGGGCTAAGATTGATCGCCTCATsTCCT |
| *Meis (CTGTCA), CTGTCA: 26-31 + | |
| *Hox/Pbx, AGATTGATCG: 40-49 + | |
| Cap, M00253, NCANHNNN: 39-46 - (0.937); 22-29 - (0.918) | |
| CDP CR1, M00104, NATCGATCGS: 41-50 + (0.964) | |
| CDP CR3+HD, M00106, NATYGATSSS: 41-50 + (0.992) | |
| CdxA, M00101, AWTWMTR: 1-7 + (0.919); 6-12 + (0.903) | |
| HSF2, M00147, NGAANNWTCK: 40-49 + (0.925) | |
| MEIS1, M00419, NNNTGACAGNNN: 23-34 - (0.951) | |
| TGIF, M00418, AGCTGTCANNA: 24-34 + (0.966) | |
| Pbx1, M00096, ANCAATCAW: 39-47 - (0.909) | |
| Hoxb2 2.1 (-) | TTGCACTTrGAGTTTACATTTTAATG |
| *Octamer-motif (ATTTgCAT), GTTTACAT: 12-19 + | |
| *Adhf-2a (TGCACTgAGA), TGCACTTrGA: 2-11 + | |
| CdxA, M00101, AWTWMTR: 20-26 + (0.978); 19-25 - (0.905); 17-23 - (0.927) | |
| SRY, M00148, AAACWAM: 14-20 - (0.905) | |
| Hoxb2 2.2 (UCSC) | AAAAnTGTACTTTTTTAGTATTTACyT |
| *HoxA5 (TTTAaTAaTTA), TTTAGTATTTA: 14-24 + | |
| CdxA, M00101, AWTWMTR: 16-22 - (0.979) | |
| SRY, M00148, AAACWAM: 7-13 - (0.928) | |
| Hoxb2 2.3 (UCSC) | GTGTGTTCTAGTGAACATTTTCATATATATTTATTGGTTAT |
| *Glucocorticoid receptor, AGTGAACA: 10-17 + | |
| *CCAAT BOX, ATTGGTT: 27-33 + | |
| Cap, M00253, NCANHNNN: 15-22 + (0.919); 21-28 + (0.906); 7-14 - (0.919) | |
| CdxA, M00101, AWTWMTR: 23-29 + (0.958); 29-35 + (0.940); 28-34 - (0.956); 26-32 - (0.951); 24-30 - (0.958); 22-28 - (0.960) | |
| FOXJ2, M00422, NNNWAAAYAAAYANNNNN: 23-40 - (0.932) | |
| HFH-3, M00289, KNNTRTTTRTTTA: 25-37 + (0.908) | |
| NF-Y, M00185, TRRCCAATSRN: 30-40 - (0.914) | |
| Oct-1, M00162, CWNAWTKWSATRYN: 14-27 + (0.913) | |
| Pbx-1, M00096, ANCAATCAW: 30-38 - (0.948) | |
| Hoxb2 2.4 (UCSC) | GTGAACATTTTCATATATATTTATTGGTTATAGCCTGTTAAAATATTTTCTTTT |
| *GATA 1, TTATAGCC: 28-35 + | |
| *CCAAT BOX, ATTGGTT: 23-29 + | |
| Cap, M00253, NCANHNNN: 5-12 + (0.919); 11-18 + (0.906) | |
| CCAAT box, M00254, NNNRRCCAATSA: 21-32 - (0.940) | |
| CdxA, M00101, AWTWMTR: 13-19 + (0.958); 19-25 + (0.940); 39-45 + (0.925); 46-52 + (0.901); 36-42 - (0.930); 18-24 - (0.957); 16-22 - (0.951); 14-20 - (0.958); 12-18 - (0.960) | |
| FOXD3, M00130, NAWTGTTTRTTT: 41-52 + (0.924) | |
| FOXJ2, M00422, NNNWAAAYAAAYANNNNN: 13-30 - (0.932) | |
| HFH-3, M00289, KNNTRTTTRTTTA: 15-27 + (0.908) | |
| HNF-3beta, M00131, KGNANTRTTTRYTTW: 39-53 + (0.920) | |
| NF-Y, M00185, TRRCCAATSRN: 20-30 - (0.914) | |
| Oct-1, M00162, CWNAWTKWSATRYN: 4-17 + (0.913) | |
| Pbx-1, M00096, ANCAATCAW: 20-28 - (0.948) | |
| SRY, M00148, AAACWAM: 47-53 - (0.961) | |
| Hoxb2 2.5 (UCSC) | AATTCyCTCTTGGAACTTTCTTTGTTCTTCmGTAG |
| HSF1, M00146, AGAANRTTCN: 12-21 + (0.915); 12-21 - (0.930) | |
| HSF2, M00147, NGAANNWTCK: 12-21 + (0.948); 12-21 - (0.930) | |
| SRY, M00148, AAACWAM: 17-23 - (0.961) | |
| Hoxb2 3.1 (UCSC) | GGCCnAGACnAGCGATTGGCGGAGrCCGGTCCCGTGACCAnGAATTCCCTGyAATTT |
| NF-Y, M00185, TRRCCAATSRN: 12-22 - (0.915) | |
| USF, M00187, CYCACGTGNC: 29-38 - (0.957) | |
| USF, M00217, NCACGTGN: 30-37 + (0.902) | |
| Hoxb2 3.2 (-) | TCCCGTGACCAnGAATTCCCTGyAATTTCGnyGGAGTCC |
| USF, M00217, NCACGTGN: 1-8 + (0.902) |