Table 5.
Comparison between previously experimentally verified B. floridae CNEs or regulatory elements (REs) and this study
| Functional B. floridae | Genomic coordinate | Literature source | Comparison with this study |
|||
|---|---|---|---|---|---|---|
| CNE/RE name | (in the B. floridae v2.0 assembly) | WGA-based CNEs | CSRM-based CNEs | CNEs- intersection | CNEs- union | |
| Elav-like CNEa | Bf_V2_69:357679-357729 | Hufton et al. (2009) | X | X | X | X |
| Engrailed RE | Bf_V2_9:1267978-1274277 | Beaster-Jones et al. (2007) | ✓ | ✓ | ✓ | ✓ |
| EvxA? RE 2473 | Bf_V2_12:378112-378330 | Acemel et al. (2016) | ✓ | ✓ | ✓ | ✓ |
| FoxD RE | Bf_V2_113:901685-902885 | Yu et al. (2004) | ✓ | ✓ | ✓ | ✓ |
| Hedgehog RE | Bf_V2_205:188300-193172 | Irimia et al. (2012a) | ✓ | ✓ | ✓ | ✓ |
| Hox1A RE | Bf_V2_12:999003-1001503 | Manzanares et al. (2000); Wada et al. (2006) | ✓ | ✓ | ✓ | ✓ |
| Hox2B RE | Bf_V2_12:986507-990914 | Manzanares et al. (2000); Wada et al. (2006) | ✓ | ✓ | ✓ | ✓ |
| Hox2C RE | Bf_V2_12:980069-981704 | Manzanares et al. (2000); Wada et al. (2006) | ✓ | ✓ | ✓ | ✓ |
| Hox3B RE | Bf_V2_12:977525-979277 | Manzanares et al. (2000); Wada et al. (2006) | ✓ | ✓ | ✓ | ✓ |
| Hox1 1655 RE | Bf_V2_12:1119489-1119959 | Acemel et al. (2016) | ✓ | ✓ | ✓ | ✓ |
| Hox1 1739 RE | Bf_V2_12:1060551-1060880 | Acemel et al. (2016) | ✓ | ✓ | ✓ | ✓ |
| Hox1 1784 RE | Bf_V2_12:1018545-1019524 | Acemel et al. (2016) | ✓ | ✓ | ✓ | ✓ |
| Hox1 1801 RE | Bf_V2_12:1002265-1002697 | Acemel et al. (2016) | ✓ | ✓ | ✓ | ✓ |
| Irx-Sowah 1a CNE | Bf_V2_14:276485-278804 | Maeso et al. (2012) | ✓ | ✓ | ✓ | ✓ |
| Irx-Sowah 5b CNE | Bf_V2_14:351877-352857 | Maeso et al. (2012) | X | ✓ | X | ✓ |
| Irx-Sowah 6a CNE | Bf_V2_14:424282-425437 | Maeso et al. (2012) | X | ✓ | X | ✓ |
| Irx-Sowah 6c CNE | Bf_V2_14:315985-317211 | Maeso et al. (2012) | X | ✓ | X | ✓ |
| Irx-Sowah 9d CNEa | Bf_V2_14:300102-300634 | Maeso et al. (2012) | X | X | X | X |
| Irx-Sowah 10b CNE | Bf_V2_14:378423-380890 | Maeso et al. (2012) | X | ✓ | X | ✓ |
| Irx-Sowah 10d CNE | Bf_V2_14:301002-303621 | Maeso et al. (2012) | ✓ | ✓ | ✓ | ✓ |
| Msx CNE | Bf_V2_40:953259-953496 | Hufton et al. (2009); Royo et al. (2011); Clarke et al. (2012) | ✓ | ✓ | ✓ | ✓ |
| Six3/6 CNE | Bf_V2_245:211307-211352 | Hufton et al. (2009); Royo et al. (2011) | ✓ | ✓ | ✓ | ✓ |
| SoxB2 CNE | Bf_V2_196:4387592-4387942 | Hufton et al. (2009); Royo et al. (2011) | ✓ | ✓ | ✓ | ✓ |
| SoxE RE | Bf_V2_174:2742068 2744567 | Van Otterloo et al. (2012) | ✓ | ✓ | ✓ | ✓ |
| Sp5 CNE | Bf_V2_149:861774-862000 | Hufton et al. (2009) | ✓ | ✓ | ✓ | ✓ |
| ZNF503/703 CNE | Bf_V2_167:2385491-2385650 | Holland et al. (2008); Royo et al. (2011); Clarke et al. (2012) | ✓ | ✓ | ✓ | ✓ |
aAlthough there is no direct overlap between our CNEs and these two regions, we found other CNEs in the immediate proximity of these regions.