Fig. 11

Pair-wise alignments of nubbin neural enhancer sequences reveal that many share conserved sequence elements. a Phylogenetic comparative analysis of nub-9 enhancer identifies multiple conserved sequence blocks. Black capital letters represent D. melanogaster bases conserved in D. simulans, D. sechellia, D. yakuba, D. erecta, D. ananassae, D. persimilis, D. pseudoobscura, D. willistoni, D. virilis, D. mojavensis and D. grimshaw orthologous DNA sequences. Lowercase gray letters represent bases not conserved in one or more species included in the analysis. Putative TF DNA-binding sequences are highlighted as follows: Castor/Hunchback DNA-binding motifs (CATAAA/TTTATG) are red highlighted sequences; bHLH DNA-binding sites (CANNTG) are blue highlighted sequences; and Hox DNA-binding motifs (ATTA/TAAT) are green highlighted sequences. b Advanced cis-Decoder search results of nub-9 for a subset of nub conserved sequence clusters (CSCs) that each contain the conserved 5’ CATAAA 3’ element. For each CSC aligned with the input nub-9 EvoPrint, the results table provides the following statistics: the number of required elements present in the CSC; number of shared elements ≥8 bp; the longest shared sequence length (sequences in red indicate that it contains the required sequence, CATAAA); total number of conserved bases; and the longest shared sequence(s). An example of an alignment is shown in panel (b). c Shown is a cis-Decoder alignment of nub-9 and nub-12 conserved sequences that highlights ≥6 bp shared elements. The readout indicates the nub-9 single copy (blue) and repeated (red) conserved sequences aligned to nub-12 CSBs (bold black). Displayed in 5’ to 3’ order, CSBs are annotated to reflect their ordered appearance within the enhancers and their alignment orientation (forward, F; reverse, R)