In all subsequent discontiguous MegaBLAST searches both the coding and non-coding seed were used.
Compared to WES, WGS facilitates sequencing of the whole genomes including both the coding and non-coding regions.
The lengths of the regions in both the coding and non-coding sets match the length distribution of fly coding exons.
This high level of sequence identity between both the coding and non-coding regions of SCGB1A1 genes created a challenge for isolation and assessment of individual genes.
In particular, for Drosophila species, natural selection has been shown to shape both the coding and non-coding parts of the genome [ 10, 11].
A total of 35 repeats structure were detected in both the coding and non-coding regions with a majority being tandem repeats.
Microsatellites, also called SSRs (simple sequence repeats) or STRs (short tandem repeats), are 1-6 bp tandem repeat motifs present in both the coding and non-coding fractions of eukaryotic and prokaryotic genomes [ 1- 3].
Their action may be directed at breaking the potentially dangerous positive feedback loop that could result if a pioneering polymerase disrupts chromatin so as to facilitate subsequent transcription events from both the coding and non-coding strands.
Therefore, both the coding region and the 3′-UTR can be more effective targets, and other factors may affect the outcome.
For all genes, both the coding sequence and splice junctions were assessed.
