Model simulations display the effects of mutation of binding sites, or perturbation of upstream gene expression.
BacPP is hence outstanding in recognition and assignment of sequences according to σ factor and provide circumstantial information about upstream gene sequences.
The distance between the stop codon of the upstream gene and the start codon of the downstream gene was demonstrated to be of key importance in translational coupling (Levin-Karp et al. 2013).
CTR1 is an upstream gene, and has been reported as the regulator of the pathway [25].
It is also possible that the distinctive VP1 unique forms coevolved with the upstream gene rep.
PE01F07 and PE01F11, isolates where evidence had indicated that may have truncated exon 1 were PCR positive for the upstream gene but negative for the downstream gene.
For example, if the upstream gene is "on" (state = 1) and is a repressor (function = 0), then the downstream gene takes the "off" state (state = 0).
The aligned region 2000 bp upstream of each gene (or until the nearest upstream gene if that was closer) was then extracted and used in subsequent analysis.
For this study, we chose to limit our validation to upstream gene promoters, as these are well characterized for their effects on silencing gene expression [44].
Interestingly, we found that while hfq is transcribed from an identical promoter region in F. novicida, it is also co-transcribed with the upstream gene miaA.
These results suggest that miR-103 and miR-107 bind the putative target sequence in the cofilin 3'UTR and functionally repress translation of the upstream gene.
