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Akin to conservation, the target organisms are behaviourally plastic, actively dispersing, multiploid eukaryotes with sexual reproduction, including both multicellular and unicellular species.
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The conservation of promoters and transcription factor (TF) binding sites are important predictors of gene expression similarity, and there is a correlation between conservation of TF binding events and conservation of the target gene expression (Hemberg and Kreiman, 2011).
Root mean square differences ranging from 0.88 to 3.26 Å indicate structural conservation between the target and template structures.
The complementarity of each miR 5' seed sequence, the low free energy and the conservation of the target site were considered as main features for target mRNA discovery.
The structural conservation between the target and template, as well as the correctness of the template alignment, are among the most important factors in generating homology models.
The miRanda algorithm is based on sequence complementarity between the mature miRNA and its target site, binding energy for the miRNA-target duplex, and the evolutionary conservation of the target site sequence and position in aligned UTRs of homologous genes found in human, mouse and rat [41].
Single miRNAs can also affect gene sets by conservation of the target site in orthologous genes.
This multiple sequence alignment showed a very few conservation with the target sequence modeled.
Therefore, the conservation of the target site is unlikely to be expected under neutral evolution but seems to be due to functional constraints.
It is conventional to screen for conservation of the target site in majority of target-prediction databases like TargetScan, miRanda, etc.
All identified sequences were further aligned on the whole genome of sequenced strains to ensure gene specificity and conservation of the target sequence between strains.
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