Kuzmenko, A. et al. Mitochondrial translation initiation machinery: conservation and diversification.
Moving from the evidence that - despite lack of translation - sequence conservation of pseudogenes suggests functionality, the authors proposed them as perfect endogenous competitors of their ancestral genes, because they retain many of the miRNA binding sites.
Variants were annotated using a custom annotation pipeline adding the following annotation for each detected variant: annotation with known polymorphism data from dbSNP130, genomic feature annotation (e.g., exon and intron), amino acid translations, and PhyloP conservation score (based on conservation of 44 vertebrate species) [Hoischen et al., 2010; Vissers et al., 2010].
These novel cases of translation readthrough exhibit lower conservation scores and lower readthrough rates than those predicted by conservation; the nucleotide character of these novel readthrough regions is intermediate between coding regions and 3′ UTRs.
More conservation in translation than transcription is also confirmed by the inheritance mode of transcription and translation between two species.
dubliniensis categories with much stronger silent site conservation than "translation," suggesting other types of silent site selection.
An extraordinary feature of the translation system is the conservation of its core across all modern cellular life forms.
When determining if and which CDS to annotate when assessing alternatively spliced transcripts, factors like NMD, translation mechanics, cross-species conservation and the presence of protein domains are taken into account.
However, neither significant translation levels nor sequence/motif conservation support their actual gene status (see examples in Supplementary Fig. S4).
The χDIA values obtained in the above manner agreed fairly well with the published values listed in Table 1, and it may be concluded that the observed translations followed the energy conservation rule (Supplementary Note B).
