The rest of the variability is attributed to factors such as protein degradation and seems to be lower compared to the effect of variability in the codon frequency.
If all homologous cassettes were conserved across their whole length and no mutation pattern reminiscent of the variability of synonymous codon positions could be observed, the cassette was confirmed as non-coding.
However, using internal correspondence analysis, the latter authors showed that the variability of synonymous codon usage between tissues represents only 2.3% of the total codon usage variability, and that most of this is explained by isochore-scale variability of GC-content that affects both coding and introns or intergenic regions.
The variability of TP53 codon 72 may then be part of the genetic "machinery" affecting the accumulation of mtDNA somatic mutations.
Alternatively, the observed variability of stop codon frequencies relative to the average expectation (compare Figure 1A and 1B) may be due to slight changes in selection pressure on TAG and the rates of A < − > G mutation between different species.
Prozzi et al. [ 28] showed that the antigenic subgroups are related to the sequence variability of the central conserved region (codon position 154 to 192) of the G protein.
Indeed, such weak selection on individual alleles can be overpowered by genetic drift, which may result in the large variability of stop codon frequencies in our data.
The model accounts for 72%, 64% and 52% of the observed variability of codon usage in prokaryotes, plants and human respectively.
4. The variability of codon usage across bacterial genomes leads to a correlation between long phase-1 overlaps and genomic GC content. 5. Our model explains the phase bias in same-strand overlapping genes by compositional factors without invoking selection.
Our experimental results confirm variability of the adaptive value of different pipo stop codons.
