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If synonymous rates are more or less equal across genes within a mitochondrial genome (as seems to be the case for P. hortorum; Fig. 1), then sampling multiple protein genes (and among many taxa) should provide another opportunity to better elucidate the tempo and pattern of rate changes.
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For genes with multiple protein products (gene models), only the representative one (if available) or the longest one was retained.
As an answer to this, various authors started to include multiple protein coding genes in their phylogenetic analyses [ 8- 10].
Elevated expression of multiple protein biosynthesis genes is a prominent feature of the transcriptome of hibernating black bears in all organs studied to date in black bears.
Second, multiple ribosomal protein genes (which are known to be down-regulated upon TOR inhibition) are also reduced for expression in hsf1-R206S, F256S cells.
The data set of multiple ribosomal protein genes was concatenated to produce a 10,971 bp-long super-gene alignment, which was then used for phylogenetic inference [ 25].
Because these chromatin association experiments measure global HMG binding and are more susceptible to experimental variability, we chose next to perform chromatin immunoprecipitation at multiple ribosomal protein genes to better quantify these effects on a gene-specific basis.
Similarly, among the 375 mlncRNAs, 51 each showed sequence similarity to 2-10 protein-coding genes, indicating some mlncRNAs are related to multiple protein-coding genes.
These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein-coding genes, without noticeable phenotypic effects.
Dysregulation of miRNA levels would be anticipated to affect the translation of multiple protein-coding genes.
The miRNAs are unique in their ability to regulate multiple protein-coding genes.
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