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SNPs within genes below the median dN/dS, suggestive of stronger constraints imposed on protein sequence, exhibited 2.55-fold enrichment (P « 10−16) for negative TE selection that was significantly higher than the group above the median (P = 0.01).
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Though HM-code divergence between duplicates in both promoter and ORF regions increase with their sequence divergence, the HM-code in ORF region evolves slower than that in promoter region, probably owing to the functional constraints imposed on protein sequences.
The observation that proteins with more interacting partners are subject to stronger levels of selective constraint suggests that direct protein protein interactions impose constraints on protein sequence evolution.
Although it has become apparent that folding imposes constraints on protein sequence evolution, the effects exerted by different chaperone classes are so far unknown.
Therefore, the question for what is the main determinant of the rate of protein evolution may have different answers, depending on how to decipher the functional constraint imposed on the protein sequence.
The first one is the (overall) selection intensity of the gene under study, S, for the overall strength of purifying selection imposed on the protein sequence; the negative sign indicates the negative (purifying) selection.
To examine this possibility, we identified gene paralogs based on protein sequence homology (Table S3).
Hence my independent ancestry models approximately account for (1) constraints on protein sequences imposed by function and (2) the prior probability of selection for function converging on similar sequences.
9 Encouragingly, evolutionary constraints on protein sequences are imposed by requirements of 3-dimensional structure and biological function, which are main aspects employed for the classification of proteins.
The reduced influence of GC12 can be explained by constraints imposed by protein sequence conservation.
Thus, there were strong constraints imposed on the PEG11 protein sequence caused by regions encoding conserved miRNA antisense to the PEG11 gene.
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