Nucleotide nonsynonymous

Polymorphisms have been identified in both UGT1 A3 and UGT1A4. Iwai et al. identified four nonsynonymous single-nucleotide polymorphisms (SNPs) in... 

Unweighted pathway Synonymous and nonsynonymous changes, with each further subdivided into three categories of nucleotide substitution 10... 

Natural variation in the genes that encode adrenergic receptors (ARs) have been identified. The variations of major interest for common diseases are those that occur with allele frequencies >1% and are termed polymorphisms. Within the coding region, polymorphic variation can result in either a change in the encoded amino acid (nonsynonymous) or, because of the redundancy of the genetic code, have no effect on the encoded residue (synonymous). The most common variants are single nucleotide polymorphisms (SNPs), but insertions and deletions are also found. AR polymorphisms have been considered as poten-... 

There are two nonsynonymous coding polymorphisms of the /i AR found in the human population (Figure 1, Table 1). At nucleotide 145, variation is present that results in either Ser or Gly at amino acid position 49. This position is within... 

In the coding region of the human AR, nine polymorphisms have been identified, three of which are nonsynonymous (Table 1) (26). A nonsynonymous variation at codon 34 has been reported (26), but the allele frequency is <1%. As shown in Figure 1, the common nonsynonymous polymorphisms occur at nucleotides 47 (amino acid 16) and 79 (amino acid 27). Both display differences in allele frequencies between Caucasians and African-Americans (Table 1) (27). Of note, the Argl6 receptor was first cloned and has been referred to as wild-type, but is in fact the minor allelic variant. 

When the lysin sequences of the first seven species were obtained, we were impressed at how much divergence had occurred between their primary structures (Figure 9 Table 1). We also discovered that amino acid replacement was mainly nonconservative regarding the class of residue replaced. Next, we made pairwise comparisons of the aligned cDNA sequences and scored the numbers of amino acid altering (nonsynonymous) and silent (synonymous) nucleotide changes in the 21 pairwise comparisons of the seven sequences. The data (Table 2) showed that the vast majority of codon differences between any two lysins are amino acid altering. For example, in the comparison of mature red and pinto abalone lysins of 136 codons, 25 of the codon differences are nonsynonymous and only one is silent (Lee and Vacquier, 1992). 

Computer programs were used to calculate the percentage of nonsynonymous nucleotide substitutions per nonsynonymous site and the percentage of... 

Li, W.-H., Wu, C.-I., and Luo, C.-C. (1985). A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2 150-174. 

Nei, M. and Gojobori, T. (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 418-426. 

The relationships between nucleotide substitution rates in eoding sequences and predicted (on the basis of a consensus of flve methods) secondary structures of encoded proteins were investigated by Chiusano et al. (1999) on 34 alignments, each one of which comprised sequences belonging to at least four mammalian orders. The rates of synonymous and nonsynonymous substitutions were found not to be signifleantly diflerent in aperiodic and o-helix, whereas they were significantly lower in /3-strand, the most hydrophobic structure, compared to the other two structures (see Table 10.1). Expeetedly, in all cases nonsynonymous rates were lower than synonymous rates. 

Evolution of nucleic acid sequence Phylogenetic analyses often examine whether nucleotide substitutions are synonymous (not altering encoded amino acid) or nonsynonymous, and trace the history of gene- TABLE 18.6 Phylogenetic databases and utilities ... 

Tabk I shows the rq)lacement of amino add residues by nonsynonymous nucleotide substitutions in the S conserved amino add sequences on the ALS enzyme. The alteration of tyrosine (Y) to histidine (H) in the first amino acid sequence (1) of R on A was found in 1 resistant bio pe. But it seems tiiat this replacement does not confer resistance, because the other resistant biotypes did not have such a replacement All S resistant biotypes had various point mutations (A, S, L) in the codon for a proline residue (P) in the second amino acid sequence (2) of Region A, whereas all 7 susceptible biotypes had the proline residue (P). Because this proline codon (P) is common with oth susceptible plants sequenced so far, it is possible tiiat its replacement confers resistance to SU herbicides in L, micrantha. Finalty, all of the resistant plants had an alteration from proline (P) to s me (A), alanine (S), or lysine (L) compared with the amino acid sequence of susceptible plants reported. 

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