mRNAs required for cell proliferation are enriched in rare codons and are poorly adapted to tRNA pools.aNIH-3T3 cells with a stably integrated FUCCI system were sorted according to the cell cycle phase, and the corresponding transcriptomes were profiled by mRNA sequencing. The scatter plot shows ...
The single-letter code for amino acids is given below the appropriate codon. (B) Expression of AU1-tagged E5 proteins in primary keratinocytes. Primary keratinocytes were infected with the indicated retroviruses and selected in G418 as described. Left: LXSN empty retrovirus; middle: wt16E5; ...
DNA transcription is a critical step in protein synthesis where genetic instructions are copied from DNA to RNA. The enzyme RNA polymerase transcribes DNA into a single-stranded RNA molecule known as messenger RNA (mRNA). Protein synthesis occurs in the cytoplasm, where the mRNA, along with ribo...
Codons with similar biochemical properties (as shown by the colours) tend to occupy adjacent regions of space. Codons encoding for the same residue (amino acid single letter codes shown over the points) tend to be closer (P = 0.017, two-sided permutation test n = 107), as do ...
Full size table Factors affecting codon usage bias Codon bias or preference varies not only with species of organisms, family or group within kingdom, but also between the genes and between different sites or positions in a gene. Species-specific codon bias is correlated with overall GC content...
There is a row and column for every single-letter aminco acid code and each cell contains a score representing how good of a match the pair of amino acids is (i.e. how similar they are). The last row and column (represented by '*') contains the minimum score. Examples of these ...
noncoding genomic %GC relies on the assumption that the species will have a similar breakdown of coding and noncoding sequence asCE. Assembly and gene calling for theBM,HC,TS, andACsequences are needed to test this assumption. Definitions of species two letter codes are provided in Table 1....
Full size table Figure 1 Phylogenetic tree used to define the relative age groups for the human and mouse genes. The labeled age classes were defined as the major evolutionary branching points with respect to the 27 genomes analyzed and the species of interest (human or mouse). Thus, genes ...
table,Table 1 – Probability Reference Table. These reference probabilities are then combined into a series of calculations, culminating in the remote likelihood of Item B below, and then finally a preliminary estimate of the codon second letter schema’s occurring naturally, based upon just three ...
Its fundamental challenge is to uncover the constraints, historical accidents, and evolutionary driving forces that could have shaped the standard codon table. The current views propose the general mechanisms of (1) stereochemical affinity between codons and attributed amino acids (stereochemical theory2,...