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Codon usage bias in Physcomitrella patens. Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA.A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons).
CUG is known to function as an initiator for one plasmid-encoded protein (RepA) in E. coli. [14] In addition to the NUG initiations, in rare cases bacteria can initiate translation from an AUU codon as e.g. in the case of poly(A) polymerase PcnB and the InfC gene that codes for translation initiation factor IF3.
The frequency of codons, also known as codon usage bias, can vary from species to species with functional implications for the control of translation. The codon varies by organism; for example, most common proline codon in E. coli is CCG, whereas in humans this is the least used proline codon. [53]
The Codon Adaptation Index (CAI) [1] is the most widespread technique for analyzing codon usage bias.As opposed to other measures of codon usage bias, such as the 'effective number of codons' (Nc), which measure deviation from a uniform bias (null hypothesis), CAI measures the deviation of a given protein coding gene sequence with respect to a reference set of genes.
A codon table can be used to translate a genetic code into a sequence of amino acids. [1] [2] The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis. [2] [3] The mRNA sequence is determined by the sequence of ...
Well-known coding regions that do not have AUG initiation codons are those of lacI (GUG) [10] [11] and lacA (UUG) [12] in the E. coli lac operon. Two more recent studies have independently shown that 17 or more non-AUG start codons may initiate translation in E. coli. [13] [14]
Well-known coding regions that do not have AUG initiation codons are those of lacI (GUG) [2] and lacA (UUG) in the E. coli lac operon. [3] Two studies have independently shown that 17 or more non-AUG start codons may initiate translation in E. coli. [4] [5] Nevertheless, AUG seems to at least be the strongest initiation codon among all ...
Effective number of codons (abbreviated as ENC or Nc) is a measure to study the state of codon usage biases in genes and genomes. [1] The way that ENC is computed has obvious similarities to the computation of effective population size in population genetics . [ 2 ]