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Stop codon (red dot) of the human mitochondrial DNA MT-ATP8 gene, and start codon (blue circle) of the MT-ATP6 gene. For each nucleotide triplet (square brackets), the corresponding amino acid is given (one-letter code), either in the +1 reading frame for MT-ATP8 (in red) or in the +3 frame for MT-ATP6 (in blue).
In the context of gene finding, the start-stop definition of an ORF therefore only applies to spliced mRNAs, not genomic DNA, since introns may contain stop codons and/or cause shifts between reading frames. An alternative definition says that an ORF is a sequence that has a length divisible by three and is bounded by stop codons.
The standard genetic code only contains 20 codons that cannot become stop codons in a frameshifted ribosomal environment (-1 frameshift: 42, +1 frameshift: 28) and 127 out of the 400 (31.75%) possible adjacent amino acid combinations in the vertebrate mitochondrial code creates an off-frame stop codon. [1]
For each codon (square brackets), the amino acid is given by the vertebrate mitochondrial code, either in the +1 frame for MT-ATP8 (in red) or in the +3 frame for MT-ATP6 (in blue). The MT-ATP8 genes terminates with the TAG stop codon (red dot) in the +1 frame. The MT-ATP6 gene starts with the ATG codon (blue circle for the M amino acid) in the ...
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).
This picture shows how Open Reading Frames (ORFs) can be used for gene prediction. Gene prediction is the process of determining where a coding gene might be in a genomic sequence. Functional proteins must begin with a Start codon (where DNA transcription begins), and end with a Stop codon (where transcription ends).
An open reading frame (ORF) is a reading frame that has the potential to be transcribed into RNA and translated into protein. It requires a continuous sequence of DNA which may include a start codon, through a subsequent region which has a length that is a multiple of 3 nucleotides, to a stop codon in the same reading frame.
They collected his DNA and amplified it using PCR. Sequencing analysis revealed a homozygous single substitution determining a stop codon. This caused an aberrant protein and the corresponding amino acid sequence indicated the exact position of the homozygous nucleotide. The substitution was localized in exon 3 and nonsense mutation at codon 68.