There is an enrichment in A's immediately upstream and downstream from the start codon.
The gene sequences downstream from the start codon show a surprising regularity in all bacteria examined.
An ORF may be incorrectly extended in the 5' direction beyond the actual start codon simply because there is an open reading frame available beyond that codon.
Synechocystis shows an exceptionally weak SD pattern and also has reasonably prominent C frequencies on either side of the start codon.
If a 5'-proximal AUG triplet can serve as a sufficient translational initiation signal, then any AUG sequence positioned in this manner might conceivably be translated, mRNA conformation permitting, regardless of whether or not the utilized start codon is part of a legitimate open reading frame ending with one of the three possible termination codons.
In an additional 8 mRNAs with short leaders of from 3 to seven nucleotides and lacking a Shine-Dalgarno homology, one 5'-proximal AUG sequence is the start codon for the phage P22 c2 repressor protein, and 5 others are blocked in-frame by termination codons upstream of known coding regions.
Finally, a short leader, if present, might sufficiently reduce the translational efficiency of a start codon so that it competes less effectively against a downstream start codon with an appropriately spaced Shine-Dalgarno homology.
Students 2 and 3 take the string with the START codon
(methionine) and the mRNA sequence and move to the A Site.
If the gene was cloned into the vector with the start codon
(ATG) next to the SP6 side, what size fragments will we get if we cut the cloned product (plasmid with our gene in it) with EcoRI ?
Only two avian strains without a start codon
were observed (A/Quail/Hong Kong/AF157/92 [H9N2] and A/duck/NC/91347/01 [H1N2]), leaving no PB1-F2 encoded.
Variability in these regions, especially in the so-called KOZAK sequence around the start codon (33), may influence efficiency of translation initiation and, thus, protein expression and virus production.
The highest frequency of nucleotide changes, deletions, and insertions was observed at the 3'- and 5'-noncoding regions just upstream of the GPC and NP start codons on the genomic and antigenomic strands, respectively (position 25-55 and 3303-3365).