Kozak sequence in vertebrae is (gcc)gccRccAUGG. A Kozak sequence of ccRccAUGG has been reported to function as well. But in the case of deletion of the -5 C, thus cRccAUGG, can it still function?
The Kozak sequence represents the consensus of the sequences observed around the initiation codon, the wikipedia page shows the sequence logo derived from 10'000 human RNAs https://en.wikipedia.org/wiki/Kozak_consensus_sequence. In vivo, this site is often not matched exactly on different mRNAs and the amount of protein synthesized from a given mRNA is dependent on the strength of the Kozak sequence. So, the effects of a deletion of the -5 base depends on what exact nucleotides are moved up by this deletion into the -5 and -6 positions.
Thank you for your answer Annemarie Honegger . However, two "T"s moved up to the -5 and -6 positions. @ Annemarie Honegger
You may try this site https://atgpr.dbcls.jp to see whether your sequence is still likely to be recognized - however, in the end, only the experiment will tell, as Kozak recognition is not an all-or-nothing process, but any changes will have a differential effect on the strength of your Kozak sequence. In addition to the actual Kozak sequence, RNA secondary structures involving this region also can have a strong effect on translation initiation.
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