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Identifying the extent of genes
Two strong beliefs, head to head
While it is gratifying that the protein sequences now align in a coherant way, your soul is certainly not at peace. You extended the sequences backwards without regard to the presence of a stop codon, and now, in two cases, there exists no start codon upstream from the conserved sequence. You are pushed therefore to one of the following very unappealing notions:
- The original annotation is correct, and the proteins start with conventional start codons. However, there is a great deal of sequence upstream from the start sites that has been conserved for a billion years without coding for anything!
- The original annotation is incorrect. The conserved sequence is explained by its presence within the coding sequence. However, at least two of the proteins do not begin with conventional start sites!
Either extraordinary conclusion requires extraordinary evidence.
How can you tell whether a sequence
is or is not likely to be part of a coding sequence?
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