Biology Genetics: Homologous Chromosomes?

I have never been too clear on exactly what an allele is. E.g. you can have two "versions of a gene" with different base sequences of DNA, that produce exactly the same protein (because some amino acids have more than one triplet code that codes for them).

Are these alleles? or not?

Be careful with the phenotypic effects, because this all depends very much on the other genes etc of the organism.

Rosie <== wishes biology had clearer terminology (a lot of the most eminent biologists cant actually agree on quite what a "gene" is - what hope do we have!)

I think (don't hold me to this) that all variations are alleles. Some may lead to phenotypic variation; some may not. Whether variations in introns count as alleles too, I don't know but you don't need to know about that.