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Variation of a gene as found at the same locus on a different chromosome in the same individual.
In a diploid individual, on each homologous pair of chromosomes there will be total of two alleles present per locus. When considering one of these two alleles, the other allele, found on the homologue, one can described as a homologous allele.
To a degree the idea of homologous as applied to alleles has taken on a different though relating meaning. That is, one can view a homologous allele, as defined above, as two very similar and, indeed, potentially identical genes in terms of their sequence. Similarly, two alleles may be described as homologous – as in the idea of homology or homologous character – if they share appreciable sequence even if they do not make up two alleles that are found on homologous chromosomes.
In other words, homology is an indication of genetic relatedness, which unquestionably is the case for two alleles found at the same locus (those two alleles with certainty both descended from similar alleles). It is also extremely likely given sufficient similarity even if those two alleles are not found at the same locus or even in the same species.
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