Up to now we have been considering genes as abstract entities and mentioning, only in passing, what they actually are. We can think about genes encoding traits, but this is perhaps the most incorrect possible view of what genes are and what they do. A gene is a region of DNA that encode a gene product, either an mRNA that itself encodes a polypeptide or a “non-coding” RNA that functions as an RNA. The gene also includes the sequences required for its proper expression, that is, when and where the gene is active, when RNAs are made from it. While we will not consider in any significant detail, it is worth noting that genes can be complex: there can be multiple regulatory regions controlling the same coding sequence and particularly in eukaryotes a single gene can produce multiple, functionally distinct gene products through the process of RNA splicing220. How differences in gene sequence influence the activity and role(s) of a gene is often not simple. One critical point to keep in mind is that a gene has meaning only in the context of a cell or an organism. Change the organism and the same, or rather, more accurately put, homologous genes (that is gene that share a common ancestor, a point we will return to) can have different roles.
Once we understand that a gene corresponds to a specific sequence of DNA, we understand that different alleles of a gene correspond to genes with different sequences. Two alleles of the same gene can differ from one another at as little as a single nucleotide position or at many positions. The most common version of an allele is often referred to as the wild type allele, but that is really just because it is the most common. There can be multiple “normal” alleles of a particular gene within any one population. Genes can overlap with one another, particularly in terms of their regulatory regions, and defining all of the regulatory regions of a gene can be difficult, particularly since different regulatory regions may be used in the different cells types present within a multicellular organism. A gene's regulatory regions can span many thousands of kilobases of DNA and be located upstream, downstream, or within the gene’s coding region. In addition, because DNA is double stranded, one gene can be located on one strand and another, completely different gene can be located on the anti-parallel strand. We will return to the basic mechanisms of gene regulation later on, but as you probably have discerned, gene regulation is complex and typically the subject of its own course.
Alleles: Different alleles of the same gene can produce quite similar gene products or their products can be different. The functional characterization of an allele is typically carried out with respect to how its presence influences a specific trait(s). Again, remember that most traits are influenced by multiple genes, and a single gene can influence multiple traits and processes. An allele can produce a gene product with completely normal function or absolutely no remaining functional activity, referred to as a null or amorphic allele. It can have less function than the "wild type" allele (hypomorphic), more function than the wild type (hypermorphic), or a new function (neomorphic). Given that many gene products function as part of multimeric complexes that are the products of multiple genes and that many organisms (like us) are diploid, there is one more possibility, the product of one allele can antagonize the activity of the other - this is known as an antimorphic allele. These different types of alleles were defined genetically by Herbert Muller, who won the Nobel prize for showing that X-rays could induce mutations, that is, new alleles.