Are alternative versions of the same gene?

An allele is a variant form of a gene. Some genes have a variety of different forms, which are located at the same position, or genetic locus, on a chromosome. Humans are called diploid organisms because they have two alleles at each genetic locus, with one allele inherited from each parent. Each pair of alleles represents the genotype of a specific gene. Genotypes are described as homozygous if there are two identical alleles at a particular locus and as heterozygous if the two alleles differ. Alleles contribute to the organism's phenotype, which is the outward appearance of the organism.

Some alleles are dominant or recessive. When an organism is heterozygous at a specific locus and carries one dominant and one recessive allele, the organism will express the dominant phenotype. Alleles can also refer to minor DNA sequence variations between alleles that do not necessarily influence the gene's phenotype.

What are variants?

In the field of genetic variation, the term variant is used to refer to a specific region of the genome which differs between two genomes.

What are alleles?

Different versions of the same variant are called alleles. For example, a SNP may have two alternative bases, or alleles, C and T4.

When working with genome scale data the term reference allele refers to the base that is found in the reference genome. Since the reference is just somebody’s genome, it is not always the major allele. In contrast, the alternative allele refers to any base, other than the reference, that is found at that locus. The alternative allele is not necessarily the minor allele and it may, or may not, be linked to a phenotype. There can be more than one alternative allele per variant.

What is linkage disequilibrium?

In the genome, alleles at variants close together on the same chromosome tend to occur together more often than is expected by chance. These blocks of alleles are called haplotypes. Linkage disequilibrium (LD) is a measure of how often two alleles or specific sequences are inherited together, with alleles that are always co-inherited said to be in linkage disequilibrium.

Genes and alleles are essential to basic genetics, but what are the differences between them? In this guide, we compare genes and alleles and provide simple definitions and examples for both.

Gene vs allele

Genes are chunks of DNA that contribute to particular traits or functions by coding for proteins that influence physiology. Alleles are different versions of a gene, which vary according to the nucleotide base present at a particular genome location. An individual's combination of alleles is known as their genotype. 

What is a gene?

Genes are sections of DNA that contribute to certain traits, characteristics or functions. Genes code for proteins or parts of proteins that influence things like the immune system, skin pigmentation, hormone production, and eye color. Genes are transcribed into RNA molecules, which are then translated into proteins. Segments of DNA demarcated as genes consist of both coding and non-coding regions. Coding regions, also called exons, are the sections transcribed into eventual protein. Non-coding regions, or introns, are not transcribed, but are thought to fulfil numerous other functions such as regulation of transcription. Humans have approximately 20,000 protein-coding genes, which represent less than 2% of the total genome.

Genes are inherited from an offspring’s parents, and they are responsible for features being passed down from one generation to the next. An organism’s genotypeconsists of its entire set of genes. Every human has a unique genotype, which explains the vast variety in human appearance and biology.

The classical understanding of a gene placed it as the singular unit of inheritance, with a rigid structure of “one gene-one RNA-one protein”. New findings in the modern era of genomics, however, have realigned this paradigm. For example, it is now known that genes are capable of producing more than one RNA molecule, through a process known as alternative splicing.

What is an allele?

There are multiple versions of a base that can be found at any given genomic location, or loci. Allele is the term used to describe these different versions of a gene. For example, at one particular loci, two alleles may exist, one that codes for a cytosine base and one that codes for a thymine base. Humans inherit two copies of their genome – one from each parent. As such, we are known as diploid organisms.

The unique combination of these alleles across a genome is known as an individual’s genotype. These gene variants still code for the same trait (i.e. eye color), but they differ in how the trait is expressed (an organism’s phenotype). In most cases, there is not one single locus whose alleles determine how a trait is expressed.

Let’s consider eye color – blue, green, brown and hazel eyes are each encoded by unique set of alleles in particular genetic loci. A more in-depth look reveals that there are roughly 16 different genes responsible for eye color, although most of the influence comes from 2 of these 16 genes.

The greater the number of potential alleles, the more diversity in a given heritable trait. This combination of genes and gene variants underlies human genetic diversity, and they are the reason why no two people are exactly alike.

Major and minor alleles

The most common form of an allele is designated the major allele, whereas less common versions are known as minor alleles.

How are genes and alleles inherited?

In humans, when a sperm cell fertilizes an egg cell, the resulting zygote will inherit 23 chromosomes from each parent. Each matching chromosome pair contains the same set of genes, but with unique alleles of each gene at each locus.

This inheritance means that individuals have two gene copies for a given trait, one inherited from their mother and the other from their father. These are known as maternal alleles and paternal alleles. It is how these alleles interact that is responsible for unique characteristics.

What is a dominant gene and what is a recessive gene?

The totality of genes encoded on a human’s 46 chromosomes is known as their genotype. But not all gene variations will be expressed. For instance, you might have one allele for brown eyes and another for blue eyes, but you will not therefore have one blue and one brown eye.

Individuals do not display the characteristics encoded on each matching pair of genes. Instead, the genes that are expressed result in the phenotype, which is how genes are expressed in observable characteristics.

How does the body know which alleles to express? This comes down to the properties of alleles that are paired.

Every individual has two copies, or alleles, or a single gene. When the alleles are the same, they are known as homozygotes. When they are different, they are called heterozygotes.

Homozygotes code for the same trait, for instance, blue eyes. If you have two blue eye alleles, your eyes will be blue. But if you have one allele for blue eyes and another for brown eyes, your eye color will be dictated by whichever allele is dominant.

A dominant allele is one that always determines the phenotype when present. On the other hand, a recessive allele is one that is not expressed when its paired allele is dominant.

With eye color, the brown eye allele is dominant to the blue eye allele. This means that a child with a blue allele from their mom and a brown allele from their dad will end up with brown eyes. But a child with two blue alleles will display the blue eye phenotype.

What does an alternative form of gene mean?

Do alternate forms of the same gene exist?