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What is a gene transcript, how is it different from an allele?

What is a gene transcript, how is it different from an allele?


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Within human genetics,

My current understanding of a transcript for a particular gene is that it's the exact nucleotide sequence and position of a particular instance of said gene in some individual.

My current understanding of an allele is that it's a less granular breakdown of the instances of a gene in a population. That is to say, one allele for a particular gene likely covers many (millions of?) unique transcripts for that particular gene, and groups them together due to their tendency to all have a similar phenotypic expression.

Is this correct?


I thought a transcript was the RNA sequence produced from transcription. The RNA copy of an allele that gets spliced and translocated to the cytoplasm for translation. Not sure if Wikipedia references are allowed here, but they seem to agree with my understanding.

An allele is a specific copy of a gene, i.e. you have two copies (alleles) of gene X; allele X1 comes from your mum, allele X2 from your dad.

I haven't heard of the less granular breakdown description of genes, so that might just be a different way of looking at it.


Alleles in the traditional sense represent genetic variation in a population at a given locus. Usually this is related to a given phenotype or observable trait. They can refer to areas of the genome that may or may NOT be transcribed into RNA, whether or NOT that RNA gets translated into protein.

Alleles can refer to a single nucleotide difference (SNP), or an insertion/deletion of one more more bases (indels). Thus for a given SNP associated with heart disease, if 97% of the population has a T and the other 3 percent have an A at that locus, then the alleles are the A and T alleles for that SNP.

Note: the variation could be in a regulatory region of DNA and never get transcribed. But the phenotype associated would be varied expression of a transcribed region it regulates.

A transcript is merely an antisense strand of a region of DNA with U replacing T. Note there are many kinds of RNA transcripts, not all of which get translated to protein. The transcript always mirrors the DNA below. If the DNA has genetic variation, the transcript will reflect it.

In the last 10 years, with the discovery of epigenetics, we also have started thinking about a genetic locus where the variation is a modification of base or histone that the base binds to as DNA is compacted. So some now also include methylation of a CpG as an allele, where one person might have 40% of CpG at that location methylated, and another have 67%. This difference can explain a trait difference and thus also be referred to as an allele (high methylation vs. lower).

Last but not least, much genetic variation results in no discernible phenotypes. Sometimes both Alleles still result in the same base being encoded during translation for example.


No.

A gene is a unit of the genome stored in the form of DNA. It can be transcribed into mRNA (the transcript) to be used as a template in protein synthesis.

A gene can come in many different versions unique to an individual. That is, individuals can have different alleles, or versions of the same gene.

For example, in mice you can have many different fur colors. The color of their hair is determined by a series of biochemical reactions that are catalyzed by proteins. If each protein is functional, the mice will have a certain color of hair. If any of these proteins are not functional (because they are carrying a certain allele), then the mouse will end up being a different color than it would be if each protein functioned.

You can also have genes that produce somewhat faulty protein-products. As is the case with insulin-resistant diabetes.


Difference Between Allele and Trait

In 1822, Mendel observed different forms of hybrids by hybridization of pea plants (Pisum sativum) and the statistical relationship between them. The offspring resulted from hybridization showed interesting clear cut differences in the length of stem, color of seed, shape and color of pod, position, and color of seed. These seven characteristics were called traits.

Through the experiment he had investigated, Mendel concluded that each characteristics of an organism is controlled by a pair of alleles and, if an organism has two different alleles, one may be expressed over the other.

He noticed that there is a “factor” which determines the characteristics (traits) of an individual, and later it was found that factor is the gene.

Gene is a small part of DNA which is located in a specific location of the chromosome, which codes for single RNA or protein. It is the molecular unit of heredity (Wilson and Walker, 2003). Allele is an alternative form of a gene which influences on the phenotypic expression of the gene.

Alleles determine different traits, which carry different phenotypes. As an example, the gene responsible for the flower color of pea plant (Pisum sativum) carries two forms, one allele determines the white color, and the other allele determines the red color. These two phenotypes red and white are not expressed simultaneously in one individual.

In mammals, most genes have two allelic forms. When two alleles are identical, it is called homozygous alleles and, when it is not identical, it is called heterozygous alleles. If alleles are heterozygous, then one phenotype is dominant over other. The allele, which is not dominant, is called recessive. If allelic forms are homozygous, it is symbolized either by RR, if it is dominant, or rr if recessive. If allelic forms are heterozygous, Rr is the symbol.

Although, most of the genes have two alleles in human and produce one characteristic, some characteristics are determined by the interaction of several genes.

When different alleles are in the same site of the genome it is called polymorphism.

The trait is a physical expression of genes such as R gene is responsible for the red color of the flower pea plant (Pisum sativum). Simply it can be explained as the physical characteristics of the genetic determination (Taylor et al, 1998), but traits can be influenced by either environmental factors or both genes and environmental factors.

Combination of different alleles expresses different traits or physical characteristics such as incomplete dominance and codominance.

What is the difference between Allele and Trait?

• Alleles are the alternative form of gene, whereas trait is the physical expression of the gene.

• Allele is in a specific location, in the chromosome, whereas trait is a physical expression.

• Alleles determine the different traits which carry different phenotype.

• Allele may be in homozygous state or heterozygous state, whereas trait does not have such state.

• Allele is a small segment of DNA, whereas trait is a product of biochemical reactions.

• Alleles carry information which is accountable for a trait of an individual, whereas trait is a characteristic of an individual.

Wilson, K., Walker, J., (2003), Practical biochemistry principles and techniques, Cambridge University Press, Cambridge


How does a gene produce two different transcripts?

I'm reading a paper about the BRCA2 gene, and the paper mentions that a breast cancer cell line with a BRCA2 mutation produced two different transcripts. These two different transcripts slightly differ in the number of base pair deletions.

I want to guess that it is because genetic mutations can happen randomly, causing different versions of the resulting transcripts. Am I correct in thinking this?

I'll start with the two main ways (not mutations) where this can happen and then talk about BRCA2. The different transcripts of genes are referred to as different isoforms. One gene can produce many isoforms. What we think of as introns and exons are really only determined by a branch site and the presence of a GU at one end and an AG at the other end. Spliceosomes can recognize potentially dozens of these sites within a gene, and the branch site and some regulatory sequences denote which splice cites actually get spliced. This is called alternative splicing. What you end up with is that the gene itself still has many EXONS that get transcribed into mRNA but only some of them are coding DNA sequences (CDS) that get translated into actual amino acids, resulting in different or slightly different proteins.

The other method that can lead to different transcripts or genes is changing polyadenylation sites. The polyA tail is a 3' end of adenosine that is recognized by the ribosome when the small subunit scans looking for a place to start translation. This is important because it not only changes the actual transcript sequence that gets produced but also changes the length of the 3' untranslated region (UTR) that can drastically change which micro RNAs are able to bind, and thus can alter the expression and regulation of the gene itself.

BRCA2 is a protein that plays a role in non-homologous end joining where double stranded DNA breaks (Caused by radiation or the environment) are repaired by splicing the ends of the broken strands and ligating them together. When BRCA is mutated, cells must use micro homology-mediated end joining (MMEJ), a more error prone method of repair. The most error-free method of double stranded break repair is homologous recombination, and BRCA mutated cells show suppressed homologous recombination activity. I honestly don't know much about NHEJ vs MMEJ but I'm sure someone else can elucidate it more or wikipedia can tell you something. Basically, this is going to produce different length transcripts because when DNA is broken into two pieces, there are overhanging ends. You can repair them (with a LOT of errors! not good for the cell!) by just breaking off the overhanging ends and ligating them together (creating a shorter molecule that isn't the same) or by using homologous recombination and doing it error-free resulting in the same length molecule.


Alleles may be dominant or recessive. A dominant allele is one that will always be expressed if present. For example, the allele for Huntington’s disease is dominant, so if an individual inherits an allele for Huntington’s from only one of the parents, they will have the disease. On the other hand, a recessive allele is one that will only be expressed if it is found on both genes.

Gregor Mendel did extensive work with plants to identify patterns in the phenotypes (expressed traits) and determine which alleles were dominant and recessive. Studying alleles can help predict traits in offspring based on the genes of parents. For example, if the allele for brown eye color (upper case B) is dominant and the allele for blue eye color (lower case b) is recessive, the various combinations of genotype and phenotype can be determined using a Punnett square diagram.

Both parents in this example have heterozygotic alleles &mdash for brown (dominant) and blue (recessive) eye color. Either of these alleles may be inherited by the offspring from each parent. The Punnett square diagram shows all combinations of alleles that are inherited, and marks the resulting phenotype for eye color. Given that brown eye color is the dominant allele, and that 3 out of 4 possibilities result in at least one brown eye color allele being inherited, the probability that the offspring will have brown eyes is 75%.

A Punnett square diagram predicts an outcome of a particular cross or breeding experiment. In this example of peas, one parent has the recessive yy set of alleles and another parent has Yy (heterozygote) set of alleles. The diagram plots the 4 possible combinations of inherited alleles in the offspring, and predicts the resulting phenotype in each case. The color yellow is determined by the dominant allele Y and the color green is determined by a recessive allele. Thus the probability of the resulting peas having a phenotype of yellow color is 50% and that of green color is 50%.

Blood Group

Another example is blood types in humans. At the gene locus three alleles—IA, IB, and IO—determine compatibility of blood transfusions. An individual has one of the six possible genotypes (AA, AO, BB, BO, AB, and OO) that produce one of four possible phenotypes: "A" (produced by AA homozygous and AO heterozygous genotypes), "B" (produced by BB homozygous and BO heterozygous genotypes), "AB" heterozygotes, and "O" homozygotes.

It is now known that each of the A, B, and O alleles is actually a class of multiple alleles with different DNA sequences that produce proteins with identical properties: more than 70 alleles are known at the ABO locus. An individual with "Type A" blood may be an AO heterozygote, an AA homozygote, or an A'A heterozygote with two different 'A' alleles.

Wild and Mutant Alleles

"Wild" alleles are used to describe phenotypic characters seen in 'wild' population of subjects like fruit flies. While wild alleles are considered dominant and normal, "mutant" alleles are recessive and harmful. Wild alleles are believed to be homozygous at most gene loci. Mutant alleles are homozygous in a small fraction of gene loci and are considered infected with a genetic disease and more frequently in heterozygous form in "carriers" for the mutant allele. Mostly all gene loci are polymorphic with multiple variations of alleles in which the genetic variations mostly produce the obvious phenotypic traits.


Allele

An allele is an essential term of genetics. Gene is the structural unit of the chromosome, which carries heredity from one generation to another. The alleles are the pair of genes, which is located in a specific area of the chromosome. On this page, we are going to define allele and discuss what is the meaning of allele.

Allele Definition - There are different variants of genes present in a chromosome. An allele is a variant of the gene, which locates in a chromosome's specific location as a pair of genes.

In the human chromosome, alleles are present in pairs and maintain the same trait. Therefore, humans are diploid organisms. Two similar alleles are present in each genetic locus, where one allele is inherited from each parent. Also, an allele can be two or more variants of a gene at one genetic locus. But all the alleles maintain the same trait at a genetic locus of the chromosome.

Alleles Meaning In Biology

Now, we will discuss alleles meaning. The word allele comes from the Greek word 'allos'. An allele is the modern formation of that word. The word 'allos' means other. In biology, an allele means different varieties of a gene. The alleles present in a particular genetic locus maintain the same trait. Though alleles are present in a locus as a pair, they can also be found in more than two numbers. In the human chromosome, alleles are present in a pair only to carry the heredity.

Genotype of Allele

Alleles are located in a particular location of the chromosome. The chromosome is the central unit of an organism. All the alleles present in an organism build its genotype. Genotype can be of two types depending on the similarity of the alleles.

When a pair of alleles are the same, they build homozygous genotypes. When the pair of alleles in a location are not similar, they build heterozygous genotypes. In the case of homozygous genotype, the allele is not dominant or recessive. But the heterozygous genotype includes one dominant allele. The dominant allele overrules the features of the recessive allele.

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Example of Allele

Now, we will be discussing some examples of alleles. Here, we are taking the example of a pea plant. The alleles for the colour of the flower build heterozygous genotype, where the purple allele is dominant, and white is recessive. For the height of the plant, tall is the dominant allele, and short is recessive. For the pea colour, the dominant allele is yellow, and the recessive allele is green. In these three cases, the dominant alleles overrule the recessive alleles' feature in the case of heterozygous genotype. Also, the eye colour and hair colour of human organisms can be observed as the example of alleles.

Difference Between a Gene and an Allele

There are some fundamental differences between gene and allele. The differences between a gene and allele are given below in a tabular form.

It is a hereditary information unit made up of DNA and consists of genetic information to transmit characteristics.

An allele is a variation of the gene.

They are located at a specific genetic locus, consisting of two copies, each of the parents.

The two copies at the specific genetic locus are called alleles.

A gene may contain different alleles.

An allele is present inside the gene upon which the character of a person is dependent.

Solved Examples

1. Give an Example of an Allele.

Solution: The genetic locus of each gene that consists of two alleles for different characteristics can be seen in the pea plant. In an experiment, it was seen that, for colour, the plants are purple due to the dominant allele and white due to the recessive allele. In height, they are tall due to the dominant allele and short due to the recessive allele. Like these, the other traits are governed by the dominant alleles in the specific genetic locus.

Conclusion

Biology is a vital subject of the Class 10 curriculum. The students should read all the chapters of biology sincerely. In Class 10, the biology syllabus contains introductory chapters of some important conceptual topics. The students should read all the chapters for their future convenience. These chapters will help them in higher studies. Genetics is a vital part of biology. The students can easily learn the primary concept of genetics in Class 10 from this page.


What is an Allele

An allele refers to one of the two or more alternative forms of a gene. Thus, a particular gene may contain more than one allele. Alleles always occur in pairs. Each allele pair occurs in the same loci on the homologous chromosomes. Alleles arise as a result of mutations in the original gene. The collection of alleles in a particular individual is known as the genotype of that individual. They pass through generations by reproduction. The process of allele transmission was first described as the law of segregation by Gregor Mendel in 1865. An allele pair with alleles containing similar nucleotide sequences is called the homozygous alleles. On the other hand, the allele pairs with different nucleotide sequences are called heterozygous alleles. In heterozygous alleles, only one allele is expressed, and the other is in the repressed form. The expressed allele is called the dominant allele, and the repressed allele is called the recessive allele. The dominant allele is called the wild type whereas the recessive allele is called the mutant. The complete masking of the recessive allele by the dominant allele is called the complete dominance. Complete dominance is a type of Mendelian inheritance. The inheritance of blood groups in humans is shown in figure 1. The A, B, and O blood types exhibit Mendelian inheritance while the AB blood type exhibits codominance.

Figure 1: Inheritance of ABO Blood Groups

The non-Mendelian inheritance patterns include incomplete dominance, codominance, multiple alleles, and the polygenic traits. In incomplete dominance, both alleles in the heterozygous pair are expressed. In codominance, a mixture of phenotypes of both alleles in the heterozygous allele pair can be observed. Multiple alleles are the presence of more than two alleles in the population to determine a particular trait. In polygenic traits, the phenotype is determined by many genes. Skin color, eye color, height, weight, and hair color of humans are polygenic traits.


Difference Between Gene and Allele

Gene vs Allele

A gene is a part of the DNA. Alleles on the other hand refer to different versions of the same gene. There are other more subtle differences between the two and this is what we are going to explore on this page:

  • Genes are the different parts of the DNA that decide the genetic traits a person is going to have. Alleles are the different sequences on the DNA-they determine a single characteristic in an individual.
  • Another important difference between the two is that alleles occur in pairs. They are also differentiated into recessive and dominant categories. Genes do not have any such differentiation.
  • An interesting difference between alleles and genes is that alleles produce opposite phenotypes that are contrasting by nature. When the two partners of a gene are homogeneous in nature, they are called homozygous. However, if the pair consists of different alleles, they are called heterozygous. In heterozygous alleles, the dominant allele gains an expression.
  • The dominance of a gene is determined by whether the AA and Aa are alike phenotypically. It is easier to find dominants because they express themselves better when they are paired with either allele.
  • Alleles are basically different types of the same gene. Let’s explain this to you in this way- If your eye color was decided by a single gene, the color blue would be carried by one allele and the color green by another. Fascinating, isn’t it?
  • All of us inherit a pair of genes from each of our parents. These genes are exactly the same for each other. So what causes the differences between individuals? It is the result of the alleles.
  • The difference between the two becomes more pronounced in the case of traits. A trait refers to what you see, so it is the physical expression of the genes themselves. Alleles determine the different versions of the genes that we see. A gene is like a machine that has been put together. However, how it will works will depend on the alleles.

Both alleles and genes play an all important role in the development of living forms. The difference is most colorfully manifest in humans of course! So next time you see the variety of hair color and eye color around you, take a moment and admire the phenomenal power of both the gene and the allele!

Summary:
1. Genes are something we inherit from our parents- alleles determine how they are expressed in an individual.
2. Alleles occur in pairs but there is no such pairing for genes.
3. A pair of alleles produces opposing phenotypes. No such generalization can be assigned to genes.
4. Alleles determine the traits we inherit.
5. The genes we inherit are the same for all humans. However, how these manifest themselves is actually determined by alleles!


What is an Allele?

Usually, genes have two alternate forms called alleles. Hence, an allele is a variant of a gene. It can be either the dominant variant or the recessive variant. Other than two alleles, some genes have multiple alleles as well.

Figure 02: Alleles

Accordingly, each allele is responsible for producing a phenotype. When there are two dominant alleles present, we call it as homozygous dominant state while when there are two recessive alleles present, we call it homozygous recessive state. The third possibility is the combination of one dominant and one recessive allele. It is the state of heterozygous. Moreover, in heterozygous and homozygous dominant states, phenotype will show the dominant phenotype while when the homozygous recessive state, phenotype shows the recessive trait.


What is an allele?

When genes mutate, they can take on multiple forms, with each form differing slightly in the sequence of their base DNA. These gene variants still code for the same trait (i.e. hair color), but they differ in how the trait is expressed (i.e. brown vs blonde hair). Different versions of the same gene are called alleles.

Genes can have two or more possible alleles. Individual humans have two alleles, or versions, of every gene. Because humans have two gene variants for each gene, we are known as diploid organisms.

The greater the number of potential alleles, the more diversity in a given heritable trait. An incredible number of genes and gene forms underly human genetic diversity, and they are the reason why no two people are exactly alike.

As an example, let’s look at eye color. In a simplified model, we will assume that there is only one gene that encodes for eye color (although there are multiple genes involved in most physical traits). Blue, green, brown, and hazel eyes are each encoded by unique alleles of said gene. The pair of alleles present on an individual’s chromosomes dictates what eye color will be expressed.


A Natural Allele of a Transcription Factor in Rice Confers Broad-Spectrum Blast Resistance

Rice feeds half the world's population, and rice blast is often a destructive disease that results in significant crop loss. Non-race-specific resistance has been more effective in controlling crop diseases than race-specific resistance because of its broad spectrum and durability. Through a genome-wide association study, we report the identification of a natural allele of a C2H2-type transcription factor in rice that confers non-race-specific resistance to blast. A survey of 3,000 sequenced rice genomes reveals that this allele exists in 10% of rice, suggesting that this favorable trait has been selected through breeding. This allele causes a single nucleotide change in the promoter of the bsr-d1 gene, which results in reduced expression of the gene through the binding of the repressive MYB transcription factor and, consequently, an inhibition of H2O2 degradation and enhanced disease resistance. Our discovery highlights this novel allele as a strategy for breeding durable resistance in rice.

Keywords: C(2)H(2) H(2)O(2) MYB blast disease broad-spectrum genome-wide association study reactive oxygen species resistance rice transcription factor.



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