This web page was produced as an assignment for Genetics 564, an undergraduate course at the University of Wisconsin-Madison.
Protein - Homology
What is homology?
Homology indicates a structure that is passed down through a common ancestor to various species. In this case homology is the existence of common ancestry between the CNGA-3 protein in the species listed below [1]. Homology can be determined by using the proteins sequence and comparing how closely related this sequence is in different species. A good starting place when looking for homologs is a website called HomoloGene. After looking at these species it is important check the accuracy with another website that utilizes a tool called BLAST. Blast is also a good tool to find additional homologous or can be used as a starting point. In this case, to find homologous for the CNGA-3 protein a website was used that allows you to "blast" species against one another. This search yields many different species and proteins that are similar and/or identical to the homo sapien sequence that was originally entered [2]. The website indicates the percent similar and the percent identical that certain species are in regards to the provided sequence. It is possible for sequences to be similar in certain locations while not being identical [2]. This occurs because there are amino acids that have very similar properties, for example some amino acids are polar while others are non-polar. As a result of this if the sequence differed because of a "similar" amino acid it would be considered similar because the function of the protein would in most cases not be altered significantly.
The BLAST website can also provide links to the FASTA for the protein in the various species. This lays out the sequence of the protein and can later be useful in depicting the phylogeny of the species. For more information on phylogeny click here.
Homology indicates a structure that is passed down through a common ancestor to various species. In this case homology is the existence of common ancestry between the CNGA-3 protein in the species listed below [1]. Homology can be determined by using the proteins sequence and comparing how closely related this sequence is in different species. A good starting place when looking for homologs is a website called HomoloGene. After looking at these species it is important check the accuracy with another website that utilizes a tool called BLAST. Blast is also a good tool to find additional homologous or can be used as a starting point. In this case, to find homologous for the CNGA-3 protein a website was used that allows you to "blast" species against one another. This search yields many different species and proteins that are similar and/or identical to the homo sapien sequence that was originally entered [2]. The website indicates the percent similar and the percent identical that certain species are in regards to the provided sequence. It is possible for sequences to be similar in certain locations while not being identical [2]. This occurs because there are amino acids that have very similar properties, for example some amino acids are polar while others are non-polar. As a result of this if the sequence differed because of a "similar" amino acid it would be considered similar because the function of the protein would in most cases not be altered significantly.
The BLAST website can also provide links to the FASTA for the protein in the various species. This lays out the sequence of the protein and can later be useful in depicting the phylogeny of the species. For more information on phylogeny click here.
Examples of homology in the CNGA3 protein:
Below is a graph that shows examples of homologous in regards to the cyclic nucleotide gate alpha-3 protein. It is helpful to explore these organisms to gain insight into what future research can be done on the protein to learn more about Achromatopsia. Humans are difficult to study, so finding homology in other organisms, especially model organisms (such as the zebra fish, fruit fly, and mouse), shows which species can be studied and possibly applied to benefit humans. Below the graph each specie is listed with its accession number (useful to study the protein in that species) and link to its FASTA page.
Below is a graph that shows examples of homologous in regards to the cyclic nucleotide gate alpha-3 protein. It is helpful to explore these organisms to gain insight into what future research can be done on the protein to learn more about Achromatopsia. Humans are difficult to study, so finding homology in other organisms, especially model organisms (such as the zebra fish, fruit fly, and mouse), shows which species can be studied and possibly applied to benefit humans. Below the graph each specie is listed with its accession number (useful to study the protein in that species) and link to its FASTA page.
Discussion of the CNGA3 homologs:
There are many homologs for this protein, including C. elegans which does not have eyes. I found this to be interesting because of the percise function of CNGA3. There were more species with homologous proteins than there was for the DNA sequence. These protein homologs will be very helpful in thinking of future research and experiments that can be done to learn more about the function of the protein and the role it plays in Achromotopsia.
There are many homologs for this protein, including C. elegans which does not have eyes. I found this to be interesting because of the percise function of CNGA3. There were more species with homologous proteins than there was for the DNA sequence. These protein homologs will be very helpful in thinking of future research and experiments that can be done to learn more about the function of the protein and the role it plays in Achromotopsia.
Rattus Norvegicus
"Brown Rat" Accession Number: CAC09431.1 Percent Identical: 77 Percent Similar: 5 FASTA Gallus Gallus
"Red Junglefowl" Accession Number: NP_990552.1 Percent Identical: 73 Percent Similar: 9 FASTA Drosophila Melanogaster
"Fruit Fly" Accession Number: CAA61760.1 Percent Identical: 57 Percent Similar: 15 FASTA Caenorhabditis Elegans
"Round Worm" Accession Number: NP_499033.1 Percent Identical: 45 Percent Similar: 15 FASTA |