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This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
AQP2 Homology
What is Homology?
Homology deals with features of organisms that are shared due to common evolutionary ancestry(1). This analysis can be done at a variety of scales, from the level of skeleton comparison down to gene and protein sequences. Comparing different protein sequences can provide insight into how the function of a given protein may have changed over evolutionary time.
How are homologs found for a protein?
Several databases will provide homologs from other species if you supply an initial query sequence, such as Homologene(2) and Ensembl(3). Homologs can also be searched for using reciprocal BLAST(4), in which a sequence is declared a homolog of a query sequence if BLAST returns the original query as the highest probability hit within the query organism using the resultant of an original BLAST search as a query.
Mouse-ear Cress(Arabidopsis thaliana)
Plasma membrane instrinsic protein 2;8
Accession = NP_191042.1
Identity= 39%
Plasma membrane instrinsic protein 2;8
Accession = NP_191042.1
Identity= 39%
Discussion of Homologs
Sequence conservation is highest within mammals, with identity dropping to less than half for zebrafish. The nematode worm is an outlier in the overall trend of sequence identity decreasing proportionally to evolutionary divergence between organisms. This suggests the possibility that C. elegans water channels may be used in a different manner than in other animals, and thus have different selective pressures influencing their sequence composition.
References
1. University of California Museum of Paleontololgy. Understanding Evolution. evolution.berkeley.edu/evolibrary/home.php. Accessed February 14th, 2017.
2. National Center for Biotechnology Information. Homologene. https://www.ncbi.nlm.nih.gov/homologene . Accessed February 14th, 2017.
3.European Bioinformatics Institute. Ensembl.http://useast.ensembl.org/index.html . Accessed February 14th, 2017.
4. Harvard Medical School. Determining Orthology. http://www.flyrnai.org/RNAi_orthology.html. Accessed February 14th, 2017.
2. National Center for Biotechnology Information. Homologene. https://www.ncbi.nlm.nih.gov/homologene . Accessed February 14th, 2017.
3.European Bioinformatics Institute. Ensembl.http://useast.ensembl.org/index.html . Accessed February 14th, 2017.
4. Harvard Medical School. Determining Orthology. http://www.flyrnai.org/RNAi_orthology.html. Accessed February 14th, 2017.