This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
What is protein homology?
Protein homology is used to analyze the similarities between two proteins based on their amino acid sequence. Proteins that have are similar enough in sequence are considered homologs. The more conserved the region of amino acids being compared, the more likely that the proteins will have similar function. By analyzing the sequences of a proteins, one can help to determine how related different species of organisms are as well (see Phylogeny). The following protein sequences were taken from the National Center for Biotechnology Information. All the FASTA sequences from the different organisms below were compared to the human COL5A1 gene product using the BLAST function.
Are there any homologs to the human gene product of COL5A1?
Homo Sapien (Human) - collagen alpha-1(V) chain ACCESSION: NP_001265003.1 FASTA Mus musculus (Mouse) - collagen alpha-1(V) chain precursor ACCESSION: NP_056549.2 FASTA % identity: 95% Rattus norvegicus (Norway Rat) - collagen alpha-1(V) chain precursor ACCESSION: NP_604447.1 FASTA % identity: 87% Gallus gallus (Chicken) - collagen alpha-1(V) chain precursor ACCESSION: NP_990121.1 FASTA % identity: 90% Xenopus tropicalis (Frog) - Predicted collagen alpha-1(V) chain ACCESSION: XP_004916702.1 FASTA % identity: 84% Danio rerio (Zebrafish) - Predicited collagen alpha-1(V) chain ACCESSION: XP_002665924.2 FASTA % identity: 83% Canis lupus familiaris (Dog) - Predicted collagen alpha-1(V) chain-like ACCESSION: XP_005625494.1 FASTA % identity: 97% Bos taurus (Cow) - Predicted collagen alpha-1(V) chain ACCESSION: XP_002691768.2 FASTA % identity: 91% Gorilla gorilla gorilla (Gorilla) - PREDICTED collagen alpha-1(V) chain ACCESSION: XP_004048883.1 FASTA % identity: 98% |
Analysis of the results
The human gene product of COL5A1 is conserved among the mammals. Using mice as a model organism would make the most sense when researching the effects rs12722 protein have on collagen ligaments. Mice have already been used to understand the effects of Ehlers-Dalos Syndrome, which is caused by a different mutation to the COL5A1 gene (1). To understand how this variant might affect muscle endurance, looking at a wide variety of animals and measuring speed could be beneficial. Further research into known peptide or DNA sequences must be done to find a variety of slow and fast organisms to compare.
References
- Sun et al. 2015. Targeted Deletion of Collagen V in Tendons and Ligaments Results in a Classic Ehlers-Danlos Syndrome Joint Phenotype. The American Journal of Pathology. 2015 March;43(4):584-9. doi: 10.1249/MSS.0b013e3181f34f4d
Website Author: Logan Silber
Contact email: [email protected]
Page last updated: 3/25/2015
Course Homepage: www.genetics564.weebly.com
Contact email: [email protected]
Page last updated: 3/25/2015
Course Homepage: www.genetics564.weebly.com