This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
What is Gene Homology?
Gene homology is defined as biological homology between two genes. This means that both genes, in two different species, are derived from a common ancestral protein [1]. There are two ways this can happen, the first is when a speciation event occurs and the genetic sequence stays the same. This type of homology happens vertically, meaning the protein is passed from parent to offspring [2]. The second way this can happen is a gene duplication event where the nucleotide sequence is present twice in the genome. Paralog genes usually have similar function, but not always due to lack to selective pressure on one copy [3]. Then a speciation even occurs and one copy goes to each new organism.
In human genetic research, it is important to identify homologous genes in model organisms in order to conduct research to discover the true nature of the gene function. In one important study, researchers used the mice to study the expression of FRMD7 protein in the fetal brain [4]. This study suggested that FRMD7 is involved in neuronal development in the mice. Since the mouse FRMD7 gene is a homolog of the human copy, this research can be applied to humans as well.
In human genetic research, it is important to identify homologous genes in model organisms in order to conduct research to discover the true nature of the gene function. In one important study, researchers used the mice to study the expression of FRMD7 protein in the fetal brain [4]. This study suggested that FRMD7 is involved in neuronal development in the mice. Since the mouse FRMD7 gene is a homolog of the human copy, this research can be applied to humans as well.
Homologs of Human FRMD7 Gene
On this page the gene homologs were found using Basic Local Alignment Tool (BLAST) via the National Center for Biotechnology Information (NCBI). What the BLAST program does is it searches for regions of local similarity between nucleotide sequences across multiple genomes at once. This information can be used to find relationships between sequences based on function and evolutionary identity. This program works by sending one sequence through the databases, and it will produce a list of statistically significant matches. It is also possible to specify exactly which organism you want the program to compare your sequence to. To further the validity of your match, you can also run the BLAST back to the sequence in the organism you started with. Below is a file containing homologous gene sequences for human FRMD7 obtained through NCBI.
genes.docx | |
File Size: | 80 kb |
File Type: | docx |
Homologous Gene Reference Numbers
Homo sapiens - Humans FRMD7
Accession Number: NG_012347 GI Number: 254039702 FASTA Canis lupus familiaris - Dog FRMD7 Accession Number: NC_006621.3 GI Number: 357579592 FASTA E-Value: 0.0 Max. Identity: 99% Bos taurus - Cattle FRMD7 Accession Number: NC_007331.4 GI Number: 355477163 FASTA E-Value: 0.0 Max. Identity: 100% Rattus norvegicus - Brown Rat FRMD7 Accession Number: NC_005120.2 GI Number: 62750821 FASTA E-Value: 0.0 Max. Identity: 95% |
Gallus gallus - Chicken FRMD7 Accession Number: NC_006091.3 GI Number: 358485508 FASTA E-Value: 2e-18 Max. Identity: 89% C. elegans frm-5 Accession Number: NC_003284.7 GI Number: 193211360 FASTA Drosophila melanogaster - Fruit Fly ferm Accession Number: NT_033777.2 GI Number: 56411841 FASTA |
Alignment
ClustalW2, T-COFFEE, and Phylogeny.fr failed to produce alignments of the human FRMD7 gene and it's homologs due to the length of the sequence. Please see the Protein Homology and Alignments page for alignments based on the protein sequence.
Analysis and Discussion
Among vertebrae - human, dog, rat, chicken, cattle - the FRMD7 gene appears to be very well conserved across taxa. This can be seen through the very small e-values which were obtained from the BLAST program. C. elegans and Drosophila showed some homology with the human FRMD7 gene, however these sequences were not able to run through a BLAST, and the sequences above were obtained from the Protein Homology and Alignments page. The accession, GI, and FASTA sequences above refer only to the entire X-chromosome present in C. elegans and Drosophila. This suggests that there are certain domains that are conserved between human FRMD7, and their invertebrate homologs.
References
[1] Reeck, G. R., de Haen, C, Teller, D. C., Doolittle, R. F., Fitch, W. M., Dickerson, R. E., Chambon, P., McLachlan, A. D., Margoliash, E., Jukes, T. H., Zuckerandl E. (1987)
“Homology” in proteins and nucleic acids: a terminology muddle and a way out of it. Cell, 1987(50), 667. doi: 10.1016/0092-8674(87)90322-9
[2] Fitch W. (1970)
Distinguishing homologous from analogous proteins. Systematic Zoology, 1970(19), 99. Retrieved from: http://www.jstor.org/stable/2412448
[3] Studer, R. A., Robinson-Rechavi, M. (2005)
How confident can we be that orthologs are similar, but paralogs differ? Trends in Genetics, 2005(25), 210. doi: 10.1016/j.tig.2009.03.004
[4] Self, J., Haitchi, H. M., Griffiths, H., Davies, D. E., Lotery, A. (2010)
FRMD7 expression in developing mouse brain. Eye, 2010(24), 165. doi: 10.1038/eye.2009.44
“Homology” in proteins and nucleic acids: a terminology muddle and a way out of it. Cell, 1987(50), 667. doi: 10.1016/0092-8674(87)90322-9
[2] Fitch W. (1970)
Distinguishing homologous from analogous proteins. Systematic Zoology, 1970(19), 99. Retrieved from: http://www.jstor.org/stable/2412448
[3] Studer, R. A., Robinson-Rechavi, M. (2005)
How confident can we be that orthologs are similar, but paralogs differ? Trends in Genetics, 2005(25), 210. doi: 10.1016/j.tig.2009.03.004
[4] Self, J., Haitchi, H. M., Griffiths, H., Davies, D. E., Lotery, A. (2010)
FRMD7 expression in developing mouse brain. Eye, 2010(24), 165. doi: 10.1038/eye.2009.44
Site created by: Kristen Klimo
Last updated: 5/11/2012
University of Wisconsin-Madison
Last updated: 5/11/2012
University of Wisconsin-Madison