This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Homologs of MYOC
Homologous genes are genes that originated from a common ancestor and have maintained many similarities while they are present in different organisms and may develop differentially in those various organisms. According to NCBI, the MYOC gene is conserved in the chimpanzee, cow, dog, mouse, rat, chicken, and zebrafish. Listed with each homologue is the percent conservation of their gene products compared to that of human myocilin (% conservation obtained from HomoloGene).
Pan troglodytes (chimpanzee) - 98.8% conserved
Gene name: MYOC
Accession number: XM 513995
Bos taurus (cow) - 82.2% conserved
Gene name: MYOC
Accession number: NM 174118
Canis lupus familaris (dog) - 83.4% conserved
Gene name: MYOC
Accession number: NM_001048030
Mus musculus (mouse) - 83% conserved
Gene name: Myoc
Accession number: NM_010865
Rattus norvegicus (rat) - 81.6% conserved
Gene name: Myoc
Accession number: NM_030865
Gallus gallus (chicken) - 66.1% conserved
Gene name: MYOC
Accession number: XM 422235
Danio rerio (zebrafish) - 51.7% conserved
Gene name: myoc
Accession number: NM 001015062
Homologue gene sequences:
| gene_homologues_.doc |
ClustalW alignment
| clustalw_gene_aligment.doc |
MUSCLE alignment
| muscle_gene_alignment.doc |
Analysis: For each alignment, I used the MYOC gene and its corresponding homologues in Homo sapiens, Mus musculus, and Danio rerio. Unlike the MYOC PROTEIN alignments, when running the MYOC gene alignments, I was unable to use the T-COFFEE analysis method for reasons that remain unknown which is disappointing as T-COFFEE alignments are color-coated to help infer the confidence level of each alignment.. This inability is particularly interesting as ClustalW and T-COFFEE are both supported by MABL (see logo at top of the page for external link). Additionally, while ClustalW kept the order of the three homologue entries the same as the original sequence entry, the MUSCLE alignment rearranged the order of the three homologues placing the Danio rerio homologue first and Homo sapiens last. I preferred the output of the ClustalW alignment over the MUSCLE alignment as I thought the formatting of the output was easier to read and I appreciated the consistency of the homologue sequence order. Interestingly, after inputting all sequence data and running each program, both reported a likelihood that portions of each homologue gene sequence were missing from the beginning and end of the sequences. This error message was most likely caused by the small number or quality of alignments at those positions. DNA sequences were confirmed and programs were re-run multiple times to eliminate the possibility of data input errors.
Above figure compares the human (A) and zebrafish (B) eye. Also shows iris-corneal angle of the zebrafish anterior chamber (C) (9).
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References:
1. Fuse, Nobuo. "Genetic Bases for Glaucoma." The Tohoku Journal of Experimental Medicine 221 (2010): 1-10. PubMed. Web. 22 Jan. 2011
http://www.jstage.jst.go.jp/article/tjem/221/1/1/_pdf
2. Rao, Kollu N., Srujana Nagireddy, and Subhabrata Chakrabarti. "Complex Genetic Mechanisms in Glaucoma: An Overview." Indian Journal of Opthamology 59.7 (2011): 31-42. PubMed. Web. 22 Jan. 2011.
http://www.ijo.in/article.asp?issn=0301-4738;year=2011;volume=59;issue=7;spage=31;epage=42;aulast=Rao
3. American Optometric Association. Answers To Your Questions About Glaucoma. St. Louis: American Optometric Association. Print.
4. http://www.forbes.com/2009/06/26/life-saving-devices-technology-personal-monitors_slide_7.html
5. http://www.youtube.com/watch?v=OJMEfGFbFMI
6. "MYOC - Myocilin, Trabecular Meshwork Inducible Glucocorticoid Response - Genetics Home Reference." Genetics Home Reference - Your Guide to Understanding Genetic Conditions. 6 Feb. 2011. Web. 08 Feb. 2011. http://ghr.nlm.nih.gov/gene/MYOC
7. Saura, Maria, Montse Cabana, Carmen Ayuso, and Diana Valverde. "European Journal of Human Genetics - Mutations including the Promoter Region of Myocilin//TIGR Gene." Nature Publishing Group : Science Journals, Jobs, and Information. 13 Oct. 2004. Web. 08 Feb. 2011. http://www.nature.com/ejhg/journal/v13/n3/full/5201299a.html
8. Fingert, John H., Elise Heon, Jefferey M. Liebmann, Tetsuya Yamamoto, Jaime E. Craig, Julian Rait, Kazuhide Kawase, Sek-Tien Hoh, Yvonne M. Buys, Joanne Dickinson, Robin R. Hockey, Donna Williams-Lyn, Graham Trope, Yoshiaki Kitazawa, Robert Ritch, David A. Mackey, Wallace L.M. Alward, Val C. Sheffield, and Edwin M. Stoned. "Analysis of Myocilin Mutations in 1703 Glaucoma Patients From Five Different Populations — Hum Mol Genet." Oxford Journals | Life Sciences & Medicine | Human Molecular Genetics. 14 Mar. 1999. Web. 08 Feb. 2011. http://hmg.oxfordjournals.org/content/8/5/899.full
9. McMahon, C., Semina, E.V., Link, B.A. "Using zebrafish to study the complex genetics of glaucoma." Comparative Biochemistry and Physiology Part C: Toxicology and Parmacology. vol 138-3. July 2004. Web. 24 Feb 2011. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6W89-4CDJG6X-1&_user=443835&_coverDate=07%2F31%2F2004&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000020958&_version=1&_urlVersion=0&_userid=443835&md5=525db1a96bf7be7620dabbcd34c426f9&search#toc2
10. Kubota, R., Noda, S., Wang, Y., Minoshima, S., Asakawa, S., Kudoh, J., Mashima, Y., Oguchi, Y., Shimizu, N. "A novel myosin-like protein (myocilin) expressed in the connecting cilium of the photoreceptor: molecular cloning, tissue expression, and chromosomal mapping." Genomics. vol 41-3.1 May 1997, Pages 360-369 Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan. http://www.sciencedirect.com.ezproxy.library.wisc.edu/science?_ob=ArticleURL&_udi=B6WG1-45M8YTG-C5&_user=443835&_coverDate=05%2F01%2F1997&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_acct=C000020958&_version=1&_urlVersion=0&_userid=443835&md5=1562ae0f98031b9d89c1c8377a859b1e&search
References:
1. Fuse, Nobuo. "Genetic Bases for Glaucoma." The Tohoku Journal of Experimental Medicine 221 (2010): 1-10. PubMed. Web. 22 Jan. 2011
http://www.jstage.jst.go.jp/article/tjem/221/1/1/_pdf
2. Rao, Kollu N., Srujana Nagireddy, and Subhabrata Chakrabarti. "Complex Genetic Mechanisms in Glaucoma: An Overview." Indian Journal of Opthamology 59.7 (2011): 31-42. PubMed. Web. 22 Jan. 2011.
http://www.ijo.in/article.asp?issn=0301-4738;year=2011;volume=59;issue=7;spage=31;epage=42;aulast=Rao
3. American Optometric Association. Answers To Your Questions About Glaucoma. St. Louis: American Optometric Association. Print.
4. http://www.forbes.com/2009/06/26/life-saving-devices-technology-personal-monitors_slide_7.html
5. http://www.youtube.com/watch?v=OJMEfGFbFMI
6. "MYOC - Myocilin, Trabecular Meshwork Inducible Glucocorticoid Response - Genetics Home Reference." Genetics Home Reference - Your Guide to Understanding Genetic Conditions. 6 Feb. 2011. Web. 08 Feb. 2011. http://ghr.nlm.nih.gov/gene/MYOC
7. Saura, Maria, Montse Cabana, Carmen Ayuso, and Diana Valverde. "European Journal of Human Genetics - Mutations including the Promoter Region of Myocilin//TIGR Gene." Nature Publishing Group : Science Journals, Jobs, and Information. 13 Oct. 2004. Web. 08 Feb. 2011. http://www.nature.com/ejhg/journal/v13/n3/full/5201299a.html
8. Fingert, John H., Elise Heon, Jefferey M. Liebmann, Tetsuya Yamamoto, Jaime E. Craig, Julian Rait, Kazuhide Kawase, Sek-Tien Hoh, Yvonne M. Buys, Joanne Dickinson, Robin R. Hockey, Donna Williams-Lyn, Graham Trope, Yoshiaki Kitazawa, Robert Ritch, David A. Mackey, Wallace L.M. Alward, Val C. Sheffield, and Edwin M. Stoned. "Analysis of Myocilin Mutations in 1703 Glaucoma Patients From Five Different Populations — Hum Mol Genet." Oxford Journals | Life Sciences & Medicine | Human Molecular Genetics. 14 Mar. 1999. Web. 08 Feb. 2011. http://hmg.oxfordjournals.org/content/8/5/899.full
9. McMahon, C., Semina, E.V., Link, B.A. "Using zebrafish to study the complex genetics of glaucoma." Comparative Biochemistry and Physiology Part C: Toxicology and Parmacology. vol 138-3. July 2004. Web. 24 Feb 2011. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6W89-4CDJG6X-1&_user=443835&_coverDate=07%2F31%2F2004&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000020958&_version=1&_urlVersion=0&_userid=443835&md5=525db1a96bf7be7620dabbcd34c426f9&search#toc2
10. Kubota, R., Noda, S., Wang, Y., Minoshima, S., Asakawa, S., Kudoh, J., Mashima, Y., Oguchi, Y., Shimizu, N. "A novel myosin-like protein (myocilin) expressed in the connecting cilium of the photoreceptor: molecular cloning, tissue expression, and chromosomal mapping." Genomics. vol 41-3.1 May 1997, Pages 360-369 Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan. http://www.sciencedirect.com.ezproxy.library.wisc.edu/science?_ob=ArticleURL&_udi=B6WG1-45M8YTG-C5&_user=443835&_coverDate=05%2F01%2F1997&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_acct=C000020958&_version=1&_urlVersion=0&_userid=443835&md5=1562ae0f98031b9d89c1c8377a859b1e&search
