Analyzing Genes responsible for the skull shape in dogs using NCBI tools Scientists have been on the hunt for the genes responsible for the plasticity that allows for the same gene(s) to give rise to very different phenotypes creating the vast diversity associated with dog breeds

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Analyzing Genes responsible for the skull shape in dogs using NCBI tools Scientists have been on the hunt for the genes responsible for the plasticity that allows for the same gene(s) to give rise to very different phenotypes creating the vast diversity associated with dog breeds. Recent studies have focused on the skull shape which can produce three different snout lengths seen in the figure below: long, slender snouts seen in Collies (Dolichocephic), shorter more rounded snouts characterized by the Bernese Mountain Dog and Border Terrier (Mesocephalic), and the awful, shortened snout seen in Pugs (brachycephalic). The subjective use of the word awful was added because is a source of many health problems seen in these breeds. A few papers have identified potential genes that may control these skull shapes (Shoenebeck papers hyperlinked below). In looking at these genes, please answer the questions as you are guided through the use of some online databases that provide information about genes. Dolichocephalic Mesocephalic Mesocephalic Brachyocephalic https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567726/pdf/317.pdf https://www.cell.com/current-biology/pdfExtended/S0960-9822(17)30502-X www.ncbi.nlm.nih.gov Using the drop down box (All Databases), select Gene. Decide if you want to research the gene, Muscle Segment Homeobox 2 (MSX2) or SPARC-related modular calcium binding (SMOC2). You only need to do one. Type in its name in search box along with canis lupus familiaris (scientific name for dog) and hit Search. 1. You should be on the page for your gene found in dogs. Take a look under the summary of the gene, what other species is this gene found in (orthologs)? Name two organisms that you recognize and one that you have never heard of. For the one you never heard of, what is the organism (do a web search to find out)? 2. What chromosome is this gene found? 3. How many exons does this gene have? 4. What is the function of this gene? There are 2 possible ways to find that out. First, there may be a section under General Gene information that lists the gene ontology where a list of potential functions is given based on features of the gene. Or, in the section on Refs of Annotated Genomes, some of the mRNA and protein sequences have descriptions of conserved domains. Select one associated with your gene and click on the hyperlink for a better description. Briefly, why is that domain important for this gene (there will be a lot of technical jargon, but you should be able to use context clues to determine why these features are important for the protein). 5. If there is a link to the protein (look for the Protein Accession box), click on the hyperlink. What are the first 5 amino acids of the protein? If your gene does not, go to the ortholog hyperlink for human. Use this information to list the first 5 amino acids of your gene. 6. Using the dropdown box again (where you selected Gene), find the OMIM (Online Mendelian Inheritance in Man). Before submitting your query, remove the canis lupus familiaris from the keyword search (OMIM is specifically looking at human genes). Click on the correct file that has your gene in the title. There may be a pop up screen asking for a donation (it once was funded by the government). Close it – this is the OMIM database. If there are diseases and mutations that are known and studied, they are discussed here along with links to other databases. Descriptions of the disease can be found here along with references. a. Where is the human gene located (what chromosomal location)? b. What disease(s) are associated with your gene? Note: if your gene does not have a known disease in humans, provide some information about what is known from animal models. c. What mode of transmission is this disease inherited? d. What are the symptoms associated with the disease? e. What is the genetic cause of the disease (change in nucleotide base, insertion, deletion, alternative splicing, regulation, etc)?