> For the complete documentation index, see [llms.txt](https://igb.mit.edu/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/viewing-cross-species-alignments.md). # Viewing cross-species alignments Cross-species Alignments and Conservation * Query the March 2006 human genome browser gateway with the gene symbol FOXP2. View the gene on chromosome 7. Adjust the tracks displayed so that base position, chromosome band and refseq are set to full. * Switch the Zebrafish, Dog and Mouse Net Alignments to Full. What portions of the gene are most highly conserved across all of these species? Compare the dog and mouse alignments. Based on what you see which species is more closely related to human? Why? Which species diverged from human more recently? ``` chr7:113,838,514-113,842,471 ``` * Examine the pan-vertebrate conservation upstream from the transcription start site (TSS). How far from the TSS is the conserved block? Can you think of a reason why it is conserved? Can you find any tracks that could support this idea? * Examine the details of the 7X Reg Potential track. Reconfigure the view so that it includes an indicator line at 0.05. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/viewing-cross-species-alignments.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.