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Thursday, July 18, 2013

How to Get a cDNA Sequence for a Gene Transcript

A paper I was reading had coordinates for mutations in a gene based off the gene's complementary DNA (cDNA) sequence.  In order to dig deeper into the finer details of the paper, I wanted to download the cDNA sequence.  Here's how I did it.  First go to Ensemble and search Human (or whatever other organism you are studying) for the gene you want the cDNA sequence for.  On the next results summary page, click on the link to the gene.  Then on the result in detail page, click on the gene id.  You should notice the next page is essentially a tab labeled with the gene you searched for.  On this page should be a table of transcripts for your gene.  Click on the transcript ID of the transcript you want the cDNA sequence for.  If you aren't sure which transcript you want, the one with the CCDS ID is a good start.  A new page will be loaded where you will be on a new tab for the transcript you selected.  On the left side of the tab is a menu of different links.  Find cDNA in this menu under sequence and click on it.  This will lead you to a page with the cDNA sequence.  Congrats, you now are able to get the cDNA sequence for a gene transcript.

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