CpG sites

[Mersha, Tesfaye]

Is there an online tool or other way that helps me to locate the types and number of CpG sites in a given gene.

 

Thanks,

T

 

[Luvina Guruvadoo]

Hello Tesfaye,

Thank you for your question. We do have a CpG track available on most of our assemblies, you can read more about it on the description page here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cpgIslandSuper

To view CpG sites on a given gene, type in the gene name in our search box and click 'go'. In this example, I will search for 'SOD1' using the human hg38 assembly. Click on the first item that appears on the search results page and you will be redirected to the genome browser display. Scroll down to the 'Regulation' track group and turn on CpG Islands by selecting 'show' from the mini drop-down menu. I have created a session for this example here: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=luvina&hgS_otherUserSessionName=CpG_example.

Also note, we have a number of tutorials that explain how to use and interpret the Genome Browser display: http://genome.ucsc.edu/training.html

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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