Finding Putative VDR binding sites in a specific gene

[Daniesha Govender]

Hi

I am emailing as I am struggling to identify VDR binding sites in the TET genes. After searching the browser and identifying my gene (TET1,TET2 and TET3) I click on the JASPAR familial binding sites tracks which does allow me to select for VDR however it indicates that the binding site exists across the entire gene even wehn adjusting the matrix similarity score. I am unsure what to do to get VDR  binding site locations or predictions for the TETs. I would appreciate any assistance with this.

Kind regards

Daniesha

[Brian Lee]

Dear Daniesha,

Thank you for using the UCSC Genome Browser and your question about VDR binding sites in the TET genes. You have helped alert us to an unexpected issue with our filters. Please try connecting to the JASPAR hub data, rather than our JASPAR internal track to resolve the issue. Here are some steps.

You can access the hub by going to the top blue menu bar and under "My Data" selecting "Track Hubs" and searching JASPAR, or clicking this link: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hubSearchTerms=JASPAR

Then click the "Connect" button next to JASPAR TFBS. You should be directed to the human hg19 assembly where you can click "GO" or first type TET1 in the position/search box and navigate to the main Browser view.

You can then decide if you only want to use the 2022 data, if so, right-click and hide the other 2018 and 2020 data tracks. Scroll down to the blue banner below the image with "JASPAR TFBS" and click the JASPAR2022 TFBS hg19 link. On this page you can then select "Vdr" and also adjust the "Minimum Score" to 0 to see all data. Click submit to return to the main browser view. You will also have to zoom in to a region that not too large as there are so many items in the track it will default to a black bar on certain scales of view. For instance, here is a session with all the above steps and zooming in on the transcription start site of TET1: http://genome.ucsc.edu/s/brianlee/TET1

Thank you again for alerting us to the issue with our JASPAR track and for using the UCSC Genome Browser. If you have any further public questions, please send new questions to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum to help others find answers to similar questions. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu, which is a private internal list to our support team.

All the best,

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[Daniesha Govender]

Thank you for your reply and assistance Brian!