Question on UCSC genome browser and thank you!

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shaoyong chen

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Jul 26, 2021, 1:06:02 PMJul 26
to gen...@soe.ucsc.edu
Hi UCSC team:

I am working at Harvard Medical School and thanks for the valuable genome browser, good Job!

Here I have a question: based on IGV I can see almost all genes based RNA Pol-2, meaning mRNA and lncRNAs; however, I can not find gene driven by RNA Pol-1 and RNA Pol-3, like ribosomal RNAs and tRNAs.

Maybe you can help?

Thank you!

Shaoyong Chen, Ph.D.

Dan Schmelter

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Jul 30, 2021, 7:08:39 PMJul 30
to shaoyong chen, gen...@soe.ucsc.edu

Hello Shaoyong,

Thank you for contacting the Genome Browser support team and for your question about RNA data.

The visualization you see on the Browser is based on the data selected and available. If you are seeing data on IGV that is not on the Genome Browser, it may be that different data sources are selected. You may want to double-check that you are looking at the same dataset with similar configuration options. Chromosome positions are also important, making sure that you are looking at your intended gene region.

The GENCODE v36 track has some annotations on tRNA and rRNA, but these types of molecules are not always well established or annotated. Additionally, this geneset only shows the Basic gene set by default instead of the Comprehensive and hides annotations marked as pseudo-genes. If you want to show everything, you can right-click into the track and select your desired options.

Here is a saved session I made showing the POLR1A, 2A, and 3A genes together in multi-region mode. This session shows all GENCODE v36 annotations without any filters. I also turned on the Human mRNA track, which may indicate transcriptional activity.

http://genome.ucsc.edu/s/dschmelt/hg38.POLR123

I hope this was helpful. If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser


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