GENCODE Comprehensive Set Appears to be Basic Set

[Dario Strbenac]

Good day,

When looking at a gene such as BRAF in UCSC, I notice only one transcript isoform. I am viewing the version 24 Comprehensive Transcript Set from the drop-down list titled GENCODE v24. I am viewing the human genome GRCh38.

I think the confusion arises because there are two tracks with similar names; GENCODE v24 and All GENCODE. It's only when the user selects All GENCODE that the other transcripts appear, even though the track title of the track shown when GENCODE v24 is selected contains "Comprehensive Transcript Set". This is incorrect.

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

[Jairo Navarro Gonzalez]

Hello Dario,

Thank you for using the UCSC Genome Browser and your question about the GENCODE v24 track for hg38. 

The GENCODE v24 track shows the basic set by default, and to view the whole set, you will have to edit the track settings in the browser. 

For example, if you navigate to this page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene 

and select "splice variants" and "show comprehensive set". You should now be able to view the different isoforms for your gene of interest.

Thank you again for your inquiry and using the UCSC Genome Browser. 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.

Jairo Navarro

UCSC Genomics Institute

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