Multi-region view does not show first exon of human transcript ENST00000649947

[Irwin Jungreis]

ENST00000649947 is a protein-coding transcript of FRMD4A in GENCODE human v44 on the '-' strand of chr10 whose first exon is 14024354-14024481. However, when I try to see this transcript in the browser with multi-region view set to "Show exons using GENCODE V44" it does not show the region containing this exon even though it is an exon of a GENCODE V44 transcript.

In the attached image ENST00000649947 is show at the bottom. You can see that the intron line starts at the multi-region boundary with no first exon.

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and reporting your issues.

To better assist with your issues, could you send us a link to your session:

https://genome.ucsc.edu/cgi-bin/hgSession

or a URL with the hgsid parameter:

https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=default&hgsid=1771431034_THTGXWSDjSTOIMfaUYPhbHlxS2PI

We cannot reproduce the display that you are experiencing in multi-region mode. In the following session, we went to your position (chr10:13,810,877-14,074,451) and entered multi-region mode:

https://genome.ucsc.edu/s/AngieHinrichs/MLQ32544

However, following these steps resulted in a 3,134 bp region compared to the 1,287 bp in your screenshot. There are also 13 regions in the session, but your screenshot only shows 7 regions. Your screenshot shows an issue with multi-region, but we cannot reproduce it at the moment.

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 Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

On Wed, Nov 1, 2023 at 2:01 PM Irwin Jungreis <ILJ...@csail.mit.edu> wrote:

ENST00000649947 is a protein-coding transcript of FRMD4A in GENCODE human v44 on the '-' strand of chr10 whose first exon is 14024354-14024481. However, when I try to see this transcript in the browser with multi-region view set to "Show exons using GENCODE V44" it does not show the region containing this exon even though it is an exon of a GENCODE V44 transcript.

In the attached image ENST00000649947 is show at the bottom. You can see that the intron line starts at the multi-region boundary with no first exon.

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[Irwin Jungreis]

Hello Jairo,

I was able to reproduce the problem. Here is a new screen shot:

[Irwin Jungreis]

Any progress on this? I just checked that the problem still occurs. Are you able to reproduce it?

On Nov 20, 2023, at 4:41 PM, Irwin Jungreis <ILJ...@csail.mit.edu> wrote:

Hello Jairo,

I was able to reproduce the problem. Here is a new screen shot:

<PastedGraphic-1.png>

The URL is: https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=exonMostly&lastVirtModeExtraState=&emGeneTable=knownGene&virtModeType=exonMostly&virtMode=1&nonVirtPosition=chr10%3A13782963%2D14074544&position=chr10%3A13782963%2D14074544&hgsid=1778905376_03d4Rq3HLLrUQhbO7n8f1f2fMTxY

In case the history matters, the way I got there is I opened the following URL: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr10:13858847-14024419&complement_hg38=1&hgt.revCmplDisp_hg38=1' then turned on Multi-region view, then zoomed out 1.5 x.

I've attached the session file.

I am on a MacBook Pro running MacOS Ventura 13.4. I tried in Safari, Chrome, and Bing, and got the same behavior.

Thanks,

Irwin

<hgSession.multiRegionBug.txt>

[Luis Nassar]

Hi, Irwin.

We're taking another look now and will be in touch soon.

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/9B350755-BC70-43BB-A4DB-7803046CE793%40csail.mit.edu.

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I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute