Question about representation of exons in the browser

[Brid Ryan]

Good afternoon, 

When looking at the genome browser, I have been trying to understand why some (internal) exons are represented as a thin and a wider rectangle combined, instead of a single unifrom rectangle. What is the significance of the former? See example below for a gene called CEBPA.

Many thanks!

Brid 

Example of exon 3 in RefSeq: NM_001367258.1

[Daniel Schmelter]

Hello Brid,

Thank you for writing to the Genome Browser support team.

The medium-thickness blocks are intended to represent UnTranslated Regions (UTR) for the transcript, in contrast to coding sequence (thicker blocks) and intron regions (thin lines). This particular situation is uncommon because the annotation shows the 3' UTR as split up across 3 exons, as opposed to the more common single exon UTR. This is still a valid annotation, however rare. You can see that the UTR is annotated as such in both NCBI RefSeq and GENCODE, across many different transcripts.

http://genome.ucsc.edu/s/dschmelt/sting1Exon

For more information on interpreting our Genome Browser view or the track itself, please look at our documentation and the RefSeq description page's display conventions section:

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite

I hope this was helpful. For further communication, please reply-all to gen...@soe.ucsc.edu. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CACKhq50cUrryMZsbbJO9HzL6PiZB7Nh7Da9ktbQGEe5gOz26yQ%40mail.gmail.com.

[Brid Ryan]

Good afternoon Daniel, 

Thank you very much for that. It explains it in part and I will note that that thinner line, even when in teh middle of the gene means that that region has been annotated to a 3'UTR. 

If you wouldn't mind me asking one follow up. You noted that the annotation as split across 3 UTRs as correct. When I look at the sequences of that exon 4, its sequence is the same across all the variants in the viewer you sent. So, the part that still confuses me somewhat, is why does the exon, which has the same sequence across all variants, show as a single width exon for 4 of the variants and as 2 widths for 2 of them. 

Thanks again very much for your time and help. 

Best wishes 

Brid 

[Brian Lee]

Dear Brid,

For your question about how transcripts can be different, where you ask, how exon 3 of NM_001367258.1, which has similar sequence across all transcripts, but is shown as a coding exon for 4 of the transcripts and as having a UTR region for two of the transcripts, these differences boil down to the fact different transcripts can have different places where translation starts and UTRs ends.

We have an entire FAQ page about interpreting genes that might be very helpful, here is the section about transcripts (note that transcripts is a different biological term from the word variants you are incorrectly using in your question): https://genome.ucsc.edu/FAQ/FAQgenes.html#genestrans

The session shared provides a valuable tool for understanding these differences, and in fact is one reason Genome Browsers are so useful for understanding genomic data. Here is that session with some green highlights of where coding begins: http://genome.ucsc.edu/s/brianlee/sting1

If you zoom in on the these regions you will see the codon frame is for a start codon (Methionine, with symbol Met or M), where each of these transcripts has a different location where the reference genome order of DNA leads to a messenger RNA (mRNA) transcript that initiates translation by a ribosome. In our session gallery we have some examples of the codon view that you might find useful: http://genome.ucsc.edu/goldenPath/help/sessions.html#dna

I hope this was helpful. For further communication, please reply-all to gen...@soe.ucsc.edu. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu.

All the best,

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CACKhq53L4JSq%2Bi6jopV2hKywB0yHdLeZ4-75a9PK0rjbMygq%3DQ%40mail.gmail.com.