Reverse Strand Chromosome

[Shannon Bonomi]

Hello,

I am trying to find the chromosome position of a specific mutation of a few different proteins. I have been able to successfully interpret the results for the mutations occurring in forward strands, however I cannot seem to interpret the position of a mutation occurring in the reverse strand. Can you please give me some guidance on how the reverse strand differs from the forward strand?

Thanks!

[Jairo Navarro Gonzalez]

Hello,

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

To view the negative strand in the Genome Browser, there is a button at the bottom of the browser image, "reverse", to get the reverse complement the genomic sequence. There is also a keyboard shortcut, r and then v, to view the negative strand. A third way to view the negative strand is to add the following URL parameter to your web browser:

hgt.toggleRevCmplDisp=1

Here is an example that uses the parameter, https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.toggleRevCmplDisp=1.

I hope this is helpful. 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

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[Shannon Bonomi]

Hey Jairo,

Thank you so much for responding. 

I am not seeing the button you are referring to and the shortcut does not seem to be working. Additionally, my output does not look like that of the example you provided, but rather the fasta sequence followed by the sequence of the chromosome and then a shortened alignment of the two. Is there any more information you can give me about correctly interpreting the chromosome sequence of a specific nucleotide?

Thank you,

Shannon

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your follow-up questions.

To help debug your issues, could you give us more information about what you are doing on the UCSC Genome Browser or the steps taken to view the FASTA sequence? A session link, https://genome.ucsc.edu/cgi-bin/hgSession, or a screenshot would help us understand what you are viewing or which tool you are using on the browser.

I look forward to your reply. 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

Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAAQRNk%2BAaH%3DGPqxcMjapAzJFYE3CZ3O1vDFEh81iAwp_22putA%40mail.gmail.com.

[Shannon Bonomi]

Thanks again for your help.

Here is a document with screenshots of what I am seeing.

 SMARCC2 alignment

[Gerardo Perez]

Hello, Shannon.

Thank you for sharing this additional information.

The coordinates of the region are displayed at the top of the page and are relative to the forward strand. In the "Human.chr12 (reverse strand)" section, the base numbering along the right-hand side starts at the end of the coordinate region noted above (56583245) and ends and the start of that coordinate region (56557476).

In the "Side by Side Alignment" section, again, the coordinates are shown relative to the forward strand, but the sequence of the reverse strand is displayed in 5' -> 3' direction for easier visualization. Interpreting the genomic coordinates of the mutations should be the same as for the forward strand, though you may have to count backwards.

I hope this is helpful. 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.

Gerardo Perez
UCSC Genomics Institute

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[Shannon Bonomi]

Thank you very much. That is what I thought, however I am receiving errors when I use this information. The error is likely not with Genome Browser. 

Thank you for your time.

[Brian Lee]

Dear Shannon,

Thank you for using the UCSC Genome Browser. I wanted to share some further links building on the information sent previously that might help illustrate the information you are investigating. For the SMARCC2 alignment information you shared you can see the Amino Acid string starts with MAVRKKDGG... in your alignment file, in the "Side by Side Alignment" section, above a sequence (atggcggtgcgg..).

Here is a link that activates the "Reverse" button and shows the codon numbering of the SMARCC2 in the region of this alignment (if the link doesn't flip the view the first time, try it again -normally you click the "Reverse" button below the main browser image).

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr12:56583217-56583256&hgt.toggleRevCmplDisp=1&knownGene=pack

What you see when the reverse strand is activating is the DNA along the top matching what is in your file (atggcggtgcgg..) matching the start MAVR... codon sequence for this gene.

If the "Reverse" button is turned off (by either clicking it or using this URL parameter): https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr12:56583217-56583256&hgt.toggleRevCmplDisp=0&knownGene=pack

You will see the sequence on the forward strand (instead of "atg" for the M1 you see "cat" and the start codon is on the right hand of the screen instead of the left side when using reverse view). So the reverse strand helps display the sequence in the order that matches the codon translation in the protein.

I hope this is helpful. 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.

All the best,
Brian Lee

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[Shannon Bonomi]

Thank you very much!