conserved regions of genome

[John Bermingham Jr]

For non-model species genomes that are accessible on the UCSC genome browser, is there a way to visualize the levels of evolutionary conservation, or is that a separate custom track that has to be generated for the species of interest?

Thank you

[Gerardo Perez]

Hello,

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

To better assist you, could you specify which non-model species genomes you are working with? We may already have the evolutionary conservation data available for it on the UCSC Genome Browser.

Also, could you clarify what type of evolutionary conservation data you are looking for? If the data is not currently available in our browser, it may be possible to upload it as a custom track.

Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. 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

On Thu, Apr 2, 2026 at 2:00 PM John Bermingham Jr <jrbermi...@gmail.com> wrote:

For non-model species genomes that are accessible on the UCSC genome browser, is there a way to visualize the levels of evolutionary conservation, or is that a separate custom track that has to be generated for the species of interest?

Thank you

--

---
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 visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/82620b56-bfa4-41e7-85ba-451c1da59716n%40soe.ucsc.edu.

[John Bermingham Jr]

Dear Dr. Perez,

I have generated a custom track for the western painted turtle L12R10 genome (GCF_011386835.1) that displays ~367 microsatellites that have been developed for use in turtles.  Most reside in introns, and I am interested in determining which of them resides in potentially conserved regions. I am looking for a track that would display conserved regions on this genome, similar to VISTA.

Thanks,

John

[Matthew Speir]

Hello, John.

Thank you for clarifying the genome you're working with. Apologies for the delay in getting back to you.

Unfortunately, we don't have any conservation data available for that genome. However, if you have some specific assemblies you want to compare your data on, we can generate LiftOver chains for those pairings (e.g. GCF_011386835.1 <-> hg38).

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.

---

Matthew Speir

UCSC Genome Browser, User Support

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CADHWnWzvXAfW8Gnt%3DqeEf%3DU%3DyW-a%2Bt%3DgXQK-Y2cq5fhDqLWX6g%40mail.gmail.com.