Locating telomere on a given chromosome

Question

[skiesareforflying]

I found some other posts suggesting to use UCSC utilities to find coordinates of centromeres and telomeres of a given chromosome. I was able to find the centromere in this way, but there don't appear to be any gaps for the telomeres. I've tried both the genome browser and table browser and get the same result:

This is a telocentric chromosome (mm9 chr13), which is why the centromere is at the very beginning. So I'm assuming I should see a telomere at the other end, but I just see "fragment"s. I got the coordinates of the whole chromosome by simply typing in "chr13" and it gave me the display for chr13 from position 1, to presumably the end. Am I doing something wrong here?

Answer 1

[Luis Nassar]

Hello,

Late to the party, but present non-the-less.

This question has come up before in the Genome Browser:

https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/telomere$20mm9|sort:date/genome/fN1dPsobIcg/8Vue9ImwKAAJ

and we have a wiki entry on how to get gaps (https://genome.ucsc.edu/FAQ/FAQtracks#tracks20). In this case you got to the right results, but the telomeres are not annotated on the mm9 assembly. Our gap data are directly imported from the NCBI public build, and so limited by that annotation. If you follow these steps on the mm10 assembly you will see the telomeres + centromeres.

585 chr13   0   100000  1   N   100000  telomere    no
9   chr13   110000  3000000 3   N   2890000 centromere  no
187 chr13   120321639   120421639   13  N   100000  telomere    no

If you have any additional questions, you can reach out to our help desk at [e-mail]. We check Biostars every now and again, but your question may go unanswered for some time. If you post a question here, using the "ucsc" helps to put it on our radar.

Lou
UCSC Genome Browser