Ucsc Genome Browser Does Not Locate Xm Genbanks: How To Overcome This?

Question

[Anima Mundi]

Hello,

when I try to get the downstream regions of a given set of genes in a sequenced genome (, using as an input their accession numbers for the UCSC Genome Browser, I fail to locate the IDs starting with the prefix XM (they are model reference sequences of the RefSeq mRNA database produced by NCBI's Genome Annotation project). How could I avoid this problem? One solution could be to extract the FASTAs of those sequences and BLAT them, but maybe there are more elegant solutions.

Answer 1

[Larry_Parnell]

Of course, you can always load the XM_ and XR_ gene models as custom tracks.

[Anima Mundi]

Thank you, Larry. I have no experience in the custom tracks usage. Could they be used for the Xenopus tropicalis genome? Unfortunately they appear to be provided only for human, mouse, rat and yest.

[Larry_Parnell]

My understanding is custom tracks of any kind can be loaded. An important element of your tracks will be the coordinates of those genes in the Xenopus genome. Try to load one or two custom tracks, view them, then scroll them out of view so that you get a feel for functionality.

[Anima Mundi]

I think I need to get familiar with custom tracks. I do not know these coordinates, maybe I would have to find the suitable tracks somewhere. I will try to sort it out, this is however a good start point!

Answer 2

[zhangzhang.lan]

I want to annotation XM. For example, XM_291816.

How to get the chromosome coordinate like this in UCSC: "85 NM_001013630 chr1 + 12704565 12727097 12704565 12726746 4 12704565,12711141,12721801,12725971, 12704733,12711358,12721865,12727097, 0 AADACL4 cmpl cmpl 0,0,1,2," ?

I also want to use the sequence to blast, but is not accurate.

Anyone can help me? Thank you.

Answer 3

[Maximilian Haeussler]

They do have them now, but on their internal site: http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031935-33041243&xmGene=pack