SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
ucsc custom track Ohad General 0 06-21-2015 04:14 AM
RepeatMasker track UCSC in R Mimoeschen Bioinformatics 0 04-17-2013 11:21 AM
UCSC refSeq Gene and hg19 coordinate thedamian Bioinformatics 6 02-07-2013 12:18 AM
Non-species refseq genes in UCSC Genome Browser stephenhart Bioinformatics 0 02-14-2012 10:03 PM
TF Motif track UCSC Livi81 General 0 06-15-2011 03:10 PM

Reply
 
Thread Tools
Old 10-01-2015, 03:29 PM   #1
deep639
Member
 
Location: Irvine

Join Date: Dec 2013
Posts: 10
Default UCSC and RefSeq Genes Track coordinate information

I had a question regarding two microRNA annotations. The two RNAs were Mir1195 and Mir5128. The reference genome was the mouse mm10 genome. They don't have the same coordinate information for UCSC and RefSeq Genes track. By that I mean, that refseq and UCSC have the microRNA on different chromosomes, for Mir1195 on the UCSC genes track it is on chr17, for refseq its on chr16. Is there an obvious reason for why this is happening? I have attached the links on UCSC for the two microRNAs showing the different coordinates.

http://genome.ucsc.edu/cgi-bin/hgTra...=2.0&dinkR=2.0

http://genome.ucsc.edu/cgi-bin/hgTra...=2.0&dinkR=2.0

Last edited by deep639; 10-01-2015 at 03:34 PM.
deep639 is offline   Reply With Quote
Old 10-01-2015, 06:27 PM   #2
blancha
Senior Member
 
Location: Montreal

Join Date: May 2013
Posts: 367
Default

I can't come up with a logical explanation.
To me, it's simply a mistake.

If you select the RefSeq gene in the UCSC Genome Browser, then click on the track for the miRNA and then click on the link with the NCBI identifier next to "RefSeq", you end up on the NCBI page where the correct chromosome is displayed. The correct chromosome is the same as for the UCSC Genes.

I would just report the mistake to the UCSC Genome Browser support team.
blancha is offline   Reply With Quote
Old 10-02-2015, 09:44 AM   #3
deep639
Member
 
Location: Irvine

Join Date: Dec 2013
Posts: 10
Default

Thanks, I let UCSC know about it.
deep639 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:07 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO