UCSC and RefSeq Genes Track coordinate information

deep639 · 10-01-2015, 04:29 PM

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

blancha · 10-01-2015, 07:27 PM

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.

deep639 · 10-02-2015, 10:44 AM

Thanks, I let UCSC know about it.

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10-01-2015, 04:29 PM	#1
deep639 Member Location: Irvine Join Date: Dec 2013 Posts: 10	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 04:34 PM.

10-01-2015, 07:27 PM	#2
blancha Senior Member Location: Montreal Join Date: May 2013 Posts: 367	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.

10-02-2015, 10:44 AM	#3
deep639 Member Location: Irvine Join Date: Dec 2013 Posts: 10	Thanks, I let UCSC know about it.