MYC
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Roderick MacLeod
Jul 22, 2016, 11:18:51 AM7/22/16
to gen...@soe.ucsc.edu
chr8:128,147,323-129,354,672
Feb. 2009 (GRCh37/hg19
UCSC genes
Dear UCSC
Why does MYC mapp to separate neiboring positions on the UCSC (but not Genbank) gene tracks?
Thanks
Rod
Roderick A. F. MacLeod PhD
Leiter AG-Cytogenetik
Leibniz Institut DSMZ
- Deutsche Sammlung v. Mikroorganismen und Zellkulturen
Inhoffenstraße 7 B
38124 Braunschweig
GERMANY
Tel. +49531-2616-157 Fax +49531-2616-150
http://www.dsmz.de
Director: Prof. Dr. Jörg Overmann
Feb. 2009 (GRCh37/hg19
UCSC genes
Dear UCSC
Why does MYC mapp to separate neiboring positions on the UCSC (but not Genbank) gene tracks?
Thanks
Rod
Roderick A. F. MacLeod PhD
Leiter AG-Cytogenetik
Leibniz Institut DSMZ
- Deutsche Sammlung v. Mikroorganismen und Zellkulturen
Inhoffenstraße 7 B
38124 Braunschweig
GERMANY
Tel. +49531-2616-157 Fax +49531-2616-150
http://www.dsmz.de
Director: Prof. Dr. Jörg Overmann
Brian Lee
Jul 22, 2016, 5:47:52 PM7/22/16
to Roderick MacLeod, gen...@soe.ucsc.edu
Dear Rod,
Thank you for using the UCSC Genome Browser and your question about the UCSC genes track on hg19 around the region of the gene MYC.
Our engineers have looked at this area and share that it appears this is consequence of the difficulty to build gene models exactly correct in all circumstances in regards to the layers of algorithms involved to collect exons into a final prediction. It does indeed look as though there was an error in the prediction of some transcripts labeling them as MYC when they are more correctly PVT1 transcripts.
On the most recent human assembly, hg38, we have switched our default displayed gene model set to be based upon Ensembl/GENCODE data, which incorporates manual annotations rather than being entirely computationally based.
Ensembl/GENCODE tracks are also available on hg19. You may wish to switch to using the Ensembl/GENCODE prediction models for hg19, here is a session link to these various tracks displayed:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.MYC.Predictions
Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead togeno...@soe.ucsc.edu.
All the best,
Brian Lee
UCSC Genomics Institute
Thank you for using the UCSC Genome Browser and your question about the UCSC genes track on hg19 around the region of the gene MYC.
Our engineers have looked at this area and share that it appears this is consequence of the difficulty to build gene models exactly correct in all circumstances in regards to the layers of algorithms involved to collect exons into a final prediction. It does indeed look as though there was an error in the prediction of some transcripts labeling them as MYC when they are more correctly PVT1 transcripts.
On the most recent human assembly, hg38, we have switched our default displayed gene model set to be based upon Ensembl/GENCODE data, which incorporates manual annotations rather than being entirely computationally based.
Ensembl/GENCODE tracks are also available on hg19. You may wish to switch to using the Ensembl/GENCODE prediction models for hg19, here is a session link to these various tracks displayed:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.MYC.Predictions
Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead togeno...@soe.ucsc.edu.
All the best,
Brian Lee
UCSC Genomics Institute
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