Obtain gene structure (Exon and CDS coordinates) for ENSMUST00000209603
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Mark Brown
Oct 26, 2016, 7:37:38 PM10/26/16
to gen...@soe.ucsc.edu
I encountered a few cases where some Ensembl transcripts cannot be found in UCSC database, e.g., ENSMUST00000209603
I wonder if it is b/c I did not search within the right table, or there is a reason that such entries are not included.
I am search within hgcentral.wgEncodeGencodeCompV19
Thanks.
Mark Brown
Oct 27, 2016, 11:46:56 AM10/27/16
to Michael Paulini, UCSC Genome Browser Discussion List
I had a typo in my initial email, the table I used is wgEncodeGencodeCompVM9
I don't think the issue is ncRNA, as the following is a ncRNA and it can be found in the table.
SELECT * FROM wgEncodeGencodeCompVM9 WHERE NAME LIKE 'ENSMUST00000195992%';
On Thu, Oct 27, 2016 at 3:49 AM, Michael Paulini <michael...@wormbase.org> wrote:
I do assume it has something to do with the fact that they are not protein-coding transcripts, so they might be in a different table.M
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Michael Paulini
Oct 27, 2016, 11:47:00 AM10/27/16
to Mark Brown, UCSC Genome Browser Discussion List
I do assume it has something to do with the fact that they are not protein-coding transcripts, so they might be in a different table.
M
On 26 October 2016 at 23:27, Mark Brown <mbro...@gmail.com> wrote:
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Cath Tyner
Oct 27, 2016, 9:54:56 PM10/27/16
to Mark Brown, Michael Paulini, UCSC Genome Browser Discussion List
Hello Mark,
Thank you for submitting your question regarding your unsuccessful search for certain Ensembl transcripts in the UCSC Genome Browser databases.
In short, some of these transcripts are in newer data set versions, which are not yet loaded into the public UCSC Genome Browser; we are currently displaying vM9.
For example, going to the Ensembl archive (M9) also returns no results for a search of ENSMUST00000209603 - this is an example of a transcript that is only in newer versions (Version M10/Ensembl 85 & Version M11/Ensembl 86), but not in Version M9/Ensembl 84 (our current set).
The correct table to query is: mm10.wgEncodeGencodeBasicVM9 (when updated, use mm10.wgEncodeGencodeBasicVM10 or whichever table you would like, such as the comprehensive table: mm10.wgEncodeGencodeCompVM10).
As noted at Ensembl: "This transcript is a member of the Gencode basic gene set."
Please note on the description page that non protein-coding transcripts are included in the GENCODE Basic Set, upon meeting certain criteria.
On our public site (genome.ucsc.edu), we are planning to update mouse assembly mm10 from vM9 to vM11 soon, but we currently do not have an estimated time for completion.
For mm10, we do have vM10 on our preview-site (and we will add vM11 soon), which you are welcome to access:
Please note that this is the UCSC Genome Browser preview site. This website is a weekly mirror of our internal development server for public access. Data and tools on this site are under development, have not been reviewed for quality, and are subject to change at any time. We provide this site for early access, with the warning that it is less available and stable than our public site. The high-quality, reviewed public site of the UCSC Genome Browser is available for use at http://genome.ucsc.edu/.
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