mm10 knownGene table different when accessing via MySQL

[Niklas Mertsch]

Good evening and greetings from Germany,

I am usually accessing the knownGene table of the mm10 mouse genome via
MySQL (as described here:
https://genome-euro.ucsc.edu/goldenPath/help/mysql.html),
but today I found that some genes I am looking for were not included.

So I double checked with the online Table Browser and was surprised to
find the genes in there.

I run MySQL from Java JDBC using the URL
"jdbc:mysql://genome-euro-mysql.soe.ucsc.edu:3306/mm10?serverTimezone=GMT&no-auto-rehash=true".
The SQL Statement I used was "SELECT name FROM knownGene where name =
'uc008itg.2'".

This did not produce an output for 'uc008itg.2', but the gene
'uc007xbe.1' was found.
Both of them appear in the output produced by the Table Browser
(https://genome-euro.ucsc.edu/cgi-bin/hgTables).

Can anyone tell me why some genes don't show up and how I can make it work?

Thank you very much in advance!

Niklas Mertsch

[Jairo Navarro Gonzalez]

Hello Niklas,

Thank you for using the UCSC Genome Browser and your inquiry.

The issues you may have been experiencing was most likely because we were updating the UCSC Genes track for mm10. The identifier, uc008itg.2, is new to the gene set and the European MySQL server could have been lagging behind. These issues should now be fixed.

If you are still experiencing issues, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

Niklas Mertsch

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