[Genome] Question about tracks and duplicate entries

[Fan Hsu]

Hi Todd,

The RefSeq track data (refGene table) is updated nightly.
The Known Genes data is not updated until next major release
(or rebuild).

I noticed that the version number for NM_004869 is 3 now.

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of Todd Riley
Sent: Tuesday, January 09, 2007 2:51 PM
To: genome at soe.ucsc.edu
Subject: [Genome] Question about tracks and duplicate entries


Hello again,

Thank you for your answers, they were very helpful.  If you don't mind,
I know have a new question for you.

How are the tracks "Known Genes", "RefSeq Genes", and "Other RefSeq"
related to each other?  I noticed that there are many RefSeq Genes in
the KnownGenes table (which makes sense).  However, I also noticed that
the RefSeq entries in the KnownGene track do not always correspond to
the entries in the RefSeq table!! Here is an example from hg17:

Known Genes track:

NM_004869    chr18    -    59207406    59240673    59209187
59240472    11
59207406,59211621,59215246,59217454,59218260,59218759,59221919,59225644,5922
8502,59229679,59240445,
59209289,59211762,59215466,59217536,59218409,59218916,59222039,59225712,5922
8659,59229791,59240673,
VPS4B_HUMAN    R8768

RefSeq Genes track:

NM_004869    chr18    -    59207406    59240732    59209187
59240472    11
59207406,59211621,59215246,59217454,59218260,59218759,59221919,59225644,5922
8502,59229679,59240445,
59209289,59211762,59215466,59217536,59218409,59218916,59222039,59225712,5922
8659,59229791,59240732,


Notice that they are not completely the same!!!  I would expect them to
be the same except for the "VPS4B_HUMAN    R8768" appended to the end of
the known gene.

Thanks,
Todd
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