Hello Raymond,
1. Wikipedia is going to do a better job than I will of describing 5'
and 3' UTR exons (plus they have pictures):
http://en.wikipedia.org/wiki/5%27UTR
It's possible you have a situation where a UTR from one gene is in the
middle of where another gene is annotated. If you have specific
examples that you'd like us to look at, feel free to send them along.
2. This is actually not an embarassing question at all. It comes up
quite often. You'll need to join the knownGene table to a table called
kgXref. In the Table Browser, where it says "output format" choose
"selected fields from primary and related tables". Check the box next
to mm9.kgXref and then click "allow selection from checked tables".
Then select the fields you want from knownGene and the fields you want
from kgXref ("geneSymbol" will give you the type of name I think you're
looking for)
I hope this information is helpful to you. Please don't hesitate to
contact us again if you require further assistance.
Kayla Smith
UCSC Genome Bioinformatics Group
Cho, Raymond wrote:
> Hello - thank you for your patience. We've pored through archives with no
> luck on these.
>
> Our goal is to isolate the sequence that codes for any protein, along with
> flanking genomic sequence. It looks like the Table should make this easy,
> but we've run into 2 distinct problems.
>
> 1. What are "5' UTR exons" and "3' UTR exons"? We had hoped that these were
> purely non-coding sequence, but BLATting some of them matched exons in the
> middle of genes. Are they sequences that CAN be alternatively spliced but
> are not always, and so sometimes code for protein? If so, are some of them
> also represented in the "CDS" file?
>
> 2. This one is embarrassing - when returning a file of sequences, how do we
> get gene names instead of merely UCSC ID's?
>
> Thank you!
>
> ray
>
>
>
>
>
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
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