[Genome] How to get alinged 3'UTR/downstream regions?

[Rachel Harte]

Hello Cei,

If you are asking how to find the sequence of 3' UTR regions from RefSeq
genes that overlap with micro-RNAs, you can do this by creating an
intersection of these two tracks using the Table Browser. Please let me know
if this is what you are trying to do and I can help you more.

Are you still having a problem with our mySQL server? I am able to
connect to it with no problem. Please let me know if this is still a
problem and I can look into it some more.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Mon, 15 Jan 2007, Cei Abreu-Goodger wrote:

> Hello,
>
> I hope you can point me in the right direction here. I work at the
> Sanger Institute, currently with micro-RNAs, and as such my main focus
> is on the 3'UTR or downstream regions of genes. It would be incredibly
> useful for me to be able to obtain the alignments corresponding to these
> regions. I can see how to download full chromosomal alignments, and can
> download 3'UTR or downstream regions from particular species using the
> Tables section. But what I really need is some way to combine both, that
> is: for a given species, get the sequence alignment for only the regions
> annotated as 3'UTR exons (I use RefSeq). Is there some way to do this?
> Btw, I don't seem to be able to connect to the mysql server:
> mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A
> ERROR 2003: Can't connect to MySQL server on 'genome-mysql.cse.ucsc.edu'
> (60)
>
>
> Many thanks,
>
> Cei
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