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

[Cei Abreu-Goodger]

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