[Genome] Retrieve Ensembl 3'UTR conserved sequence

[Ann Zweig]

Hello Ken-

	Your solution is very close.  Just a small change and one more step, 
and you will have the sequence you need.

	First you make a custom track in the table browser by intersecting the 
ensGene table with the phastConsElements17way table.  The 
phastConsElements17way table supports the Most Conserved track in the 
browser.  This track shows predictions of conserved elements across the 
set of aligned species in the Conservation track.

	To make your custom track, choose the ensGene table, then intersect it 
with the phastConsElements17way table (group = Comparative Genomics, 
track = Most Conserved).  Choose All Ensembl Genes records that have any 
overlap with Most Conserved.  Submit.  Back at the main page of the 
table browser, you may want to restrict your region to one chromosome 
(and do the query again for each chrom).  For all of chromosome 7, there 
are 1,600 Ensembl Genes that have one or more phastConsElements in them 
(out of the 1,686 Ensembl Genes on chr7).

	As the output format, choose Custom Track.  After pressing get output, 
choose "Create one BED record per Whole Gene", then press get custom 
track in table browser.

	Now, choose your custom track in the table browser, clear the 
intersection (if it's still on), and as output format choose sequence. 
Press get output.  From this page choose 3'UTR, and select other items 
as you prefer.  Press get sequence.  You will see the sequence for the 
3'UTR end of Ensembl Genes that are conserved.

	Hope this is helpful to you.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Ken wrote:
> Hello,
>  
> I need to retrieve human conserved 3'-UTR sequences which can map to Ensembl
> transcripts.
> I try to download these sequences using Table Browser.
> http://genome.ucsc.edu/cgi-bin/hgTables?command=start
> 1. I choose clade: Vertebrate; 
> genome: human; 
> assembly: May 2004;
>             group: Genes and Gene Prediction Tracks;
>             track: Ensembl Genes;
>             table: ensGene
> region: genome;
> output format: custom track;
> and then press "get output"button.
> Next choose:
> Create one BED record per: 3' UTR Exons
>             And then press "get custom track in table browser".
> 2. I choose clade: Vertebrate; 
> genome: human; 
> assembly: May 2004;
>             group: Comparative genomics;
>             track: Conservation;
>             table: multiz17way
> region: genome;
> intersection: create
>    Group: custom track;
>    Track: tb_ensGene;
>    Table: tb_ensGene;
>    All Conservation records that have at least 80% overlap with tb_ensGene
> output format: MAF;
> output file:hg17_ens_3UTR_multiz17way.maf
> and then press "get output"button.
>  
> And I want to known this 3'-UTR regions multiz alignments further. And how
> can I plot the conservation plot showed in UCSC genome browser?
>  
> Thank you for you help,
> Ken Hsu
> 
>  
> 
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