[Genome] Annotation for a gene

[Brooke Rhead]

Hello Hao,

To visualize the untranslated regions for any gene, type the gene name 
into the "position/search" box in the Genome Browser.  The UTRs are 
represented by the thinner lines on each end of the gene.  More 
information about gene track displays is located here:
http://hgwdev.cse.ucsc.edu/goldenPath/help/hgTracksHelp.html#GeneDisplay

Note that there are several gene annotation tracks, and the annotations 
may differ from one another.  It is up to you to determine which 
annotation track to use.

To obtain the genome coordinates and sequence of the UTRs, click on a 
gene in the gene track you wish to use and look for the genomic sequence 
link.  When you click on it, you will be taken to a page where you can 
select the regions of the gene for which to retrieve sequence.  Select 
the checkboxes for "5' UTR Exons" and "3' UTR Exons", and de-select the 
checkboxes for the other regions.  Also select the option for "One FASTA 
record per region".  When you hit "submit", you should get the genomic 
sequence of the UTRs in FASTA format.  The header for each region should 
include the genomic coordinates of the sequence and look similar to this:

 >hg18_knownGene_uc001jfa.1_0 range=chr10:48036700-48036859 5'pad=0 
3'pad=0 revComp=TRUE strand=- repeatMasking=none

Another way to get this information is with the Table Browser (the 
"Tables" link in the blue bar at the top of the page).  For detailed 
instructions on using the Table Browser, see:

http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

I hope this information is helpful.  Should you have further questions, 
please feel free to contact us again at the genome mailing list address, 
genome at soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Hao Chen wrote:
> Hi there,
> 
> I am trying to find the 5'UTR and 3'UTR of a gene Gdf2. I used to be able to
> do it, but could not figure out how I did it earlier. Could you give me
> instructions on how to find annotation of a gene?
> 
> Thanks!
> Hao
> _______________________________________________
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