[Genome] get the sequnence by using an Ensembl gene ID

[Archana Thakkapallayil]

Hello Yu,

Unfortunately, you cannot retrieve sequence using our MySql server 
because the sequence is not stored in database tables. One way to do 
this is by clicking on the gene alignment in the Browser and and then on 
the details page looking for the "Sequence" section and then clicking on 
the Genomic sequence link there. This will give you the option to get 
introns and UTR. But, you will have to do this individually for each gene.

Inorder to get this information for many genes, the more efficient way 
is to use the Table Browser. More information on using the Table Browser 
is here:
http://www.genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

I hope this is helpful to you. Please feel free to write back if you 
need more instruction.

Regards,

Archana
UCSC genome Bioinformatics Group


Yu Zhou wrote:
> Hi,
>
> If I know the Ensembl gene ID of a gene, how can I get the sequence (5'UTR,
> exons, introns, 3'UTR) of the gene by using a SQL query to the database?
> Because I have many genes to query and to do further processing, I would not
> use the Table Browser which is very good!
>
> I know connect to the database, but I don't know exactly the relationships
> between the tables. Could you tell me how to write the SQL clause to do
> that?
>
>
>