[Genome] query

[Kayla Smith]

Hello Jamel,

Our Table Browser can be used to retrieve the information you've requested.

First click on the "Tables" button on the blue bar on the top of the 
main page.  Then set the following options:

clade: Vertebrate
genome: Human
assembly: Mar. 2006
group: Genes and Gene Prediction Tracks
track: RefSeq Genes
table: refGene
position: chrX
output format:  sequence

click "get output"

select "genomic" and press "submit".

Here you can choose to extract only exons, and if desired, you can ask 
for bases upstream and downstream of those exons.  You could also select 
to have introns as well.  Finally, you can click the radio button for 
one FASTA record per gene, or the other radio button for one FASTA 
record per exon.

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group



Chelly Jamel wrote:
> Dear Colleague,
> I am an extensive user of the UCSC genome browser 
> and data base, and I would like to know if there 
> is an automatic way (I mean not by analyzing 
> "manually" gene by gene) to obtain a file with 
> only exonic and their flanking intronic sequences 
> and their position in the genome. For example a 
> file with exonic sequences (and their intronic 
> sequences) of all genes (refseq) on  the X 
> chromosome. Of course, this file could be 
> constructed by analyzing manually each individual 
> gene, but such approach would take days and 
> days...
> 
> Thank you in advance for your valuable help,
> With my best regards
> Jamel Chelly