[Genome] Obtaining Chromosome position from an Accession Number ID list

[Kayla Smith]

Carlos,

I'll walk you through how to get exactly what you're looking for.  Since I 
don't know which genes you're looking at, I'll make a sample list:

(some refSeqs)
NM_004045
NM_021987

(some ESTs)
BF090527
BF332306
BE147074

Copy the refSeq identifiers.

Go to the Table Browser and select the following options:

clade: Vertebrate
genome: Human
assembly: Mar.2006
group: Genes and Gene Prediction Tracks
track: RefSeq Genes
table: refGene
region: genome

identifiers: click on "paste list" and paste the refSeq identifiers.
Press "submit" to return to the Table Browser.

output format: "selected fields from primary and related tables"

click on "get output"

You will now be prompted for which columns you want displayed.  I believe 
you are interested in "name", "chrom", "txStart" and "txEnd".  Please 
check the corresponding boxes then click "get output".

Your results will be the two refSeq genes followed by the chromosome they 
are on, and their position on that chromosome.


Likewise for the ESTs, change the settings in the table browser to:

clade: Vertebrate
genome: Human
assembly: Mar.2006
group: mRNA and EST Tracks
track: Human ESTs
table: all_est
region: genome

identifiers: click on "paste list" and paste the list of EST identifiers.
Press 'submit' to return to the Table Browser.
output format: "selected fields from primary and related tables"
click on "get output"

You will now be prompted for which columns you want displayed.  I believe 
you are interested in "qName", "tName", "tStart" and "tEnd".  Please check 
the corresponding boxes then click "get output".

Your results will be the three ESTs followed by the chromosome they are 
on, and their position on that chromosome.

I hope this helps to answer your question.  If you are still having 
trouble with the table browser, please do not hesitate to contact us again 
for more assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


On Wed, 12 Jul 2006, Carlos Plasencia wrote:

> Hi,
>
> I have a large list of Genes identified by Accession Number. The list contains RefSeq, and ESTs genes. I want to get the chromosome coordinates for all my genes. I have used the table browser for other purposes, but I couldn´t get in the list the original identifier, then the table obtained is very complicated to use.
>
>
> Best regards.
>
>
> ---------------------------------
> Yahoo! Music Unlimited - Access over 1 million songs.Try it free.
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>

-- 
Kayla Smith
UCSC Genome Bioinformatics Group