[Genome] from EST to Gene

[Ann Zweig]

Hello Xi,

	If you have several GenBank accessions, it's easiest to use the Table 
Browser tool to find the corresponding Ref Seq ID.  Press 'Tables' from 
the top blue navigation bar.  Read more about using the Table Browser 
here:  http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

	I'll walk you through using an example of one GenBank accession: BC028629.

- Set up the Table Browser like so:
group: mRNA and EST Tracks
track: Human mRNAs
table: all_mrna
region: genome

- identifiers (paste your list here (in this case: BC028629))

- output format: selected fields from primary and related tables

- press 'get output'

On the next page, you will join the all_mrna table with the mrnaRefSeq 
table.  The mrnaRefSeq table contains the cross-referenced information 
you are looking for: mRNA accessions <--> RefSeq IDs.

Configure this page so that you choose the following fields from the two 
tables:

all_mrna.qName
mrnaRefseq.mrna
mrnaRefseq.refseq

- press 'get output'.
In this example, the output will look like this:

#hg18.all_mrna.qName	hg18.mrnaRefseq.mrna	hg18.mrnaRefseq.refseq
BC028629	BC028629	NM_000808

	I hope this information is helpful to you.  Please don't hesitate to 
contact the mail list again if you require further assistance.

Regards,

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

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Xi Wang wrote:
> Hi,
> 
> I've got a problem as follows:
> if I have a EST query name or Genbank/EMBL accession, how can I get the Gene Symbol Name or Refseq ID which the EST located?
> 
> Thanks!
> 
> Best wishes,
> Xi
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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