<p>I have a list of gene symbols. </p>

<blockquote>
  <p>APOB, TTC39B, ATF3, RGS1, LIPG, </p>
</blockquote>

<p>I am trying to get the genomic coordinates (as in bp) with +/-5KB position of these genes via UCSC TableBrowser / MySQL server  using NCBI 36/hg18 build. I have tried to get this information via <a href='http://genome.ucsc.edu/cgi-bin/hgTables'>TableBrowser</a>, but I can't find the chromStart and chromEnd field in the given table. Am I missing something ? </p>

<p>Also, please share your favorite tutorial / docs that explain the schema/tables in UCSC MySQL server. </p>

<p>Thanks in advance. </p>

From [the table browser][1], select group= Genes , track= UCSC gene , table=knownGene and then '**describe table schema**'

You'll see that `knownGene` is linked to `kgXref`:

    hg18.kgXref.kgID (via knownGene.name)

and `kgXref` contains a column named `geneSymbol`.

All in one, you can get the positions of the transcripts for those genes:

    mysql  -h  genome-mysql.cse.ucsc.edu -A -u genome -D hg18 -e 'select distinct X.geneSymbol,G.chrom,G.txStart-5000,G.txEnd+5000 from knownGene as G, kgXref as X where X.geneSymbol in ("APOB", "TTC39B", "ATF3", "RGS1", "LIPG") and X.kgId=G.name'
    +------------+-------+----------------+--------------+
    | geneSymbol | chrom | G.txStart-5000 | G.txEnd+5000 |
    +------------+-------+----------------+--------------+
    | APOB       | chr2  |       21072805 |     21125450 |
    | ATF3       | chr1  |      210843616 |    210865739 |
    | ATF3       | chr1  |      210800319 |    210865739 |
    | ATF3       | chr1  |      210843616 |    210865704 |
    | ATF3       | chr1  |      210849982 |    210864212 |
    | LIPG       | chr18 |       45337424 |     45378276 |
    | LIPG       | chr18 |       45337424 |     45367217 |
    | RGS1       | chr1  |      190806479 |    190820782 |
    | TTC39B     | chr9  |       15156560 |     15302244 |
    | TTC39B     | chr9  |       15156560 |     15227442 |
    | TTC39B     | chr9  |       15171584 |     15302244 |
    | TTC39B     | chr9  |       15172968 |     15268702 |
    | TTC39B     | chr9  |       15172968 |     15227442 |
    +------------+-------+----------------+--------------+

I agree that the information is hard to find: I only knew where to find it because I use to play regularly with those tables.

The **UCSC mailing list** is a good place to find this kind of information.

I also did a lot of reverse engineering by just 'greping' the flat files available from the UCSC.

 [1]: http://genome.ucsc.edu/cgi-bin/hgTables?command=start