I am interested in designing primers to determine amplification or deletion of my gene in the genome. On e-PCR (NCBI) I get results in my "genomic section" of the same species I am interested in. Now most of these seem to locate to the same chromosome, however, I was wondering how I determine whether they are infact of my gene of interest, or other genes targeted by my PCR primer set. It does not show any results in the "cross-references" section that is not the orginal gene of interest.

However, I do have another gene that does show "cross-reference" to another gene in all primers designed by e-PCR. What would be an appropriate methodology for designing primers for this gene. Thank you.

I would suggest that you go for primer design that is specific to your gene and avoids other genes in your chromosome. Use AlleleID or Beacon Designer software. They automatically interpret the homology with a database (that you have to specify). You can also create a custom database by downloading all the sequences in your chromosome locally and then BLASTing using Beacon Designer. The algorithm of the software will avoid regions that are similar between your gene and other genes.

Set it up first and then ask for a trial to the Bioinformatics company
that authors the software. Here is a direct link to Beacon Designer website
http://www.premierbiosoft.com/molecular_beacons/index.html

the software price is a bit steep at $2585. You can ask them if they will design these sort of primers for you. They do IMO.