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i have designed primers for HLA locus DPA1(exon 2 region) based on Real-Time PCR (qPCR) Primer Design guidelines. primer will start from intron regions to cover full exonic region.

F-CAGCAACAGAGAATGTCAGC

R-CCCTGAAGCAGCAATTGATG

to check for amplification of only a single region i have used in silico PCR UCSC but it shows multiple region from chr6.

pls kindly help me with solving this.

thanks

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    $\begingroup$ Well the obvious solution is to redesign new primers that anneal elsewhere in the introns. Is it other HLA genes that are being amplified? Presumably you've hit a conserved region. $\endgroup$
    – canadianer
    Commented Mar 2, 2015 at 4:56

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When designing rtPCR primers always check the extensive and well validated taqman library for the ABI system, the primers for the region you want are already well characterized:

http://www.lifetechnologies.com/order/genome-database/details/gene-expression/Hs01072897_m1#more-information-section

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