Agreed with the above commentator
Primer BLAST is my program of choice especially when trying to design isoform specific primers
2 other sites that are useful, and more direct than Primer BLAST are IDTs primer quest tool which is specifically for designing qPCR (Exon junction) primers and an equivalent facility by Roche:
http://www.idtdna.com/primerquest/home/index
https://lifescience.roche.com/webapp/wcs/stores/servlet/CategoryDisplay?tab=Assay+Design+Center&identifier=Universal+Probe+Library&langId=-1
Both of these packages allow you to input the NCBI Ref sequence (as a FASTA) file or simply the BCBI Ref Se accession number and will return forward and reverse primers embedded in the Ref seq file
Also, with ref to another answer provided by Karen Reece:
Any of these are nice:
Primer3 - http://primer3.sourceforge.net/
Primer-BLAST - http://www.ncbi.nlm.nih.gov/tools/primer-blast/
IDT PrimerQuest - http://www.idtdna.com/Scitools/Applications/Primerquest/
Primer Bank - http://pga.mgh.harvard.edu/primerbank/
RTPrimerDB - http://medgen.ugent.be/rtprimerdb
Real-time PCR primer designing software? - ResearchGate. Available from: https://www.researchgate.net/post/Real-time_PCR_primer_designing_software/1 [accessed Apr 28, 2016].
I have used all such packages and they are excellent
Find attached 2 x SOPs detailing how to use primer BLAST to access NCBI Ref sequence and then make primers and an equivalent SOP for IDT primer quest
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