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:
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: