NCBI Primer designing tool not recognizing exon-exon junction?
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11 months ago
gpreising ▴ 10

I have been trying to design PCR primers that span a splice junction using the NCBI Primer design tool for a gene (NW_005179589.1). It seems like said gene has 4 exons. When I go to pick primers, I select the "Primer must span an exon-exon junction" option, but even when I have everything else on default settings, I get the error message:

"No primers were found...see explanation below: Exon/exon junction cannot be found for submitted PCR template. Try search again without exon/intron requirements."

Am I missing something here? There are several introns in the gene so I'm confused as to why I'm getting this message.

Any help would be appreciated.

gene primer splice junction intron PCR • 753 views
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Which specific gene are you trying to get primers for? The accession number (NW_005179589.1) posted is for a scafold.

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My apologies, I'm looking at neurotensin (nts).

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11 months ago
GenoMax 108k

I was able to get results using XM_005935615.1.

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Oops, I was trying to make primers using the scaffold accession. The mRNA accession works. Thanks!