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NCBI Primer designing tool not recognizing exon-exon junction?

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
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written by gpreising • gpreising

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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written by GenoMax GenoMax

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

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written by gpreising • gpreising

1 answer

I was able to get results using XM_005935615.1.

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written by GenoMax GenoMax

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

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written by gpreising • gpreising

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