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Can't cope with NCBI Primer BLAST

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#1 Maharisha



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Posted 10 January 2014 - 09:03 AM

Hi everyone!


I've been fighting with Primer Blast for a couple of days already. I'm trying to get primers for RT-PCR for 2 genes. Because of the mRNA template, I'm choosing the option "exon-exon junction spanning" BUT the Primer Blast cannot see any exons in some RefSeq templates although they ARE listed in the reference sequence.



the Claudin 7 gene has 3 transcript variants.

- I enter accession number of the transcript variant 2  ->  here they are, primers specific for all 3 transcript variants, beautifully spanning exon-exon junctions in all 3 transcript variants!

- I enter accession number of the transcript variant 1 or 3  -> "Exon/exon junction cannot be found for submitted PCR template"!


The second gene has only 1 transcript variant and it does not search for primers because also "Exon/exon junction cannot be found for submitted PCR template". Although exons ARE there, I tell you!


I tried other online tools, sometimes they may help but I would really like to have the same algorythm for all genes I need (I'll need primers for more genes in near future)!


I feel solution is somewhere near only I don't see it... perhaps I should just check some option or something like that.


Thanks to anyone who could help me!


UPDATED: I've just repeated the SAME search and it worked! Now I don't understand it at all! Perhaps the tool does not work when it's overloaded with queries? Or it just is frightened by the fact I wrote a complaint here on the forum?))

Edited by Maharisha, 10 January 2014 - 09:14 AM.

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