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how to check for intron-exon junctions

primer sequence

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#1 moljul



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Posted 27 October 2015 - 07:00 AM

Can anyone of you tell me how to check, if primers we are currently using, span intron-exon junctions? There is some application on pubmed/NCBI, but I can not remember in detail.


Thank you in advance!!

#2 Rosewater



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Posted 27 October 2015 - 04:27 PM

You can find the nucleotide sequence on your gene on http://www.ncbi.nlm.nih.gov/nuccore/.  The files starting with "NM_" will indicate the location where two exons join.  If your primers align with the cDNA (by BlastN), you can assume they don't contain and intron DNA.  If the primers align with the genomic copy of the gene, but not the cDNA, then they may contain some untranslated region (intron) sequence.

#3 Trof


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Posted 07 November 2015 - 10:56 AM

Also PrimerBLAST will show positions of exons and exon-spanning, if you input an accession number (NM_...) as a template.

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