Genome Assembly no matches

Question

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I am very new to this and am matching primers to the genome assembly and GENCODE before running PCR. When targeting the "GENCODE Genes" I get a successful output of 170 bp. However, when targeting "genome assembly", I get no matches. What does this mean, and how do you get around this error?

Thank you for your help

[GenoMax]

Are you able to provide example sequences?

Answer 1

[Maximilian Haeussler]

You probably mean "isPCR". If you get a match on the transcripts but not the genome, then your primers probably are designed to do this, to avoid genomic contamination. Check your primers, they probably go over a splice site, they go over two exons, so they will only amplify the transcript, not the genomic DNA. Is that possible?