PCR Primer Design Related

Question

[Bhavya]

Hello

I was in the process of designing PCR primers.

On the Exon 3----(2326..2824)= 499 bp .........of Human SERPING1 gene

I used this sequence (downloaded from NCBI [https://www.ncbi.nlm.nih.gov/nuccore/NG_009625.1?from=5001&to=22300&report=genbank]) for primer designing

I used NCBI-Primer Blast to design primers on this sequence.

Now I am trying to confirm from UCSC-in-silico PCR for these primer sets. I am not getting any results.

Has anybody faced this kind of problem?

Thanks, and Regards

Bhavya

Answer 1

[GenoMax]

Here is the sequence I tried (this should be exon 3)

>NC_000011.10:57599879-57600377 Homo sapiens chromosome 11, GRCh38.p14 Primary Assembly
GATAGAGCCTCCTCAAATCCAAATGCTACCAGCTCCAGCTCCCAGGATCCAGAGAGTTTGCAAGACAGAG
GCGAAGGGAAGGTCGCAACAACAGTTATCTCCAAGATGCTATTCGTTGAACCCATCCTGGAGGTTTCCAG
CTTGCCGACAACCAACTCAACAACCAATTCAGCCACCAAAATAACAGCTAATACCACTGATGAACCCACC
ACACAACCCACCACAGAGCCCACCACCCAACCCACCATCCAACCCACCCAACCAACTACCCAGCTCCCAA
CAGATTCTCCTACCCAGCCCACTACTGGGTCCTTCTGCCCAGGACCTGTTACTCTCTGCTCTGACTTGGA
GAGTCATTCAACAGAGGCCGTGTTGGGGGATGCTTTGGTAGATTTCTCCCTGAAGCTCTACCACGCCTTC
TCAGCAATGAAGAAGGTGGAGACCAACATGGCCTTTTCCCCATTCAGCATCGCCAGCCTCCTTACCCAGG
TCCTGCTCG

I got a set of primers from Primer blast. When I try one of the primer sets (that gives a long product) in in-silico PCR tool at UCSC I get a result