Locating Genomic Location of qPCR Primers

[Flynn, Robert]

To whom it may concern, 

Do you know if it is possible to locate the genomic location of qPCR primers on UCSC genome browser? As they are complementary to cDNA, I would imagine I would need to query an mRNA refseq library? 

Many thanks for your help, 

Rob. 

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You may be interested in using the link to exonPrimer available from the details page for an item on the knownGene track.

GENCODE V41 for hg38
UCSC Genes for hg19

There is also the external tool, Primer3Plus, from NCBI that you can access from the blue navigation bar "View --> External Tools".

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro

UCSC Genome Browser

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[Flynn, Robert]

Hi Jairo, 

Thank you for your help. I have attempted to query UCSC genome browser for my 20nt primer sequence with Gencode V41 set to pack and NCBI RefSeq set to pack (everything else on hide). However, I still get the error message under Human hg38 BLAT results: "Sorry, no matches found (with a score of at least 20)."

Secondly, the link to Primer3Plus under the view menu is greyed out and appears to be unavailable. 

Many thanks again, 

Rob. 

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From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: 12 October 2022 18:25
To: Flynn, Robert <robert....@ucl.ac.uk>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Locating Genomic Location of qPCR Primers

 

⚠ Caution: External sender

[Galt Barber]

In addition to BLAT,  UCSC In-Silico PCR searches are available, and for human and mouse the option of searching genes instead of DNA so that it can find things broken up by introns better.  Select genes under target dropdown.

https://genome.ucsc.edu/cgi-bin/hgPcr

If PCR cannot find it, it might be because it has highly repetitive sequence in a short query.

And usually those do not make great primer sequences anyways.

Galt

Ar Luan 17 DFómh 2022 ag 09:30, scríobh Flynn, Robert <robert....@ucl.ac.uk>:

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