GeneExplorer - design gene specific PCR primers!

The tool directly queries the ENSEMBL core database to find all annotated transcripts of a gene and merges them together into one virtual gene. Subsequently all amplicons catching PCR primer pairs and internal primers are designed by Primer3plus (help).

Use the Span Exons feature to catch many exons in one fragment and Split Exons to split large Exons into many fragments.

Tip for Microsoft Word user: You can transfer the output to Word with all format information by using Microsoft Internet Explorer and copy/paste!

Ensemble settings


Gene Symbol or ENSEMBL-ID

GeneExplorer settings

Span CDS (3-4, 7-9, ...)

Split CDS (1+2, 4+3, ...)

Choose amplicons (1,5,6 ...)

CDS flanking region

Primer design buffer

Show SNPs

Amplicons for CDS

Amplicons for UTR

Primer3plus settings

Mispriming library

CG Clamp

Max Poly-X

Primer Size Min

Primer Size Opt

Primer Size Max

Primer Tm Min

Primer Tm Opt

Primer Tm Max