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To use the Primer3, open a DNA sequence and select the Analyze ‣ Primer3... context menu item. The dialog will appear:
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All available parameters are the same as in the original Primer3.
However there is one additional option feature available which allows to design primer for RTPCR experiments and allows setting is not originally a part of Primer3 tool. It allows user design primers for RT-PCR experiments by choosing which exons/introns to span with the primer product. This feature is described below.
RTPCR primer design
This feature allows to span corresponding intron sequences on the genomic sequence or junction sequences between exons.
Overview
Note: ths feature is only available for mRNA/cDNA sequences with annotated exons. There are several ways to obtain the cDNA for a corresponding DNA sequence.
- From NCBI or ENSEMBLE database
- Align the genomic and cDNA sequences using spliced aligner
Options
Exon annotation name
Span exon-exon junction
Exon range
Span at least one intron: the default mode
in detailed below. When you select the parameters you can save and load settings with a help of the corresponding buttons in the right corner of the dialog.
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