qPrimerDB Plants
v1.0A comprehensive qPCR primer database for medicinal plants
A comprehensive qPCR primer database for medicinal plants
qPrimerDB Plants is a dedicated qPCR primer database for medicinal plants. We pre-designed thermodynamically optimized primer pairs for all coding genes across 459 species using Primer3, with rigorous quality filters (Tm 57–63°C, GC 40–60%, amplicon 70–200 bp).
Uniquely, we integrate KEGG metabolic pathway annotations for 51 traditional Chinese medicine species, enabling researchers to search primers by biological function — not just gene ID.
Browse Primers — Search by species name or gene ID to retrieve optimized primer pairs.
Download — Export complete primer datasets per species in CSV format.
Pathways — Explore genes organized by KEGG secondary metabolite pathways (phenylpropanoids, flavonoids, terpenoids, alkaloids).
| Category | Metric | Description |
|---|---|---|
| Species | 459 | Medicinal and related plant species from IMP database |
| Genes | 27.5 M | Total coding sequences processed |
| Primer pairs | 81,840,120 | 3 pairs per gene, ranked by Primer3 quality score |
| Pathway annotations | 1,315,346 | Gene-pathway associations across 24 KEGG pathways |
| Primer length | 18–25 bp | Optimal for standard qPCR conditions |
| Tm range | 57–63 °C | Forward/Reverse Tm difference ≤ 2°C |
| Amplicon size | 70–200 bp | Ideal for SYBR Green-based detection |
All 459 species · Click to download complete primer dataset in CSV format
| Species | Genes | Primer Pairs | Avg Tm | Download |
|---|---|---|---|---|
| Loading species list... | ||||
Click a species to expand → click a pathway to see genes → click to view primer details
Loading pathway data...
Browse Primers: Enter a species scientific name to list all primers, or add a gene ID to see the 3 best pairs with thermodynamic data.
Download: Filter by species and download the complete CSV file with all primer pairs and metadata.
Pathways: Navigate the four-level hierarchy: Species → Pathway → Genes → Primers.
If you use qPrimerDB Plants in your research, please cite our paper (under review).
Primer3 v2.3.0 · Tm 57–63°C · GC 40–60% · Amplicon 70–200 bp · KEGG pathway annotation · IMP genome data (bic.ac.cn)
Hubei University of Chinese Medicine
School of Pharmacy
suwei123@hbu.edu.cn