Written and maintained by CASRAI Editorial Board
Last updated
Short answer: PrimerBank is a public database of PCR primer pairs for detecting and quantifying gene expression by real-time PCR, run from Harvard-affiliated Massachusetts General Hospital (pga.mgh.harvard.edu/primerbank). It covers human and mouse genes. It is a primer database, not a bank and not an NCBI resource; searches for “primer bank” are shared with Premier Bank credit-card pages.
This guide is general reference for researchers and lab staff. It describes what the database states about itself and what its validation figure does and does not tell you before you order oligonucleotides.
What PrimerBank is
PrimerBank is a resource of pre-designed primer pairs, built for gene expression detection and quantification by real-time PCR. Its home page states that it “contains over 306,800 primers covering most known human and mouse genes” (read 2026-11-08). That home page text is older than the database’s 2012 update paper (Wang X, Spandidos A, Wang H, Seed B. Nucleic Acids Research 2012;40(D1):D1144-D1149), which reports 497,156 primers after adding primers for 17,076 human and 18,086 mouse genes, and describes coverage of about 94% of known protein-coding genes using current NCBI annotation. The two counts differ because the site text predates the update, so cite the paper, not the home page, when you report coverage.
How to search it
According to the PrimerBank search page, you can look up primers by GenBank accession, NCBI protein accession, Gene ID, PrimerBank ID, gene symbol or keyword, filter by species (human or mouse), or BLAST your own sequence against the PrimerBank sequence database. Each result page links to the primer details; for mouse primers, it links to the validation data.
What the 82.6% validation figure means
PrimerBank reports an experimental test of 26,855 primer pairs for 27,681 mouse genes, using real-time PCR, agarose gel electrophoresis and sequencing of the product. It states that the “design success rate is 82.6% (22,187 successful primer pairs) based on agarose gel electrophoresis.”
| Question | What the PrimerBank page states |
|---|---|
| Which species were tested? | Mouse. The page presents mouse validation data on each primer page; it does not describe an equivalent human validation. |
| What counted as success? | A result judged by agarose gel electrophoresis, as the 82.6% wording says. |
| Is that the same as qPCR efficiency? | No. A clean gel band shows a product of the expected kind was made; it is not a measured amplification efficiency or a melt-curve result for your cDNA and instrument. |
| Does it cover every primer? | No. 26,855 pairs were tested, out of hundreds of thousands in the database. |
The practical reading, which is an editorial interpretation rather than a PrimerBank claim: a PrimerBank pair is a well-designed starting point, and the validation figure should not replace your own check on your template.
A pre-order checklist tied to what is stated
- Check the gene and transcript. The 2012 paper states that the shortest transcript per gene was chosen; confirm the primers fall in the isoform you intend to measure, using an accession such as those described in NCBI RefSeq.
- Re-check specificity yourself. Run the pair through a specificity tool such as NCBI BLAST for primers or in silico PCR, because annotations change after a database is built.
- Inspect thermodynamics. Look at melting temperature and secondary structure with a tool such as OligoAnalyzer.
- Plan your own validation. Confirm product identity (gel and/or melt curve) in your system, since the published success figure is a gel result from mouse genes.
- Cite the right paper. The PrimerBank page lists these citations: Wang and Seed, Nucleic Acids Research 2003;31(24):e154; Spandidos et al., BMC Genomics 2008;9:633; Spandidos et al., Nucleic Acids Research 2010;38:D792-D799; and Wang et al., Nucleic Acids Research 2012;40(D1):D1144-D1149.
Related primer databases
Several resources share the “primer bank” name or purpose. The table lists scope only, as stated by each resource.
| Resource | Scope as stated by the resource |
|---|---|
| PrimerBank (pga.mgh.harvard.edu/primerbank) | Human and mouse primers for real-time PCR gene expression |
| FlyPrimerBank (flyrnai.org/flyprimerbank) | Drosophila melanogaster primers from DRSC/TRiP at Harvard; searchable by gene or primer ID, file upload or BLAST of a sequence; can check overlap with RNAi collections (DRSC amplicons, TRiP VALIUM1/10, NIG-Fly, VDRC GD/KK); has a feedback form for problem primers. Method paper: Hu et al. 2013, PubMed 23893746. |
| qPrimerDB (qprimerdb.biodb.org) | A resource for real-time quantitative PCR primers |
Other resources named in the literature on qPCR primer databases include qPrimerDepot, GETPrime and ChIPprimersDB. For designing new primers instead of retrieving existing ones, see Primer3 and how to choose primers for PCR.
Common misunderstandings
- “Primer bank” is not a financial bank. Credit-card and banking results use the similar phrase “Premier Bank”; they are unrelated.
- It is not an NCBI database. It is hosted at Massachusetts General Hospital’s pga.mgh.harvard.edu site. It uses NCBI annotation and accessions as search keys.
- It is not limited to mouse. Mouse is where validation data is shown; the database covers human and mouse genes.
- The home page count is not the current count. See the 2012 paper above.
FAQ
Is PrimerBank the same as the NCBI primer tool?
No. PrimerBank retrieves pre-designed primers from a Harvard-affiliated database. NCBI’s Primer-BLAST designs and checks primers against NCBI databases. Using both is a normal workflow: retrieve from PrimerBank, then confirm specificity.
Is there a PrimerBank for fruit flies?
Yes. FlyPrimerBank covers Drosophila melanogaster; see the table above.
What is the difference between Primer3 and Primer-BLAST?
Primer3 is the primer-design engine; Primer-BLAST combines primer design with a BLAST specificity check. Neither is a database of pre-made pairs. See our Primer3 guide.
Sources
- PrimerBank home page, Massachusetts General Hospital: https://pga.mgh.harvard.edu/primerbank/ (read 2026-11-08)
- FlyPrimerBank, DRSC/TRiP: https://www.flyrnai.org/flyprimerbank (read 2026-11-08)
- Wang X, Spandidos A, Wang H, Seed B. PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. Nucleic Acids Res 2012;40(D1):D1144-D1149. doi:10.1093/nar/gkr1013 (PubMed 22086960)
- Hu et al. 2013, FlyPrimerBank method paper (PubMed 23893746)
