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qPCR · Primer3 · RefSeq mRNA · Exon-junction-aware

qPCR Primer Designer

Type a gene name — get ready-to-order qPCR primers in seconds. We fetch the RefSeq mRNA and design with Primer3 (Tm ≈ 60 °C, 70–200 bp), ranking exon-junction-spanning pairs first so genomic-DNA contamination won't amplify. Every pair has a one-click UCSC In-Silico PCR verify link. Human & mouse. No sequence pasting.

Gene symbol
Organism
How it works & how to read the results ▼

Pipeline: your gene → its RefSeq mRNA (via mygene.info) → sequence + exon map from NCBI → Primer3 designs candidate pairs over the transcript. Nothing is pre-canned — primers are generated fresh for the current reference transcript.

Exon-junction badge: EXON-JUNCTION = a primer sits directly on an exon–exon boundary (gold standard — it cannot bind genomic DNA). SPANS INTRON = the amplicon crosses a junction, so genomic DNA would give a larger product. Pairs with these properties are ranked first.

Defaults: Tm ≈ 60 °C (±2), length 18–25 nt, GC 40–60 %, GC-clamp, amplicon 70–200 bp — standard SYBR-Green qPCR settings.

Always verify: hit UCSC In-Silico PCR ↗ on any pair to confirm it amplifies a single, correct product against the genome before you order. Then grab the order CSV for IDT / Sigma bulk entry.

Primers designed on-the-fly with primer3-py over NCBI RefSeq mRNA; gene resolution via mygene.info. Exon junctions parsed from the RefSeq GenBank record. Results are a starting point — always validate specificity (UCSC In-Silico PCR) and efficiency (standard curve) before publishing. Built by Bharat Prajapati · free, no login.

🧺 Primer Bucket