Primer database
cyclin dependent kinase inhibitor 2A
Mus musculus
No official gene symbol for Mus musculus — filed by NCBI/Ensembl as Cdkn2a
Sequences
Forward (5′→3′)
CCGAACTCTTTCGGTCGTACReverse (5′→3′)
AGTTCGAATCTGCACCGTAGTAmplicon
94 bp
Primer Tm (°C)
| Conditions | Forward | Reverse | Average | Δ F/R |
|---|---|---|---|---|
| qPCR master mix | 61.7 | 62.7 | 62.2 | 1.0 |
| Primer-BLAST default | 58.4 | 59.5 | 58.9 | 1.1 |
qPCR master mix: Owczarzy 2004/2008 · 250 nM primer · 50 mM Na⁺ · 3 mM Mg²⁺ · 0.8 mM dNTP
Primer-BLAST default: SantaLucia 1998 salt corr. · 50 nM primer · 50 mM Na⁺ · 1.5 mM Mg²⁺ · 0.6 mM dNTP
Bold, underlined base = 3′ end (polymerase extension point).
Primer QC
GC% · Forward
55.0%GC% · Reverse
47.6%Self-dimer ΔG · Fwd (any position)
-4.3 kcal/molSelf-dimer ΔG · Fwd (3′ end)
-1.6 kcal/molSelf-dimer ΔG · Rev (any position)
-4.8 kcal/molSelf-dimer ΔG · Rev (3′ end)
0.5 kcal/molHeterodimer ΔG (F×R, any position)
-5.2 kcal/molHeterodimer ΔG (F×R, 3′ end)
-0.7 kcal/molΔG at 37 °C · SantaLucia 1998 NN parameters · < −6 kcal/mol = significant dimer risk · "3′ end" is restricted to duplexes anchored at a primer's own 3′ terminal base (polymerase-extendable); "any position" is the most stable duplex anywhere in the primer. Estimated screening value. For comprehensive dimer analysis, validate with Primer3.
Source
Citation
Mendes-Silva et al. 2022Genomic mapping
Each row is one transcript, aligned on a shared axis. A gap means that isoform skips this exonic region. Each row's box is drawn at that isoform's own real exon length, which can be narrower than the column (alternative splice site); hover a box for its exact size. A ~amber header bp means isoforms don't all agree on this region's boundary, while a plain header means they do. Navy blocks mark where the primers bind, and green (with a ✓ by the name) means this isoform has a confirmed working amplicon, not just exon overlap. A row with a “‹ exons” / “exons ›” hint instead of any box means that isoform's exons exist but sit outside the current scroll position (a truncated isoform or alternate transcription start site) — click the hint to jump to them. Click a row to load it below.
★ = Ensembl canonical transcript (reference model, not necessarily the most expressed isoform)
Showing: ENSMUST00000060501 ★
Off-target specificity
SpecificNo paired forward+reverse off-target amplicon found against nt (whole genome/transcriptome). Screen requires >=2 total mismatches including >=2 within the last 5bp at the 3' end to clear a hit (NCBI Primer-BLAST-style stringency); hits with >=6 total mismatches are dropped as implausible.
Efficiency measurements
Ideal range:Dilution series 1.90–2.10·LinRegPCR 1.70–1.90·unknown method: not scoredAnalyse your qPCR run with LinRegPCR efficiency correction and a MIQE 2.0 report.