★ Founders price. 40% off the first two years of an annual plan started by June 30, 2027, then the standard price. See the plans →
← Primer database

Primer database

PPIA

peptidylprolyl isomerase A

Homo sapiens

PublicationDong et al. 2022

Sequences

Forward (5′→3′)

AGACAAGGTCCCAAAGAC

Reverse (5′→3′)

ACCACCCTGACACATAAA

Amplicon

118 bp

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix57.656.757.20.9
Primer-BLAST default53.652.853.20.8

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

50.0%

GC% · Reverse

44.4%

Self-dimer ΔG · Fwd (any position)

-0.8 kcal/mol

Self-dimer ΔG · Fwd (3′ end)

-0.8 kcal/mol

Self-dimer ΔG · Rev (any position)

0.5 kcal/mol

Self-dimer ΔG · Rev (3′ end)

No duplex found

Heterodimer ΔG (F×R, any position)

-1.3 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

No duplex found

ΔG 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

PMID

36568365(Europe PMC)

Citation

Dong et al. 2022

Genomic mapping

Ensembl gene

ENSG00000196262 ↗

NCBI Gene ID

5478

Assembly

GRCh38

Cross-check

✓ENST00000451562
✓ENST00000489459
✓ENST00000355968
✓ENST00000677107
✓ENST00000468812★
ENST00000620047
✓ENST00000678789
✓ENST00000677022
✓ENST00000678805
✓ENST00000891940
ENST00000915253
ENST00000915254
✓ENST00000915255
✓ENST00000915256
ENST00000915257
ENST00000915258
ENST00000915259
ENST00001079075
✓ENST00001079076
ENST00001104305
ENST00001104306
✓ENST00001104307
✓ENST00001104308
✓ENST00001104309
✓ENST00001104310
ENST00001104311
✓ENST00001104313
✓ENST00001139356
~164bpThis is the outer span across every isoform's exon here. They don't all agree on the exact boundary (alternative splice site), so hover a row's own box below for its real length.158bp~1.1kbThis is the outer span across every isoform's exon here. They don't all agree on the exact boundary (alternative splice site), so hover a row's own box below for its real length.741bp~157bpThis is the outer span across every isoform's exon here. They don't all agree on the exact boundary (alternative splice site), so hover a row's own box below for its real length.342bp~31bpThis is the outer span across every isoform's exon here. They don't all agree on the exact boundary (alternative splice site), so hover a row's own box below for its real length.114bp89bp221bp~310bpThis is the outer span across every isoform's exon here. They don't all agree on the exact boundary (alternative splice site), so hover a row's own box below for its real length.412bp~2.7kbThis is the outer span across every isoform's exon here. They don't all agree on the exact boundary (alternative splice site), so hover a row's own box below for its real length.
exon presentprimer binds hereconfirmed amplicongap = exon skipped~bp = boundary varies
How do I read this diagram?

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: ENST00000451562

164bp12.5kb31bp2114bp89bp3221bp310bp4FRPredicted from the amplicon's own GC%+length (von Ahsen et al. 2001, at the same qPCR buffer as the primer Tm above: 50 mM Na⁺ plus 3 mM Mg²⁺ less 0.8 mM dNTP, as a sodium equivalent), not the SantaLucia model used for primer Tm, which isn't valid at this length. A screening estimate for ranking amplicons — that relation was fitted on oligonucleotide duplexes, so applying it at amplicon length carries more error than its published ±1.9 °C, and it is not a melt-peak prediction.118 bp amplicon · predicted amplicon Tm 83.2 °C
PPIA · ENST00000451562✓ Exon-junction spanning · gDNA-safe by primer design

Off-target specificity

Specific

No 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.

Mean efficiency · Standard curve

1.990

from 1 measurement

Efficiency measurements

Ideal range:Dilution series 1.90–2.10·LinRegPCR 1.70–1.90·unknown method: not scored
EfficiencyR²MethodSourcePCR mixInstrumentAnnealingn
1.99099.0%
—Literature-reportedvia dilution seriesPMID 36568365All-in-One qPCR Mix (GeneCopoeia)Roche LightCycler 480 (Roche Diagnostics, Germany)55 °C3

Using these primers?

Analyse your qPCR run with LinRegPCR efficiency correction and a MIQE 2.0 report.

Analyse your data →