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← Primer database

Primer database

PPP2R1B

protein phosphatase 2 scaffold subunit Abeta

Homo sapiens

PublicationWeng et al. 2023

Sequences

Forward (5′→3′)

AGTCTCTCCTTCCTGCCATAG

Reverse (5′→3′)

CACGAGCCAAGCCATACATAA

Amplicon

152 bp

estimated from mapping

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix62.161.761.90.4
Primer-BLAST default58.358.458.40.1

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

52.4%

GC% · Reverse

47.6%

Self-dimer ΔG · Fwd (any position)

-0.3 kcal/mol

Self-dimer ΔG · Fwd (3′ end)

0.7 kcal/mol

Self-dimer ΔG · Rev (any position)

-0.3 kcal/mol

Self-dimer ΔG · Rev (3′ end)

No duplex found

Heterodimer ΔG (F×R, any position)

-0.7 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

1.0 kcal/mol

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

36760798(Europe PMC)

Citation

Weng et al. 2023

Genomic mapping

Ensembl gene

ENSG00000137713 ↗

NCBI Gene ID

5519

Assembly

GRCh38

Cross-check

ENST00000531890
ENST00000531373
ENST00000876845
✓ENST00000311129
✓ENST00000426998
✓ENST00000527614★
✓ENST00000341980
✓ENST00000393055
✓ENST00000876846
✓ENST00000876847
✓ENST00000876848
✓ENST00000876849
✓ENST00000925452
✓ENST00000925453
✓ENST00000925454
✓ENST00000925455
✓ENST00000925456
✓ENST00000996481
✓ENST00000996482
✓ENST00000996483
✓ENST00001113869
✓ENST00001113870
✓ENST00001113871
✓ENST00001144531
~466bpThis 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.265bp91bp101bp~233bpThis 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.~148bpThis 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.156bp~115bpThis 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.71bp135bp174bp~3.0kbThis 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.~812bpThis 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.143bp~92bpThis 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.~3.7kbThis 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.~836bpThis 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.150bp
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: ENST00000531890

59bp1538bp71bp21.1kb135bp31.4kb174bp49.8kb143bp5607bp88bp6F
PPP2R1B · ENST00000531890No amplicon found on this isoform (exon_only / intron_only)

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.

Efficiency measurements

Ideal range:Dilution series 1.90–2.10·LinRegPCR 1.70–1.90·unknown method: not scored
No measurements yet for this primer pair.

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