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← Primer database

Primer database

STAT3

signal transducer and activator of transcription 3

Homo sapiens

PublicationAghamohammad et al. 2022⇄ Compare with 2 other candidates →

Sequences

Forward (5′→3′)

ACCAGCAGTATAGCCGCTTC

Reverse (5′→3′)

GCCACAATCCGGGCAATCT

Amplicon

124 bp

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix63.664.864.21.2
Primer-BLAST default59.960.860.30.9

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

57.9%

Self-dimer ΔG · Fwd (any position)

-1.5 kcal/mol

Self-dimer ΔG · Fwd (3′ end)

No duplex found

Self-dimer ΔG · Rev (any position)

-3.9 kcal/mol

Self-dimer ΔG · Rev (3′ end)

No duplex found

Heterodimer ΔG (F×R, any position)

-2.1 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

0.7 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

36397951(Europe PMC)

Citation

Aghamohammad et al. 2022

Genomic mapping

Ensembl gene

ENSG00000168610 ↗

NCBI Gene ID

6774

Assembly

GRCh38

Cross-check

✓ENST00000264657★
✓ENST00000678960
✓ENST00000678906
✓ENST00000715205
✓ENST00000677421
✓ENST00000678048
✓ENST00000678674
✓ENST00000678913
✓ENST00000678792
✓ENST00000679166
✓ENST00000677442
✓ENST00000677723
✓ENST00000678043
✓ENST00000679014
✓ENST00000677030
✓ENST00000678572
ENST00000677479
✓ENST00000678905
✓ENST00000679185
✓ENST00000678827
✓ENST00000677002
ENST00000677152
✓ENST00000677603
✓ENST00000585517
✓ENST00000678535
✓ENST00000389272
✓ENST00000588969
✓ENST00000404395
✓ENST00000858552
✓ENST00000858553
✓ENST00000858554
✓ENST00000858555
✓ENST00000858556
✓ENST00000858557
✓ENST00000858558
ENST00000858559
ENST00000858560
✓ENST00000858561
✓ENST00000858562
✓ENST00000922763
✓ENST00000922764
✓ENST00000922765
ENST00000922766
✓ENST00000922767
✓ENST00000922768
✓ENST00000922769
✓ENST00000922770
✓ENST00000943782
✓ENST00000943783
✓ENST00000943784
✓ENST00000943785
✓ENST00000943786
✓ENST00000943787
ENST00000943788
ENST00000943789
✓ENST00000943790
✓ENST00000943791
✓ENST00000943792
✓ENST00000943793
✓ENST00000943794
✓ENST00000943795
✓ENST00000943796
✓ENST00000943797
✓ENST00000943798
✓ENST00000943799
ENST00000943800
✓ENST00000943801
✓ENST00000943802
ENST00000943803
✓ENST00000943804
✓ENST00000943805
✓ENST00000977992
✓ENST00000977996
✓ENST00000977997
✓ENST00001052204
✓ENST00001052205
✓ENST00001052219
✓ENST00001108152
✓ENST00001108153
✓ENST00001134369
~290bpThis 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.118bp148bp47bp~151bpThis 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.145bp99bp96bp82bp95bp152bp159bp93bp60bp~45bpThis 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.~835bpThis 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.~631bpThis 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.99bp~136bpThis 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.53bp~95bpThis 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.140bp~213bpThis 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.43bp~113bpThis 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.~2.5kbThis 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: ENST00000264657 ★

164bp140.1kb151bp22.0kb145bp31.2kb99bp46.3kb96bp5677bp82bp61.0kb95bp7421bp152bp83.7kb159bp9375bp93bp102.3kb60bp111.8kb30bp12221bp94bp13236bp48bp143.3kb84bp151.2kb99bp16349bp136bp171.3kb53bp18364bp95bp19349bp140bp20860bp213bp215.3kb43bp22434bp113bp233.6kb2.5kb24FRPredicted 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.124 bp amplicon · predicted amplicon Tm 84.8 °C
STAT3 · ENST00000264657 (NM_001369512) · canonical✓ Exon-junction spanning · gDNA-safe (>1.0kb intron)

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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