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← Primer database

Primer database

Col1a1

collagen, type I, alpha 1

Mus musculus

PublicationSun et al. 2025⇄ Compare with 3 other candidates →

Sequences

Forward (5′→3′)

CTGACTGGAAGAGCGGAGAG

Reverse (5′→3′)

ACATTAGGCGCAGGAAGGTC

Amplicon

276 bp

estimated from mapping

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix63.463.963.60.5
Primer-BLAST default59.560.159.80.6

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

60.0%

GC% · Reverse

55.0%

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)

-4.7 kcal/mol

Self-dimer ΔG · Rev (3′ end)

0.7 kcal/mol

Heterodimer ΔG (F×R, any position)

-2.5 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

-0.8 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

39898320(Europe PMC)

Citation

Sun et al. 2025

Genomic mapping

Ensembl gene

ENSMUSG00000001506 ↗

NCBI Gene ID

12842

Assembly

GRCm39

Cross-check

✓ENSMUST00000001547★
✓ENSMUST00000430346
✓ENSMUST00000430349
ENSMUST00000430350
✓ENSMUST00000430351
✓ENSMUST00000430352
✓ENSMUST00000430353
✓ENSMUST00000430354
ENSMUST00000430355
✓ENSMUST00000430357
✓ENSMUST00000430358
✓ENSMUST00000430359
✓ENSMUST00000430360
✓ENSMUST00000430361
✓ENSMUST00000430362
✓ENSMUST00000430363
✓ENSMUST00000430364
✓ENSMUST00000430365
✓ENSMUST00000430366
✓ENSMUST00000430367
221bp1.5kb~195bpThis 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.122bp~32bpThis 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.119bp36bp90bp102bp785bp~69bpThis 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.237bp45bp162bp54bp160bp54bp373bp54bp119bp54bp330bp54bp81bp45bp98bp54bp113bp45bp136bp54bp234bp99bp89bp45bp93bp99bp119bp54bp181bp108bp103bp54bp283bp99bp148bp54bp89bp~103bpThis 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.519bp~54bpThis 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.189bp54bp100bp54bp108bp54bp400bp45bp87bp99bp212bp108bp356bp~108bpThis 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.191bp54bp148bp~54bpThis 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.244bp108bp88bp54bp110bp54bp130bp~162bpThis 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.103bp~108bpThis 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.341bp108bp103bp54bp109bp~108bpThis 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.367bp54bp121bp108bp256bp54bp323bp108bp86bp283bp135bp~191bpThis 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.201bp~243bpThis 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.129bp~1.6kbThis 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: ENSMUST00000001547 ★

221bp11.5kb195bp2122bp32bp3119bp36bp490bp102bp5785bp69bp6237bp45bp7162bp54bp8160bp54bp9373bp54bp10119bp54bp11330bp54bp1281bp45bp1398bp54bp14113bp45bp15136bp54bp16234bp99bp1789bp45bp1893bp99bp19119bp54bp20181bp108bp21103bp54bp22283bp99bp23148bp54bp2489bp99bp25523bp54bp26189bp54bp27100bp54bp28108bp54bp29400bp45bp3087bp99bp31212bp108bp32356bp108bp33191bp54bp34148bp54bp35244bp108bp3688bp54bp37110bp54bp38130bp162bp39103bp108bp40341bp108bp41103bp54bp42109bp108bp43367bp54bp44121bp108bp45256bp54bp46323bp108bp4786bp283bp48135bp191bp49201bp243bp50129bp1.6kb51FRPredicted 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.276 bp amplicon · predicted amplicon Tm 90.8 °C
Col1a1 · ENSMUST00000001547 (NM_007742) · canonical✓ 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.

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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