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Primer database

Col3a1

collagen, type III, alpha 1

Mus musculus

PublicationJiang et al. 2024⇄ Compare with 3 other candidates →

Sequences

Forward (5′→3′)

GAGGAATGGGTGGCTATCCG

Reverse (5′→3′)

TCGTCCAGGTCTTCCTGACT

Amplicon

215 bp

estimated from mapping

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix64.063.963.90.1
Primer-BLAST default60.059.959.90.1

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

60.0%

GC% · Reverse

55.0%

Self-dimer ΔG · Fwd (any position)

-1.1 kcal/mol

Self-dimer ΔG · Fwd (3′ end)

-0.2 kcal/mol

Self-dimer ΔG · Rev (any position)

-2.6 kcal/mol

Self-dimer ΔG · Rev (3′ end)

0.7 kcal/mol

Heterodimer ΔG (F×R, any position)

-3.4 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

-0.2 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

39916997(Europe PMC)

Citation

Jiang et al. 2024

Genomic mapping

Ensembl gene

ENSMUSG00000026043 ↗

NCBI Gene ID

12825

Assembly

GRCm39

Cross-check

✓ENSMUST00000087883★
ENSMUST00000185687
ENSMUST00000186021
✓ENSMUST00000387672
✓ENSMUST00000387673
✓ENSMUST00000387675
✓ENSMUST00000387676
✓ENSMUST00000387679
✓ENSMUST00000387681
✓ENSMUST00000387683
✓ENSMUST00000387684
✓ENSMUST00000387685
✓ENSMUST00000387686
✓ENSMUST00000387691
✓ENSMUST00000387692
✓ENSMUST00000387693
✓ENSMUST00000387694
✓ENSMUST00000387695
✓ENSMUST00000387697
✓ENSMUST00000387698
✓ENSMUST00000387699
✓ENSMUST00000387700
✓ENSMUST00000387701
✓ENSMUST00000387702
✓ENSMUST00000387703
✓ENSMUST00000387704
✓ENSMUST00000387705
✓ENSMUST00000387707
ENSMUST00000387708
✓ENSMUST00000387709
✓ENSMUST00000387710
✓ENSMUST00000387711
ENSMUST00000387712
✓ENSMUST00000387713
✓ENSMUST00000387714
✓ENSMUST00000387715
✓ENSMUST00000387716
✓ENSMUST00000387719
✓ENSMUST00000387720
✓ENSMUST00000387721
✓ENSMUST00000387723
✓ENSMUST00000387724
✓ENSMUST00000387725
✓ENSMUST00000387726
✓ENSMUST00000387727
295bp9.7kb~200bpThis 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.245bp51bp413bp114bp1.2kb~75bpThis 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.1.6kb54bp391bp54bp712bp54bp964bp54bp167bp54bp569bp~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.390bp45bp131bp54bp996bp45bp407bp54bp497bp99bp312bp45bp116bp99bp196bp54bp108bp108bp722bp54bp544bp99bp345bp~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.153bp99bp284bp~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.110bp~81bpThis 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.293bp54bp539bp~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.878bp~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.536bp99bp86bp~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.424bp54bp562bp54bp82bp~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.595bp~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.461bp~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.273bp~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.321bp~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.182bp162bp110bp~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.877bp108bp1.0kb54bp84bp108bp464bp54bp439bp~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.230bp~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.101bp~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.788bp~295bpThis 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.977bp~188bpThis 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.328bp~247bpThis 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.718bp~1.3kbThis 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.6.6kb208bp
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: ENSMUST00000087883 ★

295bp19.7kb200bp2245bp51bp3413bp114bp41.2kb75bp51.6kb54bp6391bp54bp7712bp54bp8964bp54bp9167bp54bp10569bp54bp11390bp45bp12131bp54bp13996bp45bp14407bp54bp15497bp99bp16312bp45bp17116bp99bp18196bp54bp19108bp108bp20722bp54bp21544bp99bp22345bp54bp23153bp99bp24284bp54bp25110bp54bp26320bp54bp27539bp54bp28878bp45bp29536bp99bp3086bp108bp31424bp54bp32562bp54bp3382bp54bp34595bp54bp35461bp108bp36273bp54bp37321bp54bp38182bp162bp39110bp108bp40877bp108bp411.0kb54bp4284bp108bp43464bp54bp44439bp108bp45230bp54bp46101bp108bp47788bp295bp48977bp188bp49328bp243bp50722bp1.1kb51FRPredicted 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.215 bp amplicon · predicted amplicon Tm 92.5 °C
Col3a1 · ENSMUST00000087883 (NM_009930) · 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.

Using these primers?

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