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← Primer database

Primer database

Gpi1

glucose-6-phosphate isomerase 1

Mus musculus

PublicationNoland et al. 2025

Sequences

Forward (5′→3′)

TCACTGGATGGACCAGCACT

Reverse (5′→3′)

ATCTTGGTGCCTTGGTGGAT

Amplicon

303 bp

estimated from mapping

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix64.963.264.01.7
Primer-BLAST default60.859.360.11.5

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

50.0%

Self-dimer ΔG · Fwd (any position)

-2.6 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)

-0.2 kcal/mol

Heterodimer ΔG (F×R, any position)

-3.2 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

1.2 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

40046510(Europe PMC)

Citation

Noland et al. 2025

Genomic mapping

Ensembl gene

ENSMUSG00000036427 ↗

NCBI Gene ID

14751

Assembly

GRCm39

Cross-check

✓ENSMUST00000038027★
ENSMUST00000205800
ENSMUST00000206415
ENSMUST00000495269
ENSMUST00000495270
✓ENSMUST00000495271
✓ENSMUST00000495272
✓ENSMUST00000495273
✓ENSMUST00000495274
✓ENSMUST00000495275
ENSMUST00000495276
✓ENSMUST00000495277
✓ENSMUST00000495278
✓ENSMUST00000495279
✓ENSMUST00000495280
✓ENSMUST00000495282
✓ENSMUST00000495284
✓ENSMUST00000495285
✓ENSMUST00000495286
✓ENSMUST00000495292
✓ENSMUST00000495295
✓ENSMUST00000495296
✓ENSMUST00000495297
ENSMUST00000495298
✓ENSMUST00000495299
ENSMUST00000495300
ENSMUST00000495301
ENSMUST00000578836
ENSMUST00000578839
ENSMUST00000578840
ENSMUST00000578849
ENSMUST00000578852
ENSMUST00000578853
ENSMUST00000578854
ENSMUST00000578855
ENSMUST00000583409
ENSMUST00000583410
ENSMUST00000583411
~264bpThis 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.~91bpThis 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.~70bpThis 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.~120bpThis 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.~492bpThis 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.84bp~147bpThis 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.~72bpThis 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.45bp124bp~123bpThis 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.84bp63bp15bp~61bpThis 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.44bp~1.4kbThis 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.~130bpThis 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.~77bpThis 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.~129bpThis 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.76bp~67bpThis 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.~1.2kbThis 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: ENSMUST00000038027 ★

264bp11.1kb91bp2444bp69bp31.9kb120bp46.4kb84bp5311bp147bp61.7kb72bp7803bp45bp82.4kb54bp97.8kb61bp10452bp44bp11293bp153bp122.0kb130bp13366bp77bp141.6kb129bp151.3kb76bp16252bp67bp171.4kb1.2kb18FRPredicted 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.303 bp amplicon · predicted amplicon Tm 91.5 °C
Gpi1 · ENSMUST00000038027 (NM_008155) · canonical✓ Exon-junction spanning · gDNA-safe by primer design⚠ 303bp is atypical for real-time qPCR (standard: 70–200bp) · verify intent before approving

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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