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← Primer database

Primer database

Ldha

lactate dehydrogenase A

Mus musculus

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

Sequences

Forward (5′→3′)

AAGACTACTGTGTAACTGCGAA

Reverse (5′→3′)

ACTTGAAGATGTTCACGTTTCG

Amplicon

114 bp

estimated from mapping

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix60.360.260.30.1
Primer-BLAST default57.457.557.50.1

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

40.9%

GC% · Reverse

40.9%

Self-dimer ΔG · Fwd (any position)

-0.3 kcal/mol

Self-dimer ΔG · Fwd (3′ end)

No duplex found

Self-dimer ΔG · Rev (any position)

-3.0 kcal/mol

Self-dimer ΔG · Rev (3′ end)

-0.2 kcal/mol

Heterodimer ΔG (F×R, any position)

-2.5 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

-2.5 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

38465221(Europe PMC)

Citation

Jiang et al. 2022

Genomic mapping

Ensembl gene

ENSMUSG00000063229 ↗

NCBI Gene ID

16828

Assembly

GRCm39

Cross-check

✓ENSMUST00000147535
✓ENSMUST00000048209★
✓ENSMUST00000210815
ENSMUST00000125862
ENSMUST00000210968
✓ENSMUST00000092621
✓ENSMUST00000210467
ENSMUST00000133062
✓ENSMUST00000209984
✓ENSMUST00000005051
✓ENSMUST00000132157
ENSMUST00000210631
✓ENSMUST00000438835
✓ENSMUST00000438836
✓ENSMUST00000438837
✓ENSMUST00000438838
✓ENSMUST00000438841
✓ENSMUST00000438842
✓ENSMUST00000438843
✓ENSMUST00000438844
✓ENSMUST00000438845
✓ENSMUST00000438846
✓ENSMUST00000438847
ENSMUST00000438848
✓ENSMUST00000438849
✓ENSMUST00000438850
ENSMUST00000438851
ENSMUST00000438852
✓ENSMUST00000438853
✓ENSMUST00000438854
ENSMUST00000438855
✓ENSMUST00000438856
✓ENSMUST00000438857
✓ENSMUST00000438858
✓ENSMUST00000438859
✓ENSMUST00000438860
✓ENSMUST00000438861
✓ENSMUST00000438862
✓ENSMUST00000438863
✓ENSMUST00000438864
✓ENSMUST00000438865
✓ENSMUST00000438866
✓ENSMUST00000438867
✓ENSMUST00000438868
✓ENSMUST00000562003
✓ENSMUST00000562004
✓ENSMUST00000581926
✓ENSMUST00000581927
ENSMUST00000581929
ENSMUST00000581932
✓ENSMUST00000581933
ENSMUST00000585312
ENSMUST00000585313
ENSMUST00000585314
ENSMUST00000585315
✓ENSMUST00000585316
ENSMUST00000585317
178bp330bp91bp1.5kb176bp1.4kb116bp438bp~1.8kbThis 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.8bp~241bpThis 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.1.2kb~133bpThis 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.1.1kb~174bpThis 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.533bp~174bpThis 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.800bp~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.1.9kb~181bpThis 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.870bp~661bpThis 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: ENSMUST00000147535

178bp15.9kb150bp21.2kb118bp31.1kb174bp4533bp174bp5818bp118bp6FRPredicted 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.114 bp amplicon · predicted amplicon Tm 88.0 °C
Ldha · ENSMUST00000147535✓ 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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