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← Primer database

Primer database

Dnmt1

DNA methyltransferase 1

Mus musculus

PublicationJi et al. 2023

Sequences

Forward (5′→3′)

GGACAAGGAGAATGCCATGAAGC

Reverse (5′→3′)

TTACTCCGTCCAGTGCCACCAA

Amplicon

123 bp

estimated from mapping

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix65.367.566.42.2
Primer-BLAST default62.063.962.91.8

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

52.2%

GC% · Reverse

54.5%

Self-dimer ΔG · Fwd (any position)

-1.9 kcal/mol

Self-dimer ΔG · Fwd (3′ end)

-0.3 kcal/mol

Self-dimer ΔG · Rev (any position)

-1.0 kcal/mol

Self-dimer ΔG · Rev (3′ end)

1.0 kcal/mol

Heterodimer ΔG (F×R, any position)

-2.7 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

-0.3 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

36704326(Europe PMC)

Citation

Ji et al. 2023

Genomic mapping

Ensembl gene

ENSMUSG00000004099 ↗

NCBI Gene ID

13433

Assembly

GRCm39

Cross-check

ENSMUST00000569685
✓ENSMUST00000178110
✓ENSMUST00000004202★
✓ENSMUST00000177754
✓ENSMUST00000216540
✓ENSMUST00000384574
✓ENSMUST00000384575
✓ENSMUST00000384576
✓ENSMUST00000384577
✓ENSMUST00000384578
✓ENSMUST00000384579
✓ENSMUST00000384580
✓ENSMUST00000384582
✓ENSMUST00000384583
✓ENSMUST00000569680
✓ENSMUST00000569684
✓ENSMUST00000569687
✓ENSMUST00000569688
156bp~571bpThis 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.~778bpThis 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.37bp~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.~232bpThis 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.~79bpThis 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.76bp32bp79bp41bp85bp41bp82bp~65bpThis 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.43bp81bp110bp119bp93bp152bp188bp178bp98bp148bp~116bpThis 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.205bp137bp~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.219bp~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.193bp85bp129bp283bp~142bpThis 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.167bp178bp196bp281bp91bp~913bpThis 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: ENSMUST00000569685

571bp110.7kb37bp2919bp105bp3429bp211bp41.1kb76bp52.5kb76bp6983bp32bp7649bp79bp82.1kb41bp92.4kb85bp102.1kb41bp111.1kb82bp122.0kb65bp13364bp43bp14216bp81bp15265bp110bp162.5kb119bp17438bp93bp181.0kb152bp19622bp188bp20457bp178bp212.1kb98bp22365bp148bp231.6kb116bp24433bp205bp25413bp137bp26744bp174bp271.7kb219bp282.0kb193bp291.5kb85bp30475bp129bp31574bp283bp32597bp142bp331.4kb167bp34612bp178bp35779bp196bp36812bp281bp37880bp91bp381.3kb913bp39
Dnmt1 · ENSMUST00000569685No amplicon found on this isoform (intron_only / intron_only)

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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