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← Primer database

Primer database

NTMT1

N-terminal Xaa-Pro-Lys N-methyltransferase 1

Homo sapiens

PublicationZeng et al. 2024

Sequences

Forward (5′→3′)

GAATGCCCACTCCAACACCT

Reverse (5′→3′)

CAACCGCGACTCTCCTGG

Amplicon

214 bp

estimated from mapping

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix64.164.464.30.2
Primer-BLAST default60.360.160.20.1

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

55.0%

GC% · Reverse

66.7%

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)

-4.6 kcal/mol

Self-dimer ΔG · Rev (3′ end)

0.1 kcal/mol

Heterodimer ΔG (F×R, any position)

-1.3 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

-1.3 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

39726744(Europe PMC)

Citation

Zeng et al. 2024

Genomic mapping

Ensembl gene

ENSG00000148335 ↗

NCBI Gene ID

28989

Assembly

GRCh38

Cross-check

✓ENST00000372486
ENST00000613644
ENST00000611055
ENST00000617943
ENST00000372483★
ENST00000459968
ENST00000482347
ENST00000372481
ENST00000372480
ENST00000900249
✓ENST00000900251
ENST00000900252
ENST00000900253
ENST00000900254
ENST00000900255
ENST00000900256
ENST00000935935
ENST00000935936
ENST00000935937
ENST00000949698
ENST00000949699
ENST00000949700
ENST00000980156
ENST00000980158
✓ENST00001024535
ENST00001024537
ENST00001024538
ENST00001024539
ENST00001024544
ENST00001024545
ENST00001079310
ENST00001079314
ENST00001079317
ENST00001103068
ENST00001103069
ENST00001103070
ENST00001103071
ENST00001110577
ENST00001117010
ENST00001122902
ENST00001137187
239bp18.7kb~388bpThis 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.1.8kb~313bpThis 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.813bp44bp10.2kb108bp5.8kb~196bpThis 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.93bp~358bpThis 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.50bp~1.9kbThis 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.2.0kb~3.0kbThis 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.377bp~2.7kbThis 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: ENST00000372486

313bp123.5kb216bp21.2kb253bp3901bp1.5kb4FRPredicted 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.214 bp amplicon · predicted amplicon Tm 92.0 °C
NTMT1 · ENST00000372486 (NM_001286796)✓ 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.

Using these primers?

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