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← Primer database

Primer database

Pparg

peroxisome proliferator activated receptor gamma

Mus musculus

PublicationHeintz et al. 2022⇄ Compare with 1 other candidate →

Sequences

Forward (5′→3′)

TGGGTGAAACTCTGGGAGATTC

Reverse (5′→3′)

AATTTCTTGTGAAGTGCTCATAGGC

Amplicon

86 bp

estimated from mapping

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix63.262.763.00.5
Primer-BLAST default59.760.159.90.4

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

50.0%

GC% · Reverse

40.0%

Self-dimer ΔG · Fwd (any position)

-0.7 kcal/mol

Self-dimer ΔG · Fwd (3′ end)

-0.3 kcal/mol

Self-dimer ΔG · Rev (any position)

-0.8 kcal/mol

Self-dimer ΔG · Rev (3′ end)

-0.3 kcal/mol

Heterodimer ΔG (F×R, any position)

-1.3 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

36520866(Europe PMC)

Citation

Heintz et al. 2022

Genomic mapping

Ensembl gene

ENSMUSG00000000440 ↗

NCBI Gene ID

19016

Assembly

GRCm39

Cross-check

ENSMUST00000171644
ENSMUST00000203732★
ENSMUST00000204305
ENSMUST00000205213
✓ENSMUST00000000450
ENSMUST00000442365
ENSMUST00000442367
ENSMUST00000442368
ENSMUST00000442373
ENSMUST00000442374
ENSMUST00000442375
ENSMUST00000442376
ENSMUST00000442377
ENSMUST00000442378
ENSMUST00000442379
ENSMUST00000442380
ENSMUST00000442381
ENSMUST00000442382
ENSMUST00000442383
ENSMUST00000442384
ENSMUST00000442385
ENSMUST00000442386
ENSMUST00000442387
ENSMUST00000442389
ENSMUST00000442390
ENSMUST00000442391
ENSMUST00000442392
ENSMUST00000442393
ENSMUST00000442394
ENSMUST00000442395
✓ENSMUST00000442396
✓ENSMUST00000442398
✓ENSMUST00000442399
~917bpThis 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.661bp~126bpThis 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.3.3kb~338bpThis 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.6.4kb61bp11.1kb~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.1.9kb37bp21.6kb79bp10.9kb105bp3.6kb~271bpThis 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.17.6kb228bp1.4kb~170bpThis 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.9.3kb139bp12.0kb~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.9.6kb~1.6kbThis 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.15.5kb1.4kb
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: ENSMUST00000171644

420bp122.3kb65bp256.1kb228bp31.4kb170bp49.3kb139bp512.0kb200bp69.6kb451bp716.6kb1.4kb8
Pparg · ENSMUST00000171644 (NM_001410262)No 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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