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← Primer database

Primer database

Cxcl12

C-X-C motif chemokine ligand 12

Rattus norvegicus

PublicationAl-Romaima et al. 2022

Sequences

Forward (5′→3′)

TATCTCGGCGGCGTCACCAG

Reverse (5′→3′)

AAACCATCGCTGCGTAGACACTG

Amplicon

80 bp

estimated from mapping

Primer Tm (°C)

ConditionsForwardReverseAverageΔ F/R
qPCR master mix68.466.667.51.8
Primer-BLAST default64.463.564.00.9

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

65.0%

GC% · Reverse

52.2%

Self-dimer ΔG · Fwd (any position)

-0.3 kcal/mol

Self-dimer ΔG · Fwd (3′ end)

0.7 kcal/mol

Self-dimer ΔG · Rev (any position)

-2.5 kcal/mol

Self-dimer ΔG · Rev (3′ end)

0.5 kcal/mol

Heterodimer ΔG (F×R, any position)

-2.5 kcal/mol

Heterodimer ΔG (F×R, 3′ end)

-0.8 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

36484062(Europe PMC)

Citation

Al-Romaima et al. 2022

Genomic mapping

Ensembl gene

ENSRNOG00000013589 ↗

NCBI Gene ID

24772

Assembly

GRCr8

Cross-check

★ = Ensembl canonical transcript (reference model, not necessarily the most expressed isoform)

Showing: ENSRNOT00000066670 ★

143bp12.8kb118bp22.1kb87bp32.5kb5.1kb4FRPredicted 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.80 bp amplicon · predicted amplicon Tm 86.6 °C
Cxcl12 · ENSRNOT00000066670 (NM_022177) · canonical⚠ Single-exon · may amplify genomic DNA

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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