Transcription Rate Estimator

Model gene transcription with physical rate constraints today. Tune promoter energy, regulators, and polymerase levels. See rates, time evolution, and steady state instantly here.

Calculator Inputs

Regulator level driving promoter activation.
Half-activation concentration in Hill model.
Cooperativity; n > 1 gives sharper response.
Proxy for polymerase recruitment capacity.
Half-saturation for RNAP availability curve.
Max initiation under saturating conditions.
Used in exp(-deltaG/RT). Lower raises rate.
Affects energetic factor through RT.
Fractional time lost to pausing or abortive steps.
Average polymerase elongation velocity.
Total transcribed length in nucleotides.
Accounts for premature termination losses.
Set ≤ 0 to ignore degradation.
Time window for mRNA accumulation estimate.
Starting amount at t = 0 for time evolution.

Example Data Table

Typical input scenarios for comparison.
Scenario TF (nM) K_TF (nM) n RNAP (nM) Vmax (1/s) deltaG (kJ/mol) v_elong (nt/s) L (nt)
Weak TF 10 30 2 100 0.05 6 35 1500
Moderate TF 50 30 2 100 0.05 6 35 1500
Strong TF 200 30 2 100 0.05 6 35 1500
Slow elongation 50 30 2 100 0.05 6 15 1500
Long gene 50 30 2 100 0.05 6 35 6000

Formula Used

1) Hill activation for regulatory input

TF_activity = TF^n / (K_TF^n + TF^n)

2) RNAP availability saturation

RNAP_activity = RNAP / (K_RNAP + RNAP)

3) Energetic factor

Energy_factor = exp( - deltaG / (R * T) )

4) Initiation rate

k_init = Vmax * TF_activity * RNAP_activity * Energy_factor * (1 - p_pause)

5) Elongation-limited throughput

k_elong = (v_elong / L) * eta_term

6) Effective transcription rate

k_eff = min(k_init, k_elong)

7) Optional mRNA time evolution

dN/dt = k_eff - k_deg * N, k_deg = ln(2) / half_life

When half-life is ≤ 0, degradation is ignored and N grows linearly.

How to Use

  1. Enter TF, K_TF, and n to describe regulation strength.
  2. Enter RNAP and K_RNAP to represent recruitment capacity.
  3. Set Vmax, deltaG, and temperature to scale initiation.
  4. Provide pausing, elongation speed, gene length, and termination efficiency.
  5. Optionally set half-life, duration, and initial mRNA for dynamics.
  6. Press Estimate Transcription Rate to see results.
  7. Use the CSV/PDF buttons to export your current results.

Related Calculators

Membrane potential calculatorGoldman equation calculatorDonnan equilibrium calculatorIon channel conductancePatch clamp sealCable length constantMembrane time constantAxon conduction velocityHodgkin Huxley solverAction potential threshold

Important Note: All the Calculators listed in this site are for educational purpose only and we do not guarentee the accuracy of results. Please do consult with other sources as well.