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Table 1 Overview of parameters, their description and default value

From: Is RNA-dependent RNA polymerase essential for transposon control?

Par. Description Value Units
j Integration of new transposon 0.1 hr-1
f Fraction of successful integration 0.1 -
v ta Transcription of active transposons 16 hr-1
v ts Transcription of silenced transposons 1.6 hr-1
t m Export of mRNA from nucleus 0.45 hr-1
t an Export of asRNA from nucleusa 0.45 hr-1
q VLP production (proteins etc) 1 · 10-5 #mol-1 hr-1
d v Decay of VLP 2.0 hr-1
u Activation of silenced transposon 0.02 hr-1
h b Basal heterochromatin formation 0.01 hr-1
h s siRNA induced heterochromatin formation 0.001 #mol-1 hr-1
p n Rate of dsRNA synthesis from nuclear RNA 0.002 hr-1
p nx dsRNA synthesis from mRNA and asRNAa, h 2 · 10-4 #mol-1 hr-1
d r Decay rate nuclear RNA 0.28 hr-1
p c Rate of dsRNA synthesis from mRNA 0.002 hr-1
p cx dsRNA synthesis from mRNA and asRNAa 2.5 · 10-4 #mol-1 hr-1
p cxx dsRNA synthesis from hairpin mRNAh 0.002 hr-1
g Primed amplification rate 0.002 #mol-1 hr-1
b RISC activity 0.008 #mol-1 hr-1
d m Decay rate nuclear/cytoplasmic mRNA 0.14 hr-1
g s Rate of dsRNA cleavage by Dicer 2.0 hr-1
n Number of siRNAs cleaved from single dsRNA 10 -
d s Decay siRNA 2.8 hr-1
v s Degradation rate by RNAse 800 #mol-1 hr-1
k s Saturation constant 5.0 #mol
  1. Units are number of molecules (#mol), and per hour (hr-1). Parameters marked in their description with a and/or h are used only in the antisense or hairpin models respectively. Parameter value sampling is performed by assuming a uniform distribution in the interval [0.1 * parameter, 10.0 * parameter] and drawing random values from this distribution. See Additional File 3 for references and estimations of parameter values.