Table 1 Reactions and kinetic parameters for the gene expression model

$\text{Pro}+\text{Rp}\stackrel{k_{\mathrm{tc}}}{\to }\text{Rp}·\text{Pro}\left({\tau }_{\mathrm{oc}}\right)$

k _tc =0.0245, τ _oc ∼N(40,4²)

$\text{Rp}·\text{Pro}+{\text{U}}_{[1,({\Delta }_{\text{P}}+1\left)\right]}\stackrel{k_m}{\to }{\text{O}}_1+\text{Pro}$

k _m =150

${\text{O}}_n\stackrel{k_a}{\to }{\text{A}}_n$

k _a =150 for n>10, k _a =30 for n≤10

${\text{A}}_n+{\text{U}}_{n+{\Delta }_{\text{P}}+1}\stackrel{k_m}{\to }{\text{O}}_{n+1}+{\text{U}}_{n-{\Delta }_{\text{P}}}+{\text{U}}_{n-{\Delta }_{\text{P}}}^R$

k _m =150

${\text{O}}_n\underset{1/{\tau }_p}{\overset{k_p}{\rightleftharpoons }}{\text{O}}_{n_p}$

k _p =0.55,τ _p =3

${\text{O}}_{n_p}+{\text{A}}_{n-2{\Delta }_{\text{P}}-1}\stackrel{0.8k_m}{\to }{\text{O}}_n+{\text{A}}_{n-2{\Delta }_{\text{P}}-1}$

k _m =150

${\text{O}}_n+{\text{A}}_{n-2{\Delta }_{\text{P}}-1}\stackrel{0.2k_m}{\to }{\text{O}}_{n_p}+{\text{A}}_{n-2{\Delta }_{\text{P}}-1}$

k _m =150

${\text{O}}_n\underset{1/{\tau }_{\mathrm{ar}}}{\overset{k_{\mathrm{ar}}}{\rightleftharpoons }}{\text{O}}_{n_{\mathrm{ar}}}$

$k_{\mathrm{ar}}=2.78·10^{-4}$, τ _ar =100

${\text{O}}_n\underset{1/d_{\mathrm{ed}}}{\overset{k_{\mathrm{ed}}}{\rightleftharpoons }}{\text{O}}_{n_{\mathrm{corr}}}$

k _ed =0.009, d _ed =5

${\text{O}}_n\stackrel{k_{\mathrm{pre}}}{\to }\text{Rp}+{\text{U}}_{\left[\right(n-{\Delta }_{\text{P}}),(n+{\Delta }_{\text{P}}\left)\right]}$

k _pre =1.9·10⁻⁴

${\text{O}}_n+{\text{U}}_{n-{\Delta }_{\text{P}}-1}+{\text{U}}_{n-{\Delta }_{\text{P}}-1}^R\stackrel{k_{\mathrm{pyr}}}{\to }{\text{O}}_{n-1}+{\text{U}}_{n+{\Delta }_{\text{P}}-1}$

k _pyr =0.75

${\text{A}}_{\mathrm{last}}\stackrel{k_f}{\to }\text{Rp}+{\text{U}}_{[\text{last},\text{last}-{\Delta }_{\text{P}}]}+\text{mRNA}$

k _f =2

$\text{mRNA}\stackrel{k_{\mathrm{dr}}}{\to }\varnothing$

k _dr =0.025

$\text{Rib}+{\text{U}}_{[1,{\Delta }_{\text{R}}+1]}^{\text{R}}\stackrel{k_{\mathrm{tl}}}{\to }{\text{O}}_1^{\text{R}}+{\text{Rib}}^{\text{R}}$

k _tl =0.53

${\text{O}}_n^{\text{R}}\stackrel{k_{\mathrm{tr}\{A,B,C\}}}{\to }{\text{A}}_n^{\text{R}}$

k _trA =35, k _trB =8, k _trC =4.5

${\text{A}}_{n-3}^{\text{R}}+{\text{U}}_{[n+{\Delta }_{\text{R}}-3,n+{\Delta }_{\text{R}}-1]}^{\text{R}}\stackrel{k_{\mathrm{tm}}}{\to }{\text{O}}_{n-2}^{\text{R}}$

k _tm =10,000

${\text{O}}_{n-2}^{\text{R}}\stackrel{k_{\mathrm{tm}}}{\to }{\text{O}}_{n-1}^{\text{R}}$

see above

${\text{O}}_{n-1}^{\text{R}}\stackrel{k_{\mathrm{tm}}}{\to }{\text{O}}_n^{\text{R}}+{\text{U}}_{[n-{\Delta }_{\text{R}}-2,n-{\Delta }_{\text{R}}]}^{\text{R}}$

see above

${\text{O}}_n^{\text{R}}+{\text{U}}_{[n-{\Delta }_{\text{R}}-2,n-{\Delta }_{\text{R}}]}^{\text{R}}\stackrel{k_{\mathrm{bt}}}{\to }{\text{A}}_{n-3}^{\text{R}}+{\text{U}}_{[n+{\Delta }_{\text{R}}-3,n+{\Delta }_{\text{R}}-1]}^{\text{R}}$

k _bt =1.5

${\text{O}}_n^{\text{R}}\stackrel{k_{\mathrm{drop}}}{\to }\text{Rib}+{\text{U}}_{[n-{\Delta }_{\text{R}},n+{\Delta }_{\text{R}}]}^{\text{R}}$

k _drop =1.14·10⁻⁴

$\text{mRNA}\stackrel{k_{\mathrm{tt}}}{\to }\left[{\text{Rib}}^{\text{R}}\right]\times \text{Rib}$

k _tt is sequence dependent

${\text{A}}_{\mathrm{last}}^{\text{R}}\stackrel{k_{t{l}_f}}{\to }\text{Rib}+{\text{U}}_{[\mathrm{last},\mathrm{last}-{\Delta }_{\text{R}}]}^{\text{R}}+\text{P}\left({\tau }_{\mathrm{fold}}\right)$

$k_{t{l}_f}=2$, τ _fold ∼N(420,100²)

$\text{P}\stackrel{k_{\mathrm{dp}}}{\to }\varnothing$

k _dp =0.0029