MODEL1012090005
type: SBMLModel
species: COPASI16
reaction: COPASI77
reaction: COPASI79
notes: This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
parameter: COPASI32
parameter: COPASI34
parameter: COPASI36
parameter: COPASI55
reaction: COPASI100
parameter: COPASI57
parameter: COPASI59
parameter: COPASI64
parameter: COPASI43
reaction: COPASI74
substance units: substance
parameter: COPASI47
reaction: COPASI81
species: COPASI3
reaction: COPASI83
parameter: COPASI67
parameter: COPASI69
parameter: COPASI60
species: COPASI22
parameter: COPASI52
species: COPASI24
reaction: COPASI88
name: Kim2011_Oscillator_ExtendedI
reaction: COPASI71
parameter: COPASI40
reaction: COPASI97
curated: false
species: COPASI4
parameter: COPASI31
parameter: COPASI35
reaction: COPASI92
reaction: COPASI94
area units: area
reaction: COPASI76
is described by: http://identifiers.org/pubmed/21283141
species: COPASI26
species: COPASI28
species: COPASI11
species: COPASI10
reaction: COPASI99
species: COPASI13
parameter: COPASI54
parameter: COPASI51
species: COPASI19
species: COPASI18
parameter: COPASI58
parameter: COPASI38
initial assignment: MODEL1012090005#
reaction: COPASI87
parameter: COPASI42
species: COPASI23
parameter: COPASI39
species: COPASI6
reaction: COPASI80
parameter: COPASI46
species: COPASI25
species: COPASI8
reaction: COPASI82
parameter: COPASI66
parameter: COPASI63
parameter: COPASI45
parameter: COPASI68
parameter: COPASI49
reaction: COPASI85
reaction: COPASI91
species: COPASI20
species: COPASI5
reaction: COPASI93
reaction: COPASI73
length unit: length
species: COPASI15
species: COPASI14
species: COPASI17
reaction: COPASI75
compartment: 153431

COPASI16
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT12A2

153431
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

COPASI77
type: Reaction
kinetic law: 972637
product: 972624
product: 972612
reactant: 972600
reactant: 972588
fast: false
reversible: false
name: Release

972624
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

COPASI12
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: rA1dI1

972612
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI5
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5E-7
initial amount: NaN
in compartment: 153431
name: A1

972600
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

COPASI11
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: A1dI1

972588
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

COPASI7
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 8.0E-7
initial amount: NaN
in compartment: 153431
name: rA1

COPASI79
type: Reaction
kinetic law: 972732
product: 972720
reactant: 972708
reactant: 972696
fast: false
reversible: true
name: RNAPbinding2

972720
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

COPASI18
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT21A1

972708
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

COPASI10
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T21A1

972696
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI14
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.25E-7
initial amount: NaN
in compartment: 153431
name: RNAP

COPASI32
type: Parameter
constant: true
value: 2.5E-7
name: A1tot

COPASI34
type: Parameter
constant: true
value: 5.0E-7
name: A2tot

COPASI36
type: Parameter
constant: true
value: 1.75E-8
name: RNaseHtot

COPASI55
type: Parameter
constant: true
value: 0.026
name: kcatON21

COPASI100
type: Reaction
kinetic law: 973853
product: 973841
reactant: 973829
reactant: 973817
fast: false
reversible: false
name: sI2activation

973841
type: SpeciesReference
stoichiometry: 1.0
species: COPASI28

COPASI28
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T12A2sI2

973829
type: SpeciesReference
stoichiometry: 1.0
species: COPASI27

COPASI27
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: A2sI2

973817
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

COPASI2
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.2E-7
initial amount: NaN
in compartment: 153431
name: T12

COPASI57
type: Parameter
constant: true
value: 0.024
name: kcatH1

COPASI59
type: Parameter
constant: true
value: 74000.0
name: kTA11

COPASI64
type: Parameter
constant: true
value: 0.002
name: kcatOFF11

COPASI43
type: Parameter
constant: true
value: 22300.0
name: kTAI12

COPASI74
type: Reaction
kinetic law: 972455
product: 972443
reactant: 972431
reactant: 972419
fast: false
reversible: false
name: Annihilation3

972443
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

COPASI13
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: A2rI2

972431
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

COPASI8
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.5E-7
initial amount: NaN
in compartment: 153431
name: rI2

972419
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

COPASI3
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 153431
name: A2

COPASI47
type: Parameter
constant: true
value: 11.3
name: kminusON12

COPASI81
type: Reaction
kinetic law: 972830
product: 972818
reactant: 972805
reactant: 972793
fast: false
reversible: true
name: RNAPbinding4

972818
type: SpeciesReference
stoichiometry: 1.0
species: COPASI19

COPASI19
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT21

972805
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI4
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5E-7
initial amount: NaN
in compartment: 153431
name: T21

972793
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI83
type: Reaction
kinetic law: 972950
product: 972938
product: 972926
product: 972914
reactant: 972902
fast: false
reversible: false
name: RNAPcat2

972938
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

972926
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

972914
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

972902
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

COPASI67
type: Parameter
constant: true
value: 0.032
name: ksminus

COPASI69
type: Parameter
constant: true
value: 5.5E-7
name: rI2init

COPASI60
type: Parameter
constant: true
value: 28000.0
name: kTAI11

COPASI22
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T11

COPASI52
type: Parameter
constant: true
value: 5.5
name: kminusH2

COPASI24
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT11A1

COPASI88
type: Reaction
kinetic law: 973229
product: 973217
product: 973205
reactant: 973193
fast: false
reversible: false
name: RNaseHcat1

973217
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

COPASI6
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-6
initial amount: NaN
in compartment: 153431
name: dI1

973205
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI15
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.75E-8
initial amount: NaN
in compartment: 153431
name: RNaseH

973193
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20

COPASI20
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNaseHrA1dI1

COPASI71
type: Reaction
kinetic law: 972311
product: 972299
reactant: 972287
reactant: 972275
fast: false
reversible: false
name: Activation2

972299
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

972287
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

972275
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI40
type: Parameter
constant: true
value: 42700.0
name: krAI1

COPASI97
type: Reaction
kinetic law: 973709
product: 973697
product: 973685
product: 973673
reactant: 973661
fast: false
reversible: false
name: RNAPcat7

973697
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

973685
type: SpeciesReference
stoichiometry: 1.0
species: COPASI28

973673
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

973661
type: SpeciesReference
stoichiometry: 1.0
species: COPASI29

COPASI29
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT12A2sI2

COPASI31
type: Parameter
constant: true
value: 2.5E-7
name: T21tot

COPASI35
type: Parameter
constant: true
value: 1.25E-7
name: RNAPtot

COPASI92
type: Reaction
kinetic law: 973433
product: 973421
reactant: 973409
reactant: 973397
fast: false
reversible: true
name: RNAPbinding5

973421
type: SpeciesReference
stoichiometry: 1.0
species: COPASI24

973409
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

COPASI23
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T11A1

973397
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI94
type: Reaction
kinetic law: 973541
product: 973529
product: 973517
product: 973505
reactant: 973493
fast: false
reversible: false
name: RNAPcat5

973529
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

973517
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

973505
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

973493
type: SpeciesReference
stoichiometry: 1.0
species: COPASI24

COPASI76
type: Reaction
kinetic law: 972576
product: 972564
product: 972552
reactant: 972540
reactant: 972528
fast: false
reversible: false
name: Inhibition2

972564
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

972552
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

972540
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

972528
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

COPASI26
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: sI2

COPASI99
type: Reaction
kinetic law: 973805
product: 973793
reactant: 973781
reactant: 973769
fast: false
reversible: true
name: sI2binding2

973793
type: SpeciesReference
stoichiometry: 1.0
species: COPASI28

973781
type: SpeciesReference
stoichiometry: 1.0
species: COPASI26

973769
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

COPASI9
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T12A2

COPASI54
type: Parameter
constant: true
value: 0.0018
name: kcatOFF12

COPASI51
type: Parameter
constant: true
value: 4.4
name: kminusH1

COPASI58
type: Parameter
constant: true
value: 0.062
name: kcatH2

COPASI38
type: Parameter
constant: true
value: 4630.0
name: kTA12

COPASI87
type: Reaction
kinetic law: 973181
product: 973168
reactant: 973155
reactant: 973142
fast: false
reversible: true
name: RNaseHbinding2

973168
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

COPASI21
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNaseHA2rI2

973155
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

973142
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI42
type: Parameter
constant: true
value: 10300.0
name: kTAI21

COPASI39
type: Parameter
constant: true
value: 10000.0
name: kAI1

COPASI80
type: Reaction
kinetic law: 972780
product: 972768
reactant: 972756
reactant: 972744
fast: false
reversible: true
name: RNAPbinding3

972768
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

COPASI17
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT12

972756
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

972744
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI46
type: Parameter
constant: true
value: 1.0E8
name: kplusH

COPASI25
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT11

COPASI82
type: Reaction
kinetic law: 972890
product: 972878
product: 972866
product: 972854
reactant: 972842
fast: false
reversible: false
name: RNAPcat1

972878
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

972866
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

972854
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

972842
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

COPASI66
type: Parameter
constant: true
value: 192000.0
name: ksplus

COPASI63
type: Parameter
constant: true
value: 0.05
name: kcatON11

COPASI45
type: Parameter
constant: true
value: 1.0E8
name: kplus

COPASI68
type: Parameter
constant: true
value: 8.0E-7
name: rA1init

COPASI49
type: Parameter
constant: true
value: 11.8
name: kminusON21

COPASI85
type: Reaction
kinetic law: 973077
product: 973064
product: 973051
product: 973038
reactant: 973025
fast: false
reversible: false
name: RNAPcat4

973064
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

973051
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

973038
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

973025
type: SpeciesReference
stoichiometry: 1.0
species: COPASI19

COPASI91
type: Reaction
kinetic law: 973385
product: 973373
product: 973361
reactant: 973349
reactant: 973337
fast: false
reversible: false
name: Inhibition3

973373
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

973361
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

973349
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

973337
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

COPASI93
type: Reaction
kinetic law: 973481
product: 973469
reactant: 973457
reactant: 973445
fast: false
reversible: true
name: RNAPbinding6

973469
type: SpeciesReference
stoichiometry: 1.0
species: COPASI25

973457
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

973445
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI73
type: Reaction
kinetic law: 972407
product: 972395
reactant: 972383
reactant: 972371
fast: false
reversible: false
name: Annihilation2

972395
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

972383
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

972371
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

COPASI75
type: Reaction
kinetic law: 972516
product: 972504
product: 972492
reactant: 972479
reactant: 972467
fast: false
reversible: false
name: Inhibition1

972504
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

972492
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

972479
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

972467
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

COPASI53
type: Parameter
constant: true
value: 0.081
name: kcatON12

COPASI33
type: Parameter
constant: true
value: 1.0E-6
name: dI1tot

COPASI37
type: Parameter
constant: true
value: 60400.0
name: kTA21

COPASI96
type: Reaction
kinetic law: 973649
product: 973637
reactant: 973625
reactant: 973613
fast: false
reversible: true
name: RNAPbinding7

973637
type: SpeciesReference
stoichiometry: 1.0
species: COPASI29

973625
type: SpeciesReference
stoichiometry: 1.0
species: COPASI28

973613
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI101
type: Reaction
kinetic law: 973913
product: 973901
product: 973889
reactant: 973877
reactant: 973865
fast: false
reversible: false
name: sI2annihilation

973901
type: SpeciesReference
stoichiometry: 1.0
species: COPASI26

973889
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

973877
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

973865
type: SpeciesReference
stoichiometry: 1.0
species: COPASI27

COPASI98
type: Reaction
kinetic law: 973757
product: 973745
reactant: 973733
reactant: 973721
fast: false
reversible: true
name: sI2binding1

973745
type: SpeciesReference
stoichiometry: 1.0
species: COPASI27

973733
type: SpeciesReference
stoichiometry: 1.0
species: COPASI26

973721
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

COPASI65
type: Parameter
constant: true
value: 0.0
name: T11tot

COPASI78
type: Reaction
kinetic law: 972684
product: 972672
reactant: 972660
reactant: 972648
fast: false
reversible: true
name: RNAPbinding1

972672
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

972660
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

972648
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI50
type: Parameter
constant: true
value: 48.0
name: kminusOFF21

COPASI30
type: Parameter
constant: true
value: 1.2E-7
name: T12tot

COPASI86
type: Reaction
kinetic law: 973129
product: 973116
reactant: 973103
reactant: 973090
fast: false
reversible: true
name: RNaseHbinding1

973116
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20

973103
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

973090
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI61
type: Parameter
constant: true
value: 24.7
name: kminusON11

COPASI56
type: Parameter
constant: true
value: 0.0024
name: kcatOFF21

COPASI89
type: Reaction
kinetic law: 973277
product: 973265
product: 973253
reactant: 973241
fast: false
reversible: false
name: RNaseHcat2

973265
type: SpeciesReference
stoichiometry: 1.0
species: COPASI27

973253
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

973241
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

COPASI62
type: Parameter
constant: true
value: 267.0
name: kminusOFF11

COPASI44
type: Parameter
constant: true
value: 79600.0
name: kAIrA1

COPASI41
type: Parameter
constant: true
value: 42800.0
name: kAI2

COPASI48
type: Parameter
constant: true
value: 161.0
name: kminusOFF12

COPASI84
type: Reaction
kinetic law: 973012
product: 973000
product: 972988
product: 972975
reactant: 972963
fast: false
reversible: false
name: RNAPcat3

973000
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

972988
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

972975
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

972963
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

COPASI90
type: Reaction
kinetic law: 973325
product: 973313
reactant: 973301
reactant: 973289
fast: false
reversible: false
name: Activation3

973313
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

973301
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

973289
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

COPASI70
type: Reaction
kinetic law: 972263
product: 972251
reactant: 972239
reactant: 972227
fast: false
reversible: false
name: Activation1

972251
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

972239
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

972227
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

COPASI72
type: Reaction
kinetic law: 972359
product: 972347
reactant: 972335
reactant: 972323
fast: false
reversible: false
name: Annihilation1

972347
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

972335
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

972323
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI95
type: Reaction
kinetic law: 973601
product: 973589
product: 973577
product: 973565
reactant: 973553
fast: false
reversible: false
name: RNAPcat6

973589
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

973577
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

973565
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

973553
type: SpeciesReference
stoichiometry: 1.0
species: COPASI25