MODEL1012090004
type: SBMLModel
species: COPASI26
reaction: COPASI74
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.
reaction: COPASI95
reaction: COPASI97
species: COPASI11
volume units: volume
reaction: COPASI77
reaction: COPASI79
parameter: COPASI41
parameter: COPASI45
compartment: 133252
parameter: COPASI62
species: COPASI5
parameter: COPASI64
parameter: COPASI28
reaction: COPASI83
parameter: COPASI68
reaction: COPASI85
parameter: COPASI48
species: COPASI17
parameter: COPASI50
parameter: COPASI52
species: COPASI15
parameter: COPASI56
parameter: COPASI36
parameter: COPASI38
parameter: COPASI55
curated: false
initial assignment: MODEL1012090004#
parameter: COPASI59
species: COPASI18
substance units: substance
reaction: COPASI88
reaction: COPASI96
reaction: COPASI94
species: COPASI27
reaction: COPASI76
species: COPASI23
species: COPASI7
species: COPASI21
area units: area
species: COPASI20
species: COPASI9
length unit: length
reaction: COPASI78
species: COPASI3
is described by: http://identifiers.org/pubmed/21283141
species: COPASI2
reaction: COPASI99
parameter: COPASI61
parameter: COPASI63
parameter: COPASI43
parameter: COPASI47
parameter: COPASI49
species: COPASI6
name: Kim2011_Oscillator_DetailedIII
parameter: COPASI31
parameter: COPASI33
parameter: COPASI71
parameter: COPASI35
reaction: COPASI80
reaction: COPASI82
species: COPASI12
parameter: COPASI66
species: COPASI25
species: COPASI24
reaction: COPASI87
reaction: COPASI91
reaction: COPASI89
species: COPASI19
reaction: COPASI93
parameter: COPASI54
reaction: COPASI73
parameter: COPASI58
reaction: COPASI75
species: COPASI8
species: COPASI10
time units: time

COPASI26
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: A3rI3

133252
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

COPASI74
type: Reaction
kinetic law: 964976
product: 964964
reactant: 964952
reactant: 964940
fast: false
reversible: false
name: Activation2

964964
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: 133252
name: T31A1

964952
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI5
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 133252
name: A1

964940
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI4
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-7
initial amount: NaN
in compartment: 133252
name: T31

COPASI95
type: Reaction
kinetic law: 966073
product: 966061
reactant: 966049
reactant: 966037
fast: false
reversible: true
name: RNAPbinding6

966061
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: 133252
name: RNAPT23

966049
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

COPASI22
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-7
initial amount: NaN
in compartment: 133252
name: T23

966037
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI14
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 7.5E-8
initial amount: NaN
in compartment: 133252
name: RNAP

COPASI97
type: Reaction
kinetic law: 966193
product: 966181
product: 966169
product: 966157
reactant: 966145
fast: false
reversible: false
name: RNAPcat6

966181
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

COPASI6
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: rI3

966169
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

966157
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

966145
type: SpeciesReference
stoichiometry: 1.0
species: COPASI25

COPASI25
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT31

COPASI11
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: A1rI1

COPASI77
type: Reaction
kinetic law: 965120
product: 965108
reactant: 965096
reactant: 965084
fast: false
reversible: false
name: Annihilation3

965108
type: SpeciesReference
stoichiometry: 1.0
species: COPASI26

965096
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

965084
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

COPASI12
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 133252
name: A3

COPASI79
type: Reaction
kinetic law: 965242
product: 965230
product: 965217
reactant: 965205
reactant: 965193
fast: false
reversible: false
name: Inhibition2

965230
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

965217
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

965205
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

COPASI7
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 7.5E-7
initial amount: NaN
in compartment: 133252
name: rI1

965193
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

COPASI41
type: Parameter
constant: true
value: 24000.0
name: kAI3

COPASI45
type: Parameter
constant: true
value: 267.0
name: kminusOFF12

COPASI62
type: Parameter
constant: true
value: 1.0E-7
name: T23tot

COPASI64
type: Parameter
constant: true
value: 0.83
name: ksminus1

COPASI28
type: Parameter
constant: true
value: 1.0E-7
name: T12tot

COPASI83
type: Reaction
kinetic law: 965434
product: 965422
reactant: 965410
reactant: 965398
fast: false
reversible: true
name: RNAPbinding4

965422
type: SpeciesReference
stoichiometry: 1.0
species: COPASI25

965410
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

965398
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI68
type: Parameter
constant: true
value: 0.05
name: kcatH3

COPASI85
type: Reaction
kinetic law: 965555
product: 965543
product: 965531
product: 965519
reactant: 965507
fast: false
reversible: false
name: RNAPcat2

965543
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

COPASI8
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: rI2

965531
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: 133252
name: T23A3

965519
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

965507
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: 133252
name: RNAPT23A3

COPASI48
type: Parameter
constant: true
value: 7.6
name: kminusH1

COPASI17
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT12

COPASI50
type: Parameter
constant: true
value: 0.08
name: kcatON12

COPASI52
type: Parameter
constant: true
value: 0.08
name: kcatON23

COPASI15
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 3.0E-8
initial amount: NaN
in compartment: 133252
name: RNaseH

COPASI56
type: Parameter
constant: true
value: 74000.0
name: kTA31

COPASI36
type: Parameter
constant: true
value: 74000.0
name: kTA12

COPASI38
type: Parameter
constant: true
value: 24000.0
name: kAI2

COPASI55
type: Parameter
constant: true
value: 0.05
name: kcatH2

COPASI2
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-7
initial amount: NaN
in compartment: 133252
name: T12

COPASI3
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 133252
name: A2

COPASI59
type: Parameter
constant: true
value: 267.0
name: kminusOFF31

COPASI88
type: Reaction
kinetic law: 965724
product: 965712
reactant: 965700
reactant: 965688
fast: false
reversible: true
name: RNaseHbinding1

965712
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: 133252
name: RNaseHA1rI1

965700
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

965688
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI96
type: Reaction
kinetic law: 966133
product: 966121
product: 966109
product: 966097
reactant: 966085
fast: false
reversible: false
name: RNAPcat5

966121
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

966109
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

966097
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

966085
type: SpeciesReference
stoichiometry: 1.0
species: COPASI24

COPASI24
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT31A1

COPASI94
type: Reaction
kinetic law: 966025
product: 966013
reactant: 966001
reactant: 965989
fast: false
reversible: true
name: RNAPbinding5

966013
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

966001
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

965989
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI27
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNaseHA3rI3

COPASI76
type: Reaction
kinetic law: 965072
product: 965060
reactant: 965048
reactant: 965036
fast: false
reversible: false
name: Annihilation2

965060
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: 133252
name: A2rI2

965048
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

965036
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

COPASI21
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNaseHA2rI2

COPASI9
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: T12A2

COPASI78
type: Reaction
kinetic law: 965181
product: 965169
product: 965157
reactant: 965145
reactant: 965132
fast: false
reversible: false
name: Inhibition1

965169
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

965157
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

965145
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

965132
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

COPASI99
type: Reaction
kinetic law: 966291
product: 966279
product: 966267
reactant: 966255
fast: false
reversible: false
name: RNaseHcat3

966279
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

966267
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

966255
type: SpeciesReference
stoichiometry: 1.0
species: COPASI27

COPASI61
type: Parameter
constant: true
value: 0.02
name: kcatOFF31

COPASI63
type: Parameter
constant: true
value: 4120.0
name: ksplus1

COPASI43
type: Parameter
constant: true
value: 1.0E8
name: kplusH

COPASI47
type: Parameter
constant: true
value: 267.0
name: kminusOFF23

COPASI49
type: Parameter
constant: true
value: 7.6
name: kminusH2

COPASI31
type: Parameter
constant: true
value: 5.0E-7
name: A3tot

COPASI33
type: Parameter
constant: true
value: 7.5E-8
name: RNAPtot

COPASI71
type: Parameter
constant: true
value: 6730.0
name: ksplus3

COPASI35
type: Parameter
constant: true
value: 74000.0
name: kTA23

COPASI80
type: Reaction
kinetic law: 965290
product: 965278
reactant: 965266
reactant: 965254
fast: false
reversible: true
name: RNAPbinding1

965278
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

COPASI16
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT12A2

965266
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

965254
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI82
type: Reaction
kinetic law: 965386
product: 965374
reactant: 965362
reactant: 965350
fast: false
reversible: true
name: RNAPbinding3

965374
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

965362
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

965350
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI66
type: Parameter
constant: true
value: 0.0
name: rI2init

COPASI87
type: Reaction
kinetic law: 965676
product: 965664
product: 965652
product: 965640
reactant: 965628
fast: false
reversible: false
name: RNAPcat4

965664
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

965652
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

965640
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

965628
type: SpeciesReference
stoichiometry: 1.0
species: COPASI19

COPASI91
type: Reaction
kinetic law: 965869
product: 965857
product: 965844
reactant: 965832
fast: false
reversible: false
name: RNaseHcat2

965857
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

965844
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

965832
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

COPASI89
type: Reaction
kinetic law: 965772
product: 965760
reactant: 965748
reactant: 965736
fast: false
reversible: true
name: RNaseHbinding2

965760
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

965748
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

965736
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI93
type: Reaction
kinetic law: 965977
product: 965965
product: 965953
reactant: 965941
reactant: 965929
fast: false
reversible: false
name: Inhibition3

965965
type: SpeciesReference
stoichiometry: 1.0
species: COPASI26

965953
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

965941
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

965929
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

COPASI54
type: Parameter
constant: true
value: 0.05
name: kcatH1

COPASI73
type: Reaction
kinetic law: 964928
product: 964916
reactant: 964904
reactant: 964892
fast: false
reversible: false
name: Activation1

964916
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

964904
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

964892
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

COPASI58
type: Parameter
constant: true
value: 24.8
name: kminusON31

COPASI75
type: Reaction
kinetic law: 965024
product: 965012
reactant: 965000
reactant: 964988
fast: false
reversible: false
name: Annihilation1

965012
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

965000
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

964988
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI98
type: Reaction
kinetic law: 966243
product: 966231
reactant: 966218
reactant: 966205
fast: false
reversible: true
name: RNaseHbinding3

966231
type: SpeciesReference
stoichiometry: 1.0
species: COPASI27

966218
type: SpeciesReference
stoichiometry: 1.0
species: COPASI26

966205
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI60
type: Parameter
constant: true
value: 0.08
name: kcatON31

COPASI40
type: Parameter
constant: true
value: 53000.0
name: kTAI12

COPASI81
type: Reaction
kinetic law: 965338
product: 965326
reactant: 965314
reactant: 965302
fast: false
reversible: true
name: RNAPbinding2

965326
type: SpeciesReference
stoichiometry: 1.0
species: COPASI24

965314
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

965302
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI42
type: Parameter
constant: true
value: 1.0E8
name: kplus

COPASI44
type: Parameter
constant: true
value: 24.8
name: kminusON12

COPASI46
type: Parameter
constant: true
value: 24.8
name: kminusON23

COPASI65
type: Parameter
constant: true
value: 7.5E-7
name: rI1init

COPASI29
type: Parameter
constant: true
value: 1.0E-7
name: T31tot

COPASI67
type: Parameter
constant: true
value: 7.6
name: kminusH3

COPASI30
type: Parameter
constant: true
value: 5.0E-7
name: A1tot

COPASI32
type: Parameter
constant: true
value: 5.0E-7
name: A2tot

COPASI69
type: Parameter
constant: true
value: 13100.0
name: ksplus2

COPASI72
type: Parameter
constant: true
value: 0.59
name: ksminus3

COPASI70
type: Parameter
constant: true
value: 0.62
name: ksminus2

COPASI34
type: Parameter
constant: true
value: 3.0E-8
name: RNaseHtot

COPASI51
type: Parameter
constant: true
value: 0.02
name: kcatOFF12

COPASI53
type: Parameter
constant: true
value: 0.02
name: kcatOFF23

COPASI57
type: Parameter
constant: true
value: 53000.0
name: kTAI31

COPASI37
type: Parameter
constant: true
value: 24000.0
name: kAI1

COPASI39
type: Parameter
constant: true
value: 53000.0
name: kTAI23

COPASI84
type: Reaction
kinetic law: 965495
product: 965483
product: 965471
product: 965458
reactant: 965446
fast: false
reversible: false
name: RNAPcat1

965483
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

965471
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

965458
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

965446
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

COPASI86
type: Reaction
kinetic law: 965616
product: 965604
product: 965592
product: 965580
reactant: 965567
fast: false
reversible: false
name: RNAPcat3

965604
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

965592
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

965580
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

965567
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

COPASI90
type: Reaction
kinetic law: 965820
product: 965808
product: 965796
reactant: 965784
fast: false
reversible: false
name: RNaseHcat1

965808
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

965796
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

965784
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20

COPASI92
type: Reaction
kinetic law: 965917
product: 965905
reactant: 965893
reactant: 965881
fast: false
reversible: false
name: Activation3

965905
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

965893
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

965881
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22