//proteindomain/cleavage
type: Collection
persistent identity: proteindomain cleavage
display id: proteindomain_cleavage
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
owned by: james
owned by: myers
member: BBa_I712015
member: BBa_K772009
member: TEVsite
member: BBa_K772002
member: AnIn
member: BBa_K772103
member: BBa_K648009
member: BBa_K1680013
member: Intein
member: BBa_I712016
member: BBa_K772008
member: AnRe
member: preSCsite
member: TEV cut si
member: BBa_K648008
member: BBa_K772001
member: BBa_K772100
member: BBa_K1680012

AnIn
type: ComponentDefinition
persistent identity: BBa K772007
display id: BBa_K772007
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: GFP - LasR anchor-inducer protein complex
creator: Mustafa Elitok
created: 2012-09-25T11:00:00Z
modified: 2015-05-08T01:13:15Z
discontinued: false
dominant: false
experience: experience/None
group u list: _1024_
m user id: 0
owner id: 9573
owning group id: 9
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: This part contains a green fluorescent protein (GFP) as a non-reactive chemical compound (anchor) in order to neutralize the active reactive fixed to it, an inducer regulatory protein (LasR is responsible to induce pLas promoter in the presence of 6HSLO3 which is a chemical compound sythesized by an enzyme that LasI gene codes.) and a TEV protease cleavage site between them to assemble these two proteins. BBa_772001 and BBa_K772002 are assembled to be used as the trigger of detection in the whole system which ends with the intracellular transfection (or activation) of TEV protease. After the activation, it is planned that TEV protease will cleave this anchor-inducer protein complex to release free the reporter. In conclusion, in this system, the inducer would activate a transcription pathway on the targeted inducible gene or the reporter would indicate that there is a change in the whole system.
mutable notes: Cleavage site, LasR and GFP sequences are gathered from Registry.
mutable provenance: Note that there is an RBS sequence just before the protein sequence in order to eliminate the need of addition of it.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/Translational Unit
role: SO:0000804
sequence annotation: GFP
sequence annotation: RBS
sequence annotation: LasR
sequence annotation: Double Terminator
sequence annotation: Anchor - Inducer
sequence annotation: TEV cleavage site
sequence: https://synbiohub.org/public/igem/BBa_K772007_sequence/1

GFP
type: SequenceAnnotation
persistent identity: annotation2203899
display id: annotation2203899
version: 1
top level: AnIn
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772007/annotation2203899/range2203899/1

https://synbiohub.org/public/igem/BBa_K772007/annotation2203899/range2203899/1
type: Range
persistent identity: range2203899
display id: range2203899
version: 1
direction: direction/forward
top level: AnIn
start: 21
end: 741
orientation: inline

RBS
type: SequenceAnnotation
persistent identity: annotation2203898
display id: annotation2203898
version: 1
top level: AnIn
role: feature/rbs
role: SO:0000139
location: https://synbiohub.org/public/igem/BBa_K772007/annotation2203898/range2203898/1

https://synbiohub.org/public/igem/BBa_K772007/annotation2203898/range2203898/1
type: Range
persistent identity: range2203898
display id: range2203898
version: 1
direction: direction/forward
top level: AnIn
start: 1
end: 20
orientation: inline

LasR
type: SequenceAnnotation
persistent identity: annotation2203901
display id: annotation2203901
version: 1
top level: AnIn
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772007/annotation2203901/range2203901/1

https://synbiohub.org/public/igem/BBa_K772007/annotation2203901/range2203901/1
type: Range
persistent identity: range2203901
display id: range2203901
version: 1
direction: direction/forward
top level: AnIn
start: 880
end: 1636
orientation: inline

Double Terminator
type: SequenceAnnotation
persistent identity: annotation2203909
display id: annotation2203909
version: 1
top level: AnIn
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K772007/annotation2203909/range2203909/1

https://synbiohub.org/public/igem/BBa_K772007/annotation2203909/range2203909/1
type: Range
persistent identity: range2203909
display id: range2203909
version: 1
direction: direction/forward
top level: AnIn
start: 1636
end: 1720
orientation: inline

Anchor - Inducer
type: SequenceAnnotation
persistent identity: annotation2203902
display id: annotation2203902
version: 1
top level: AnIn
role: SO:0000316
role: feature/protein
location: https://synbiohub.org/public/igem/BBa_K772007/annotation2203902/range2203902/1

https://synbiohub.org/public/igem/BBa_K772007/annotation2203902/range2203902/1
type: Range
persistent identity: range2203902
display id: range2203902
version: 1
direction: direction/forward
top level: AnIn
start: 21
end: 1636
orientation: inline

TEV cleavage site
type: SequenceAnnotation
persistent identity: annotation2203900
display id: annotation2203900
version: 1
top level: AnIn
role: feature/cds
role: SO:0000316
location: https://synbiohub.org/public/igem/BBa_K772007/annotation2203900/range2203900/1

https://synbiohub.org/public/igem/BBa_K772007/annotation2203900/range2203900/1
type: Range
persistent identity: range2203900
display id: range2203900
version: 1
direction: direction/forward
top level: AnIn
start: 782
end: 871
orientation: inline

TEV cut si
type: ComponentDefinition
persistent identity: BBa K128002
display id: BBa_K128002
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: TEV tobacco etch virus protease cleavage site
creator: Sara Mouradian
created: 2008-07-09T11:00:00Z
modified: 2015-05-08T01:09:46Z
discontinued: false
dominant: false
experience: experience/None
group u list: _178_
m user id: 0
owner id: 2822
owning group id: 9
sample status: In stock
status: status/Available
bookmark: false
mutable description: This codes for the seven amino acid sequences that is recognized by the Tobacco Etch Virus protease. The amino acid sequenced used is: Glu-Asn-Leu-Tyr-Phe-Gln-Gly. The TEV protease cuts between Gln and Gly. It is often used in Ni-Nta protein column purifications to cut off the binding tag. This part uses the modified Silver BioBrick prefix and suffix to allow for protein construction.
mutable notes: The TEV cut site is almost always used in conjunction with other peptides, either to release the protein of interest from a binding assay, or to cut two proteins apart post-translationally. Because of this, we used the modified Silver BioBrick prefix and suffix to make the construction of funcitonal fusion peptides possible.
mutable provenance: This is the cut sequence for TEV protease put forth by the Dougherty Lab (North Carolina State University). The general form is E-X-X-Y-X-Q-(G/S), but ENLYFQS was found to be most efficient
owned by: james
owned by: myers
star: true
type: DnaRegion
role: SO:0000324
role: partType/Tag
sequence annotation: TEV cut site
sequence: https://synbiohub.org/public/igem/BBa_K128002_sequence/1

TEV cut site
type: SequenceAnnotation
persistent identity: annotation1966491
display id: annotation1966491
version: 1
top level: TEV cut si
role: SO:0000324
role: feature/tag
location: https://synbiohub.org/public/igem/BBa_K128002/annotation1966491/range1966491/1

https://synbiohub.org/public/igem/BBa_K128002/annotation1966491/range1966491/1
type: Range
persistent identity: range1966491
display id: range1966491
version: 1
direction: direction/forward
top level: TEV cut si
start: 1
end: 21
orientation: inline

BBa_K1680013
type: ComponentDefinition
persistent identity: BBa K1680013
display id: BBa_K1680013
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: NDegron
creator: Katharina Sporbeck
created: 2015-09-16T11:00:00Z
modified: 2015-10-27T01:42:39Z
discontinued: false
dominant: false
experience: experience/None
group u list: _2098_
m user id: 15693
owner id: 26460
owning group id: 9
status: status/Planning
bookmark: false
mutable description: Protein coding region for the firefly [Photinus pyralis] luciferase, codon optimized for yeast.
mutable notes: Shipped in RFC10
mutable provenance: gBlock designed by Team Tuebingen
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/Coding
role: SO:0000316
sequence annotation: SV40 NLS
sequence annotation: Spacer
sequence annotation: Nuclear export sequence
sequence annotation: TEV cleavage sites
sequence annotation: NDegron
sequence: https://synbiohub.org/public/igem/BBa_K1680013_sequence/1

SV40 NLS
type: SequenceAnnotation
persistent identity: annotation2477348
display id: annotation2477348
version: 1
top level: BBa_K1680013
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K1680013/annotation2477348/range2477348/1

https://synbiohub.org/public/igem/BBa_K1680013/annotation2477348/range2477348/1
type: Range
persistent identity: range2477348
display id: range2477348
version: 1
direction: direction/forward
top level: BBa_K1680013
start: 13
end: 33
orientation: inline

Spacer
type: SequenceAnnotation
persistent identity: annotation2477352
display id: annotation2477352
version: 1
top level: BBa_K1680013
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K1680013/annotation2477352/range2477352/1

https://synbiohub.org/public/igem/BBa_K1680013/annotation2477352/range2477352/1
type: Range
persistent identity: range2477352
display id: range2477352
version: 1
direction: direction/forward
top level: BBa_K1680013
start: 34
end: 66
orientation: inline

Nuclear export sequence
type: SequenceAnnotation
persistent identity: annotation2477351
display id: annotation2477351
version: 1
top level: BBa_K1680013
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K1680013/annotation2477351/range2477351/1

https://synbiohub.org/public/igem/BBa_K1680013/annotation2477351/range2477351/1
type: Range
persistent identity: range2477351
display id: range2477351
version: 1
direction: direction/forward
top level: BBa_K1680013
start: 130
end: 147
orientation: inline

TEV cleavage sites
type: SequenceAnnotation
persistent identity: annotation2477349
display id: annotation2477349
version: 1
top level: BBa_K1680013
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K1680013/annotation2477349/range2477349/1

https://synbiohub.org/public/igem/BBa_K1680013/annotation2477349/range2477349/1
type: Range
persistent identity: range2477349
display id: range2477349
version: 1
direction: direction/forward
top level: BBa_K1680013
start: 67
end: 86
orientation: inline

NDegron
type: SequenceAnnotation
persistent identity: annotation2477350
display id: annotation2477350
version: 1
top level: BBa_K1680013
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K1680013/annotation2477350/range2477350/1

https://synbiohub.org/public/igem/BBa_K1680013/annotation2477350/range2477350/1
type: Range
persistent identity: range2477350
display id: range2477350
version: 1
direction: direction/forward
top level: BBa_K1680013
start: 97
end: 138
orientation: inline

NDegron
type: SequenceAnnotation
persistent identity: annotation2477347
display id: annotation2477347
version: 1
top level: BBa_K1680013
role: feature/cds
role: SO:0000316
location: https://synbiohub.org/public/igem/BBa_K1680013/annotation2477347/range2477347/1

https://synbiohub.org/public/igem/BBa_K1680013/annotation2477347/range2477347/1
type: Range
persistent identity: range2477347
display id: range2477347
version: 1
direction: direction/forward
top level: BBa_K1680013
start: 1
end: 165
orientation: inline

BBa_K772001
type: ComponentDefinition
persistent identity: BBa K772001
display id: BBa_K772001
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: EpCAM Binding Dock: C-terminus
creator: Mustafa Elitok
created: 2012-09-23T11:00:00Z
modified: 2015-05-08T01:13:15Z
discontinued: false
dominant: false
experience: experience/Works
group u list: _1024_
m user id: 0
owner id: 9573
owning group id: 9
sample status: Not in stock
status: status/Unavailable
bookmark: true
mutable description: This gene sequence includes an EpCAM (Epithelial Cell Adhesion Molecule) antigen binding domain, OmpA transmembrane protein (dock) and TEV protease C terminus. It is planned to use this subpart with BBa_772, which contains only TEV protease N terminus differently instead of C terminus, in order to induce a signal reaction in the case of EpCAM presence. EpCAM is an natural antigen which is found high significantly in the cases of some breast and colorectal cancer subtypes. On the upstream region of protein sequence, there are a constitutive pLac promoter and appropiate RBS. To see how this part works: Experience.
mutable notes: There are two protein sequences between domains and the dock: One between the binding domain (antibody) and dock and one between the part of TEV protease.
mutable provenance: CD225 (EpCAM antibody) is commonly used for the test of presence of EpCAM in the laboratories. The sequences of OmpA and TEV protease terminuses are acquired from the Registry.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/Translational Unit
role: SO:0000804
sequence annotation: pCons Promoter
sequence annotation: RBS
sequence annotation: TEV Protease C terminus
sequence annotation: OmpA (Dock)
sequence annotation: CD215 Antibody
sequence annotation: Binding Dock
sequence: https://synbiohub.org/public/igem/BBa_K772001_sequence/1

pCons Promoter
type: SequenceAnnotation
persistent identity: annotation2203669
display id: annotation2203669
version: 1
top level: BBa_K772001
role: SO:0000167
role: feature/promoter
location: https://synbiohub.org/public/igem/BBa_K772001/annotation2203669/range2203669/1

https://synbiohub.org/public/igem/BBa_K772001/annotation2203669/range2203669/1
type: Range
persistent identity: range2203669
display id: range2203669
version: 1
direction: direction/forward
top level: BBa_K772001
start: 1
end: 72
orientation: inline

RBS
type: SequenceAnnotation
persistent identity: annotation2203670
display id: annotation2203670
version: 1
top level: BBa_K772001
role: feature/rbs
role: SO:0000139
location: https://synbiohub.org/public/igem/BBa_K772001/annotation2203670/range2203670/1

https://synbiohub.org/public/igem/BBa_K772001/annotation2203670/range2203670/1
type: Range
persistent identity: range2203670
display id: range2203670
version: 1
direction: direction/forward
top level: BBa_K772001
start: 73
end: 93
orientation: inline

TEV Protease C terminus
type: SequenceAnnotation
persistent identity: annotation2203672
display id: annotation2203672
version: 1
top level: BBa_K772001
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772001/annotation2203672/range2203672/1

https://synbiohub.org/public/igem/BBa_K772001/annotation2203672/range2203672/1
type: Range
persistent identity: range2203672
display id: range2203672
version: 1
direction: direction/forward
top level: BBa_K772001
start: 94
end: 419
orientation: inline

OmpA (Dock)
type: SequenceAnnotation
persistent identity: annotation2203671
display id: annotation2203671
version: 1
top level: BBa_K772001
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772001/annotation2203671/range2203671/1

https://synbiohub.org/public/igem/BBa_K772001/annotation2203671/range2203671/1
type: Range
persistent identity: range2203671
display id: range2203671
version: 1
direction: direction/forward
top level: BBa_K772001
start: 420
end: 857
orientation: inline

CD215 Antibody
type: SequenceAnnotation
persistent identity: annotation2203673
display id: annotation2203673
version: 1
top level: BBa_K772001
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772001/annotation2203673/range2203673/1

https://synbiohub.org/public/igem/BBa_K772001/annotation2203673/range2203673/1
type: Range
persistent identity: range2203673
display id: range2203673
version: 1
direction: direction/forward
top level: BBa_K772001
start: 858
end: 1159
orientation: inline

Binding Dock
type: SequenceAnnotation
persistent identity: annotation2203674
display id: annotation2203674
version: 1
top level: BBa_K772001
role: SO:0000316
role: feature/protein
location: https://synbiohub.org/public/igem/BBa_K772001/annotation2203674/range2203674/1

https://synbiohub.org/public/igem/BBa_K772001/annotation2203674/range2203674/1
type: Range
persistent identity: range2203674
display id: range2203674
version: 1
direction: direction/forward
top level: BBa_K772001
start: 94
end: 1159
orientation: inline

BBa_K772002
type: ComponentDefinition
persistent identity: BBa K772002
display id: BBa_K772002
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: EpCAM Binding Dock: N terminus
creator: Mustafa Elitok
created: 2012-09-23T11:00:00Z
modified: 2015-05-08T01:13:15Z
discontinued: false
dominant: false
experience: experience/Works
group u list: _1024_
m user id: 0
owner id: 9573
owning group id: 9
sample status: Not in stock
status: status/Unavailable
bookmark: true
mutable description: This gene sequence includes an EpCAM (Epithelial p? Cell Adhesion Molecule) antigen binding domain, OmpA transmembrane protein (dock) and TEV protease N terminus. It is planned to use this subpart with BBa_772, which contains only TEV protease C terminus differently instead of N terminus, in order to induce a signal reaction in the case of EpCAM presence. EpCAM is an natural antigen which is found high significantly in the cases of some breast and colorectal cancer subtypes. On the upstream region of protein sequence, there are a constitutive pLac promoter and appropiate RBS. To see how this part works: Experience.
mutable notes: There are two protein sequences between domains and the dock: One between the binding domain (antibody) and dock and one between the part of TEV protease.
mutable provenance: CD225 (EpCAM antibody) is commonly used for the test of presence of EpCAM in the laboratories. The sequences of OmpA and TEV protease terminuses are acquired from the Registry.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/Translational Unit
role: SO:0000804
sequence annotation: RBS
sequence annotation: TEV Protease N terminus
sequence annotation: OmpA (Dock)
sequence annotation: pCons Promoter
sequence annotation: CD215 antibody
sequence annotation: Binding Dock
sequence: https://synbiohub.org/public/igem/BBa_K772002_sequence/1

RBS
type: SequenceAnnotation
persistent identity: annotation2203683
display id: annotation2203683
version: 1
top level: BBa_K772002
role: feature/rbs
role: SO:0000139
location: https://synbiohub.org/public/igem/BBa_K772002/annotation2203683/range2203683/1

https://synbiohub.org/public/igem/BBa_K772002/annotation2203683/range2203683/1
type: Range
persistent identity: range2203683
display id: range2203683
version: 1
direction: direction/forward
top level: BBa_K772002
start: 73
end: 93
orientation: inline

TEV Protease N terminus
type: SequenceAnnotation
persistent identity: annotation2203685
display id: annotation2203685
version: 1
top level: BBa_K772002
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772002/annotation2203685/range2203685/1

https://synbiohub.org/public/igem/BBa_K772002/annotation2203685/range2203685/1
type: Range
persistent identity: range2203685
display id: range2203685
version: 1
direction: direction/forward
top level: BBa_K772002
start: 94
end: 398
orientation: inline

OmpA (Dock)
type: SequenceAnnotation
persistent identity: annotation2203682
display id: annotation2203682
version: 1
top level: BBa_K772002
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772002/annotation2203682/range2203682/1

https://synbiohub.org/public/igem/BBa_K772002/annotation2203682/range2203682/1
type: Range
persistent identity: range2203682
display id: range2203682
version: 1
direction: direction/forward
top level: BBa_K772002
start: 399
end: 836
orientation: inline

pCons Promoter
type: SequenceAnnotation
persistent identity: annotation2203681
display id: annotation2203681
version: 1
top level: BBa_K772002
role: SO:0000167
role: feature/promoter
location: https://synbiohub.org/public/igem/BBa_K772002/annotation2203681/range2203681/1

https://synbiohub.org/public/igem/BBa_K772002/annotation2203681/range2203681/1
type: Range
persistent identity: range2203681
display id: range2203681
version: 1
direction: direction/forward
top level: BBa_K772002
start: 1
end: 72
orientation: inline

CD215 antibody
type: SequenceAnnotation
persistent identity: annotation2203686
display id: annotation2203686
version: 1
top level: BBa_K772002
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772002/annotation2203686/range2203686/1

https://synbiohub.org/public/igem/BBa_K772002/annotation2203686/range2203686/1
type: Range
persistent identity: range2203686
display id: range2203686
version: 1
direction: direction/forward
top level: BBa_K772002
start: 837
end: 1138
orientation: inline

Binding Dock
type: SequenceAnnotation
persistent identity: annotation2203684
display id: annotation2203684
version: 1
top level: BBa_K772002
role: SO:0000316
role: feature/protein
location: https://synbiohub.org/public/igem/BBa_K772002/annotation2203684/range2203684/1

https://synbiohub.org/public/igem/BBa_K772002/annotation2203684/range2203684/1
type: Range
persistent identity: range2203684
display id: range2203684
version: 1
direction: direction/forward
top level: BBa_K772002
start: 94
end: 1138
orientation: inline

TEVsite
type: ComponentDefinition
persistent identity: BBa J18918
display id: BBa_J18918
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: TEV cleavage site (E. coli)
creator: Raik Gruenberg
created: 2010-01-26T12:00:00Z
modified: 2015-08-31T04:08:36Z
discontinued: false
dominant: true
experience: experience/None
group u list: _165_
m user id: 0
owner id: 2175
owning group id: 165
sample status: It's complicated
status: status/Planning
bookmark: false
mutable description: TEV cleaves the following AA sequence with high specificity: * Glu-Asn-Leu-Tyr-Phe-Gln↓Gly but: * Glu-Asn-Leu-Tyr-Phe-Gln↓Ser is also reported Note, the part suggested by the Voigt lab, also contains 2 additional 1xGly flanks for increased accessibility. See also: * BBa_I712077 (TEV N-term) * BBa_I712078 (TEV C-term) * BBa_I712016 (myri+TEV site, Slovenia team igem2007) * BBa_J64007 (Dan Widmaier, Voigt lab) References =========== Dougherty et al. (1989): Molecular genetic analysis of a plant virus polyprotein cleavage site: a model. PMID: 2669323
mutable notes: * gene synthesis * codon optimized for E. coli
mutable provenance: gene synthesis
owned by: james
owned by: myers
star: false
type: DnaRegion
role: SO:0000417
role: partType/Protein Domain
sequence: https://synbiohub.org/public/igem/BBa_J18918_sequence/1

BBa_I712015
type: ComponentDefinition
persistent identity: BBa I712015
display id: BBa_I712015
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: HIV-1 protease cleavage site
creator: Katja Kolar
created: 2007-10-20T11:00:00Z
modified: 2015-08-31T04:07:46Z
discontinued: false
dominant: false
experience: experience/Works
group u list: _130_
m user id: 0
owner id: 1883
owning group id: 9
sample status: In stock
status: status/Available
bookmark: false
mutable description: This is proteolytic cleavage site for HIV-1 protease.
owned by: james
owned by: myers
star: true
type: DnaRegion
role: SO:0000324
role: partType/Tag
sequence: https://synbiohub.org/public/igem/BBa_I712015_sequence/1

BBa_K1680012
type: ComponentDefinition
persistent identity: BBa K1680012
display id: BBa_K1680012
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: Cleavage site for HCV protease
creator: Katharina Sporbeck
created: 2015-09-16T11:00:00Z
modified: 2015-10-27T01:43:40Z
discontinued: false
dominant: false
group u list: _2098_
m user id: 15693
owner id: 26460
owning group id: 9
status: status/Planning
bookmark: false
mutable description: Protein coding region for the cleavage site of the HCV NS3-4A protease (Part BBa_K1680011).
mutable notes: Shipped in RFC 25
mutable provenance: gBlock designed by Team Tuebingen
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/Coding
role: SO:0000316
sequence: https://synbiohub.org/public/igem/BBa_K1680012_sequence/1

BBa_I712016
type: ComponentDefinition
persistent identity: BBa I712016
display id: BBa_I712016
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: myristoilation signal sequence fused to Tobacco Etch Virus (TEV) protease cleavage site
creator: Katja Kolar
created: 2007-10-22T11:00:00Z
modified: 2015-08-31T04:07:46Z
discontinued: false
dominant: false
experience: experience/Works
group u list: _130_
m user id: 0
owner id: 1883
owning group id: 9
sample status: In stock
status: status/Available
bookmark: false
mutable description: Signal sequence for myristoilation with proteolytic cleavage site for TEV protease.
owned by: james
owned by: myers
star: true
type: DnaRegion
role: SO:0000324
role: partType/Tag
sequence: https://synbiohub.org/public/igem/BBa_I712016_sequence/1

BBa_K772008
type: ComponentDefinition
persistent identity: BBa K772008
display id: BBa_K772008
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: GFP - LacZ protein complex with flag tags
creator: Mustafa Elitok
created: 2012-09-25T11:00:00Z
modified: 2015-05-08T01:13:15Z
discontinued: false
dominant: false
group u list: _1024_
m user id: 0
owner id: 9573
owning group id: 9
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: This part contains a green fluorescent protein (GFP) as a non-reactive chemical compound (anchor) in order to neutralize the active reactive fixed to it, a reporter device (LacZ enzyme catalyses the reaction of the cleavage of X-Gal which results with blue color change) and a TEV protease cleavage site between them to assemble these two proteins. BBa_772001 and BBa_K772002 are assembled to be used as the trigger of detection in the whole system which ends with the intracellular transfection (or activation) of TEV protease. After the activation, it is planned that TEV protease will cleave this anchor-inducer protein complex to release free the reporter. In conclusion, in this system, the inducer would activate a transcription pathway on the targeted inducible gene or the reporter would indicate that there is a change in the whole system. This part contains flag tags extra from BBa_K772006 in the GFP region; because it is planned to be used in the Co-IP/SDS-PAGE assay to be isolated.
mutable notes: Cleavage site, LacZ and GFP sequences are gathered from Registry.
mutable provenance: Note that there is an RBS sequence just before the protein sequence in order to eliminate the need of addition of it.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: SO:0000804
role: partType/Measurement
sequence annotation: Flag Tag
sequence annotation: TEV cleavage site
sequence annotation: Double Terminator
sequence annotation: GFP
sequence annotation: Anchor-Reporter + Flag
sequence annotation: RBS
sequence annotation: LacZ
sequence: https://synbiohub.org/public/igem/BBa_K772008_sequence/1

Flag Tag
type: SequenceAnnotation
persistent identity: annotation2203911
display id: annotation2203911
version: 1
top level: BBa_K772008
role: SO:0000324
role: feature/tag
location: https://synbiohub.org/public/igem/BBa_K772008/annotation2203911/range2203911/1

https://synbiohub.org/public/igem/BBa_K772008/annotation2203911/range2203911/1
type: Range
persistent identity: range2203911
display id: range2203911
version: 1
direction: direction/forward
top level: BBa_K772008
start: 21
end: 46
orientation: inline

TEV cleavage site
type: SequenceAnnotation
persistent identity: annotation2203913
display id: annotation2203913
version: 1
top level: BBa_K772008
role: feature/cds
role: SO:0000316
location: https://synbiohub.org/public/igem/BBa_K772008/annotation2203913/range2203913/1

https://synbiohub.org/public/igem/BBa_K772008/annotation2203913/range2203913/1
type: Range
persistent identity: range2203913
display id: range2203913
version: 1
direction: direction/forward
top level: BBa_K772008
start: 768
end: 857
orientation: inline

Double Terminator
type: SequenceAnnotation
persistent identity: annotation2203915
display id: annotation2203915
version: 1
top level: BBa_K772008
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K772008/annotation2203915/range2203915/1

https://synbiohub.org/public/igem/BBa_K772008/annotation2203915/range2203915/1
type: Range
persistent identity: range2203915
display id: range2203915
version: 1
direction: direction/forward
top level: BBa_K772008
start: 1102
end: 1232
orientation: inline

GFP
type: SequenceAnnotation
persistent identity: annotation2203912
display id: annotation2203912
version: 1
top level: BBa_K772008
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772008/annotation2203912/range2203912/1

https://synbiohub.org/public/igem/BBa_K772008/annotation2203912/range2203912/1
type: Range
persistent identity: range2203912
display id: range2203912
version: 1
direction: direction/forward
top level: BBa_K772008
start: 47
end: 767
orientation: inline

Anchor-Reporter + Flag
type: SequenceAnnotation
persistent identity: annotation2203916
display id: annotation2203916
version: 1
top level: BBa_K772008
role: SO:0000316
role: feature/protein
location: https://synbiohub.org/public/igem/BBa_K772008/annotation2203916/range2203916/1

https://synbiohub.org/public/igem/BBa_K772008/annotation2203916/range2203916/1
type: Range
persistent identity: range2203916
display id: range2203916
version: 1
direction: direction/forward
top level: BBa_K772008
start: 21
end: 1101
orientation: inline

RBS
type: SequenceAnnotation
persistent identity: annotation2203910
display id: annotation2203910
version: 1
top level: BBa_K772008
role: feature/rbs
role: SO:0000139
location: https://synbiohub.org/public/igem/BBa_K772008/annotation2203910/range2203910/1

https://synbiohub.org/public/igem/BBa_K772008/annotation2203910/range2203910/1
type: Range
persistent identity: range2203910
display id: range2203910
version: 1
direction: direction/forward
top level: BBa_K772008
start: 1
end: 20
orientation: inline

LacZ
type: SequenceAnnotation
persistent identity: annotation2203914
display id: annotation2203914
version: 1
top level: BBa_K772008
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772008/annotation2203914/range2203914/1

https://synbiohub.org/public/igem/BBa_K772008/annotation2203914/range2203914/1
type: Range
persistent identity: range2203914
display id: range2203914
version: 1
direction: direction/forward
top level: BBa_K772008
start: 858
end: 1101
orientation: inline

BBa_K772009
type: ComponentDefinition
persistent identity: BBa K772009
display id: BBa_K772009
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: GFP - LasR protein complex with flag tags
creator: Mustafa Elitok
created: 2012-09-25T11:00:00Z
modified: 2015-05-08T01:13:15Z
discontinued: false
dominant: false
group u list: _1024_
m user id: 0
owner id: 9573
owning group id: 9
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: This part contains a green fluorescent protein (GFP) as a non-reactive chemical compound (anchor) in order to neutralize the active reactive fixed to it, an inducer regulatory protein (LasR is responsible to induce pLas promoter in the presence of 6HSLO3 which is a chemical compound sythesized by an enzyme that LasI gene codes.) and a TEV protease cleavage site between them to assemble these two proteins. BBa_772001 and BBa_K772002 are assembled to be used as the trigger of detection in the whole system which ends with the intracellular transfection (or activation) of TEV protease. After the activation, it is planned that TEV protease will cleave this anchor-inducer protein complex to release free the reporter. In conclusion, in this system, the inducer would activate a transcription pathway on the targeted inducible gene or the reporter would indicate that there is a change in the whole system. This part contains flag tags extra from BBa_K772006 in the GFP region; because it is planned to be used in the Co-IP/SDS-PAGE assay to be isolated.
mutable notes: Note that there is an RBS sequence just before the protein sequence in order to eliminate the need of addition of it.
mutable provenance: Cleavage site, LasR and GFP sequences are gathered from Registry.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: SO:0000804
role: partType/Measurement
sequence annotation: Flag tag
sequence annotation: RBS
sequence annotation: GFP
sequence annotation: Double terminator
sequence annotation: LasR
sequence annotation: Anchor-inducer + flag
sequence annotation: TEV cleavage site
sequence: https://synbiohub.org/public/igem/BBa_K772009_sequence/1

Flag tag
type: SequenceAnnotation
persistent identity: annotation2203918
display id: annotation2203918
version: 1
top level: BBa_K772009
role: SO:0000324
role: feature/tag
location: https://synbiohub.org/public/igem/BBa_K772009/annotation2203918/range2203918/1

https://synbiohub.org/public/igem/BBa_K772009/annotation2203918/range2203918/1
type: Range
persistent identity: range2203918
display id: range2203918
version: 1
direction: direction/forward
top level: BBa_K772009
start: 21
end: 46
orientation: inline

RBS
type: SequenceAnnotation
persistent identity: annotation2203917
display id: annotation2203917
version: 1
top level: BBa_K772009
role: feature/rbs
role: SO:0000139
location: https://synbiohub.org/public/igem/BBa_K772009/annotation2203917/range2203917/1

https://synbiohub.org/public/igem/BBa_K772009/annotation2203917/range2203917/1
type: Range
persistent identity: range2203917
display id: range2203917
version: 1
direction: direction/forward
top level: BBa_K772009
start: 1
end: 20
orientation: inline

GFP
type: SequenceAnnotation
persistent identity: annotation2203919
display id: annotation2203919
version: 1
top level: BBa_K772009
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772009/annotation2203919/range2203919/1

https://synbiohub.org/public/igem/BBa_K772009/annotation2203919/range2203919/1
type: Range
persistent identity: range2203919
display id: range2203919
version: 1
direction: direction/forward
top level: BBa_K772009
start: 47
end: 767
orientation: inline

Double terminator
type: SequenceAnnotation
persistent identity: annotation2203922
display id: annotation2203922
version: 1
top level: BBa_K772009
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K772009/annotation2203922/range2203922/1

https://synbiohub.org/public/igem/BBa_K772009/annotation2203922/range2203922/1
type: Range
persistent identity: range2203922
display id: range2203922
version: 1
direction: direction/forward
top level: BBa_K772009
start: 1615
end: 1745
orientation: inline

LasR
type: SequenceAnnotation
persistent identity: annotation2203921
display id: annotation2203921
version: 1
top level: BBa_K772009
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772009/annotation2203921/range2203921/1

https://synbiohub.org/public/igem/BBa_K772009/annotation2203921/range2203921/1
type: Range
persistent identity: range2203921
display id: range2203921
version: 1
direction: direction/forward
top level: BBa_K772009
start: 858
end: 1614
orientation: inline

Anchor-inducer + flag
type: SequenceAnnotation
persistent identity: annotation2203923
display id: annotation2203923
version: 1
top level: BBa_K772009
role: SO:0000316
role: feature/protein
location: https://synbiohub.org/public/igem/BBa_K772009/annotation2203923/range2203923/1

https://synbiohub.org/public/igem/BBa_K772009/annotation2203923/range2203923/1
type: Range
persistent identity: range2203923
display id: range2203923
version: 1
direction: direction/forward
top level: BBa_K772009
start: 21
end: 1614
orientation: inline

TEV cleavage site
type: SequenceAnnotation
persistent identity: annotation2203920
display id: annotation2203920
version: 1
top level: BBa_K772009
role: feature/cds
role: SO:0000316
location: https://synbiohub.org/public/igem/BBa_K772009/annotation2203920/range2203920/1

https://synbiohub.org/public/igem/BBa_K772009/annotation2203920/range2203920/1
type: Range
persistent identity: range2203920
display id: range2203920
version: 1
direction: direction/forward
top level: BBa_K772009
start: 768
end: 857
orientation: inline

Intein
type: ComponentDefinition
persistent identity: BBa K1947002
display id: BBa_K1947002
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: Intein
creator: zhang xucheng
created: 2016-10-12T11:00:00Z
modified: 2016-10-14T02:59:19Z
discontinued: false
dominant: false
experience: experience/None
group u list: _2414_
m user id: 33528
owner id: 34115
owning group id: 9
status: status/Planning
bookmark: false
mutable description: This sequence encodes a short polypeptide which can be specifically recognized and spliced by DL-Dithiothreitol（DTT）. In our case we add this short sequence between the recombinant protein which we want to purify and the linker protein Spytag, in order to separate the recombinant protein form the Magnetosome.
mutable notes: Our project is to use Magnetosome to purify recombinant protein, and we need to remove the protein from the compound after the protein we are interested combined with Magnetosome. As this short polypeptide can be spliced by DTT, we can meet this need by adding the intein between the recombinant protein and magnetosome.
mutable provenance: This sequence comes form the gyrA gene of Mycobacterium xenopi
owned by: james
owned by: myers
star: false
type: DnaRegion
role: SO:0000417
role: partType/Protein Domain
sequence: https://synbiohub.org/public/igem/BBa_K1947002_sequence/1

AnRe
type: ComponentDefinition
persistent identity: BBa K772006
display id: BBa_K772006
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: GFP - LacZ anchor-inducer protein complex
creator: Mustafa Elitok
created: 2012-09-24T11:00:00Z
modified: 2015-05-08T01:13:15Z
discontinued: false
dominant: false
experience: experience/None
group u list: _1024_
m user id: 0
owner id: 9573
owning group id: 9
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: This part contains a green fluorescent protein (GFP) as a non-reactive chemical compound (anchor) in order to neutralize the active reactive fixed to it, a reporter/inducer device or protein (enzyme etc.) and a TEV protease cleavage site between them to assemble these two proteins. BBa_772001 and BBa_K772002 are assembled to be used as the trigger of detection in the whole system which ends with the intracellular transfection (or activation) of TEV protease. After the activation, it is planned that TEV protease will cleave this anchor-inducer protein complex to release free the inducer/reporter. In conclusion, the inducer would activate a transcription pathway on the targeted inducible gene or the reporter would indicate that there is a change in the whole system.
mutable notes: Note that there is an RBS sequence just before the protein sequence in order to eliminate the need of addition of it.
mutable provenance: Cleavage site, LacZ and GFP sequences are gathered from Registry.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/Translational Unit
role: SO:0000804
sequence annotation: LacZ
sequence annotation: RBS
sequence annotation: Double Terminator
sequence annotation: GFP
sequence annotation: Anchor - Reporter
sequence annotation: TEV cleavage site
sequence: https://synbiohub.org/public/igem/BBa_K772006_sequence/1

LacZ
type: SequenceAnnotation
persistent identity: annotation2203906
display id: annotation2203906
version: 1
top level: AnRe
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772006/annotation2203906/range2203906/1

https://synbiohub.org/public/igem/BBa_K772006/annotation2203906/range2203906/1
type: Range
persistent identity: range2203906
display id: range2203906
version: 1
direction: direction/forward
top level: AnRe
start: 832
end: 1075
orientation: inline

RBS
type: SequenceAnnotation
persistent identity: annotation2203903
display id: annotation2203903
version: 1
top level: AnRe
role: feature/rbs
role: SO:0000139
location: https://synbiohub.org/public/igem/BBa_K772006/annotation2203903/range2203903/1

https://synbiohub.org/public/igem/BBa_K772006/annotation2203903/range2203903/1
type: Range
persistent identity: range2203903
display id: range2203903
version: 1
direction: direction/forward
top level: AnRe
start: 1
end: 20
orientation: inline

Double Terminator
type: SequenceAnnotation
persistent identity: annotation2203907
display id: annotation2203907
version: 1
top level: AnRe
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K772006/annotation2203907/range2203907/1

https://synbiohub.org/public/igem/BBa_K772006/annotation2203907/range2203907/1
type: Range
persistent identity: range2203907
display id: range2203907
version: 1
direction: direction/forward
top level: AnRe
start: 1076
end: 1207
orientation: inline

GFP
type: SequenceAnnotation
persistent identity: annotation2203904
display id: annotation2203904
version: 1
top level: AnRe
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_K772006/annotation2203904/range2203904/1

https://synbiohub.org/public/igem/BBa_K772006/annotation2203904/range2203904/1
type: Range
persistent identity: range2203904
display id: range2203904
version: 1
direction: direction/forward
top level: AnRe
start: 21
end: 741
orientation: inline

Anchor - Reporter
type: SequenceAnnotation
persistent identity: annotation2203908
display id: annotation2203908
version: 1
top level: AnRe
role: SO:0000316
role: feature/protein
location: https://synbiohub.org/public/igem/BBa_K772006/annotation2203908/range2203908/1

https://synbiohub.org/public/igem/BBa_K772006/annotation2203908/range2203908/1
type: Range
persistent identity: range2203908
display id: range2203908
version: 1
direction: direction/forward
top level: AnRe
start: 21
end: 1075
orientation: inline

TEV cleavage site
type: SequenceAnnotation
persistent identity: annotation2203905
display id: annotation2203905
version: 1
top level: AnRe
role: feature/cds
role: SO:0000316
location: https://synbiohub.org/public/igem/BBa_K772006/annotation2203905/range2203905/1

https://synbiohub.org/public/igem/BBa_K772006/annotation2203905/range2203905/1
type: Range
persistent identity: range2203905
display id: range2203905
version: 1
direction: direction/forward
top level: AnRe
start: 742
end: 831
orientation: inline

BBa_K772103
type: ComponentDefinition
persistent identity: BBa K772103
display id: BBa_K772103
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: GFP - LacZ protein complex generator
creator: Mustafa Elitok
created: 2012-09-25T11:00:00Z
modified: 2015-05-08T01:13:15Z
discontinued: false
dominant: false
experience: experience/None
group u list: _1024_
m user id: 0
owner id: 9573
owning group id: 9
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: GFP - LacZ protein generator is generated with the aim of inducing a reporting reaction aftermath of the activation of EpCAM detection system. (BBa_K772100) For more information: BBa_K772006
mutable notes: To achieve a constitutive production, pTetR promoter is added in the upstream region of the original part.
mutable provenance: Cleavage site, LacZ and GFP sequences are gathered from Registry.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: SO:0000804
role: partType/Generator
component: BBa_R0040
component: BBa_K772006
sequence annotation: BBa_R0040
sequence annotation: BBa_K772006
sequence: https://synbiohub.org/public/igem/BBa_K772103_sequence/1

BBa_R0040
type: Component
persistent identity: component2211349
display id: component2211349
version: 1
top level: BBa_K772103
access: public
definition: https://synbiohub.org/public/igem/BBa_R0040/1

BBa_K772006
type: Component
persistent identity: component2211360
display id: component2211360
version: 1
top level: BBa_K772103
access: public
definition: AnRe

BBa_R0040
type: SequenceAnnotation
persistent identity: annotation2211349
display id: annotation2211349
version: 1
top level: BBa_K772103
location: https://synbiohub.org/public/igem/BBa_K772103/annotation2211349/range2211349/1
component: BBa_R0040

https://synbiohub.org/public/igem/BBa_K772103/annotation2211349/range2211349/1
type: Range
persistent identity: range2211349
display id: range2211349
version: 1
direction: direction/forward
top level: BBa_K772103
start: 1
end: 54
orientation: inline

BBa_K772006
type: SequenceAnnotation
persistent identity: annotation2211360
display id: annotation2211360
version: 1
top level: BBa_K772103
location: https://synbiohub.org/public/igem/BBa_K772103/annotation2211360/range2211360/1
component: BBa_K772006

https://synbiohub.org/public/igem/BBa_K772103/annotation2211360/range2211360/1
type: Range
persistent identity: range2211360
display id: range2211360
version: 1
direction: direction/reverse
top level: BBa_K772103
start: 63
end: 1269
orientation: inline

BBa_K648008
type: ComponentDefinition
persistent identity: BBa K648008
display id: BBa_K648008
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: TEV protease cleaveage site with Standard 25 Prefix/Suffix
creator: Jim Rose
created: 2011-07-03T11:00:00Z
modified: 2015-05-08T01:12:59Z
discontinued: false
dominant: false
experience: experience/None
group u list: _825_
m user id: 0
owner id: 9871
owning group id: 9
sample status: In stock
status: status/Available
bookmark: false
mutable description: This is the cleaveage site for th Tobacco etch virus(TEV) protease commonly used for cleaving fusion proteins. It encodes for the amino acids E N L Y F Q G which are cleaved by the TEV protease. This part also contains the prefix/suffix required for standard 25 assembly into fusion parts.
mutable notes: This part contains the AgeI and NgoMIV sites as part of it's prefix/suffix that allows it to be used in standard 25 assembly. This part was synthesized through PCR oligo synthesis methods using the following primers: Forward 5'---ATTAGAATTCGCGGCCGCTTCTAGATGGCCGGCGAGAATTTGTATTTTCAGGG---3' Reverse 5'---TAATCTGCAGCGGCCGCTACTAGTATTAACCGGTACCCTGAAAATACAAATTCTC---3'
mutable provenance: Phan, J., Zdanov, A., Evdokimov, A. G., Tropea, J. E., Peters, H. P. K., Kapust, R. B., Li, M., Wlodawer, A., and Waugh, D. S. (2002). Structural basis for the substrate specificity of tobacco etch virus protease. J. Biol. Chem. 277: 50564-50572.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: SO:0000417
role: partType/Protein Domain
sequence: https://synbiohub.org/public/igem/BBa_K648008_sequence/1

preSCsite
type: ComponentDefinition
persistent identity: BBa J18919
display id: BBa_J18919
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: preScission protease cleavage site (E. coli-optimized)
creator: Raik Gruenberg
created: 2010-01-26T12:00:00Z
modified: 2015-08-31T04:08:36Z
discontinued: false
dominant: false
experience: experience/Works
group u list: _165_
m user id: 0
owner id: 2175
owning group id: 165
sample status: It's complicated
status: status/Planning
bookmark: false
mutable description: cleavage site for PreScission??? protease. preScission protease cleavage site (PreScission??? protease is a genetically engineered form of human rhinovirus 3C protease with a GST fusion, allowing for facile cleavage and purification of GST-tagged proteins along with protease removal after recombinant protein cleavage. Enables low-temperature cleavage of fusion proteins containing the eight-residue recognition sequence.) cleavage site: * Leu-Glu-Val-Leu-Phe-Gln↓Gly-Pro References ============== Walker et al. (1994): Efficient and rapid affinity purification of proteins using recombinant fusion proteases. PMID: 7764949
mutable notes: * gene synthesis * codon optimized for E. coli
mutable provenance: gene synthesis
owned by: james
owned by: myers
star: false
type: DnaRegion
role: SO:0000417
role: partType/Protein Domain
sequence: https://synbiohub.org/public/igem/BBa_J18919_sequence/1

BBa_K648009
type: ComponentDefinition
persistent identity: BBa K648009
display id: BBa_K648009
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: RecA Cleavage Site with Standard 25 Prefix/Suffix
creator: Jim Rose
created: 2011-07-03T11:00:00Z
modified: 2015-05-08T01:12:59Z
discontinued: false
dominant: false
experience: experience/None
group u list: _825_
m user id: 0
owner id: 9871
owning group id: 9
sample status: It's complicated
status: status/Planning
bookmark: false
mutable description: This part encodes for the amino acids V Q A G M F S which are cleavage by the RecA protein within the cell. This sequence was taken from the CI repressor protein which is also cleaved by RecA.
mutable notes: This part contains the AgeI and NgoMIV sites as part of it's prefix/suffix that allows it to be used in standard 25 assembly. This part was synthesized through PCR oligo synthesis methods using the following primers: Forward Primer 5'---ATTAGAATTCGCGGCCGCTTCTAGATGGCCGGCgttCAGGCAGGGATGTTC---3??? Reverse Primer 5???---TAATCTGCAGCGGCCGCTACTAGTATTAACCGGTtgagaacatccctgcctg ---3???
mutable provenance: Kim, B, and Little, LB. "LexA and lambda Cl repressors as enzymes: specific cleavage in an intermolecular reaction.." Cell 73.6 (1993): 1165-73. Web. 4 Jul 2011. <http://www.ncbi.nlm.nih.gov/pubmed/8513500>.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: SO:0000417
role: partType/Protein Domain
sequence: https://synbiohub.org/public/igem/BBa_K648009_sequence/1

BBa_K772100
type: ComponentDefinition
persistent identity: BBa K772100
display id: BBa_K772100
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: EpCAM Detection Device
creator: Mustafa Elitok
created: 2012-09-25T11:00:00Z
modified: 2015-05-08T01:13:15Z
discontinued: false
dominant: false
experience: experience/Works
group u list: _1024_
m user id: 0
owner id: 9573
owning group id: 9
sample status: It's complicated
status: status/Planning
bookmark: true
mutable description: This gene sequence includes both of EpCAM Binding Docks; BBa_K772001 and BBa_K772002. Thus, this composite part is the main component of CTC (Circulating Tumor Cell) detection system. Docks include an EpCAM (Epithelial Cell Adhesion Molecule) antigen binding domain, OmpA transmembrane protein (dock) and TEV protease C or N terminus. Hopefully, after binding to the EpCAM antigen, TEV protease domains will fix together to form the full structure in order to activate the signalling pathway. (For more information: BBa_K772003) EpCAM is an natural antigen which is found high significantly in the cases of some breast and colorectal cancer subtypes. On the upstream region of protein sequences, there are a constitutive pLac promoter and appropriate RBS. To see how this part works: Experience.
mutable notes: There are two protein sequences between domains and the dock: One between the binding domain (antibody) and dock and one between the domain of TEV protease.
mutable provenance: CD225 (EpCAM antibody) is commonly used for the test of presence of EpCAM in the laboratories. The sequences of OmpA and TEV protease terminuses are acquired from the Registry.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: SO:0000804
role: partType/Project
component: BBa_K772001
component: BBa_K772002
sequence annotation: BBa_K772002
sequence annotation: BBa_K772001
sequence: https://synbiohub.org/public/igem/BBa_K772100_sequence/1

BBa_K772001
type: Component
persistent identity: component2211341
display id: component2211341
version: 1
top level: BBa_K772100
access: public
definition: BBa_K772001

BBa_K772002
type: Component
persistent identity: component2211348
display id: component2211348
version: 1
top level: BBa_K772100
access: public
definition: BBa_K772002

BBa_K772002
type: SequenceAnnotation
persistent identity: annotation2211348
display id: annotation2211348
version: 1
top level: BBa_K772100
location: https://synbiohub.org/public/igem/BBa_K772100/annotation2211348/range2211348/1
component: BBa_K772002

https://synbiohub.org/public/igem/BBa_K772100/annotation2211348/range2211348/1
type: Range
persistent identity: range2211348
display id: range2211348
version: 1
direction: direction/reverse
top level: BBa_K772100
start: 1168
end: 2305
orientation: inline

BBa_K772001
type: SequenceAnnotation
persistent identity: annotation2211341
display id: annotation2211341
version: 1
top level: BBa_K772100
location: https://synbiohub.org/public/igem/BBa_K772100/annotation2211341/range2211341/1
component: BBa_K772001

https://synbiohub.org/public/igem/BBa_K772100/annotation2211341/range2211341/1
type: Range
persistent identity: range2211341
display id: range2211341
version: 1
direction: direction/reverse
top level: BBa_K772100
start: 1
end: 1159
orientation: inline