//dna/bioscaffold
type: Collection
persistent identity: dna bioscaffold
display id: dna_bioscaffold
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
owned by: james
owned by: myers
member: BioScaffol
member: BBa_J70030
member: BBa_J70034
member: BBa_J70032
member: BBa_K259009
member: BBa_J70012
member: BBa_J70052
member: BBa_J70050
member: tetO array
member: BBa_J70036
member: BBa_K259008
member: BBa_J70040
member: BBa_J70010

tetO array
type: ComponentDefinition
persistent identity: BBa K606026
display id: BBa_K606026
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: tetO Array
creator: K??vin Yauy
created: 2011-07-26T11:00:00Z
modified: 2015-05-08T01:12:51Z
discontinued: false
dominant: false
experience: experience/Works
group u list: _778_
m user id: 0
owner id: 8972
owning group id: 9
sample status: It's complicated
status: status/Planning
bookmark: true
mutable description: tetO Array Contains lots of tetO where bind YFP:tetR (<partinfo>BBa_K606025</partinfo>).
mutable notes: Reduce sequence to avoid restriction sites
mutable provenance: Andrew Wright, Dave Lane, Fran??ois-Xavier Barre, pDAG479 plasmid.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/Coding
role: SO:0000316
sequence annotation: tetO array
sequence: https://synbiohub.org/public/igem/BBa_K606026_sequence/1

tetO array
type: SequenceAnnotation
persistent identity: annotation2124086
display id: annotation2124086
version: 1
top level: tetO array
role: SO:0000057
role: feature/operator
location: https://synbiohub.org/public/igem/BBa_K606026/annotation2124086/range2124086/1

https://synbiohub.org/public/igem/BBa_K606026/annotation2124086/range2124086/1
type: Range
persistent identity: range2124086
display id: range2124086
version: 1
direction: direction/forward
top level: tetO array
start: 1
end: 3628
orientation: inline

BBa_K259008
type: ComponentDefinition
persistent identity: BBa K259008
display id: BBa_K259008
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: BioScaffold Linker - Removes Stop Codons & scars & replaces with a Gly-Ser linker
creator: Petros Mina
created: 2009-10-12T11:00:00Z
modified: 2015-05-08T01:11:42Z
discontinued: false
dominant: false
group u list: _357_
m user id: 0
owner id: 5318
owning group id: 9
sample status: It's complicated
status: status/Planning
bookmark: false
mutable description: This part is part of a family of Bioscaffold - Linkers. This part will help users interested in protein-fusion. The usage of the part will allow in frame assembly of 2(+) proteins by: *Removing the stop codons from the upstream protein. *Removing the scar created by the Assembly Standard 10 (RFC10) construction of 2(+) protein coding sequences. *Maintaining the start codon of the downstream protein. *Adding a flexible (Gly-Ser-Gly) linker between the two protein coding sequences. *Acting as a translational buffer if ligation is incorrect. ===Assembly Instructions=== *Create an Assembly Standard 10 fusion as below ; **Upstream Protein Part - Bioscaffold Linker - Downstream Protein Part** *Use the BioScaffold Specific Enzymes (i)Restrict with BpuEI to remove upstream scar (created between Upstream Protein - Bioscaffold) and stop codons from upstream protein part. (ii)Ligate and you will get the intermediate product; **Upstream Protein (w/out Stop codons) - Tyr - BioScaffold Linker - Downstream Protein** *Restrict with CspCI to remove downstream scar. *Ligate to get the final product; **Upstream Protein - Tyr-Gly-Ser-Gly- Downstream Protein** ====N.B.==== CspCI cuts with a 1 b.p discrepancy depending on the sequence. However this should not affect the restriction/ligation process as this has been taken into account and incorporated into the design. Even with the discrepancy involved the restriction/ligation process will still give the same product and in-frame fusion. The other restriction variants of CspCI have also been taken into account and relevant BioScaffolds are being produced to be tested. Updates will soon follow on this. This version accounts for cleaving DNA 12/10bp (top/bottom) on the 5' of the recognition sequence and 10…
mutable notes: CspCI enzyme has different variations in the distance of restricting DNA from the recognition site.This biobrick is almost identical to part BBa_K259004 but modified to account for this discrepancy.
mutable provenance: This part is completely designed de novo. This sequence does not occur naturally.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: Translational buffer
sequence annotation: BpuEI
sequence annotation: Gly-Ser-Gly Linker
sequence annotation: Translational Buffer
sequence annotation: 5' CspCI recognition site
sequence annotation: BpuEI (rev.comp)
sequence annotation: Tyr involved in Restriction/Ligation
sequence annotation: Met involved in Restriction/Ligation
sequence annotation: 3' CspCI Recognition site
sequence: https://synbiohub.org/public/igem/BBa_K259008_sequence/1

Translational buffer
type: SequenceAnnotation
persistent identity: annotation2037358
display id: annotation2037358
version: 1
top level: BBa_K259008
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K259008/annotation2037358/range2037358/1

https://synbiohub.org/public/igem/BBa_K259008/annotation2037358/range2037358/1
type: Range
persistent identity: range2037358
display id: range2037358
version: 1
direction: direction/forward
top level: BBa_K259008
start: 68
end: 72
orientation: inline

BpuEI
type: SequenceAnnotation
persistent identity: annotation2037352
display id: annotation2037352
version: 1
top level: BBa_K259008
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259008/annotation2037352/range2037352/1

https://synbiohub.org/public/igem/BBa_K259008/annotation2037352/range2037352/1
type: Range
persistent identity: range2037352
display id: range2037352
version: 1
direction: direction/forward
top level: BBa_K259008
start: 21
end: 26
orientation: inline

Gly-Ser-Gly Linker
type: SequenceAnnotation
persistent identity: annotation2037353
display id: annotation2037353
version: 1
top level: BBa_K259008
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_K259008/annotation2037353/range2037353/1

https://synbiohub.org/public/igem/BBa_K259008/annotation2037353/range2037353/1
type: Range
persistent identity: range2037353
display id: range2037353
version: 1
direction: direction/forward
top level: BBa_K259008
start: 44
end: 52
orientation: inline

Translational Buffer
type: SequenceAnnotation
persistent identity: annotation2037355
display id: annotation2037355
version: 1
top level: BBa_K259008
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K259008/annotation2037355/range2037355/1

https://synbiohub.org/public/igem/BBa_K259008/annotation2037355/range2037355/1
type: Range
persistent identity: range2037355
display id: range2037355
version: 1
direction: direction/forward
top level: BBa_K259008
start: 56
end: 64
orientation: inline

5' CspCI recognition site
type: SequenceAnnotation
persistent identity: annotation2037356
display id: annotation2037356
version: 1
top level: BBa_K259008
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259008/annotation2037356/range2037356/1

https://synbiohub.org/public/igem/BBa_K259008/annotation2037356/range2037356/1
type: Range
persistent identity: range2037356
display id: range2037356
version: 1
direction: direction/forward
top level: BBa_K259008
start: 65
end: 67
orientation: inline

BpuEI (rev.comp)
type: SequenceAnnotation
persistent identity: annotation2037350
display id: annotation2037350
version: 1
top level: BBa_K259008
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259008/annotation2037350/range2037350/1

https://synbiohub.org/public/igem/BBa_K259008/annotation2037350/range2037350/1
type: Range
persistent identity: range2037350
display id: range2037350
version: 1
direction: direction/reverse
top level: BBa_K259008
start: 3
end: 8
orientation: inline

Tyr involved in Restriction/Ligation
type: SequenceAnnotation
persistent identity: annotation2037351
display id: annotation2037351
version: 1
top level: BBa_K259008
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259008/annotation2037351/range2037351/1

https://synbiohub.org/public/igem/BBa_K259008/annotation2037351/range2037351/1
type: Range
persistent identity: range2037351
display id: range2037351
version: 1
direction: direction/forward
top level: BBa_K259008
start: 41
end: 43
orientation: inline

Met involved in Restriction/Ligation
type: SequenceAnnotation
persistent identity: annotation2037354
display id: annotation2037354
version: 1
top level: BBa_K259008
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259008/annotation2037354/range2037354/1

https://synbiohub.org/public/igem/BBa_K259008/annotation2037354/range2037354/1
type: Range
persistent identity: range2037354
display id: range2037354
version: 1
direction: direction/forward
top level: BBa_K259008
start: 53
end: 55
orientation: inline

3' CspCI Recognition site
type: SequenceAnnotation
persistent identity: annotation2037357
display id: annotation2037357
version: 1
top level: BBa_K259008
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259008/annotation2037357/range2037357/1

https://synbiohub.org/public/igem/BBa_K259008/annotation2037357/range2037357/1
type: Range
persistent identity: range2037357
display id: range2037357
version: 1
direction: direction/forward
top level: BBa_K259008
start: 73
end: 76
orientation: inline

BioScaffol
type: ComponentDefinition
persistent identity: BBa K259004
display id: BBa_K259004
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: BioScaffold Linker - Removes Stop Codons & scars & replaces with a Gly-Ser linker
creator: Petros Mina
created: 2009-07-31T11:00:00Z
modified: 2015-05-08T01:11:42Z
discontinued: false
dominant: false
experience: experience/None
group u list: _357_
m user id: 0
owner id: 5318
owning group id: 9
sample status: It's complicated
status: status/Planning
bookmark: false
mutable description: This part is part of a family of Bioscaffold - Linkers. This part will help users interested in protein-fusion. The usage of the part will allow in frame assembly of 2(+) proteins by: *Removing the stop codons from the upstream protein. *Removing the scar created by the Assembly Standard 10 (RFC10) construction of 2(+) protein coding sequences. *Maintaining the start codon of the downstream protein. *Adding a flexible (Gly-Ser-Gly) linker between the two protein coding sequences. *Acting as a translational buffer if ligation is incorrect. ===Assembly Instructions=== *Create an Assembly Standard 10 fusion as below ; **Upstream Protein Part - Bioscaffold Linker - Downstream Protein Part** *Use the BioScaffold Specific Enzymes (i)Restrict with BpuEI to remove upstream scar (created between Upstream Protein - Bioscaffold) and stop codons from upstream protein part. (ii)Ligate and you will get the intermediate product; **Upstream Protein (w/out Stop codons) - Tyr - BioScaffold Linker - Downstream Protein** *Restrict with CspCI to remove downstream scar. *Ligate to get the final product; **Upstream Protein - Tyr-Gly-Ser-Gly- Downstream Protein**
mutable notes: This part was designed taking into consideration the requirements by Assembly Standard 10 (RFC10).
mutable provenance: This part is completely designed ''de novo''. This sequence does not occur naturally.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: Tyr Involved in Restriction/Ligation
sequence annotation: Met Involved in Restriction/Ligation
sequence annotation: Gly-Ser-Gly Linker
sequence annotation: BpuEI
sequence annotation: CspCI (3' Recognition Seq)
sequence annotation: Translational Buffer
sequence annotation: CspCI (5' Recognition Seq)
sequence: https://synbiohub.org/public/igem/BBa_K259004_sequence/1

Tyr Involved in Restriction/Ligation
type: SequenceAnnotation
persistent identity: annotation2014599
display id: annotation2014599
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259004/annotation2014599/range2014599/1

https://synbiohub.org/public/igem/BBa_K259004/annotation2014599/range2014599/1
type: Range
persistent identity: range2014599
display id: range2014599
version: 1
direction: direction/forward
top level: BioScaffol
start: 41
end: 43
orientation: inline

Met Involved in Restriction/Ligation
type: SequenceAnnotation
persistent identity: annotation2014601
display id: annotation2014601
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259004/annotation2014601/range2014601/1

https://synbiohub.org/public/igem/BBa_K259004/annotation2014601/range2014601/1
type: Range
persistent identity: range2014601
display id: range2014601
version: 1
direction: direction/forward
top level: BioScaffol
start: 53
end: 55
orientation: inline

Gly-Ser-Gly Linker
type: SequenceAnnotation
persistent identity: annotation2014600
display id: annotation2014600
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_K259004/annotation2014600/range2014600/1

https://synbiohub.org/public/igem/BBa_K259004/annotation2014600/range2014600/1
type: Range
persistent identity: range2014600
display id: range2014600
version: 1
direction: direction/forward
top level: BioScaffol
start: 44
end: 52
orientation: inline

BpuEI
type: SequenceAnnotation
persistent identity: annotation2014597
display id: annotation2014597
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259004/annotation2014597/range2014597/1

https://synbiohub.org/public/igem/BBa_K259004/annotation2014597/range2014597/1
type: Range
persistent identity: range2014597
display id: range2014597
version: 1
direction: direction/reverse
top level: BioScaffol
start: 3
end: 8
orientation: inline

CspCI (3' Recognition Seq)
type: SequenceAnnotation
persistent identity: annotation2014605
display id: annotation2014605
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259004/annotation2014605/range2014605/1

https://synbiohub.org/public/igem/BBa_K259004/annotation2014605/range2014605/1
type: Range
persistent identity: range2014605
display id: range2014605
version: 1
direction: direction/forward
top level: BioScaffol
start: 74
end: 77
orientation: inline

Translational Buffer
type: SequenceAnnotation
persistent identity: annotation2014604
display id: annotation2014604
version: 1
top level: BioScaffol
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K259004/annotation2014604/range2014604/1

https://synbiohub.org/public/igem/BBa_K259004/annotation2014604/range2014604/1
type: Range
persistent identity: range2014604
display id: range2014604
version: 1
direction: direction/forward
top level: BioScaffol
start: 70
end: 72
orientation: inline

BpuEI
type: SequenceAnnotation
persistent identity: annotation2014598
display id: annotation2014598
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259004/annotation2014598/range2014598/1

https://synbiohub.org/public/igem/BBa_K259004/annotation2014598/range2014598/1
type: Range
persistent identity: range2014598
display id: range2014598
version: 1
direction: direction/forward
top level: BioScaffol
start: 21
end: 26
orientation: inline

Translational Buffer
type: SequenceAnnotation
persistent identity: annotation2014602
display id: annotation2014602
version: 1
top level: BioScaffol
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K259004/annotation2014602/range2014602/1

https://synbiohub.org/public/igem/BBa_K259004/annotation2014602/range2014602/1
type: Range
persistent identity: range2014602
display id: range2014602
version: 1
direction: direction/forward
top level: BioScaffol
start: 56
end: 65
orientation: inline

CspCI (5' Recognition Seq)
type: SequenceAnnotation
persistent identity: annotation2014603
display id: annotation2014603
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259004/annotation2014603/range2014603/1

https://synbiohub.org/public/igem/BBa_K259004/annotation2014603/range2014603/1
type: Range
persistent identity: range2014603
display id: range2014603
version: 1
direction: direction/forward
top level: BioScaffol
start: 66
end: 68
orientation: inline

BBa_J70034
type: ComponentDefinition
persistent identity: BBa J70034
display id: BBa_J70034
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: A BioScaffold Part (Uses AarI) for Library Vector Preparation (see Part Design page)
creator: Julie Norville
created: 2008-12-27T12:00:00Z
modified: 2015-05-08T01:08:20Z
discontinued: false
dominant: false
experience: experience/None
group u list: _41_
m user id: 0
owner id: 1201
owning group id: 41
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: When placed in a BioBrick assembly and cut with the restriction enzyme AarI, this part will direct the restriction enzyme to cut within the BioBrick scar still in testing, uses AarI (2) XmaI (1) See part design page or BBFRFC15, for details about use
mutable notes: TBA
mutable provenance: Designed
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: XmaI
sequence annotation: AarI
sequence: https://synbiohub.org/public/igem/BBa_J70034_sequence/1

XmaI
type: SequenceAnnotation
persistent identity: annotation2000049
display id: annotation2000049
version: 1
top level: BBa_J70034
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70034/annotation2000049/range2000049/1

https://synbiohub.org/public/igem/BBa_J70034/annotation2000049/range2000049/1
type: Range
persistent identity: range2000049
display id: range2000049
version: 1
direction: direction/forward
top level: BBa_J70034
start: 20
end: 25
orientation: inline

AarI
type: SequenceAnnotation
persistent identity: annotation2000048
display id: annotation2000048
version: 1
top level: BBa_J70034
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70034/annotation2000048/range2000048/1

https://synbiohub.org/public/igem/BBa_J70034/annotation2000048/range2000048/1
type: Range
persistent identity: range2000048
display id: range2000048
version: 1
direction: direction/forward
top level: BBa_J70034
start: 38
end: 44
orientation: inline

AarI
type: SequenceAnnotation
persistent identity: annotation2000047
display id: annotation2000047
version: 1
top level: BBa_J70034
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70034/annotation2000047/range2000047/1

https://synbiohub.org/public/igem/BBa_J70034/annotation2000047/range2000047/1
type: Range
persistent identity: range2000047
display id: range2000047
version: 1
direction: direction/forward
top level: BBa_J70034
start: 1
end: 7
orientation: inline

BBa_J70032
type: ComponentDefinition
persistent identity: BBa J70032
display id: BBa_J70032
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: A Composite BioScaffold Part (PpiI and PsrI) for Protein Fusions (see Design Page)
creator: Julie Norville
created: 2008-12-12T12:00:00Z
modified: 2015-05-08T01:08:20Z
discontinued: false
dominant: false
experience: experience/None
group u list: _41_
m user id: 0
owner id: 1201
owning group id: 41
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: Brings together a BioScaffold part that removes protein tails with one that removes protein heads in order to create a BioScaffold part that can help create protein fusions using standard assembly
mutable notes: The part that links the two BioScaffold parts can be altered as desired--here I just wanted to leave at least 7 bp beyond the internal scars.
mutable provenance: Designed
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
component: BBa_J70012
component: BBa_J70031
component: BBa_J70030
sequence annotation: BBa_J70012
sequence annotation: BBa_J70031
sequence annotation: BBa_J70030
sequence: https://synbiohub.org/public/igem/BBa_J70032_sequence/1

BBa_J70012
type: Component
persistent identity: component2000365
display id: component2000365
version: 1
top level: BBa_J70032
access: public
definition: BBa_J70012

BBa_J70031
type: Component
persistent identity: component2000357
display id: component2000357
version: 1
top level: BBa_J70032
access: public
definition: https://synbiohub.org/public/igem/BBa_J70031/1

BBa_J70030
type: Component
persistent identity: component2000353
display id: component2000353
version: 1
top level: BBa_J70032
access: public
definition: BBa_J70030

BBa_J70012
type: SequenceAnnotation
persistent identity: annotation2000365
display id: annotation2000365
version: 1
top level: BBa_J70032
location: https://synbiohub.org/public/igem/BBa_J70032/annotation2000365/range2000365/1
component: BBa_J70012

https://synbiohub.org/public/igem/BBa_J70032/annotation2000365/range2000365/1
type: Range
persistent identity: range2000365
display id: range2000365
version: 1
direction: direction/reverse
top level: BBa_J70032
start: 87
end: 138
orientation: inline

BBa_J70031
type: SequenceAnnotation
persistent identity: annotation2000357
display id: annotation2000357
version: 1
top level: BBa_J70032
location: https://synbiohub.org/public/igem/BBa_J70032/annotation2000357/range2000357/1
component: BBa_J70031

https://synbiohub.org/public/igem/BBa_J70032/annotation2000357/range2000357/1
type: Range
persistent identity: range2000357
display id: range2000357
version: 1
direction: direction/reverse
top level: BBa_J70032
start: 57
end: 78
orientation: inline

BBa_J70030
type: SequenceAnnotation
persistent identity: annotation2000353
display id: annotation2000353
version: 1
top level: BBa_J70032
location: https://synbiohub.org/public/igem/BBa_J70032/annotation2000353/range2000353/1
component: BBa_J70030

https://synbiohub.org/public/igem/BBa_J70032/annotation2000353/range2000353/1
type: Range
persistent identity: range2000353
display id: range2000353
version: 1
direction: direction/reverse
top level: BBa_J70032
start: 1
end: 48
orientation: inline

BBa_J70012
type: ComponentDefinition
persistent identity: BBa J70012
display id: BBa_J70012
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: A BioScaffold Part (Uses PsrI), Protein Head Remover see Part Design page
creator: Julie Norville
created: 2008-05-08T11:00:00Z
modified: 2015-05-08T01:08:20Z
discontinued: false
dominant: false
experience: experience/None
group u list: _41_
m user id: 0
owner id: 1201
owning group id: 41
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: still in testing
mutable notes: still in testing
mutable provenance: designed
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: Mab 2
sequence annotation: PsrI 1
sequence annotation: AscI 1
sequence annotation: PsrI 2
sequence annotation: Mab 1
sequence annotation: AscI 2
sequence: https://synbiohub.org/public/igem/BBa_J70012_sequence/1

Mab 2
type: SequenceAnnotation
persistent identity: annotation1963020
display id: annotation1963020
version: 1
top level: BBa_J70012
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70012/annotation1963020/range1963020/1

https://synbiohub.org/public/igem/BBa_J70012/annotation1963020/range1963020/1
type: Range
persistent identity: range1963020
display id: range1963020
version: 1
direction: direction/forward
top level: BBa_J70012
start: 47
end: 52
orientation: inline

PsrI 1
type: SequenceAnnotation
persistent identity: annotation1963016
display id: annotation1963016
version: 1
top level: BBa_J70012
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70012/annotation1963016/range1963016/1

https://synbiohub.org/public/igem/BBa_J70012/annotation1963016/range1963016/1
type: Range
persistent identity: range1963016
display id: range1963016
version: 1
direction: direction/forward
top level: BBa_J70012
start: 10
end: 12
orientation: inline

AscI 1
type: SequenceAnnotation
persistent identity: annotation1963021
display id: annotation1963021
version: 1
top level: BBa_J70012
role: feature/binding
role: SO:0001091
location: https://synbiohub.org/public/igem/BBa_J70012/annotation1963021/range1963021/1

https://synbiohub.org/public/igem/BBa_J70012/annotation1963021/range1963021/1
type: Range
persistent identity: range1963021
display id: range1963021
version: 1
direction: direction/forward
top level: BBa_J70012
start: 20
end: 27
orientation: inline

PsrI 2
type: SequenceAnnotation
persistent identity: annotation1963017
display id: annotation1963017
version: 1
top level: BBa_J70012
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70012/annotation1963017/range1963017/1

https://synbiohub.org/public/igem/BBa_J70012/annotation1963017/range1963017/1
type: Range
persistent identity: range1963017
display id: range1963017
version: 1
direction: direction/forward
top level: BBa_J70012
start: 43
end: 46
orientation: inline

PsrI 1
type: SequenceAnnotation
persistent identity: annotation1963015
display id: annotation1963015
version: 1
top level: BBa_J70012
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70012/annotation1963015/range1963015/1

https://synbiohub.org/public/igem/BBa_J70012/annotation1963015/range1963015/1
type: Range
persistent identity: range1963015
display id: range1963015
version: 1
direction: direction/forward
top level: BBa_J70012
start: 1
end: 3
orientation: inline

Mab 1
type: SequenceAnnotation
persistent identity: annotation1963018
display id: annotation1963018
version: 1
top level: BBa_J70012
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70012/annotation1963018/range1963018/1

https://synbiohub.org/public/igem/BBa_J70012/annotation1963018/range1963018/1
type: Range
persistent identity: range1963018
display id: range1963018
version: 1
direction: direction/forward
top level: BBa_J70012
start: 4
end: 10
orientation: inline

AscI 2
type: SequenceAnnotation
persistent identity: annotation1963022
display id: annotation1963022
version: 1
top level: BBa_J70012
role: feature/binding
role: SO:0001091
location: https://synbiohub.org/public/igem/BBa_J70012/annotation1963022/range1963022/1

https://synbiohub.org/public/igem/BBa_J70012/annotation1963022/range1963022/1
type: Range
persistent identity: range1963022
display id: range1963022
version: 1
direction: direction/forward
top level: BBa_J70012
start: 28
end: 34
orientation: inline

BBa_J70040
type: ComponentDefinition
persistent identity: BBa J70040
display id: BBa_J70040
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: A BioScaffold Part (Uses AarI, MabI) for Library Vector Preparation (see Part Design page)
creator: Julie Norville
created: 2009-01-22T12:00:00Z
modified: 2015-05-08T01:08:20Z
discontinued: false
dominant: false
experience: experience/None
group u list: _41_
m user id: 0
owner id: 1201
owning group id: 41
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: When placed in a BioBrick assembly and cut with the restriction enzyme AarI, this part will direct the restriction enzyme to cut within the BioBrick scar still in testing, uses AarI (2), MabI(2), XmaI (1) * XmaI does not work in vector for BioScaffold part manipulations See part design page or BBFRFC15, for details about use
mutable notes: See BBa_J70034, this is an analogous part except it uses MabI
mutable provenance: Designed
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: XmaI
sequence annotation: AarI
sequence annotation: MabI
sequence: https://synbiohub.org/public/igem/BBa_J70040_sequence/1

XmaI
type: SequenceAnnotation
persistent identity: annotation2000128
display id: annotation2000128
version: 1
top level: BBa_J70040
role: feature/binding
role: SO:0001091
location: https://synbiohub.org/public/igem/BBa_J70040/annotation2000128/range2000128/1

https://synbiohub.org/public/igem/BBa_J70040/annotation2000128/range2000128/1
type: Range
persistent identity: range2000128
display id: range2000128
version: 1
direction: direction/forward
top level: BBa_J70040
start: 20
end: 25
orientation: inline

AarI
type: SequenceAnnotation
persistent identity: annotation2000127
display id: annotation2000127
version: 1
top level: BBa_J70040
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70040/annotation2000127/range2000127/1

https://synbiohub.org/public/igem/BBa_J70040/annotation2000127/range2000127/1
type: Range
persistent identity: range2000127
display id: range2000127
version: 1
direction: direction/forward
top level: BBa_J70040
start: 38
end: 44
orientation: inline

MabI
type: SequenceAnnotation
persistent identity: annotation2000129
display id: annotation2000129
version: 1
top level: BBa_J70040
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70040/annotation2000129/range2000129/1

https://synbiohub.org/public/igem/BBa_J70040/annotation2000129/range2000129/1
type: Range
persistent identity: range2000129
display id: range2000129
version: 1
direction: direction/forward
top level: BBa_J70040
start: 11
end: 17
orientation: inline

MabI
type: SequenceAnnotation
persistent identity: annotation2000130
display id: annotation2000130
version: 1
top level: BBa_J70040
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70040/annotation2000130/range2000130/1

https://synbiohub.org/public/igem/BBa_J70040/annotation2000130/range2000130/1
type: Range
persistent identity: range2000130
display id: range2000130
version: 1
direction: direction/forward
top level: BBa_J70040
start: 29
end: 34
orientation: inline

AarI
type: SequenceAnnotation
persistent identity: annotation2000126
display id: annotation2000126
version: 1
top level: BBa_J70040
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70040/annotation2000126/range2000126/1

https://synbiohub.org/public/igem/BBa_J70040/annotation2000126/range2000126/1
type: Range
persistent identity: range2000126
display id: range2000126
version: 1
direction: direction/forward
top level: BBa_J70040
start: 1
end: 7
orientation: inline

BioScaffol
type: ComponentDefinition
persistent identity: BBa K259002
display id: BBa_K259002
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: BioScaffold Linker - Removes Stop Codons & scars & replaces with a Gly-Ser linker
creator: Petros Mina
created: 2009-07-31T11:00:00Z
modified: 2015-05-08T01:11:42Z
discontinued: false
dominant: false
experience: experience/None
group u list: _357_
m user id: 0
owner id: 5318
owning group id: 9
sample status: It's complicated
status: status/Planning
bookmark: false
mutable description: This part is part of a family of Bioscaffold - Linkers. This part will help users interested in protein-fusion. The usage of the part will allow in frame assembly of 2(+) proteins by: *Removing the stop codons from the upstream protein. *Removing the scar created by the Assembly Standard 10 (RFC10) construction of 2(+) protein coding sequences. *Maintaining the start codon of the downstream protein. *Adding a flexible (Gly-Ser-Gly) linker between the two protein coding sequences. *Acting as a translational buffer if ligation is incorrect. ===Assembly Instructions==== *Create an Assembly Standard 10 fusion giving ; **Upstream Protein Part - Bioscaffold Linker - Downstream Protein Part *Use the BioScaffold Specific Enzymes **Restrict with BpuEI to remove upstream scar (created between Upstream Protein - Bioscaffold) and stop codons from upstream protein part. **Ligate and you will get the intermediate product; Upstream Protein (w/out Stop codons) - Tyr - BioScaffold Linker - Downstream Protein **Restrict with BseRI to remove downstream scar. **Ligate to get the final product; Upstream Protein - Tyr-Gly-Ser-Gly- Downstream Protein
mutable notes: Part was designed taking into account RFC10 assembly standard and as an attempt to be upwards compatible with RFC10.
mutable provenance: This part was designed ''de novo''. The sequence does not occur naturally.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: BseRI Site
sequence annotation: Gly-Ser-Gly Linker
sequence annotation: BpuEI Site
sequence annotation: Tyr Residue involved in Restriction/Ligation
sequence annotation: Translational Buffer
sequence annotation: Met involved in Restriction/Ligation
sequence: https://synbiohub.org/public/igem/BBa_K259002_sequence/1

BseRI Site
type: SequenceAnnotation
persistent identity: annotation2014595
display id: annotation2014595
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259002/annotation2014595/range2014595/1

https://synbiohub.org/public/igem/BBa_K259002/annotation2014595/range2014595/1
type: Range
persistent identity: range2014595
display id: range2014595
version: 1
direction: direction/reverse
top level: BioScaffol
start: 63
end: 68
orientation: inline

BseRI Site
type: SequenceAnnotation
persistent identity: annotation2014596
display id: annotation2014596
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259002/annotation2014596/range2014596/1

https://synbiohub.org/public/igem/BBa_K259002/annotation2014596/range2014596/1
type: Range
persistent identity: range2014596
display id: range2014596
version: 1
direction: direction/forward
top level: BioScaffol
start: 81
end: 86
orientation: inline

Gly-Ser-Gly Linker
type: SequenceAnnotation
persistent identity: annotation2014592
display id: annotation2014592
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_K259002/annotation2014592/range2014592/1

https://synbiohub.org/public/igem/BBa_K259002/annotation2014592/range2014592/1
type: Range
persistent identity: range2014592
display id: range2014592
version: 1
direction: direction/forward
top level: BioScaffol
start: 44
end: 52
orientation: inline

BpuEI Site
type: SequenceAnnotation
persistent identity: annotation2014591
display id: annotation2014591
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259002/annotation2014591/range2014591/1

https://synbiohub.org/public/igem/BBa_K259002/annotation2014591/range2014591/1
type: Range
persistent identity: range2014591
display id: range2014591
version: 1
direction: direction/forward
top level: BioScaffol
start: 21
end: 26
orientation: inline

BpuEI Site
type: SequenceAnnotation
persistent identity: annotation2014590
display id: annotation2014590
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259002/annotation2014590/range2014590/1

https://synbiohub.org/public/igem/BBa_K259002/annotation2014590/range2014590/1
type: Range
persistent identity: range2014590
display id: range2014590
version: 1
direction: direction/reverse
top level: BioScaffol
start: 3
end: 8
orientation: inline

Tyr Residue involved in Restriction/Ligation
type: SequenceAnnotation
persistent identity: annotation2014589
display id: annotation2014589
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259002/annotation2014589/range2014589/1

https://synbiohub.org/public/igem/BBa_K259002/annotation2014589/range2014589/1
type: Range
persistent identity: range2014589
display id: range2014589
version: 1
direction: direction/forward
top level: BioScaffol
start: 41
end: 43
orientation: inline

Translational Buffer
type: SequenceAnnotation
persistent identity: annotation2014594
display id: annotation2014594
version: 1
top level: BioScaffol
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K259002/annotation2014594/range2014594/1

https://synbiohub.org/public/igem/BBa_K259002/annotation2014594/range2014594/1
type: Range
persistent identity: range2014594
display id: range2014594
version: 1
direction: direction/forward
top level: BioScaffol
start: 56
end: 62
orientation: inline

Met involved in Restriction/Ligation
type: SequenceAnnotation
persistent identity: annotation2014593
display id: annotation2014593
version: 1
top level: BioScaffol
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259002/annotation2014593/range2014593/1

https://synbiohub.org/public/igem/BBa_K259002/annotation2014593/range2014593/1
type: Range
persistent identity: range2014593
display id: range2014593
version: 1
direction: direction/forward
top level: BioScaffol
start: 53
end: 55
orientation: inline

BBa_J70010
type: ComponentDefinition
persistent identity: BBa J70010
display id: BBa_J70010
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: A BioScaffold Part (Uses PpiI), for offset see Part Design page
creator: Julie Norville
created: 2008-05-08T11:00:00Z
modified: 2015-05-08T01:08:20Z
discontinued: false
dominant: false
experience: experience/None
group u list: _41_
m user id: 0
owner id: 1201
owning group id: 41
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: still in testing
mutable notes: still in testing
mutable provenance: designed
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: PpiI2
sequence annotation: PpiI 2
sequence annotation: PpiI 1
sequence annotation: PacI 2
sequence annotation: PacI3
sequence annotation: MabI 1
sequence annotation: PacI 1
sequence annotation: MabI 2
sequence: https://synbiohub.org/public/igem/BBa_J70010_sequence/1

PpiI2
type: SequenceAnnotation
persistent identity: annotation1963029
display id: annotation1963029
version: 1
top level: BBa_J70010
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70010/annotation1963029/range1963029/1

https://synbiohub.org/public/igem/BBa_J70010/annotation1963029/range1963029/1
type: Range
persistent identity: range1963029
display id: range1963029
version: 1
direction: direction/forward
top level: BBa_J70010
start: 51
end: 53
orientation: inline

PpiI 2
type: SequenceAnnotation
persistent identity: annotation1963028
display id: annotation1963028
version: 1
top level: BBa_J70010
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70010/annotation1963028/range1963028/1

https://synbiohub.org/public/igem/BBa_J70010/annotation1963028/range1963028/1
type: Range
persistent identity: range1963028
display id: range1963028
version: 1
direction: direction/forward
top level: BBa_J70010
start: 42
end: 45
orientation: inline

PpiI 1
type: SequenceAnnotation
persistent identity: annotation1963026
display id: annotation1963026
version: 1
top level: BBa_J70010
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70010/annotation1963026/range1963026/1

https://synbiohub.org/public/igem/BBa_J70010/annotation1963026/range1963026/1
type: Range
persistent identity: range1963026
display id: range1963026
version: 1
direction: direction/forward
top level: BBa_J70010
start: 1
end: 3
orientation: inline

PacI 2
type: SequenceAnnotation
persistent identity: annotation1963033
display id: annotation1963033
version: 1
top level: BBa_J70010
role: feature/binding
role: SO:0001091
location: https://synbiohub.org/public/igem/BBa_J70010/annotation1963033/range1963033/1

https://synbiohub.org/public/igem/BBa_J70010/annotation1963033/range1963033/1
type: Range
persistent identity: range1963033
display id: range1963033
version: 1
direction: direction/forward
top level: BBa_J70010
start: 27
end: 34
orientation: inline

PacI3
type: SequenceAnnotation
persistent identity: annotation1963034
display id: annotation1963034
version: 1
top level: BBa_J70010
role: feature/binding
role: SO:0001091
location: https://synbiohub.org/public/igem/BBa_J70010/annotation1963034/range1963034/1

https://synbiohub.org/public/igem/BBa_J70010/annotation1963034/range1963034/1
type: Range
persistent identity: range1963034
display id: range1963034
version: 1
direction: direction/forward
top level: BBa_J70010
start: 23
end: 30
orientation: inline

MabI 1
type: SequenceAnnotation
persistent identity: annotation1963030
display id: annotation1963030
version: 1
top level: BBa_J70010
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70010/annotation1963030/range1963030/1

https://synbiohub.org/public/igem/BBa_J70010/annotation1963030/range1963030/1
type: Range
persistent identity: range1963030
display id: range1963030
version: 1
direction: direction/forward
top level: BBa_J70010
start: 13
end: 19
orientation: inline

PacI 1
type: SequenceAnnotation
persistent identity: annotation1963032
display id: annotation1963032
version: 1
top level: BBa_J70010
role: feature/binding
role: SO:0001091
location: https://synbiohub.org/public/igem/BBa_J70010/annotation1963032/range1963032/1

https://synbiohub.org/public/igem/BBa_J70010/annotation1963032/range1963032/1
type: Range
persistent identity: range1963032
display id: range1963032
version: 1
direction: direction/forward
top level: BBa_J70010
start: 19
end: 24
orientation: inline

MabI 2
type: SequenceAnnotation
persistent identity: annotation1963031
display id: annotation1963031
version: 1
top level: BBa_J70010
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70010/annotation1963031/range1963031/1

https://synbiohub.org/public/igem/BBa_J70010/annotation1963031/range1963031/1
type: Range
persistent identity: range1963031
display id: range1963031
version: 1
direction: direction/forward
top level: BBa_J70010
start: 35
end: 41
orientation: inline

PpiI 1
type: SequenceAnnotation
persistent identity: annotation1963027
display id: annotation1963027
version: 1
top level: BBa_J70010
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70010/annotation1963027/range1963027/1

https://synbiohub.org/public/igem/BBa_J70010/annotation1963027/range1963027/1
type: Range
persistent identity: range1963027
display id: range1963027
version: 1
direction: direction/forward
top level: BBa_J70010
start: 9
end: 12
orientation: inline

BBa_J70050
type: ComponentDefinition
persistent identity: BBa J70050
display id: BBa_J70050
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: Left Library Insert Preparation Part (To use with J70052, and J70040)
creator: Julie Norville
created: 2009-01-22T12:00:00Z
modified: 2015-05-08T01:08:20Z
discontinued: false
dominant: false
experience: experience/None
group u list: _41_
m user id: 0
owner id: 1201
owning group id: 41
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: Still in Testing Surround a part with J70050 and J70052, digest with AarI Insert into a vector that contained J70040, and had J70040 removed by AarI and MabI
mutable notes: Not sure if single AarI site will be good enough
mutable provenance: Designed
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: Spacer
sequence annotation: AarI
sequence: https://synbiohub.org/public/igem/BBa_J70050_sequence/1

Spacer
type: SequenceAnnotation
persistent identity: annotation2000145
display id: annotation2000145
version: 1
top level: BBa_J70050
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70050/annotation2000145/range2000145/1

https://synbiohub.org/public/igem/BBa_J70050/annotation2000145/range2000145/1
type: Range
persistent identity: range2000145
display id: range2000145
version: 1
direction: direction/forward
top level: BBa_J70050
start: 8
end: 11
orientation: inline

AarI
type: SequenceAnnotation
persistent identity: annotation2000144
display id: annotation2000144
version: 1
top level: BBa_J70050
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70050/annotation2000144/range2000144/1

https://synbiohub.org/public/igem/BBa_J70050/annotation2000144/range2000144/1
type: Range
persistent identity: range2000144
display id: range2000144
version: 1
direction: direction/forward
top level: BBa_J70050
start: 1
end: 7
orientation: inline

BBa_J70052
type: ComponentDefinition
persistent identity: BBa J70052
display id: BBa_J70052
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: Right Library Insert Preparation Part (To use with J70050, and J70040)
creator: Julie Norville
created: 2009-01-22T12:00:00Z
modified: 2015-05-08T01:08:20Z
discontinued: false
dominant: false
experience: experience/None
group u list: _41_
m user id: 0
owner id: 1201
owning group id: 41
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: Still in Testing Surround a part with J70050 and J70052, digest with AarI Insert into a vector that contained J70040 and had J70040 removed by AarI and MabI
mutable notes: Not sure if one AarI site on each site will be enough.
mutable provenance: Designed
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: Spacer
sequence annotation: AarI
sequence: https://synbiohub.org/public/igem/BBa_J70052_sequence/1

Spacer
type: SequenceAnnotation
persistent identity: annotation2000146
display id: annotation2000146
version: 1
top level: BBa_J70052
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70052/annotation2000146/range2000146/1

https://synbiohub.org/public/igem/BBa_J70052/annotation2000146/range2000146/1
type: Range
persistent identity: range2000146
display id: range2000146
version: 1
direction: direction/forward
top level: BBa_J70052
start: 1
end: 3
orientation: inline

AarI
type: SequenceAnnotation
persistent identity: annotation2000147
display id: annotation2000147
version: 1
top level: BBa_J70052
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70052/annotation2000147/range2000147/1

https://synbiohub.org/public/igem/BBa_J70052/annotation2000147/range2000147/1
type: Range
persistent identity: range2000147
display id: range2000147
version: 1
direction: direction/forward
top level: BBa_J70052
start: 4
end: 10
orientation: inline

BBa_J70036
type: ComponentDefinition
persistent identity: BBa J70036
display id: BBa_J70036
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: A BioScaffold Part (Uses AarI) for Library Insert Preparation (see Part Design page)
creator: Julie Norville
created: 2008-12-27T12:00:00Z
modified: 2015-05-08T01:08:20Z
discontinued: false
dominant: false
experience: experience/None
group u list: _41_
m user id: 0
owner id: 1201
owning group id: 41
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: When placed in a BioBrick assembly and cut with the restriction enzyme AarI, this part will direct the restriction enzyme to cut within the BioBrick scar still in testing, uses AarI (2) XmaI (1) See part design page or BBFRFC15, for details about use
mutable notes: TBA
mutable provenance: Designed
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: XmaI
sequence annotation: AarI
sequence: https://synbiohub.org/public/igem/BBa_J70036_sequence/1

XmaI
type: SequenceAnnotation
persistent identity: annotation2000052
display id: annotation2000052
version: 1
top level: BBa_J70036
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70036/annotation2000052/range2000052/1

https://synbiohub.org/public/igem/BBa_J70036/annotation2000052/range2000052/1
type: Range
persistent identity: range2000052
display id: range2000052
version: 1
direction: direction/forward
top level: BBa_J70036
start: 23
end: 28
orientation: inline

AarI
type: SequenceAnnotation
persistent identity: annotation2000050
display id: annotation2000050
version: 1
top level: BBa_J70036
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70036/annotation2000050/range2000050/1

https://synbiohub.org/public/igem/BBa_J70036/annotation2000050/range2000050/1
type: Range
persistent identity: range2000050
display id: range2000050
version: 1
direction: direction/forward
top level: BBa_J70036
start: 4
end: 10
orientation: inline

AarI
type: SequenceAnnotation
persistent identity: annotation2000051
display id: annotation2000051
version: 1
top level: BBa_J70036
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70036/annotation2000051/range2000051/1

https://synbiohub.org/public/igem/BBa_J70036/annotation2000051/range2000051/1
type: Range
persistent identity: range2000051
display id: range2000051
version: 1
direction: direction/forward
top level: BBa_J70036
start: 41
end: 47
orientation: inline

BBa_J70030
type: ComponentDefinition
persistent identity: BBa J70030
display id: BBa_J70030
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: A BioScaffold Part (Uses PpiI), Protein Tail Remover see Part Design Page
creator: Julie Norville
created: 2008-12-07T12:00:00Z
modified: 2015-05-08T01:08:20Z
discontinued: false
dominant: false
experience: experience/None
group u list: _41_
m user id: 0
owner id: 1201
owning group id: 41
sample status: Not in stock
status: status/Unavailable
bookmark: false
mutable description: When placed in a BioBrick assembly and cut with the restriction enzyme PpiI, this part will direct the restriction enzymes to cut outside the BioBrick scar still in testing, uses restriction enzyme sites PpiI (2) PacI (2) MabI (2), will place in pSB1AK3 vector
mutable notes: Can be used to removed protein tails for protein fusions, see BBF RFC 15 XXXXX^ XXX TACTAGAG BioScaffold Part BBa_J70030 TACTAGAT XXXXX^ ^XXXXX XXX ATGATCAC ATGATCTA^XXXXX XXXXX^ TAA TACTAGAG BioScaffold Part BBa_J70030 TACTAGAT XXXXX^ ^XXXXX ATT ATGATCAC ATGATCTA^XXXXX
mutable provenance: this part is designed
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: PpiI 2
sequence annotation: MabI 2
sequence annotation: MabI 1
sequence annotation: PacI3
sequence annotation: PpiI 1
sequence annotation: PacI 2
sequence annotation: PacI 1
sequence: https://synbiohub.org/public/igem/BBa_J70030_sequence/1

PpiI 2
type: SequenceAnnotation
persistent identity: annotation2000015
display id: annotation2000015
version: 1
top level: BBa_J70030
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70030/annotation2000015/range2000015/1

https://synbiohub.org/public/igem/BBa_J70030/annotation2000015/range2000015/1
type: Range
persistent identity: range2000015
display id: range2000015
version: 1
direction: direction/forward
top level: BBa_J70030
start: 46
end: 48
orientation: inline

PpiI 2
type: SequenceAnnotation
persistent identity: annotation2000014
display id: annotation2000014
version: 1
top level: BBa_J70030
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70030/annotation2000014/range2000014/1

https://synbiohub.org/public/igem/BBa_J70030/annotation2000014/range2000014/1
type: Range
persistent identity: range2000014
display id: range2000014
version: 1
direction: direction/forward
top level: BBa_J70030
start: 37
end: 40
orientation: inline

MabI 2
type: SequenceAnnotation
persistent identity: annotation2000013
display id: annotation2000013
version: 1
top level: BBa_J70030
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70030/annotation2000013/range2000013/1

https://synbiohub.org/public/igem/BBa_J70030/annotation2000013/range2000013/1
type: Range
persistent identity: range2000013
display id: range2000013
version: 1
direction: direction/forward
top level: BBa_J70030
start: 30
end: 36
orientation: inline

MabI 1
type: SequenceAnnotation
persistent identity: annotation2000009
display id: annotation2000009
version: 1
top level: BBa_J70030
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_J70030/annotation2000009/range2000009/1

https://synbiohub.org/public/igem/BBa_J70030/annotation2000009/range2000009/1
type: Range
persistent identity: range2000009
display id: range2000009
version: 1
direction: direction/forward
top level: BBa_J70030
start: 8
end: 14
orientation: inline

PacI3
type: SequenceAnnotation
persistent identity: annotation2000011
display id: annotation2000011
version: 1
top level: BBa_J70030
role: feature/binding
role: SO:0001091
location: https://synbiohub.org/public/igem/BBa_J70030/annotation2000011/range2000011/1

https://synbiohub.org/public/igem/BBa_J70030/annotation2000011/range2000011/1
type: Range
persistent identity: range2000011
display id: range2000011
version: 1
direction: direction/forward
top level: BBa_J70030
start: 18
end: 24
orientation: inline

PpiI 1
type: SequenceAnnotation
persistent identity: annotation2000008
display id: annotation2000008
version: 1
top level: BBa_J70030
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_J70030/annotation2000008/range2000008/1

https://synbiohub.org/public/igem/BBa_J70030/annotation2000008/range2000008/1
type: Range
persistent identity: range2000008
display id: range2000008
version: 1
direction: direction/forward
top level: BBa_J70030
start: 4
end: 7
orientation: inline

PacI 2
type: SequenceAnnotation
persistent identity: annotation2000012
display id: annotation2000012
version: 1
top level: BBa_J70030
role: feature/binding
role: SO:0001091
location: https://synbiohub.org/public/igem/BBa_J70030/annotation2000012/range2000012/1

https://synbiohub.org/public/igem/BBa_J70030/annotation2000012/range2000012/1
type: Range
persistent identity: range2000012
display id: range2000012
version: 1
direction: direction/forward
top level: BBa_J70030
start: 22
end: 29
orientation: inline

PacI 1
type: SequenceAnnotation
persistent identity: annotation2000010
display id: annotation2000010
version: 1
top level: BBa_J70030
role: feature/binding
role: SO:0001091
location: https://synbiohub.org/public/igem/BBa_J70030/annotation2000010/range2000010/1

https://synbiohub.org/public/igem/BBa_J70030/annotation2000010/range2000010/1
type: Range
persistent identity: range2000010
display id: range2000010
version: 1
direction: direction/forward
top level: BBa_J70030
start: 14
end: 20
orientation: inline

BBa_K259009
type: ComponentDefinition
persistent identity: BBa K259009
display id: BBa_K259009
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: BioScaffold Linker - Removes Stop Codons & scars & replaces with a Gly-Ser linker
creator: Petros Mina
created: 2009-10-12T11:00:00Z
modified: 2015-05-08T01:11:42Z
discontinued: false
dominant: false
group u list: _357_
m user id: 0
owner id: 5318
owning group id: 9
sample status: It's complicated
status: status/Planning
bookmark: false
mutable description: This part is part of a family of Bioscaffold - Linkers. This part will help users interested in protein-fusion. The usage of the part will allow in frame assembly of 2(+) proteins by: *Removing the stop codons from the upstream protein. *Removing the scar created by the Assembly Standard 10 (RFC10) construction of 2(+) protein coding sequences. *Maintaining the start codon of the downstream protein. *Adding a flexible (Gly-Ser-Gly) linker between the two protein coding sequences. *Acting as a translational buffer if ligation is incorrect. ===Assembly Instructions=== *Create an Assembly Standard 10 fusion as below ; **Upstream Protein Part - Bioscaffold Linker - Downstream Protein Part** *Use the BioScaffold Specific Enzymes (i)Restrict with BpuEI to remove upstream scar (created between Upstream Protein - Bioscaffold) and stop codons from upstream protein part. (ii)Ligate and you will get the intermediate product; **Upstream Protein (w/out Stop codons) - Tyr - BioScaffold Linker - Downstream Protein** *Restrict with CspCI to remove downstream scar. *Ligate to get the final product; **Upstream Protein - Tyr-Gly-Ser-Gly- Downstream Protein** ====N.B.==== CspCI cuts with a 1 b.p discrepancy depending on the sequence. However this should not affect the restriction/ligation process as this has been taken into account and incorporated into the design. Even with the discrepancy involved the restriction/ligation process will still give the same product and in-frame fusion. The other restriction variants of CspCI have also been taken into account and relevant BioScaffolds are being produced to be tested. This version is for when CspCI cuts 13/10b.p. (top/bottom) on the 5' of the recognition sequence and 10/13bp (top/bottom) on the 3' of the…
mutable notes: The CspCI discrepancy had to be taken into account
mutable provenance: This part is completely designed ''de novo''. This sequence does not occur naturally.
owned by: james
owned by: myers
star: false
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: Translational Buffer
sequence annotation: 5' CspCI Recognition sequence
sequence annotation: 3' CspCI recognition sequence
sequence annotation: BpuEI
sequence annotation: BpuEI (rev. complement)
sequence annotation: Met involved in restriction/ligation
sequence annotation: Gly-Ser-Gly linker
sequence annotation: Tyr involved in restriction/ligation
sequence: https://synbiohub.org/public/igem/BBa_K259009_sequence/1

Translational Buffer
type: SequenceAnnotation
persistent identity: annotation2037405
display id: annotation2037405
version: 1
top level: BBa_K259009
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K259009/annotation2037405/range2037405/1

https://synbiohub.org/public/igem/BBa_K259009/annotation2037405/range2037405/1
type: Range
persistent identity: range2037405
display id: range2037405
version: 1
direction: direction/forward
top level: BBa_K259009
start: 56
end: 65
orientation: inline

Translational Buffer
type: SequenceAnnotation
persistent identity: annotation2037439
display id: annotation2037439
version: 1
top level: BBa_K259009
role: SO:0000319
role: feature/stop
location: https://synbiohub.org/public/igem/BBa_K259009/annotation2037439/range2037439/1

https://synbiohub.org/public/igem/BBa_K259009/annotation2037439/range2037439/1
type: Range
persistent identity: range2037439
display id: range2037439
version: 1
direction: direction/forward
top level: BBa_K259009
start: 69
end: 73
orientation: inline

5' CspCI Recognition sequence
type: SequenceAnnotation
persistent identity: annotation2037437
display id: annotation2037437
version: 1
top level: BBa_K259009
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259009/annotation2037437/range2037437/1

https://synbiohub.org/public/igem/BBa_K259009/annotation2037437/range2037437/1
type: Range
persistent identity: range2037437
display id: range2037437
version: 1
direction: direction/forward
top level: BBa_K259009
start: 66
end: 68
orientation: inline

3' CspCI recognition sequence
type: SequenceAnnotation
persistent identity: annotation2037438
display id: annotation2037438
version: 1
top level: BBa_K259009
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259009/annotation2037438/range2037438/1

https://synbiohub.org/public/igem/BBa_K259009/annotation2037438/range2037438/1
type: Range
persistent identity: range2037438
display id: range2037438
version: 1
direction: direction/forward
top level: BBa_K259009
start: 74
end: 77
orientation: inline

BpuEI
type: SequenceAnnotation
persistent identity: annotation2037401
display id: annotation2037401
version: 1
top level: BBa_K259009
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259009/annotation2037401/range2037401/1

https://synbiohub.org/public/igem/BBa_K259009/annotation2037401/range2037401/1
type: Range
persistent identity: range2037401
display id: range2037401
version: 1
direction: direction/forward
top level: BBa_K259009
start: 21
end: 26
orientation: inline

BpuEI (rev. complement)
type: SequenceAnnotation
persistent identity: annotation2037400
display id: annotation2037400
version: 1
top level: BBa_K259009
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259009/annotation2037400/range2037400/1

https://synbiohub.org/public/igem/BBa_K259009/annotation2037400/range2037400/1
type: Range
persistent identity: range2037400
display id: range2037400
version: 1
direction: direction/reverse
top level: BBa_K259009
start: 3
end: 8
orientation: inline

Met involved in restriction/ligation
type: SequenceAnnotation
persistent identity: annotation2037404
display id: annotation2037404
version: 1
top level: BBa_K259009
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259009/annotation2037404/range2037404/1

https://synbiohub.org/public/igem/BBa_K259009/annotation2037404/range2037404/1
type: Range
persistent identity: range2037404
display id: range2037404
version: 1
direction: direction/forward
top level: BBa_K259009
start: 53
end: 55
orientation: inline

Gly-Ser-Gly linker
type: SequenceAnnotation
persistent identity: annotation2037403
display id: annotation2037403
version: 1
top level: BBa_K259009
role: SO:0000110
role: feature/dna
location: https://synbiohub.org/public/igem/BBa_K259009/annotation2037403/range2037403/1

https://synbiohub.org/public/igem/BBa_K259009/annotation2037403/range2037403/1
type: Range
persistent identity: range2037403
display id: range2037403
version: 1
direction: direction/forward
top level: BBa_K259009
start: 44
end: 52
orientation: inline

Tyr involved in restriction/ligation
type: SequenceAnnotation
persistent identity: annotation2037402
display id: annotation2037402
version: 1
top level: BBa_K259009
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_K259009/annotation2037402/range2037402/1

https://synbiohub.org/public/igem/BBa_K259009/annotation2037402/range2037402/1
type: Range
persistent identity: range2037402
display id: range2037402
version: 1
direction: direction/forward
top level: BBa_K259009
start: 41
end: 43
orientation: inline