//dna/spacer
type: Collection
persistent identity: dna spacer
display id: dna_spacer
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
owned by: james
owned by: myers
member: spacer
member: BioScaffol
member: BBa_K259008
member: BBa_K259009

spacer
type: ComponentDefinition
persistent identity: BBa B0040
display id: BBa_B0040
version: 1
was generated by: https://synbiohub.org/public/igem/igem2sbol/1
description: Spacer.1 (generic)
creator: Vinay S. Mahajan, Brian Chow, Peter Carr
created: 2003-01-31T12:00:00Z
modified: 2015-08-31T04:07:20Z
discontinued: false
dominant: false
experience: experience/Works
group u list: _1_
m user id: 0
owner id: 24
owning group id: 7
part status: Released HQ 2013
sample status: In stock
status: status/Available
bookmark: false
mutable description: Generic spacer for ensuring a 70 bp distance between the end of the suffix of the BioBrick part containing the double terminator and the prefix of the BioBrick part containing the promoter of the new gene. Please, use the AlignX function of Vector NT to check for homology with the components in your plasmid before using this spacer.
mutable notes: The size of the spacer was choosed to meet the minimum length of a sequence that can be queried using the BLAST search engine. However, subsequences of it can be used to design shorter spacers. The sequence was selected from many more sequences randomly generated using the Random DNA Generator engine; the GC% parameter used as input was 50%. The sequences were selected based on the following constraints listed in their order of importance: the absence of any putative promoter regions, a low degree of homology with the Elowitz plasmid (whose components are widely used in our designs), no homology with other E.coli sequences as shown by BLASTN search results and the presence of a number of TAA stop codons. The second constraint was the most stringent leading to the elimination of most sequences. DE made the following changes to the original sequence in order to add stop codons in the -3 frame and more in the +2 frame (note, not all of these stop codons are UAA. Thus, if used in an organism that inserts an amino acid @ UGA or UAG the obvious will occur): T->A @ 85 T->A @ 42 C->T @ 79 A->T @ 64 A->T @ 31 T->A @ 34 C->A @ 37 Also, note that the above changes further reduce (the already very weak) homology to current NCBI-stored sequences. In the process of selecting the best sequence it appeared that a good alternative sequence for a spacer would be: AGGTTCTGATATGTAACTGTGCCCAATGTCGTTAGTGACGCATACCTCTTAAGAGGCCACTGTCCTAACA. The sequence contains no putative promoters and shows moderate homology with the 5' end of the Ampicillin resistance gene. However a strong promoter sequence starts 12 bp downstream of this sequence, and therefore the sequence presented above was preferred. The sequence is compatible (does not show significant homology) with the components in the Elowitz repressilator plasmid.
mutable provenance: Randomly generated and optimized for several parameters (see Design notes).
owned by: james
owned by: myers
star: true
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: Spacer-1
sequence annotation: BBa_B0040
sequence: https://synbiohub.org/public/igem/BBa_B0040_sequence/1

Spacer-1
type: SequenceAnnotation
persistent identity: annotation1721
display id: annotation1721
version: 1
top level: spacer
role: SO:0000110
role: feature/misc
location: https://synbiohub.org/public/igem/BBa_B0040/annotation1721/range1721/1

https://synbiohub.org/public/igem/BBa_B0040/annotation1721/range1721/1
type: Range
persistent identity: range1721
display id: range1721
version: 1
direction: direction/forward
top level: spacer
start: 1
end: 70
orientation: inline

BBa_B0040
type: SequenceAnnotation
persistent identity: annotation7030
display id: annotation7030
version: 1
top level: spacer
role: SO:0000804
role: feature/BioBrick
location: https://synbiohub.org/public/igem/BBa_B0040/annotation7030/range7030/1

https://synbiohub.org/public/igem/BBa_B0040/annotation7030/range7030/1
type: Range
persistent identity: range7030
display id: range7030
version: 1
direction: direction/forward
top level: spacer
start: 1
end: 70
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: Tyr Residue involved in Restriction/Ligation
sequence annotation: Translational Buffer
sequence annotation: BseRI Site
sequence annotation: Gly-Ser-Gly Linker
sequence annotation: BpuEI Site
sequence annotation: Met involved in Restriction/Ligation
sequence: https://synbiohub.org/public/igem/BBa_K259002_sequence/1

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

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

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

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

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

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: Gly-Ser-Gly linker
sequence annotation: 3' CspCI recognition sequence
sequence annotation: Met involved in restriction/ligation
sequence annotation: Translational Buffer
sequence annotation: BpuEI (rev. complement)
sequence annotation: Tyr involved in restriction/ligation
sequence annotation: 5' CspCI Recognition sequence
sequence annotation: BpuEI
sequence: https://synbiohub.org/public/igem/BBa_K259009_sequence/1

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

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

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

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

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

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

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

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

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

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: BpuEI
sequence annotation: Translational Buffer
sequence annotation: CspCI (5' Recognition Seq)
sequence annotation: Gly-Ser-Gly Linker
sequence annotation: Tyr Involved in Restriction/Ligation
sequence annotation: Met Involved in Restriction/Ligation
sequence annotation: CspCI (3' Recognition Seq)
sequence: https://synbiohub.org/public/igem/BBa_K259004_sequence/1

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: 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

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

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

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

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

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

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: BpuEI (rev.comp)
sequence annotation: 5' CspCI recognition site
sequence annotation: Tyr involved in Restriction/Ligation
sequence annotation: BpuEI
sequence annotation: Met involved in Restriction/Ligation
sequence annotation: 3' CspCI Recognition site
sequence annotation: Translational buffer
sequence annotation: Gly-Ser-Gly Linker
sequence annotation: Translational Buffer
sequence: https://synbiohub.org/public/igem/BBa_K259008_sequence/1

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

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

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

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

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

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

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