Team:UCL/Science/Sequences
From 2014.igem.org
Summary
For ease of reference, the sequences for (1) our BioBrick Gene Designs, (2) Plasmid / Vector Backbones, and (3) BioBricks that we have used from that iGEM Registry Distribution, have been provided below. Clicking on the Gene/Plasmid/BioBrick headers will take you to pages describing the part in more detail and the source of the sequences.
Note: format is a little horrendous, will change to all CAPS, and at a set width (70-75 char), and add "br" for all later.
BioBrick Designs for Our Genes
[New] BBa_K1336000 / AzoR Part-only sequence (612bp)
Sequence taken from Lisbon.
1 |
ATG AAA CTG TTG CAC ATC GAT TCG AGC ATC CTG GGC GAC AAT TCC GCC TCG CGT CAG CTG AGC CGT GAA GTG GTC GAA GCC TGG AAG GCT GCA GAC CCA |
[New] BBa_K1336001 / AzoR 1B6 (heat-stable AzoR mutant) Part-only sequence (612bp)
Sequence given from Lisbon group directly.
1 |
ATG AAA CTG TTG CAC ATC GAT TCG AGC ATC CTG GGC GAC AAT TCC GCC TCG CGC CAG CTG AGC CGT GAA GTG GTC GAA GCC TGG AAG GCT GCA GAC CCA |
[Proposed] BBa_K1336002 / CotA Part-only sequence (1542bp)
Sequence given from Lisbon group directly.
1 |
ATG ACA CTT GAA AAA TTT GTG GAT GCT CTC CCA ATC CCA GAT ACA CTA AAG CCA GTA CAG CAA TCA AAA GAA AAA ACA TAC TAC GAA GTC ACC ATG GAG |
[New] BBa_K1336003 / BsDyP Part-only sequence (1251bp)
Sequence given from Lisbon group directly.
1 |
ATG AGC GAT GAA CAG AAA AAG CCA GAA CAA ATT CAC AGA CGG GAC ATT TTA AAA TGG GGA GCG ATG GCG GGG GCA GCC GTT GCG ATC GGT GCC AGC GGT |
[Proposed] BBa_K1336004 / PpDyP Part-only sequence (864bp)
Sequence taken from Lisbon.
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ATG CCG TTC CAG CAA GGT CTG CTT GCC ACC CCG GTG CCG GCC CAC GCC CGT CAC CTG TTC TTC ACC CTG CAG TCG CCC GAG GCG TTG CCT GCC GCG CTG |
[Improvement] BBa_K500000 / LiP Part-only sequence (1116bp)
Sequence taken from the initial page; not currently showing our improvements.
1 |
ATG GCT TTT AAA CAA TTA TTC GCC GCT ATT TCC TTG GCT TTG TCT TTG TCT GCT GCT AAT GCT GCT GCT GTT ATT GAA AAA AGA GCT ACT TGT TCC AAC |
[Improvement] BBa_K729006 / CueO Part-only sequence (1612bp)
Sequence taken from the initial page; not currently showing our improvements.
1 |
TTG ACA GCT AGC TCA GTC CTA GGT ATA ATG CTA GCT ACT AGA GAA AGA GGA GAA ATA CTA GAT GCA ACG TCG TGA TTT CTT AAA ATA TTC CGT CGC GCT |
[New] BBa_K1336005 / ispB Part-only sequence (562bp)
The first sequence below shows the "sense" ispB gene, but we use the second sequence, the Reverse Complement to design primers to produce an antisense fragment for gene knockdown (i.e. as RNAi).
"Sense" ispB sequence (972bp)
Black = region for PCR. Underlined CTG CAG = illegal PstI restriction site.
1 |
ATG AAT TTA GAA AAA ATC AAT GAG TTA ACC GCG CAA GAT ATG GCG GGT GTT AAT GCG GCA ATC CTT GAG CAG CTT AAT TCC GAC GTC CAA CTG ATC AAT |
"Antisense" ispB sequence (972bp)
To create the RNAi/antisense fragment, we first get the reverse complement of the full ispB gene, before designing the primers to amplify the black region.
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TTA ACG ATC GCG TTG AAC AGC GAT GTG CGC GAG GCC GAT GAG TGC TTC TCG CCA AGG GGT GTC CGG GAG CAC CTG TAA CGC TGC GAT GGC TTT GTC TGC |
"Antisense" RNAi ispB sequence PCR fragment (562bp)
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G GCC TTT CTC CTC CTC CGG CGT ACA GCC AGC CAG AAT CCC GGA ACA CTG CGC GGC AGC CTC AAA CAG ACG CGC GGT TTT GCT ATA GAT AAC GCG CAT |
[New] BBa_K1336006 / LacI Expression Cassette + ispB Part-only sequence (Xbp)
LacI EC + K1336005.
LacI EC + "Antisense" ispB Device sequence
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LACIEC NEEDED + PREFIX NEEDED + TTA ACG ATC GCG TTG AAC AGC GAT GTG CGC GAG GCC GAT GAG TGC TTC TCG CCA AGG GGT GTC CGG GAG CAC CTG TAA CGC TGC GAT GGC TTT GTC TGC |
[New] BBa_K1336007 / LacI Expression Cassette + BsDyP Part-only sequence (XXXbp)
LacI EC + K1336003.
LacI EC + BsDyP Device sequence
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LACIEC NEEDED + PREFIX NEEDED + [[BsDyP NEEDED]] + SUFFIX NEEDED |
Plasmid Backbone / Vectors
pET-21a (+) sequence (5443bp) [Link, see DT]
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1 |
ATC CGG ATA TAG TTC CTC CTT TCA GCA AAA AAC CCC TCA AGA CCC GTT TAG AGG CCC CAA GGG GTT ATG CTA GTT ATT GCT CAG CGG TGG CAG CAG CCA |
pSB1C3 Part-only sequence (2070bp)
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1 |
TAC TAG TAG CGG CCG CTG CAG TCC GGC AAA AAA GGG CAA GGT GTC ACC ACC CTG CCC TTT TTC TTT AAA ACC GAA AAG ATT ACT TCG CGT TAT GCA GGC |
pSB1A3 Part-only sequence (2155bp)
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1 |
TAC TAG TAG CGG CCG CTG CAG TCC GGC AAA AAA GGG CAA GGT GTC ACC ACC CTG CCC TTT TTC TTT AAA ACC GAA AAG ATT ACT TCG CGT TAT GCA GGC |
pSB1K3 Part-only sequence (2204bp)
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1 |
TAC TAG TAG CGG CCG CTG CAG TCC GGC AAA AAA GGG CAA GGT GTC ACC ACC CTG CCC TTT TTC TTT AAA ACC GAA AAG ATT ACT TCG CGT TAT GCA GGC |
BioBricks from iGEM Parts Registry Distributions
[Test use] J04450 Part-only sequence (1069bp)
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1 |
CAA TAC GCA AAC CGC CTC TCC CCG CGC GTT GGC CGA TTC ATT AAT GCA GCT GGC ACG ACA GGT TTC CCG ACT GGA AAG CGG GCA GTG AGC GCA ACG CAA |
[Used] K314103 Part-only sequence (1638bp)
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1 |
ACG CGC CCT GTA GCG GCG CAT TAA GCG CGG CGG GTG TGG TGG TTA CGC GCA GCG TGA CCG CTA CAC TTG CCA GCG CCC TAG CGC CCG CTC CTT TCG CTT |
[Test use] R0010 Part-only sequence (200bp)
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CAA TAC GCA AAC CGC CTC TCC CCG CGC GTT GGC CGA TTC ATT AAT GCA GCT GGC ACG ACA GGT TTC CCG ACT GGA AAG CGG GCA GTG AGC GCA ACG CAA |
[Not used] R0011 Part-only sequence (55bp)
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AAT TGT GAG CGG ATA ACA ATT GAC ATT GTG AGC GGA TAA CAA GAT ACT GAG CAC A |
[Not used] K206000 Part-only sequence (130bp)
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ACA TTG ATT ATT TGC ACG GCG TCA CAC TTT GCT ATG CCA TAG CAA GAT AGT CCA TAA GAT TAG CGG ATC CTA CCT GAC GCT TTT TAT CGC AAC TCT CTA |
[Test use] B0034 Part-only sequence (12bp)
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AAA GAG GAG AAA |
[Test use] K518012 Part-only sequence (828bp)
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TCA CAC AGG AAA GTA CTA GAT GGC TTC CTC CGA AGA CGT TAT CAA AGA GTT CAT GCG TTT CAA AGT TCG TAT GGA AGG TTC CGT TAA CGG TCA CGA GTT |
[Not used] B0012 Part-only sequence (41bp)
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TCA CAC TGG CTC ACC TTC GGG TGG GCC TTT CTG CGT TTA TA |
Full table
No. | ID | Name / Function | Source | State / Concentration / Date Made | Gene Size / Sequence | Initial Plasmid / Vector | Comments |
---|---|---|---|---|---|---|---|
1 | pAzoR / BBa_K1336000 | FMN-dependent NADH-azoreductase 1 | Pseudomonas putida | Miniprep,
48 ng/uL, 15/07/17, TO. |
612 bp | Expression vector pET-21a (+) (ampicillin resistant (ampR)), initially cloned between NdeI and BamHI. | Plasmid provided by Lisbon; with Paper. |
2 | p1B6 (AzoR 1B6) / BBa_K1336001 | Mutant: Heat-stable; FMN-dependent NADH-azoreductase 1 | Pseudomonas putida | Miniprep,
68 ng/uL, 15/07/14, TO. |
612 bp | Expression vector pET-21a (+) (ampR), initially cloned between NdeI and BamHI. | Plasmid provided by Lisbon; with Paper. |
3 | pCotA / BBa_K1336002 | Spore Coat Protein Laccase | Bacillus subtilis | Miniprep,
103 ng/uL, 15/07/14, TO. |
1542 bp | Expression vector pET-21a (+) (ampR), initially cloned between NheI and BamHI. | Plasmid provided by Lisbon; with Paper. |
4 | pBsDyP / BBa_K1336003 | Dye Decolourising Peroxidase BSU38260 | Bacillus subtilis | Miniprep,
51 ng/uL, 15/07/14, TO. |
1251 bp | Expression vector pET-21a (+) (ampR), initially cloned between NdeI and BamHI. | Plasmid provided by Lisbon; with Paper. |
5 | pPpDyP / BBa_K1336004 | Dye Decolourising Peroxidase PP_3248 | Pseudomonas putida | Miniprep,
55 ng/uL, 15/07/14, TO. |
864 bp | Expression vector pET-21a (+) (ampR), initially cloned between NdeI and BamHI. | Plasmid provided by Lisbon; with Paper. |
6 | LiP / BBa_K500000 | Lignin Peroxidase | Phanerochaete chrysosporium (White-Rot Fungi) | [Taken from BBa_K500000, and optimised for use in E. coli; being synthesised by Gene Oracle],
X ng/uL, dd/mm/yy, Gene Oracle. |
1116 bp | [To be cloned directly into expression vector, pSB1C3, between EcoRI and PstI.] | Synthesised (for free) by Gene Oracle. Sequence from Paper. |
7 | CueO / BBa_K729006 | Laccase | Escherichia coli | Miniprep,
X ng/uL, dd/mm/yy, TO. |
1612 bp | Plasmid Backbone: pSB1C3, i.e. chloramphenicol resistant (camR). | A device consisting of: a constituitive promoter (J23119), a strong RBS (B0034), and laccase for polyethylene degradation (K729002). |
8 | ispB / BBa_K1336005 | Octaprenyl Diphosphate Synthase | Escherichia coli, strain K-12 | Miniprep,
X ng/uL, dd/mm/yy, EG. |
972 bp | [To be cloned directly into expression vector, pSB1C3, between EcoRI and PstI.] | Using the antisense/reverse complement gene as a method of gene knockdown (i.e. as RNAi); in collaboration with the Edinburgh iGEM 2014 Team. |
9 | BBa_J04450 | RFP Coding Device | Spring 2014 BioBrick Distribution.
Plate 4, Well 4B. [Check! DT?]. |
(1) Miniprep,
333 ng/uL, 01/07/14, TO. (2) Miniprep, 38 ng/uL (NanoDrop, dodgy!) 01/07/14, TO. |
1069 bp,
Genomic Sequence[Add sequence! Made from combined BioBricks?] |
Plasmid Backbone: pSB1C3, i.e. chloramphenicol resistant (camR). | LacI-, and CAP-, sensitive; can fail if system contains LacI or CAP protein!
RFP Coding Device contains: LacI (R0010), strong RBS (B0034), mRFP1 (E1010), and double terminator (B0015 = B0010+B0012). |
10 | BBa_K314103 | Lac induced expression cassette | Spring 2014 BioBrick Distribution.
Plate 1, Well 4D. [Check! DT?]. |
Miniprep,
334 ng/uL, 01/07/14, TO. |
1638 bp,
Genomic Sequence[Add sequence!] |
Plasmid Backbone: pSB1C3, i.e. chloramphenicol resistant (camR).
Plasmid / Vector Map. |
Lactose (IPTG) inducible protein expression insert includes f1 origin (K314110), a Lac I generator (K314111), a lactose inducible promoter (R0011), and the Elowitz standard RBS (B0034). |
11 | BBa_R0010 | Promoter (LacI regulated) | Spring 2014 BioBrick Distribution.
Plate 3, Well 4G. [Check! DT?]. |
Miniprep,
329.1 ng/uL, 01/07/14, TO. |
200 bp,
Genomic Sequence[Add sequence!] |
Plasmid Backbone: pSB1C3, i.e. chloramphenicol resistant (camR).
Plasmid / Vector Map. |
This part is an inverting regulator sensitive to LacI and CAP. In the absence of LacI and CAP proteins, this part promotes transcription; in their presence, the part inhibits transcription. LacI can be inhibited by IPTG. |
12 | BBa_R0011 | Promoter (LacI regulated, lambda pL hybrid) | Spring 2014 BioBrick Distribution.
Plate 2, Well 6D (Inconsistent sequencing!). [Check! DT? / Maybe use Spring 2013 Distribution, Plate 5, Well 6G.]. |
Miniprep,
38 ng/uL (NanoDrop, dodgy!), 01/07/14, TO. |
55 bp,
Genomic Sequence[Add sequence!] |
Plasmid Backbone: pSB1C3, i.e. chloramphenicol resistant (camR).
Plasmid / Vector Map. |
Inverting regulatory region controlled by LacI (BBa_C0010, BBa_C0012, etc.) The PLlac 0-1 promoter is a hybrid regulatory region consisting of the promoter P(L) of phage lambda with the cI binding sites replaced with lacO1. |
13 | BBa_K206000 | pBAD Strong Promoter | Spring 2014 BioBrick Distribution.
Plate 3, Well 14A. [Check! DT?]. |
Miniprep,
144 ng/uL, 01/07/14, TO. |
130 bp,
Genomic Sequence[Add sequence!] |
Plasmid Backbone: pSB1C3, i.e. chloramphenicol resistant (camR).
Plasmid / Vector Map |
pBAD is an E. coli promoter that is induced by L-arabinose. In the absence of arabinose, the repressor protein AraC (BBa_I13458) binds to the AraI1 operator site of pBAD and the upstream operator site AraO2, blocking transcription; in its presence, transcription is permitted. |
14 | BBa_B0034 | RBS | Spring 2014 BioBrick Distribution.
Plate 4, Well 1N. [Check! DT?]. |
Miniprep,
156.5 ng/uL, 01/07/14, TO. |
12 bp,
Genomic Sequence[Add sequence!] |
Plasmid Backbone: pSB1A2, i.e. ampicillin resistant (ampR).
Plasmid / Vector Map |
RBS based on Elowitz (1999) repressilator. |
15 | BBa_K518012 | RBS + RFP + double Terminator | Spring 2014 BioBrick Distribution.
Plate 1, Well 18C. [Check! DT?]. |
(1) Miniprep,
49 ng/uL, 01/07/14, TO. (2) Miniprep, 219.2 ng/uL, 08/08/14, YKH. |
828 bp,
Genomic Sequence[Add sequence!] |
Plasmid Backbone: pSB1C3, i.e. chloramphenicol resistant (camR).
Plasmid / Vector Map |
This Coding Device contains: RBS.3 (medium) (B0032), mRFP1 (E1010), and double terminator (B0014 = B0012+B0011). |
16 | [CHECK: BAD PART !]
BBa_B0012 (2) |
Transcription Terminator for E. coli RNA polymerase | Spring 2014 BioBrick Distribution.
Plate 2, Well 2B. [Check! DT?]. |
Miniprep,
128 ng/uL, 01/07/14, TO. |
41 bp,
Genomic Sequence[Add sequence!] |
Plasmid Backbone: pSB1C3, i.e. chloramphenicol resistant (camR).
Plasmid / Vector Map |
TE from coliphage T7. This is a bad terminator (Experience: Fails). It is a promoter in the reverse direction. |
# | ID | Name / Function | Source | State / Concentration / Date Made | Gene Size / Sequence | Initial Plasmid / Vector | Comments |