Team:UCL/Science/Sequences
From 2014.igem.org
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<h3>Summary</h3> | <h3>Summary</h3> | ||
- | <p>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 | + | <p>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 iGEM Parts Registry pages describing the part(s) in more detail.</p> |
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<h3>BioBrick Designs for Our Genes</h3> | <h3>BioBrick Designs for Our Genes</h3> | ||
- | <h4><a name="K1336000" href="http://parts.igem.org/Part:BBa_K1336000">[ | + | |
- | <p class="widthCorrect">Sequence | + | <font size="2"> |
+ | <table border="1px" width="100%" height="auto"> | ||
+ | <thead> | ||
+ | <tr> | ||
+ | <th> </th> | ||
+ | <th> Registry ID </th> | ||
+ | <th> Gene ID</th> | ||
+ | <th> Name / Function </th> | ||
+ | <th> Source </th> | ||
+ | <th> Size </th> | ||
+ | <th> Status </th> | ||
+ | </tr> | ||
+ | </thead> | ||
+ | <tbody> | ||
+ | <!--Lisbon plasmids--> | ||
+ | <tr> | ||
+ | <td> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K1336000">BBa_K1336000</a> </td> | ||
+ | <td> AzoR </td> | ||
+ | <td> FMN-dependent NADH-azoreductase 1 </td> | ||
+ | <td> <em>Pseudomonas putida</em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K1336000">612 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Primers">In Progress</a>]: primers designed </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K1336001">BBa_K1336001</a> </td> | ||
+ | <td> 1B6 </td> | ||
+ | <td> AzoR heat-stable mutant</td> | ||
+ | <td> <em>Pseudomonas putida</em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K1336001">612 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Experiments">In Progress</a>]: to remove 2 illegal PstI sites </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K1336002">BBa_K1336002</a> </td> | ||
+ | <td> CotA </td> | ||
+ | <td> Spore Coat Protein Laccase</td> | ||
+ | <td> <em>Bacillus subtilis</em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K1336002">1542 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Primers">In Progress</a>]: primers designed </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> <center><img src="https://static.igem.org/mediawiki/2014/e/e0/UCL_Bronze-metal-star.jpg" width="25px"></center> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K1336003">BBa_K1336003</a> </td> | ||
+ | <td> BsDyP </td> | ||
+ | <td> Dye Decolourising Peroxidase BSU38260</td> | ||
+ | <td> <em>Bacillus subtilis</em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K1336003">1251 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Experiments">New BioBrick Part</a>]: submitted </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K1336004">BBa_K1336004</a> </td> | ||
+ | <td> PpDyP </td> | ||
+ | <td> Dye Decolourising Peroxidase PP_3248 </td> | ||
+ | <td> <em>Pseudomonas putida</em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K1336004">864 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Primers">In Progress</a>]: primers designed </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> <center><img src="https://static.igem.org/mediawiki/2014/e/e0/UCL_Bronze-metal-star.jpg" width="25px"></center> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K1336005">BBa_K1336005</a> </td> | ||
+ | <td> ispB RNAi </td> | ||
+ | <td> RNAi of Octaprenyl Diphosphate <br>Synthase fragment </td> | ||
+ | <td> <em>Escherichia coli, K12 strain</em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K1336005">562 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Experiment">New BioBrick Part</a>]: submitted </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> <center><img src="https://static.igem.org/mediawiki/2014/e/e0/UCL_Bronze-metal-star.jpg" width="25px"></center> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K1336006">BBa_K1336006</a> </td> | ||
+ | <td> LacIEC+ispB </td> | ||
+ | <td> IPTG inducible ispB RNAi </td> | ||
+ | <td> <em>Escherichia coli, K12 strain </em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K1336006">2208 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Experiment">New BioBrick Device</a>]: submitted </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> <center><img src="https://static.igem.org/mediawiki/2014/e/e0/UCL_Bronze-metal-star.jpg" width="25px"></center> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K1336007">BBa_K1336007</a> </td> | ||
+ | <td> LacIEC+BsDyP </td> | ||
+ | <td> IPTG inducible BsDyP </td> | ||
+ | <td> <em>Bacillus subtilis</em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K1336007">2895 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Experiment">New BioBrick Device</a>]: submitted </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K729006">BBa_K729006</a> </td> | ||
+ | <td> CueO </td> | ||
+ | <td> Laccase </td> | ||
+ | <td> <em>Escherichia coli </em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K729006">1612 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Experiment">In Progress</a>]: ascertaining identity </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> <center>(<img src="https://static.igem.org/mediawiki/2014/3/36/UCL_Gold-metal-star.jpg" width="25px">)</center> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K500000">BBa_K500000</a> </td> | ||
+ | <td> LiP </td> | ||
+ | <td> Lignin Peroxidase </td> | ||
+ | <td> <em>Phanerochaete chrysosporium</em> </td> <!-- <br>(White-Rot Fungi) --> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K500000">1116 bp</a> </td> <!--Check size!--> | ||
+ | <td> [<a href="/Team:UCL/Science/Results">Improved Characterisation</a>]: toxicity issues in gene synthesis. <br> [<a href="/Team:UCL/Science/Experiment">In Progress</a>]: to subclone into pSB1C3/pSB3C5. </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> <center><img src="https://static.igem.org/mediawiki/2014/3/36/UCL_Gold-metal-star.jpg" width="25px"></center> </td> | ||
+ | <td> <a href="http://parts.igem.org/Part:BBa_K729004">BBa_K729004</a> </td> | ||
+ | <td> nucB </td> | ||
+ | <td> Extracellular nuclease </td> | ||
+ | <td> <em>Staphylococcus aureus</em> </td> | ||
+ | <td> <a href="/Team:UCL/Science/Sequences#BBa_K729004">561 bp</a> </td> | ||
+ | <td> [<a href="/Team:UCL/Science/Results">Improved Function</a>] </td> | ||
+ | </tr> | ||
+ | |||
+ | |||
+ | </tbody> | ||
+ | </table> | ||
+ | </font> | ||
+ | |||
+ | <h4><a name="K1336000" href="http://parts.igem.org/Part:BBa_K1336000">[In progress] BBa_K1336000 / AzoR Part-only sequence (612bp)</a></h4> | ||
+ | <p class="widthCorrect">FMN-dependent NADH-azoreductase 1 (from <em>Pseudomonas putida</em>) <a href="http://www.ncbi.nlm.nih.gov/pubmed/21655981">[1]</a>. <br> | ||
+ | Gene provided by the <a href="http://www.itqb.unl.pt/martins">Microbial & Enzyme Technology Lab</a> led by Dr Lígia O. Martins at the Universidade Nova de Lisboa. <br> | ||
+ | In expression vector: pET-21a (+) (ampicillin resistant (ampR)) <a href="http://www.addgene.org/browse/sequence_vdb/2549/ ">[2] <a href=" http://biochem.web.utah.edu/hill/links/pET21.pdf">[3] </a>, initially cloned between <em>NdeI</em> and <em>BamHI</em> restriction sites. <br> | ||
+ | Sequence obtained from <a href="http://www.ncbi.nlm.nih.gov/nuccore/26986745?report=fasta&from=3267527&to=3268138">NCBI</a>.</p> | ||
<font size="2"><table class="table table-striped table-bordered"> | <font size="2"><table class="table table-striped table-bordered"> | ||
<tr> | <tr> | ||
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<br> | <br> | ||
- | <h4><a name="K1336001" href="http://parts.igem.org/Part:BBa_K1336001">[ | + | <h4><a name="K1336001" href="http://parts.igem.org/Part:BBa_K1336001">[In progress] BBa_K1336001 / AzoR 1B6 (heat-stable AzoR mutant) Part-only sequence (612bp)</a></h4> |
- | <p class="widthCorrect"> | + | <p class="widthCorrect">Heat-stable mutant of FMN-dependent NADH-azoreductase 1 (from <em>Pseudomonas putida</em>) <a href="http://www.ncbi.nlm.nih.gov/pubmed/24475252">[4]</a>. <br> |
+ | Gene and sequence provided by the <a href="http://www.itqb.unl.pt/martins">Microbial & Enzyme Technology Lab</a> led by Dr Lígia O. Martins at the Universidade Nova de Lisboa. <br> | ||
+ | In expression vector: pET-21a (+) (ampicillin resistant (ampR)) <a href="http://www.addgene.org/browse/sequence_vdb/2549/ ">[2] <a href=" http://biochem.web.utah.edu/hill/links/pET21.pdf">[3] </a>, initially cloned between <em>NdeI</em> and <em>BamHI</em> restriction sites. <br></p> | ||
<font size="2"><table class="table table-striped table-bordered"> | <font size="2"><table class="table table-striped table-bordered"> | ||
<tr> | <tr> | ||
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<br> | <br> | ||
- | <h4><a name="K1336002" href="http://parts.igem.org/Part:BBa_K1336002">[ | + | <h4><a name="K1336002" href="http://parts.igem.org/Part:BBa_K1336002">[In progress] BBa_K1336002 / CotA Part-only sequence (1542bp)</a></h4> |
- | <p class="widthCorrect"> | + | <p class="widthCorrect">Spore Coat Protein Laccase (from <em>Bacillus subtilis</em>) <a href="http://www.itqb.unl.pt/martins/index_files/JBC2002.pdf">[5]</a>. <br> |
+ | Gene and sequence provided by the <a href="http://www.itqb.unl.pt/martins">Microbial & Enzyme Technology Lab</a> led by Dr Lígia O. Martins at the Universidade Nova de Lisboa. <br> | ||
+ | In expression vector: pET-21a (+) (ampicillin resistant (ampR)) <a href="http://www.addgene.org/browse/sequence_vdb/2549/ ">[2] <a href=" http://biochem.web.utah.edu/hill/links/pET21.pdf">[3] </a>, initially cloned between <strong><em>NheI</em></strong> and <em>BamHI</em> restriction sites. <br></p> | ||
<font size="2"><table class="table table-striped table-bordered"> | <font size="2"><table class="table table-striped table-bordered"> | ||
<tr> | <tr> | ||
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<br> | <br> | ||
- | <h4><a name="K1336003" href="http://parts.igem.org/Part:BBa_K1336003">[New] BBa_K1336003 / BsDyP Part-only sequence (1251bp)</a></h4> | + | <h4><a name="K1336003" href="http://parts.igem.org/Part:BBa_K1336003">[New Part] BBa_K1336003 / BsDyP Part-only sequence (1251bp)</a></h4> |
- | <p class="widthCorrect"> | + | <p class="widthCorrect">Dye Decolourising Peroxidase BSU38260 (from <em>Bacillus subtilis</em>) <a href="http://www.ncbi.nlm.nih.gov/pubmed/23820555">[6]</a>. <br> |
+ | Gene and sequence provided by the <a href="http://www.itqb.unl.pt/martins">Microbial & Enzyme Technology Lab</a> led by Dr Lígia O. Martins at the Universidade Nova de Lisboa. <br> | ||
+ | In expression vector: pET-21a (+) (ampicillin resistant (ampR)) <a href="http://www.addgene.org/browse/sequence_vdb/2549/ ">[2] <a href=" http://biochem.web.utah.edu/hill/links/pET21.pdf">[3] </a>, initially cloned between <em>NdeI</em> and <em>BamHI</em> restriction sites. <br></p> | ||
<font size="2"><table class="table table-striped table-bordered"> | <font size="2"><table class="table table-striped table-bordered"> | ||
<tr> | <tr> | ||
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<br> | <br> | ||
- | <h4><a name="K1336004" href="http://parts.igem.org/Part:BBa_K1336004">[ | + | <h4><a name="K1336004" href="http://parts.igem.org/Part:BBa_K1336004">[In progress] BBa_K1336004 / PpDyP Part-only sequence (864bp)</a></h4> |
- | <p class="widthCorrect">Sequence | + | |
+ | <p class="widthCorrect">Dye Decolourising Peroxidase PP_3248 (from <em>Pseudomonas putida</em>) <a href="http://www.ncbi.nlm.nih.gov/pubmed/23820555">[6]</a>. <br> | ||
+ | Gene provided by the <a href="http://www.itqb.unl.pt/martins">Microbial & Enzyme Technology Lab</a> led by Dr Lígia O. Martins at the Universidade Nova de Lisboa. <br> | ||
+ | In expression vector: pET-21a (+) (ampicillin resistant (ampR)) <a href="http://www.addgene.org/browse/sequence_vdb/2549/ ">[2] <a href=" http://biochem.web.utah.edu/hill/links/pET21.pdf">[3] </a>, initially cloned between <em>NdeI</em> and <em>BamHI</em> restriction sites. <br> | ||
+ | Sequence obtained from <a href="http://www.ncbi.nlm.nih.gov/nuccore/24987239?from=3681833&to=3682696&sat=4&sat_key=105780727&report=fasta">NCBI</a>.</p> | ||
<font size="2"><table class="table table-striped table-bordered"> | <font size="2"><table class="table table-striped table-bordered"> | ||
<tr> | <tr> | ||
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<br> | <br> | ||
- | + | <h4><a name="K1336005" href="http://parts.igem.org/Part:BBa_K1336005">[New Part] BBa_K1336005 / ispB Part-only sequence (562bp)</a></h4> | |
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- | <h4><a name="K1336005" href="http://parts.igem.org/Part:BBa_K1336005">[New] BBa_K1336005 / ispB Part-only sequence (562bp)</a></h4> | + | |
<p class="widthCorrect">The first sequence below shows the <a href="http://www.ncbi.nlm.nih.gov/protein/16131077">"sense" ispB gene</a>, but we use the second sequence, the Reverse Complement to design primers to produce an antisense fragment for <a href="http://jb.asm.org/content/179/9/3058.short">gene knockdown</a> (i.e. as RNAi).</p><br> | <p class="widthCorrect">The first sequence below shows the <a href="http://www.ncbi.nlm.nih.gov/protein/16131077">"sense" ispB gene</a>, but we use the second sequence, the Reverse Complement to design primers to produce an antisense fragment for <a href="http://jb.asm.org/content/179/9/3058.short">gene knockdown</a> (i.e. as RNAi).</p><br> | ||
<p>"Sense" ispB sequence (972bp)</p> | <p>"Sense" ispB sequence (972bp)</p> | ||
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</table></font> | </table></font> | ||
- | <p>"Antisense" RNAi ispB sequence PCR fragment (562bp)</p> | + | <p>"Antisense" RNAi ispB sequence PCR fragment (562bp):</p> |
- | + | ||
<font size="2"><table class="table table-striped table-bordered"> | <font size="2"><table class="table table-striped table-bordered"> | ||
<tr> | <tr> | ||
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</table></font> | </table></font> | ||
- | <h4><a name="K1336006" href="http://parts.igem.org/Part:BBa_K1336006">[New] BBa_K1336006 / LacI Expression Cassette + ispB Part-only sequence ( | + | <h4><a name="K1336006" href="http://parts.igem.org/Part:BBa_K1336006">[New Device] BBa_K1336006 / LacI Expression Cassette + ispB Part-only sequence (2208bp)</a></h4> |
- | <p class="widthCorrect">LacI EC + | + | <p class="widthCorrect"><a href="/Team:UCL/Science/Sequences#BBa_K314103">LacI EC</a> + <a href="/Team:UCL/Science/Sequences#BBa_K1336005">"Antisense" ispB</a> Device sequence</p> |
- | <p>LacI EC + " | + | <br> |
+ | |||
+ | <h4><a name="K1336007" href="http://parts.igem.org/Part:BBa_K1336007">[New Device] BBa_K1336007 / LacI Expression Cassette + BsDyP Part-only sequence (2895 bp)</a></h4> | ||
+ | <p class="widthCorrect"><a href="/Team:UCL/Science/Sequences#BBa_K314103">LacI EC</a> + <a href="/Team:UCL/Science/Sequences#BBa_K1336003">BsDyP</a> Device sequence</p> | ||
+ | <br> | ||
+ | |||
+ | <!--https://2012.igem.org/Team:University_College_London/BioBricks | ||
+ | http://parts.igem.org/wiki/index.php?title=Part:BBa_K729006 (1612bp) Device. | ||
+ | http://parts.igem.org/wiki/index.php?title=Part:BBa_K729002 (1551bp) Part-only.--> | ||
+ | <h4><a name="K729006" href="http://parts.igem.org/Part:BBa_K729006">[In progress] BBa_K729006 / CueO Part-only sequence (1612bp)</a></h4> | ||
+ | <p class="widthCorrect">Sequence taken from the initial page; not currently showing our improvements.</p> | ||
<font size="2"><table class="table table-striped table-bordered"> | <font size="2"><table class="table table-striped table-bordered"> | ||
<tr> | <tr> | ||
<td style="text-align:right;"> | <td style="text-align:right;"> | ||
- | <pre>1<br />100<br />199<br />298<br />397<br />496<br />595<br />694<br />793<br />892</pre> | + | <pre>1<br />100<br />199<br />298<br />397<br />496<br />595<br />694<br />793<br />892<br />991<br />1090<br />1189<br />1288<br />1387<br />1486<br />1585</pre> |
</td> | </td> | ||
<td style="text-align:left;"> | <td style="text-align:left;"> | ||
- | <pre> | + | <pre>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 <br />GGG TGT GGC TTC GGC TTT GCC GCT GTG GAG CCG CGC AGT ATT TGC GGC AGA ACG CCC AAC GTT ACC GAT CCC TGA TTT GCT CAC GAC CGA TGC CCG TAA <br />TCG CAT TCA GTT AAC TAT TGG CGC AGG CCA GTC CAC CTT TGG CGG GAA AAC TGC AAC TAC CTG GGG CTA TAA CGG CAA TCT GCT GGG GCC GGC GGT GAA <br />ATT ACA GCG CGG CAA AGC GGT AAC GGT TGA TAT CTA CAA CCA ACT GAC GGA AGA GAC AAC GTT GCA CTG GCA CGG GCT GGA AGT ACC GGG TGA AGT CGA <br />CGG CGG CCC GCA GGG AAT TAT TCC GCC AGG TGG CAA GCG CTC GGT GAC GTT GAA CGT TGA TCA ACC TGC CGC TAC CTG CTG GTT CCA TCC GCA TCA GCA <br />CGG CAA AAC CGG GCG ACA GGT GGC GAT GGG GCT GGC TGG GCT GGT GGT GAT TGA AGA TGA CGA GAT CCT GAA ATT AAT GCT GCC AAA ACA GTG GGG TAT <br />CGA TGA TGT TCC GGT GAT CGT TCA GGA TAA GAA ATT TAG CGC CGA CGG GCA GAT TGA TTA TCA ACT GGA TGT GAT GAC CGC CGC CGT GGG CTG GTT TGG <br />CGA TAC GTT GCT GAC CAA CGG TGC AAT CTA CCC GCA ACA CGC TGC CCC GCG TGG TTG GCT GCG CCT GCG TTT GCT CAA TGG CTG TAA TGC CCG TTC GCT <br />CAA TTT CGC CAC CAG CGA CAA TCG CCC GCT GTA TGT GAT TGC CAG CGA CGG TGG TCT GCT ACC TGA ACC AGT GAA GGT GAG CGA ACT GCC GGT GCT GAT <br />GGG CGA GCG TTT TGA AGT GCT GGT GGA GGT TAA CGA TAA CAA ACC CTT TGA CCT GGT GAC GCT GCC GGT CAG CCA GAT GGG GAT GGC GAT TGC GCC GTT <br />TGA TAA GCC TCA TCC GGT AAT GCG GAT TCA GCC GAT TGC TAT TAG TGC CTC CGG TGC TTT GCC AGA CAC ATT AAG TAG CCT GCC TGC GTT ACC TTC GCT <br />GGA AGG GCT GAC GGT ACG CAA GCT GCA ACT CTC TAT GGA CCC GAT GCT CGA TAT GAT GGG GAT GCA GAT GCT AAT GGA GAA ATA TGG CGA TCA GGC GAT <br />GGC CGG GAT GGA TCA CAG CCA GAT GAT GGG CCA TAT GGG GCA CGG CAA TAT GAA TCA TAT GAA CCA CGG CGG GAA GTT CGA TTT CCA CCA TGC CAA CAA <br />AAT CAA CGG TCA GGC GTT TGA TAT GAA CAA GCC GAT GTT TGC GGC GGC GAA AGG GCA ATA CGA ACG TTG GGT TAT CTC TGG CGT GGG CGA CAT GAT GCT <br />GCA TCC GTT CCA TAT CCA CGG CAC GCA GTT CCG TAT CTT GTC AGA AAA TGG CAA ACC GCC AGC GGC TCA TCG CGC GGG CTG GAA AGA TAC CGT TAA GGT <br />AGA AGG TAA TGT CAG CGA AGT GCT GGT GAA GTT TAA TCA CGA TGC ACC GAA AGA ACA TGC TTA TAT GGC GCA CTG CCA TCT GCT GGA GCA TGA AGA TAC <br />GGG GAT GAT GTT AGG GTT TAC GGT ATA A</pre> |
</td> | </td> | ||
</tr> | </tr> | ||
Line 176: | Line 286: | ||
<br> | <br> | ||
- | + | <h4><a name="K500000" href="http://parts.igem.org/Part:BBa_K500000">[Improved Characterisation / In Progress] BBa_K500000 / LiP Part-only sequence (1116bp)</a></h4> | |
- | <p class="widthCorrect"> | + | <p class="widthCorrect">Sequence taken from the initial page; not currently showing our improvements.</p> |
- | + | ||
<font size="2"><table class="table table-striped table-bordered"> | <font size="2"><table class="table table-striped table-bordered"> | ||
<tr> | <tr> | ||
<td style="text-align:right;"> | <td style="text-align:right;"> | ||
- | <pre>1<br />100<br />199<br />298<br />397<br />496<br />595<br />694<br />793<br />892</pre> | + | <pre>1<br />100<br />199<br />298<br />397<br />496<br />595<br />694<br />793<br />892<br />991<br />1090</pre> |
+ | </td> | ||
+ | <td style="text-align:left;"> | ||
+ | <pre>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 <br />GGT AAG ACT GTT GGT GAT GCT TGT TCT TGT GCT TGG TTT GAT GTT TTG GAC GAC ATC CAA CAA AAC TTG TTT CAT GGT GGT CAA TGT GGT GCT GAA GCT <br />CAT GAA TCT ATC AGA TTG GTT TTC CAT GAC TCC ATT GCT ATT TCT CCA GCT ATG GAA GCT CAA GGT AAA TTT GGT GGA GGT GGT GCT GAT GGT TCC ATT <br />ATG ATT TTC GAT GAT ATC GAA ACC GCC TTC CAT CCA AAT ATT GGT TTG GAC GAA ATC GTC AAG TTG CAA AAG CCA TTT GTT CAA AAG CAC GGT GTT ACT <br />CCA GGT GAT TTT ATT GCT TTT GCT GGT GCT GTT GCT TTG TCT AAT TGT CCA GGT GCT CCA CAA ATG AAT TTC TTT ACT GGT AGA GCA CCA GCT ACT CAA <br />CCA GCT CCA GAT GGT TTG GTT CCA GAA CCA TTT CAT ACC GTT GAC CAA ATC ATC AAC AGA GTT AAT GAC GCC GGT GAA TTT GAC GAA TTG GAA TTG GTT <br />TGG ATG TTG TCT GCT CAT TCT GTT GCT GCT GTT AAT GAT GTT GAT CCA ACT GTT CAA GGT TTG CCA TTT GAT TCT ACC CCA GGT ATT TTC GAT TCC CAA <br />TTC TTC GTT GAA ACC CAA TTG AGA GGT ACT GCT TTT CCA GGT TCT GGT GGT AAT CAA GGT GAA GTT GAA TCT CCA TTG CCA GGT GAA ATT AGA ATC CAA <br />TCC GAT CAT ACC ATT GCC AGA GAT TCA AGA ACT GCT TGT GAA TGG CAA TCC TTC GTT AAC AAT CAA TCC AAG TTG GTT GAC GAC TTC CAA TTC ATT TTC <br />TTG GCT TTG ACT CAA TTG GGT CAA GAT CCA AAT GCT ATG ACT GAT TGC TCC GAT GTT ATT CCA CAA TCT AAA CCT ATC CCA GGT AAC TTG CCA TTT TCA <br />TTT TTT CCA GCT GGT AAG ACC ATC AAG GAT GTT GAA CAA GCT TGT GCT GAA ACT CCA TTT CCA ACT TTG ACT ACT TTG CCA GGT CCA GAA ACT TCT GTT <br />CAA AGA ATA CCA CCA CCA CCA GGT GCT </pre> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table></font> | ||
+ | <br> | ||
+ | |||
+ | <h4><a name="K729004" href="http://parts.igem.org/Part:BBa_K729004">[Improved Function] BBa_K729004 / nucB Part-only sequence (561bp)</a></h4> | ||
+ | <p class="widthCorrect">Sequence taken from the initial page; not currently showing our improvements.</p> | ||
+ | <font size="2"><table class="table table-striped table-bordered"> | ||
+ | <tr> | ||
+ | <td style="text-align:right;"> | ||
+ | <pre>1<br />100<br />199<br />298<br />397<br />496</pre> | ||
</td> | </td> | ||
<td style="text-align:left;"> | <td style="text-align:left;"> | ||
- | <pre> | + | <pre>ATG AAA AAG ATT TGG CTG GCG CTG GCT GGT TTA GTT TTA GCG TTT AGC GCA TCG GCG CAA ACA GAT AAC GGC GTA AAT AGA AGT GGT TCT GAA GAT CCA <br />ACA GTA TAT AGT GCA ACT TCA ACT AAA AAA TTA CAT AAA GAA CCT GCG ACT TTA ATT AAA GCG ATT GAT GGT GAT ACG GTT AAA TTA ATG TAC AAA GGT <br />CAA CCA ATG ACA TTC AGA CTA TTA TTG GTT GAT ACA CCT GAA ACA AAG CAT CCT AAA AAA GGT GTA GAG AAA TAT GGT CCT GAA GCA AGT GCA TTT ACG <br />AAA AAA ATG GTA GAA AAT GCA AAG AAA ATT GAA GTC GAG TTT GAC AAA GGT CAA AGA ACT GAT AAA TAT GGA CGT GGC TTA GCG TAT ATT TAT GCT GAT <br />GGA AAA ATG GTA AAC GAA GCT TTA GTT CGT CAA GGC TTG GCT AAA GTT GCT TAT GTT TAC AAA CCT AAC AAT ACA CAT GAA CAA CAT TTA AGA AAA AGT <br />GAA GCA CAA GCG AAA AAA GAG AAA TTA AAT ATT TGG AGC GAA GAC AAC GCT GAT TCA GGT CAA TAA </pre> |
</td> | </td> | ||
</tr> | </tr> | ||
Line 193: | Line 316: | ||
<h3>Plasmid Backbone / Vectors</h3> | <h3>Plasmid Backbone / Vectors</h3> | ||
- | <h4><a name="pET21a+" href="http://www.addgene.org/browse/sequence_vdb/2549/">pET-21a (+) sequence (5443bp) | + | <h4><a name="pET21a+" href="http://www.addgene.org/browse/sequence_vdb/2549/">pET-21a (+) sequence (5443bp)</a></h4> |
<p class="widthCorrect">...</p> | <p class="widthCorrect">...</p> | ||
<font size="2"><table class="table table-striped table-bordered"> | <font size="2"><table class="table table-striped table-bordered"> | ||
Line 363: | Line 486: | ||
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Latest revision as of 17:10, 16 October 2014
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 iGEM Parts Registry pages describing the part(s) in more detail.
BioBrick Designs for Our Genes
Registry ID | Gene ID | Name / Function | Source | Size | Status | |
---|---|---|---|---|---|---|
BBa_K1336000 | AzoR | FMN-dependent NADH-azoreductase 1 | Pseudomonas putida | 612 bp | [In Progress]: primers designed | |
BBa_K1336001 | 1B6 | AzoR heat-stable mutant | Pseudomonas putida | 612 bp | [In Progress]: to remove 2 illegal PstI sites | |
BBa_K1336002 | CotA | Spore Coat Protein Laccase | Bacillus subtilis | 1542 bp | [In Progress]: primers designed | |
|
BBa_K1336003 | BsDyP | Dye Decolourising Peroxidase BSU38260 | Bacillus subtilis | 1251 bp | [New BioBrick Part]: submitted |
BBa_K1336004 | PpDyP | Dye Decolourising Peroxidase PP_3248 | Pseudomonas putida | 864 bp | [In Progress]: primers designed | |
|
BBa_K1336005 | ispB RNAi | RNAi of Octaprenyl Diphosphate Synthase fragment |
Escherichia coli, K12 strain | 562 bp | [New BioBrick Part]: submitted |
|
BBa_K1336006 | LacIEC+ispB | IPTG inducible ispB RNAi | Escherichia coli, K12 strain | 2208 bp | [New BioBrick Device]: submitted |
|
BBa_K1336007 | LacIEC+BsDyP | IPTG inducible BsDyP | Bacillus subtilis | 2895 bp | [New BioBrick Device]: submitted |
BBa_K729006 | CueO | Laccase | Escherichia coli | 1612 bp | [In Progress]: ascertaining identity | |
|
BBa_K500000 | LiP | Lignin Peroxidase | Phanerochaete chrysosporium | 1116 bp | [Improved Characterisation]: toxicity issues in gene synthesis. [In Progress]: to subclone into pSB1C3/pSB3C5. |
|
BBa_K729004 | nucB | Extracellular nuclease | Staphylococcus aureus | 561 bp | [Improved Function] |
[In progress] BBa_K1336000 / AzoR Part-only sequence (612bp)
FMN-dependent NADH-azoreductase 1 (from Pseudomonas putida) [1].
Gene provided by the Microbial & Enzyme Technology Lab led by Dr Lígia O. Martins at the Universidade Nova de Lisboa.
In expression vector: pET-21a (+) (ampicillin resistant (ampR)) [2] [3] , initially cloned between NdeI and BamHI restriction sites.
Sequence obtained from NCBI.
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 |
[In progress] BBa_K1336001 / AzoR 1B6 (heat-stable AzoR mutant) Part-only sequence (612bp)
Heat-stable mutant of FMN-dependent NADH-azoreductase 1 (from Pseudomonas putida) [4].
Gene and sequence provided by the Microbial & Enzyme Technology Lab led by Dr Lígia O. Martins at the Universidade Nova de Lisboa.
In expression vector: pET-21a (+) (ampicillin resistant (ampR)) [2] [3] , initially cloned between NdeI and BamHI restriction sites.
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 |
[In progress] BBa_K1336002 / CotA Part-only sequence (1542bp)
Spore Coat Protein Laccase (from Bacillus subtilis) [5].
Gene and sequence provided by the Microbial & Enzyme Technology Lab led by Dr Lígia O. Martins at the Universidade Nova de Lisboa.
In expression vector: pET-21a (+) (ampicillin resistant (ampR)) [2] [3] , initially cloned between NheI and BamHI restriction sites.
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 Part] BBa_K1336003 / BsDyP Part-only sequence (1251bp)
Dye Decolourising Peroxidase BSU38260 (from Bacillus subtilis) [6].
Gene and sequence provided by the Microbial & Enzyme Technology Lab led by Dr Lígia O. Martins at the Universidade Nova de Lisboa.
In expression vector: pET-21a (+) (ampicillin resistant (ampR)) [2] [3] , initially cloned between NdeI and BamHI restriction sites.
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 |
[In progress] BBa_K1336004 / PpDyP Part-only sequence (864bp)
Dye Decolourising Peroxidase PP_3248 (from Pseudomonas putida) [6].
Gene provided by the Microbial & Enzyme Technology Lab led by Dr Lígia O. Martins at the Universidade Nova de Lisboa.
In expression vector: pET-21a (+) (ampicillin resistant (ampR)) [2] [3] , initially cloned between NdeI and BamHI restriction sites.
Sequence obtained from NCBI.
1 |
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 |
[New Part] 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.
1 |
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):
1 |
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 Device] BBa_K1336006 / LacI Expression Cassette + ispB Part-only sequence (2208bp)
LacI EC + "Antisense" ispB Device sequence
[New Device] BBa_K1336007 / LacI Expression Cassette + BsDyP Part-only sequence (2895 bp)
LacI EC + BsDyP Device sequence
[In progress] 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 |
[Improved Characterisation / In Progress] 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 |
[Improved Function] BBa_K729004 / nucB Part-only sequence (561bp)
Sequence taken from the initial page; not currently showing our improvements.
1 |
ATG AAA AAG ATT TGG CTG GCG CTG GCT GGT TTA GTT TTA GCG TTT AGC GCA TCG GCG CAA ACA GAT AAC GGC GTA AAT AGA AGT GGT TCT GAA GAT CCA |
Plasmid Backbone / Vectors
pET-21a (+) sequence (5443bp)
...
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)
...
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)
...
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)
...
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)
...
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)
...
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)
...
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 |
[Not used] R0011 Part-only sequence (55bp)
...
1 |
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)
...
1 |
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)
...
1 |
AAA GAG GAG AAA |
[Test use] K518012 Part-only sequence (828bp)
...
1 |
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)
...
1 |
TCA CAC TGG CTC ACC TTC GGG TGG GCC TTT CTG CGT TTA TA |