Difference between revisions of "Part:BBa K3425019"

 
 
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<partinfo>BBa_K3425019 short</partinfo>
 
<partinfo>BBa_K3425019 short</partinfo>
  
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This part is the constitutive promoter BBa_J23108 adopted to the iGEM Type IIS standard (RFC1000). The BBa_J23108 sequence is flanked by the Type IIS prefix and suffix which allows cloning into the Level 0 backbone (pSB1C00). BBa_J23108 is part of the Anderson promoter family and its relative strength is 0.51. BBa_K3425017 can be ordered as two overlapping primers, see iGEM Type IIS guide.
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<html>
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<p>This series of iGEM Type IIS templates present easy to use blueprints to design parts for this assembly standard. These parts provide ready-made sequences which contain the different fusion sites for a promoter, RBS, CDS and terminator part according to the following image*.</p>
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</html>
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<center>https://static.igem.org/mediawiki/parts/b/b7/PCR_for_pSB1C00.png</center>
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<html>
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<p>By adding the fusion and restriction sites by DNA synthesis or PCR, the part is ready to be cloned into the Type IIS universal acceptor </html>[[Part:pSB1C00|<partinfo>pSB1C00</partinfo>]]<html>. More information about this backbone can be found in its page. It can also be found, together with all our experience in this cloning method, in Team Uppsala 2020's <a href="https://2020.igem.org/Team:UofUppsala/Engineering#TypeIIS">iGEM Type IIS standard guidebook</a>.</p>
  
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<!-- Add more about the biology of this part here
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<p>*<b>Note:</b> This image was taken from the </html>[[Part:pSB1C00|<partinfo>pSB1C00</partinfo>]]<html> page to provide visual aid for the explanation without redirecting to another page.</p>
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===Usage and Biology===
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</html>
  
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This part is part of iGEM Uppsala 2020's <html><a href="https://parts.igem.org/Collections/iGEM_Type_IIS_Collections">iGEM Type IIS standard collection</a></html>.
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K3425019 SequenceAndFeatures</partinfo>
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===Usage and biology===
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<html>
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<p>This part is a CDS template, and it is used to clone coding sequences into </html>[[Part:pSB1C00|<partinfo>pSB1C00</partinfo>]]<html>, the first step towards assembling transcriptional units with iGEM Type IIS assembly. The template is flanked by fusion sites FS_c (AATG) and FS_e (GCTT), which will allow it to take the third position when using it for assembly to a Level 1 or pOdd plasmid (such as </html>[[Part:pSB1K01|<partinfo>pSB1K01</partinfo>]]<html>).</p>
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<p>Follow these steps to use this template:</p>
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<ol>
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<li>Obtain the template sequence from "Sequence and features"</li>
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<li>Substitute the A homopolymer (annotated as CDS template) by the desired coding sequence </li>
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<li>Remove the start codon from your sequence, since the 5' fusion site (FS_c) contains ATG
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<li>Order the part as dsDNA or primers to obtain it by PCR.</li>
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</ol>
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<p>For ease of use, we provide a .dna file which also contains example primers. This file can be found in Team Uppsala 2020's <a href="https://2020.igem.org/Team:UofUppsala/Parts#Collection">Parts page</a>.</p>
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<p>The following table details the part numbers and names of the design templates.</p>
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<center>
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<style>
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.parts-table {
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border: 3px solid #ccc;
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border-collapse: collapse;
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}
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.parts-table td {
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padding: 5px;
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border: 1px solid #ccc;
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vertical-align: center;
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//border-collapse: collapse;
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}
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.parts-table th {
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background-color: #464646;
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//border-collapse: collapse;
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border: 1px solid #ccc;
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padding: 5px;
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color: #f2f2f2;
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vertical-align: text-top;
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text-align: center;
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}
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</style>
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<table class="parts-table">
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<tr>
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<th>Registry Number</th>
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<th>Name</th>
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</tr>
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<tr>
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<td></html>[[Part:BBa_K3425017|<partinfo>BBa_K3425017</partinfo>]]<html></td>
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<td>Promoter template</td>
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</tr>
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<tr>
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<td></html>[[Part:BBa_K3425018|<partinfo>BBa_K3425018</partinfo>]]<html></td>
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<td>RBS template</td>
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</tr>
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<tr>
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<td></html>[[Part:BBa_K3425019|<partinfo>BBa_K3425019</partinfo>]]<html></td>
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<td>CDS template</td>
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</tr>
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<tr>
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<td></html>[[Part:BBa_K3425020|<partinfo>BBa_K3425020</partinfo>]]<html></td>
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<td>Terminator template</td>
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</tr>
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</table>
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</center>
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</html>
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<html><span class='h3bb'><b>Sequence and Features</b></span></html>
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<partinfo>BBa_K3425019 SequenceAndFeatures</partinfo>
  
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'''Note:''' The part contains restriction sites for its cloning into Level 0 universal Type IIS acceptor pSB1C00, therefore it is marked as not compatible with RFC1000 standard, even though it is.
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
 
<partinfo>BBa_K3425019 parameters</partinfo>
 
<partinfo>BBa_K3425019 parameters</partinfo>
 
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Latest revision as of 21:05, 25 October 2020


iGEM Type IIS standard CDS template

This series of iGEM Type IIS templates present easy to use blueprints to design parts for this assembly standard. These parts provide ready-made sequences which contain the different fusion sites for a promoter, RBS, CDS and terminator part according to the following image*.

PCR_for_pSB1C00.png

By adding the fusion and restriction sites by DNA synthesis or PCR, the part is ready to be cloned into the Type IIS universal acceptor pSB1C00. More information about this backbone can be found in its page. It can also be found, together with all our experience in this cloning method, in Team Uppsala 2020's iGEM Type IIS standard guidebook.

*Note: This image was taken from the pSB1C00 page to provide visual aid for the explanation without redirecting to another page.

This part is part of iGEM Uppsala 2020's iGEM Type IIS standard collection.

Usage and biology

This part is a CDS template, and it is used to clone coding sequences into pSB1C00, the first step towards assembling transcriptional units with iGEM Type IIS assembly. The template is flanked by fusion sites FS_c (AATG) and FS_e (GCTT), which will allow it to take the third position when using it for assembly to a Level 1 or pOdd plasmid (such as pSB1K01).

Follow these steps to use this template:

  1. Obtain the template sequence from "Sequence and features"
  2. Substitute the A homopolymer (annotated as CDS template) by the desired coding sequence
  3. Remove the start codon from your sequence, since the 5' fusion site (FS_c) contains ATG
  4. Order the part as dsDNA or primers to obtain it by PCR.

For ease of use, we provide a .dna file which also contains example primers. This file can be found in Team Uppsala 2020's Parts page.

The following table details the part numbers and names of the design templates.

Registry Number Name
BBa_K3425017 Promoter template
BBa_K3425018 RBS template
BBa_K3425019 CDS template
BBa_K3425020 Terminator template
Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI site found at 5
    Illegal SapI.rc site found at 39

Note: The part contains restriction sites for its cloning into Level 0 universal Type IIS acceptor pSB1C00, therefore it is marked as not compatible with RFC1000 standard, even though it is.