Difference between revisions of "Part:BBa K4041004"
Line 21: Line 21:
 
                     <td>TDH Forward</td>
 
                     <td>TDH Forward</td>
 
<td>CCCGGTTCTGATGAGATATTGT</td>
 
<td>CCCGGTTCTGATGAGATATTGT</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>vcgC Reverse</td>
 +
<td>CGCCAATAGCCTGTTCAGAT</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>vcgC Forward</td>
 +
<td>GCAGTTCAAACATGGTCTCAAA</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>ctxA Reverse</td>
 +
<td>GGTCTTATGCCAAGAGGACAGA</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>ctxA Forward</td>
 +
<td>CCATCATCGTGCCTAACAAATC</td>
 
                  
 
                  
 
                 </tr>
 
                 </tr>
  
 +
                <tr>
 +
                    <td>The following RPA primer were proved to work in this block in in Vibrio</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>TDH Reverse</td>
 +
<td>CTTATAGCCAGACACCGCTGCCATTGTATAGT</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>TDH Forward</td>
 +
<td>CCCGGTTCTGATGAGATATTGTTTGTTGTTCG</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>vcgC Reverse</td>
 +
<td>GCGAGTAGTGAGCCGATCCCGCCAATAGCCTG</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>vcgC Forward</td>
 +
<td>GGCGCAGTTCAAACATGGTCTCAAAAAGGAGC</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>ctxA Reverse</td>
 +
<td>GCAGTCAGGTGGTCTTATGCCAAGAGGACAGA</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>ctxA Forward</td>
 +
<td>ACATATCCATCATCGTGCCTAACAAATCCCGT</td>
 +
               
 +
                </tr>
 +
 +
  <tr>
 +
                    <td>The following crRNA were proved to work in this block in in Vibrio</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>TDH forward (crRNA1)</td>
 +
<td>ACTGTGAACATTAATGATAA</td>
 +
               
 +
                </tr>
 +
 +
<tr>
 +
                    <td>vcgC forward (crRNA3)</td>
 +
<td>ATAGCACTAATGTGTCATCT</td>
 +
               
 +
                </tr>
 +
<tr>
 +
                    <td>vcgC reverse (crRNA4, with PAM)</td>
 +
<td>GCGGAGACGAGATCGCTATC</td>
 +
               
 +
                </tr>
 +
             
 +
<tr>
 +
                    <td>ctxA Forward (crRNA5)</td>
 +
<td>TGATCATGCAAGAGGAACTC</td>
 +
               
 +
                </tr>
 +
 +
<tr>
 +
                    <td>crRNA 2 (high background) and crRNA 6 (no cleavage signal) is not functional from design, and is discarded</td>
 +
<td>TGATCATGCAAGAGGAACTC</td>
 +
               
 +
                </tr>
 
                  
 
                  
 
         </table>
 
         </table>

Revision as of 19:18, 21 October 2021


Composite vibrio CDS template (TDH-vcgC-ctxA)

This is a non-coding part that consist of the TDH gene of the Vibrio Parahaemolyticus, vcgC gene of Vibrio vulnificus and the ctxA gene of Vibrio Cholerae. The genome template is used for cloning into a plasmid and contains conserved regions so teams could design detection kit based on the conserved regions.

The genes is one of the central and important gene that makes the Vibrios pathogenic. While it is important for its cytotoxicity, it itself could be served as a biomarker for the strains.

The following qPCR primer were proved to work in this block in in Vibrio
TDH Reverse GACACCGCTGCCATTGTATAGT
TDH Forward CCCGGTTCTGATGAGATATTGT
vcgC Reverse CGCCAATAGCCTGTTCAGAT
vcgC Forward GCAGTTCAAACATGGTCTCAAA
ctxA Reverse GGTCTTATGCCAAGAGGACAGA
ctxA Forward CCATCATCGTGCCTAACAAATC
The following RPA primer were proved to work in this block in in Vibrio
TDH Reverse CTTATAGCCAGACACCGCTGCCATTGTATAGT
TDH Forward CCCGGTTCTGATGAGATATTGTTTGTTGTTCG
vcgC Reverse GCGAGTAGTGAGCCGATCCCGCCAATAGCCTG
vcgC Forward GGCGCAGTTCAAACATGGTCTCAAAAAGGAGC
ctxA Reverse GCAGTCAGGTGGTCTTATGCCAAGAGGACAGA
ctxA Forward ACATATCCATCATCGTGCCTAACAAATCCCGT
The following crRNA were proved to work in this block in in Vibrio
TDH forward (crRNA1) ACTGTGAACATTAATGATAA
vcgC forward (crRNA3) ATAGCACTAATGTGTCATCT
vcgC reverse (crRNA4, with PAM) GCGGAGACGAGATCGCTATC
ctxA Forward (crRNA5) TGATCATGCAAGAGGAACTC
crRNA 2 (high background) and crRNA 6 (no cleavage signal) is not functional from design, and is discarded TGATCATGCAAGAGGAACTC

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 BsaI.rc site found at 295
    Illegal BsaI.rc site found at 477