Difference between revisions of "Part:BBa K1104301:Design"

 
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__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K1104301 short</partinfo>
 
<partinfo>BBa_K1104301 short</partinfo>
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===Design Notes===
 
===Design Notes===
−
None
+
==Exons and Introns==
 +
CDS from exons:
 +
exon1: atgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg
 +
exon2: aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa
 +
exon3: aaccagtttcaaagatctctgggacaaacgtttcggttaa
 +
 
 +
mRNA from exons:
 +
exon1 (001-137): gtcagacacttctcagtcttttttcgaatagtttgaatatctattgaagtttaacacgtatttagccaatatgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg
 +
exon2 (138-318): aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa
 +
exon3 (319-680):
 +
aaccagtttcaaagatctctgggacaaacgtttcggttaagtgccattatgaagattcaacgatgaaattttttaacaaaaaatatgaaaacgcgaaatgattaagaaatgaaaaatgaaaaactgtattatcattgaaaattctatgaactttaatttacttatttaataaataatataagtaaattatcttttggt
 +
ttaatttctttaaagtattatcttttgaataaataaatttttttatatagataaattagataataatagaaaataaattttttttctaaatatactaattattatattcattattttaataattaaattgttaaatgcagtaattaacaatagaaatttaaaaa
 +
 
 +
material peptide based on mRNA sequence (200 to 355)
 +
exon2:
 +
8887754
 +
gtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa
 +
8887872
 +
8888151
 +
exon3: aaccagtttcaaagatctctgggacaaacgtttcggt
 +
8888187
 +
 
 +
[[File:NYMU_Group 5 Defensin 1.png|1000px]]
 +
 
 +
See more:[http://www.ncbi.nlm.nih.gov/gene/406143 http://www.ncbi.nlm.nih.gov/gene/406143]
 +
 
 +
 
 +
final defensin sequence:
 +
ATGgtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaaaaccagtttcaaagatctctgggacaaacgtttcggtTAA
 +
 
 +
Final defensin primers:         
 +
ATGGTAACTTGTGACCTTCTCTCATTCA
 +
          TGTGACCTTCTCTCATTCAAAGGACAAGTTAATGACAGTGCTTGCGCTGCTAACTGTCT
 +
                                                    GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT                                                                                               
 +
                                                                                              GCGAGAAAGGAGTTTGTATTTGTCGAAAAACCAGTTTCAAAGATCTCTGGGACAAACGTTTCGGTTAA
 +
              19nt,51C                                  16nt,52C;                                  17nt,50C
  
 +
D_a_RP: AGACAGTTAGCAGCGCAAGCACTGTCATTAACTTGTCCTTTGAATGAGAGAAGGTCACA (59nt)
 +
D_b_FP: GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT (59nt)
  
  

Revision as of 06:33, 5 October 2013

Defensin1


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 135
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Exons and Introns

CDS from exons: exon1: atgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg exon2: aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa exon3: aaccagtttcaaagatctctgggacaaacgtttcggttaa

mRNA from exons: exon1 (001-137): gtcagacacttctcagtcttttttcgaatagtttgaatatctattgaagtttaacacgtatttagccaatatgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg exon2 (138-318): aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa exon3 (319-680): aaccagtttcaaagatctctgggacaaacgtttcggttaagtgccattatgaagattcaacgatgaaattttttaacaaaaaatatgaaaacgcgaaatgattaagaaatgaaaaatgaaaaactgtattatcattgaaaattctatgaactttaatttacttatttaataaataatataagtaaattatcttttggt ttaatttctttaaagtattatcttttgaataaataaatttttttatatagataaattagataataatagaaaataaattttttttctaaatatactaattattatattcattattttaataattaaattgttaaatgcagtaattaacaatagaaatttaaaaa

material peptide based on mRNA sequence (200 to 355) exon2: 8887754 gtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa 8887872 8888151 exon3: aaccagtttcaaagatctctgggacaaacgtttcggt 8888187

NYMU Group 5 Defensin 1.png

See more:[http://www.ncbi.nlm.nih.gov/gene/406143 http://www.ncbi.nlm.nih.gov/gene/406143]


final defensin sequence: ATGgtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaaaaccagtttcaaagatctctgggacaaacgtttcggtTAA

Final defensin primers: ATGGTAACTTGTGACCTTCTCTCATTCA 

         TGTGACCTTCTCTCATTCAAAGGACAAGTTAATGACAGTGCTTGCGCTGCTAACTGTCT 
                                                    GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT                                                                                                
                                                                                              GCGAGAAAGGAGTTTGTATTTGTCGAAAAACCAGTTTCAAAGATCTCTGGGACAAACGTTTCGGTTAA
              19nt,51C                                   16nt,52C;                                   17nt,50C

D_a_RP: AGACAGTTAGCAGCGCAAGCACTGTCATTAACTTGTCCTTTGAATGAGAGAAGGTCACA (59nt) D_b_FP: GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT (59nt)


Source

Apis melliferra

References