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

(→‎Exons and Introns)
(→‎Final defensin sequence:)
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===Final defensin sequence:===
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===''Final defensin sequence:''===
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ATGgtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaaaaccagtttcaaagatctctgggacaaacgtttcggtTAA
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<p>ATGgtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaaaaccagtttcaaagatctctgggacaaacgtttcggtTAA</p>
  
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Final defensin primers:          
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<p>Final defensin primers:</p>
 
ATGGTAACTTGTGACCTTCTCTCATTCA
 
ATGGTAACTTGTGACCTTCTCTCATTCA
 
           TGTGACCTTCTCTCATTCAAAGGACAAGTTAATGACAGTGCTTGCGCTGCTAACTGTCT  
 
           TGTGACCTTCTCTCATTCAAAGGACAAGTTAATGACAGTGCTTGCGCTGCTAACTGTCT  
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               19nt,51C                                  16nt,52C;                                  17nt,50C
 
               19nt,51C                                  16nt,52C;                                  17nt,50C
  
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D_a_RP: AGACAGTTAGCAGCGCAAGCACTGTCATTAACTTGTCCTTTGAATGAGAGAAGGTCACA (59nt)
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<p>D_a_RP: AGACAGTTAGCAGCGCAAGCACTGTCATTAACTTGTCCTTTGAATGAGAGAAGGTCACA (59nt)</p>
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D_b_FP: GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT (59nt)
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<p>D_b_FP: GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT (59nt)</p>
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+
  
 
===Source===
 
===Source===

Revision as of 06:37, 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