Coding

Part:BBa_K1104301:Design

Designed by: Jou-Chien Liao, Rohan Shina, Yucheng Huang   Group: iGEM13_NYMU-Taipei   (2013-09-11)
Revision as of 06:35, 5 October 2013 by JRDeath (Talk | contribs) (→‎Exons and Introns)

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