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

(→‎Final defensin primers:)
(→‎Final defensin primers)
 
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===Design Notes===
 
===Design Notes===
−
===''Exons and Introns''===
+
==''Exons and Introns''==
−
CDS from exons:
+
<p>CDS from exons:</p>
−
exon1: atgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg
+
<p>exon1: atgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg</p>
−
exon2: aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa
+
<p>exon2: aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa</p>
−
exon3: aaccagtttcaaagatctctgggacaaacgtttcggttaa
+
<p>exon3: aaccagtttcaaagatctctgggacaaacgtttcggttaa</p>
−
 
+
−
mRNA from exons:
+
<p>mRNA from exons</p>
−
exon1 (001-137): gtcagacacttctcagtcttttttcgaatagtttgaatatctattgaagtttaacacgtatttagccaatatgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg
+
<p>exon1 (001-137):</p> <p>gtcagacacttctcagtcttttttcgaatagtttgaatatctattgaagtttaacacgtatttagccaatatgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg</p>
−
exon2 (138-318): aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa
+
<p>exon2 (138-318):</p> <p>aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa</p>
−
exon3 (319-680):  
+
<p>exon3 (319-680):</p>
−
aaccagtttcaaagatctctgggacaaacgtttcggttaagtgccattatgaagattcaacgatgaaattttttaacaaaaaatatgaaaacgcgaaatgattaagaaatgaaaaatgaaaaactgtattatcattgaaaattctatgaactttaatttacttatttaataaataatataagtaaattatcttttggt
+
<p>aaccagtttcaaagatctctgggacaaacgtttcggttaagtgccattatgaagattcaacgatgaaattttttaacaaaaaatatgaaaacgcgaaatgattaagaaatgaaaaatgaaaaactgtattatcattgaaaattctatgaactttaatttacttatttaataaataatataagtaaattatcttttggt
−
ttaatttctttaaagtattatcttttgaataaataaatttttttatatagataaattagataataatagaaaataaattttttttctaaatatactaattattatattcattattttaataattaaattgttaaatgcagtaattaacaatagaaatttaaaaa
+
ttaatttctttaaagtattatcttttgaataaataaatttttttatatagataaattagataataatagaaaataaattttttttctaaatatactaattattatattcattattttaataattaaattgttaaatgcagtaattaacaatagaaatttaaaaa</p>
−
 
+
−
material peptide based on mRNA sequence (200 to 355)
+
<p>material peptide based on mRNA sequence (200 to 355)</p>
−
exon2:  
+
<p>exon2:</p>
−
8887754
+
<p>8887754</p>
−
gtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa
+
<p>gtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa</p>
−
8887872
+
<p>8887872</p>
−
8888151
+
<p>exon3:</p>
−
exon3: aaccagtttcaaagatctctgggacaaacgtttcggt
+
<p>8888151</p>
−
8888187
+
<p>aaccagtttcaaagatctctgggacaaacgtttcggt</p>
−
 
+
<p>8888187</p>
 +
 
[[File:NYMU_Group 5 Defensin 1.png|1000px]]
 
[[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]
+
*See more:[http://www.ncbi.nlm.nih.gov/gene/406143 http://www.ncbi.nlm.nih.gov/gene/406143]
−
 
+
−
 
+
==''Defensin1 primers(example)''==
−
===''Final defensin primers:''===
+
ATGGTAACTTGTGACCTTCTCTCATTCA
−
 
+
          TGTGACCTTCTCTCATTCAAAGGACAAGTTAATGACAGTGCTTGCGCTGCTAACTGTCT  
−
ATGGTAACTTGTGACCTTCTCTCATTCA
+
−
        TGTGACCTTCTCTCATTCAAAGGACAAGTTAATGACAGTGCTTGCGCTGCTAACTGTCT  
+
 
                                                     GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT                                                                                                 
 
                                                     GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT                                                                                                 
 
                                                                                               GCGAGAAAGGAGTTTGTATTTGTCGAAAAACCAGTTTCAAAGATCTCTGGGACAAACGTTTCGGTTAA
 
                                                                                               GCGAGAAAGGAGTTTGTATTTGTCGAAAAACCAGTTTCAAAGATCTCTGGGACAAACGTTTCGGTTAA
−
               19nt,51C                                  16nt,52C;                                  17nt,50C
+
               19nt,51C                                  16nt,52C                                   17nt,50C
−
 
+
−
<p>D_a_RP: AGACAGTTAGCAGCGCAAGCACTGTCATTAACTTGTCCTTTGAATGAGAGAAGGTCACA (59nt)</p>
+
−
<p>D_b_FP: GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT (59nt)</p>
+
  
 
===Source===
 
===Source===

Latest revision as of 07:47, 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

exon3:

8888151

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]

Defensin1 primers(example)

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

Source

Apis melliferra

References