Difference between revisions of "Part:BBa K1104301:Design"
| Line 11: | Line 11: | ||
<p>exon2: aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa</p> | <p>exon2: aggatgaattcgagccacttgagcattttgagaatgaagaacgtgccgacagacatagaagagtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa</p> | ||
<p>exon3: aaccagtttcaaagatctctgggacaaacgtttcggttaa</p> | <p>exon3: aaccagtttcaaagatctctgggacaaacgtttcggttaa</p> | ||
| − | + | ||
<p>mRNA from exons</p> | <p>mRNA from exons</p> | ||
<p>exon1 (001-137):</p> <p>gtcagacacttctcagtcttttttcgaatagtttgaatatctattgaagtttaacacgtatttagccaatatgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg</p> | <p>exon1 (001-137):</p> <p>gtcagacacttctcagtcttttttcgaatagtttgaatatctattgaagtttaacacgtatttagccaatatgaaaatctattttattgtcggccttctcttcatggctatggttgctatcatggctgcacctgttg</p> | ||
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<p>aaccagtttcaaagatctctgggacaaacgtttcggttaagtgccattatgaagattcaacgatgaaattttttaacaaaaaatatgaaaacgcgaaatgattaagaaatgaaaaatgaaaaactgtattatcattgaaaattctatgaactttaatttacttatttaataaataatataagtaaattatcttttggt | <p>aaccagtttcaaagatctctgggacaaacgtttcggttaagtgccattatgaagattcaacgatgaaattttttaacaaaaaatatgaaaacgcgaaatgattaagaaatgaaaaatgaaaaactgtattatcattgaaaattctatgaactttaatttacttatttaataaataatataagtaaattatcttttggt | ||
ttaatttctttaaagtattatcttttgaataaataaatttttttatatagataaattagataataatagaaaataaattttttttctaaatatactaattattatattcattattttaataattaaattgttaaatgcagtaattaacaatagaaatttaaaaa</p> | ttaatttctttaaagtattatcttttgaataaataaatttttttatatagataaattagataataatagaaaataaattttttttctaaatatactaattattatattcattattttaataattaaattgttaaatgcagtaattaacaatagaaatttaaaaa</p> | ||
| − | + | ||
<p>material peptide based on mRNA sequence (200 to 355)</p> | <p>material peptide based on mRNA sequence (200 to 355)</p> | ||
<p>exon2:</p> | <p>exon2:</p> | ||
| Line 24: | Line 24: | ||
<p>gtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa</p> | <p>gtaacttgtgaccttctctcattcaaaggacaagttaatgacagtgcttgcgctgctaactgtctcagtttgggtaaagctggaggtcattgcgagaaaggagtttgtatttgtcgaaa</p> | ||
<p>8887872</p> | <p>8887872</p> | ||
| − | |||
<p>exon3:</p> | <p>exon3:</p> | ||
<p>8888151</p> | <p>8888151</p> | ||
<p>aaccagtttcaaagatctctgggacaaacgtttcggt</p> | <p>aaccagtttcaaagatctctgggacaaacgtttcggt</p> | ||
<p>8888187</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] | ||
| − | + | ||
| − | + | ||
===''Final defensin primers:''=== | ===''Final defensin primers:''=== | ||
| Line 41: | Line 39: | ||
GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT | GCGCTGCTAACTGTCTCAGTTTGGGTAAAGCTGGAGGTCATTGCGAGAAAGGAGTTTGT | ||
GCGAGAAAGGAGTTTGTATTTGTCGAAAAACCAGTTTCAAAGATCTCTGGGACAAACGTTTCGGTTAA | GCGAGAAAGGAGTTTGTATTTGTCGAAAAACCAGTTTCAAAGATCTCTGGGACAAACGTTTCGGTTAA | ||
| − | + | 19nt,51C 16nt,52C; 17nt,50C | |
<p>D_a_RP: AGACAGTTAGCAGCGCAAGCACTGTCATTAACTTGTCCTTTGAATGAGAGAAGGTCACA (59nt)</p> | <p>D_a_RP: AGACAGTTAGCAGCGCAAGCACTGTCATTAACTTGTCCTTTGAATGAGAGAAGGTCACA (59nt)</p> | ||
Revision as of 07:34, 5 October 2013
Defensin1
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 135
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE 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
- See more:[http://www.ncbi.nlm.nih.gov/gene/406143 http://www.ncbi.nlm.nih.gov/gene/406143]
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