IGEM:Stanford/2009/Project Homeostasis/Primer: Difference between revisions
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''Forward'': TATAgaattcgcggccgcttctagagGGAGTCATAATGGATTCTTGTC | ''Forward'': TATAgaattcgcggccgcttctagagGGAGTCATAATGGATTCTTGTC | ||
''Reverse'': TATAtactagtagcggccgctgcagGTTAGTCTGACTGTAACTG | ''Reverse'': '''''TATAtactagtagcggccgctgcagGTTAGTCTGACTGTAACTG''''' | ||
| Line 15: | Line 15: | ||
''Forward'': TATAgaattcgcggccgcttctagATGAAAACATGGTTAATGGGGTTCAGCG | ''Forward'': TATAgaattcgcggccgcttctagATGAAAACATGGTTAATGGGGTTCAGCG | ||
''Reverse'': TATAtactagtagcggccgctgcagCTCTGAGACTTAACGCTCATG | ''Reverse'': '''''TATAtactagtagcggccgctgcagCTCTGAGACTTAACGCTCATG''''' | ||
| Line 22: | Line 22: | ||
''Forward'': TATAgaattcgcggccgcttctagagGCAAATGAAGAAATTGCTCC | ''Forward'': TATAgaattcgcggccgcttctagagGCAAATGAAGAAATTGCTCC | ||
''Reverse'': TATAtactagtagcggccgctgcagCGTCATCAGTTACGGAAAGGG | ''Reverse'': '''''TATAtactagtagcggccgctgcagCGTCATCAGTTACGGAAAGGG''''' | ||
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*'''HlyB (from CFT073)''' | *'''HlyB (from CFT073)''' | ||
TATAgaattcgcggccgcttctag ATGGATTCTTGTCATAAAATTG | "Forward": TATAgaattcgcggccgcttctag ATGGATTCTTGTCATAAAATTG | ||
TATAtactagtagcggccgctgcag TTAGTCTGACTGTAACTG | "Reverse": '''''TATAtactagtagcggccgctgcag TTAGTCTGACTGTAACTG''''' | ||
*'''HlyD (from CFT073)''' | *'''HlyD (from CFT073)''' | ||
TATA gaattcgcggccgcttctag ATGAAAACATGGTTAATG | "Forward":TATA gaattcgcggccgcttctag ATGAAAACATGGTTAATG | ||
TATAtactagtagcggccgctgcag TTAACGCTCATGTAAACTTTC | "Reverse": '''''TATAtactagtagcggccgctgcag TTAACGCTCATGTAAACTTTC''''' | ||
*'''TolC''' | *'''TolC''' | ||
TATAgaattcgcggccgcttctagATGAAGAAATTGCTCCCCATTC | "Forward": TATAgaattcgcggccgcttctagATGAAGAAATTGCTCCCCATTC | ||
TATAtactagtagcggccgctgcagTCAGTTACGGAAAGGGTTATG | "Reverse": '''''TATAtactagtagcggccgctgcagTCAGTTACGGAAAGGGTTATG'''''' | ||
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*'''IL-6 fusion gene''' | *'''IL-6 fusion gene''' | ||
TATAGAATTCGCGGCCGCTTCTAGAGGGATGCATCACCGGTTCCGC | "Forward": TATAGAATTCGCGGCCGCTTCTAGAGGGATGCATCACCGGTTCCGC | ||
ATATTACTAGTAGCGGCCGCTGCAGGGATGCATTCATTTGACGAAGAG | "Reverse": '''''ATATTACTAGTAGCGGCCGCTGCAGGGATGCATTCATTTGACGAAGAG''''' | ||
| Line 60: | Line 60: | ||
''Forward'': TATAgaattcgcggccgcttctagATGGCCCAACAATCACCCTATTCAGC | ''Forward'': TATAgaattcgcggccgcttctagATGGCCCAACAATCACCCTATTCAGC | ||
''Reverse'': TATAtactagtagcggccgctgcagTCAATCGCTTTTCAGCAACACCTCTTCCAGCCACTGGC | ''Reverse'': ''''''TATAtactagtagcggccgctgcagTCAATCGCTTTTCAGCAACACCTCTTCCAGCCACTGGC''''' | ||
Revision as of 15:44, 1 July 2009
Anti-Immunosuppression Device
Primers
Added 7/1/09 - Mark
- HlyB (from E. coli str. CFT073)
Forward: TATAgaattcgcggccgcttctagagGGAGTCATAATGGATTCTTGTC
Reverse: TATAtactagtagcggccgctgcagGTTAGTCTGACTGTAACTG
- HlyD (from E. coli str. CFT073)
Forward: TATAgaattcgcggccgcttctagATGAAAACATGGTTAATGGGGTTCAGCG
Reverse: TATAtactagtagcggccgctgcagCTCTGAGACTTAACGCTCATG
- TolC (from E. coli str. CFT073)
Forward: TATAgaattcgcggccgcttctagagGCAAATGAAGAAATTGCTCC
Reverse: TATAtactagtagcggccgctgcagCGTCATCAGTTACGGAAAGGG
Added 7/1/09 - Ming
- HlyB (from CFT073)
"Forward": TATAgaattcgcggccgcttctag ATGGATTCTTGTCATAAAATTG
"Reverse": TATAtactagtagcggccgctgcag TTAGTCTGACTGTAACTG
- HlyD (from CFT073)
"Forward":TATA gaattcgcggccgcttctag ATGAAAACATGGTTAATG
"Reverse": TATAtactagtagcggccgctgcag TTAACGCTCATGTAAACTTTC
- TolC
"Forward": TATAgaattcgcggccgcttctagATGAAGAAATTGCTCCCCATTC
"Reverse": TATAtactagtagcggccgctgcagTCAGTTACGGAAAGGGTTATG'
Added 6/28/09 - Robert, Ariana
- IL-6 fusion gene
"Forward": TATAGAATTCGCGGCCGCTTCTAGAGGGATGCATCACCGGTTCCGC "Reverse": ATATTACTAGTAGCGGCCGCTGCAGGGATGCATTCATTTGACGAAGAG
- TrpR (E. coli str. IAI1)
Forward: TATAgaattcgcggccgcttctagATGGCCCAACAATCACCCTATTCAGC
Reverse: 'TATAtactagtagcggccgctgcagTCAATCGCTTTTCAGCAACACCTCTTCCAGCCACTGGC
- Protease-binding sequence?
Gene Sequences
- HylB
ATGATCATCAATAAATTTTCCCTTAAATGGATGTTGGCTATTGCCGTCGCCATCCCTGCGATAGCACTGTTGTTTGTGGCTTTCACCAGTCTAAACACCATGTCAGTGATGCAAGCGCAGTCCAACAGCTTGTATGCCAACACGGCTGCACCAATGCGTGCCATGGCTGAAGCAACCTCACGTATTCCTCGGATGCGTGTCGGTATCGATATGATGCTACTGCAAGAAACGGCGCTCAAAGATGCGAAAGGGGTCCTCAAACGAGTCGAAGAGGCAAGAACCGAAGATATCCCAGAAATGCGTCAAGCAATGCAAGTTGCGGTTGATTCTCAGGTTAATCCGGAACTCAAAGAGCAGGCACGCAAACTTCAAGCTCGTTTTGAACAAATGGTACGTGAAGAGTTAGAGCCTATGCTGCAAGCCTTCGCCAATAACGATATGACCACGGCACAAAACATTTACCGCGATAAATACGCGCCGACCTATGGTGAAATGCGTAAACAAGCCAACCAGATCCTCGATACGCTTTTGCAGCAAGCGGAGCAGCAAAACCATGCCAGTGTGGAAAGCTTCGAAGCAGGACGCACCAAGCAAATGGTGATCATTGCAGCAGGCTTGATCATTTCATTCATCACTTCACTGGTTATCATAACGAACTTACGTAGCCGAGTGGCTTACCTGAAAGATCGTATGAGTTCTGCGGCGGCGAATCTTTCACTGCGTACTCGATTGGAGTTGGATGGTAACGATGAACTGTGTGACATCGGTAAAAGCTTCAATGCGTTCATTGATAAAGTGCATCACTCGATTGAAGAAGTGGCAGAAAACTCAAAAGAGCTGGCGACGATGGCCTCTAGTGTGTCGCAGCGCGCGCACATGACGCAATCTAACTGTGCTTCGCAGCGAGATAGAACAGTGCAAGTTGCGACGGCGATTCATGAGCTTGGTGCCACCGTATCCGAAATCGCTTCCAATGCGGCCATGGCTGCCGATGTCGCGAAGCAAGCGACGCTGCATTCTGGTGAAGGGAAAAAAGTGGTAGGCGAAGTGCAAAATCGGATCCAAACACTGGTCAATGAACTCGATAATGCCACTCAAGTTGTCTCATCACTGGCGACCCAAATTAACGGTATTAGCTCAACACTTGATACCATTCGCAGTATTTCTGAGCAAACGAACCTATTGGCGCTCAACGCTGCGATTGAAGCTGCGCGAGCGGGTGAACAAGGTCGTGGTTTTGCGGTGGTGGCGGATGAAGTTCGCACATTAGCAAGTCGTTCAGCGGCATCGACGGAAGAGATCCAGCAAGTCATTAATCGCCTTCAAACGGAGTCAACTCGCGCAGTAGAAGCAATGGAAAAAGGTCGCTCGCAAAGTGATGTGGTGGTTGAGTTTTCCGCTAAAGCGAACCAATCTCTCACAGAGATCAACAGCCAAATTGATCAGATTAATGATCAAAATATTCAAGTTGCGACCGCGACAGAGGAACAATCAACCGTGGTGGAAGACATTAATCGCAACGTTGAAGACATCAACCAACTGACGACAGAAACCTCGCATGTTGCGGATGAGTTAAGCCGAGCCAGTGCAAGCTTGCAACGTCTCTCTTCGCAACTGGATAAACTGGTGGGCAGTTTTGAACTTTAA http://www.ncbi.nlm.nih.gov/nuccore/NC_012583.1/?from=274978&to=276624&report=fasta NCBI Reference Sequence: NC_012583.1 from Vibrio cholerae O395 chromosome II, complete genome
- HylD
ATGGCTGCGTTCGGACAAGACGTCTTCAGGCGCTTCGGCACGGTCACCGAACGCTTCTCCGGCACCGGCGGCAAACTCTTCGGCGGCCTGCTCGCGCGCCTGTCGAGCGTGGAGCGCGACGACAGCCTGGACTGGGCGAGCGACGCCGACTGGGCGCGCCTGCAGCAGGAGCCGCTGCGCGCGCGCGCGGTACTCAAGGTCAGCGCGATCGCGCTGCTGGTGCTGCTCGGCTGGGCCGCGGTGGCGCATGTGGACGAGGTGACCAAGGGCGACGGCAAGGTGATCCCGTCCAGCCAGCTGCAGATCATCCAGTCGGTCGATGGCGGCGTGGTGGAGTCGATCGCGGTGCGCGAGGGCGAGGTGGTCGAGGCCGGGCAGCTGCTGCTCAAGGTCGATCCCACCCGTTTCATGTCCTCGCTGCTGGAAAACCGCGCCGAGTTCCTCGCGCTGGAAATCAAGCGCCGGCGGCTCGAGGCGCTGACCCAGGGGACGCCGTTCTCGGTGCCGGCCGAGCTGGAGAAGGAGGCGGCGGACATCGCCGCCCACGAGCGCCGGCTGTATGAATCCAGCCGCGCCGAGATGGACGCGCAGCAGTCGATCGCGCGCGACCAGCTGCGCCAGCGCGAGCAGGAACTCAACGAGGTGCGCGCCCGCAGTGAGAACGCCGCCCGCGCCTACGAACTGGTGCAGCAGGAACTCAAGGTCACCAAGCCGCTCGCGGCCTCCGGCGCGGTATCCGAGGTCGAGCTGCTGCGTCTGGAGCGCGACGTGTCGCGCTTGCGCGGCGAGCGCGAGCAGAGCGCGGCGCAGATTTCGCGCATCCAGTCGGCCATCGCCGAATCCACGCGCAAGATCCAGGAGATCGAGCTGACGGTGCGCAACCAGCTGCGCAACGAGCTTTCGGACACCATGGCGCGGCTGGGCAGCCTGACCCAGGGCAGCCGCATGCTGGCCGACCGCGTCAAGCACGCCGAAATCCGCGCGCCGATGCGCGGCACGGTCAAGCGCATCCTCGTCAACACCGTGGGTGGCGTGGTCCAGCCGGGCAAGGAAGTGGCCGAGATCGTGCCGCTCGACGACGCGCTGATCCTCGAAGCGCAGGTCAAGCCGAGCGACATCGCCTTCCTGCGCCCGGGTCAGTCGGCGCTGGTCAAGTTCTCCGCGTACGACTTCTCGATCTACGGCGGCCTGGAGGCGGTCGTGGACCAGATTTCCGCCGACACCGTGGTCGATGCAAAGGGTTCCGCGTTCTACGTGGTGCGGGTGCGCACGCTGCATTCCTCTCTGGGTGAAAACCTGCCGATCATTCCGGGCATGGTGGCCGAAGTGGACATCCTGACCGGCAAGAAGACCATCCTCTCCTACCTGCTGAAGCCCGTGCTGCGGGCCAAGGCCAACGCACTGTCCGAACGATGA http://www.ncbi.nlm.nih.gov/nuccore/NC_008702.1/?from=674498&to=675913&report=fasta NCBI Reference Sequence: NC_008702.1 from Azoarcus sp. BH72, complete genome
- TolC
ATGAAGAAATTGCTCCCCATTCTTATCGGCCTGAGCCTTTCTGGGTTCAGTTCGTTGAGCCAGGCCGAGAACCTGATGCAAGTTTATCAGCAAGCACGCCTTAGTAACCCGGAATTGCGTAAGTCTGCCGCCGATCGTGATGCTGCCTTTGAAAAAATTAATGAAGCGCGCAGTCCATTACTGCCACAGCTAGGTTTAGGTGCAGATTACACCTATAGCAACGGCTACCGCGACGCGAACGGCATCAACTCTAACGCGACCAGTGCGTCCTTGCAGTTAACTCAATCCATTTTTGATATGTCGAAATGGCGTGCGTTAACGCTGCAGGAAAAAGCAGCAGGGATTCAGGACGTCACGTATCAGACCGATCAGCAAACCTTGATCCTCAACACCGCGACCGCTTATTTCAACGTGTTGAATGCTATTGACGTTCTTTCCTATACACAGGCACAAAAAGAAGCGATCTACCGTCAATTAGATCAAACCACCCAACGTTTTAACGTGGGCCTGGTAGCGATCACCGACGTGCAGAACGCCCGCGCACAGTACGATACCGTGCTGGCGAACGAAGTGACCGCACGTAATAACCTTGATAACGCGGTAGAGCAGCTGCGCCAGATCACCGGTAACTACTATCCGGAACTGGCTGCGCTGAATGTCGAAAACTTTAAAACCGACAAACCACAGCCGGTTAACGCGCTGCTGAAAGAAGCCGAAAAACGCAACCTGTCGCTGTTACAGGCACGCTTGAGCCAGGACCTGGCGCGCGAGCAAATTCGCCAGGCGCAGGATGGTCACTTACCGACTCTGGATTTAACGGCTTCTACCGGGATTTCTGACACCTCTTATAGCGGTTCGAAAACCCGTGGTGCCGCTGGTACCCAGTATGACGATAGCAATATGGGCCAGAACAAAGTTGGCCTGAGCTTCTCGCTGCCGATTTATCAGGGCGGAATGGTTAACTCGCAGGTGAAACAGGCACAGTACAACTTTGTCGGTGCCAGCGAGCAACTGGAAAGTGCCCATCGTAGCGTCGTGCAGACCGTGCGTTCCTCCTTCAACAACATTAATGCATCTATCAGTAGCATTAACGCCTACAAACAAGCCGTAGTTTCCGCTCAAAGCTCATTAGACGCGATGGAAGCGGGCTACTCGGTCGGTACGCGTACCATTGTTGATGTGTTGGATGCGACCACCACGTTGTACAACGCCAAGCAAGAGCTGGCGAATGCGCGTTATAACTACCTGATTAATCAGCTGAATATTAAGTCAGCTCTGGGTACGTTGAACGAGCAGGATCTGCTGGCACTGAACAATGCGCTGAGCAAACCGGTTTCCACTAATCCGGAAAACGTTGCACCGCAAACGCCGGAACAGAATGCTATTGCTGATGGTTATGCGCCTGATAGCCCGGCACCAGTCGTTCAGCAAACATCCGCACGCACTACCACCAGTAACGGTCATAACCCTTTCCGTAACTGA http://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2/?from=3176137&to=3177618&report=fasta NCBI Reference Sequence: NC_000913.2 from Escherichia coli str. K-12 substr. MG1655, complete genome
- IL-6 fusion gene
- Protease-binding sequence?
Anti-Inflammatory Device
Primers:
SoxR (Escherichia coli E24377A)
Forward: TATAgaattcgcggccgcttctagATGGAAAAGAAATTACCCCGC
Reverse: TATAtactagtagcggccgctgcagTTAGTTTTGTTCATCTTCCAGCAAGCGTG
CrtB (Erwinia Uredovora)
Forward: TATAgaattcgcggccgcttctagATGGCAGTTGGCTCGAAAAG
Reverse: TATAtactagtagcggccgctgcagCTAGAGCGGGCGCTGCCAG
CrtE (Erwinia Uredovora)
Forward: TATAgaattcgcggccgcttctagATGACGGTCTGCGCAAAAAAAC
Reverse: TATAtactagtagcggccgctgcagTTAACTGACGGCAGCGAGTTTTTTG
CrtI (Erwinia Uredovora)
Forward: TATAgaattcgcggccgcttctag ATGAAACCAACTACGGTAATTGGTGC
Reverse: TATAtactagtagcggccgctgcag TGATTGAGTAACGACGG
CrtY (Erwinia Uredovora)
Forward: TATAgaattcgcggccgcttctag ATGCAACCGCATTATGATCTG
Reverse: TATAtactagtagcggccgctgcag TTAACGATGAGTCGTCATAATGGC
Soxs: primer dimers
Blh (Halobacterium sp. NRC1)
Forward: TATAgaattcgcggccgcttctagATGCCACACGGCGCGATCG
Reverse: TATAtactagtagcggccgctgcagTCAGAGGACGCCCTGCAC
RalDH(II) (Rattus Norvegicus)
Forward: TATAgaattcgcggccgcttctagATGCCCGGCGAGGTGAAGGC
Reverse: TATAtactagtagcggccgctgcagTTAGGAGTTCTTCTGGGGGATC
Gene sequences:
SoxR
ATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGATGTGTTGCGATATGTTGCAATTATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAA
http://www.ncbi.nlm.nih.gov/nuccore/NC_009801.1/?from=4616553&to=4617017&report=fasta
(NCBI Reference Sequence: NC_009801.1 from Escherichia coli E24377A, complete genome)
Crt genes GenBank accession no. D90087—should we do as the entire cluster (in this case how should we design primers) or in parts?
Blh ATGGGTCTGATGCTGATTGATTGGTGTGCACTGGCTCTGGTTGTTTTCATTGGCCTGCCGCACGGCGCGCTGGATGCTGCCATTTCTTTTTCTATGATCTCTTCTGCAAAACGCATTGCTCGTCTGGCTGGTATTCTGCTGATCTATCTGCTGCTGGCGACCGCGTTCTTCCTGATCTGGTATCAGCTGCCAGCGTTTAGCCTGCTGATCTTCCTGCTGATCTCCATTATCCACTTTGGTATGGCAGACTTCAACGCGTCCCCAAGCAAACTGAAATGGCCGCATATCATCGCCCACGGCGGTGTTGTTACTGTTTGGCTGCCGCTGATCCAGAAAAACGAAGTAACTAAACTGTTTAGCATCCTGACTAACGGTCCGACTCCGATCCTGTGGGACATCCTGCTGATTTTCTTCCTGTGTTGGTCTATTGGCGTGTGTCTGCACACGTACGAAACCCTGCGCTCTAAACATTACAACATCGCCTTTGAACTGATCGGTCTGATTTTCCTGGCGTGGTATGCGCCGCCTCTGGTTACGTTTGCCACTTACTTCTGCTTCATTCATTCCCGTCGCCACTTCTCCTTTGTGTGGAAGCAGCTGCAACACATGTCTTCCAAAAAGATGATGATTGGCAGCGCGATTATCCTGTCCTGTACCTCTTGGCTGATCGGCGGTGGTATCTATTTCTTCCTGAACTCCAAAATGATCGCCTCTGAGGCTGCGCTGCAGACTGTGTTCATCGGTCTGGCGGCACTGACCGTGCCGCACATGATTCTGATCGACTTCATCTTCCGTCCGCACTCTTCCCGTATCAAAATCAAAAACTGA
Kim et al. In vitro characterization of a recombinant Blh protein from an uncultured marine bacterium as a beta-carotene 15,15'-dioxygenase. J Biol Chem. 2009 Jun 5;284(23):15781-93. (supplementary material; 15,15'-Dioxygenase, product of Blh gene, codon-optimized and expressed in E. coli, forms a 64k protein of two 32 kDa dimers)
RALDH?
