Team:Edinburgh/Sequences

It may or may not be useful to have annotated nucleotide sequences of various stuff that we use. Some of this information can be retrieved from the Registry, but it may be useful to have it in a more nicely usable form. Copying DNA sequences from the Registry using the web-browser's normal copy function is strangely broken...

Note that any biobricks we submit to the Registry will still have to be properly documented there.

We have BBa_K523000 to BBa_K523999 available this year.

Biobrick prefix, suffix, scar

• gaattcgcggccgcttctag - prefix, short
• gaattcgcggccgcttctagag - prefix, long
• tactagtagcggccgctgcag - suffix
• tactag - scar, short
• tactagag - scar, long

Restriction sites

• gaattc - EcoRI (prefix 1)
• tctaga - XbaI (prefix 2)
• actagt - SpeI (suffix 1)
• ctgcag - PstI (suffix 2)

• gcggccgc - NotI (in both prefix and suffix)

• agatct - BglII (not part of RFC10, we use it internally after the prefix)

• tacgta - SnaBI (might become relevant)

pSB1C3 vector

• This is the official sequence from the Registry ([http://partsregistry.org/wiki/index.php?title=Part:pSB1C3 here])
• Red is CmlR coding sequence ([http://en.wikipedia.org/wiki/Chloramphenicol_acetyltransferase chloramphenicol acetyltransferase])
• Blue is restriction sites for the 4 main enzymes (SpeI, PstI, EcoRI, XbaI)

tactagtagcggccgctgcagtccggcaaaaaagggcaaggtgtcaccaccctgcccttt ttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgct gcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggtt atccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggc caggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacga gcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagata ccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttac cggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctg taggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccc cgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaag acacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgt aggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagt atttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttg atccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattac gcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctca gtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcac ctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaac ttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgag cgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtcc aagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaatt cattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgcca gcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcga agaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattgg ctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgt aacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcac tccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacac tatcccatatcaccagctcaccgtctttcattgccatacgaaattccggatgagcattca tcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacgg tctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactg actgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatc cagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaa atacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccga tcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaa aataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggat
gatttctggaattcgcggccgcttctagag

Plac-LacZα insert (clone 2)

• Assigned code <partinfo>BBa_K523000</partinfo>
• A modified version (seems to lack about 45 bases at the start) of [http://partsregistry.org/wiki/index.php?title=Part:BBa_J33207 BBa_J33207]
• Sanger sequencing seemed to confirm that all was well with clone 2, though in a few regions the chromatograms were poor.
• Sequence below includes BioBrick prefix and suffix (blue) as well as the BglII site (bold), which is partly in the prefix
• lacZα is in red.
• Both forward and reverse sequencing reactions failed to give good info about the suffix; so I have simply added the standard suffix. However we've not conclusively proved that the SpeI site exists; this should be verified by digest.

gaattcgcggccgcttctagagatctgctggggcaaaccagcgtggaccgcttgctgcaa ctctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaaga aaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcatta atgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaa tgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtat gttgtgtgaaattgtgagcggataacaatttcacacaggaaacagctatgaccatgatta cggattcactggccgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaac ttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaagaggcccgca ccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgctttgcctggtttc cggcaccagaagcggtgccggaaagctggctggagtgatactagtagcggccgctgcag

malS using primers f1/r1 (colony 1)

• Assigned code <partinfo>BBa_K523001</partinfo>
• Prefix and suffix in blue.
• Pre-coding sequence in CAPITALS and contains native RBS.
• BglII site in bold.
• Double stop codon is present.
• This has been sequenced and looks good.

gaattcgcggccgcttctagagatctGAAATCGCAGCAATAAGGACTCATCCGCCatgaa actcgccgcctgttttctgacactccttcctggcttcgccgttgccgccagctggacttc tccggggtttcccgcctttagcgaacaggggacaggaacatttgtcagccacgcgcagtt gcccaaaggtacgcgtccactaacgctaaattttgaccaacagtgctggcagcctgcgga tgcgataaaactcaatcagatgctttccctgcaaccttgtagcaacacgccgcctcaatg gcgattgttcagggacggcgaatatacgctgcaaatagacacccgctccggtacgccaac attgatgatttccatccagaacgccgccgaaccggtagcaagcctggtccgtgaatgccc gaaatgggatggattaccgctcacagtggatgtcagcgccactttcccggaaggagccgc cgtacgggattattacagccagcaaattgcgatagtgaagaacggtcaaataatgttaca acccgctgccaccagcaacggtttactcctgctggaacgggcagaaactgacacatccgc ccctttcgactggcataacgccacggtttactttgtgctgacagatcgtttcgaaaacgg cgatcccagtaatgaccagagttacggacgtcataaagacggtatggcggaaattggcac ttttcacggcggcgatttacgcggcctgaccaacaaactggattacctccagcagttggg cgttaatgctttatggataagcgccccatttgagcaaattcacggctgggtcggcggcgg tacaaaaggcgatttcccgcattatgcctaccacggttattacacacaggactggacgaa tcttgatgccaatatgggcaacgaagccgatctacggacgctggttgatagcgcacatca gcgcggtattcgtattctctttgatgtcgtgatgaaccacaccggctatgccacgctggc ggatatgcaggagtatcagtttggcgcgttatatctttctggtgacgaagtgaaaaaatc gctgggtgaacgctggagcgactggaaacctgccgccgggcaaacctggcatagctttaa cgattacattaatttcagcgacaaaacaggctgggataaatggtggggaaaaaactggat cagaacggatatcggcgattacgacaatcctggattcgacgatctcactatgtcgctagc ctttttgccggatatcaaaaccgaatcaactaccgcttctggtctgccggtgttctataa aaacaaaatggatacccacgccaaagccattgacggctatacgccgcgcgattacttaac ccactggttaagtcagtgggtccgcgactatgggattgatggttttcgggtcgataccgc caaacatgttgagttgcccgcctggcagcaactgaaaaccgaagccagcgccgcgcttcg cgaatggaaaaaagctaaccccgacaaagcattagatgacaaacctttctggatgaccgg tgaagcctggggccacggcgtgatgcaaagtgactactatcgccacggcttcgatgcgat gatcaatttcgattatcaggagcaggcggcgaaagcagtcgactgtctggcgcagatgga tacgacctggcagcaaatggcggagaaattgcagggtttcaacgtgttgagctacctctc gtcgcatgatacccgcctgttccgtgaagggggcgacaaagcagcagagttattactatt agcgccaggcgcggtacaaatcttttatggtgatgaatcctcgcgtccgttcggtcctac aggttctgatccgctgcaaggtacacgttcggatatgaactggcaggatgttagcggtaa atctgccgccagcgtcgcgcactggcagaaaatcagccagttccgcgcccgccatcccgc aattggcgcgggcaaacaaacgacacttttgctgaagcagggctacggctttgttcgtga gcatggcgacgataaagtgctggtcgtctgggcagggcaacagtaataatactagtagcg
gccgctgcag

malS using primers f2/r2 (colony 1)

• This is essentially as above but starting at the start codon, and with no stop codon, and adding two bases at the end of the BioBrick, which (together with the T at the start of the suffix) code for a glycine when using BioSandwich assembly.
• This has been sequenced and looks good.

<code> gaattcgcggccgcttctagagatctatgaa actcgccgcctgttttctgacactccttcctggcttcgccgttgccgccagctggacttc tccggggtttcccgcctttagcgaacaggggacaggaacatttgtcagccacgcgcagtt gcccaaaggtacgcgtccactaacgctaaattttgaccaacagtgctggcagcctgcgga tgcgataaaactcaatcagatgctttccctgcaaccttgtagcaacacgccgcctcaatg gcgattgttcagggacggcgaatatacgctgcaaatagacacccgctccggtacgccaac attgatgatttccatccagaacgccgccgaaccggtagcaagcctggtccgtgaatgccc gaaatgggatggattaccgctcacagtggatgtcagcgccactttcccggaaggagccgc cgtacgggattattacagccagcaaattgcgatagtgaagaacggtcaaataatgttaca acccgctgccaccagcaacggtttactcctgctggaacgggcagaaactgacacatccgc ccctttcgactggcataacgccacggtttactttgtgctgacagatcgtttcgaaaacgg cgatcccagtaatgaccagagttacggacgtcataaagacggtatggcggaaattggcac ttttcacggcggcgatttacgcggcctgaccaacaaactggattacctccagcagttggg cgttaatgctttatggataagcgccccatttgagcaaattcacggctgggtcggcggcgg tacaaaaggcgatttcccgcattatgcctaccacggttattacacacaggactggacgaa tcttgatgccaatatgggcaacgaagccgatctacggacgctggttgatagcgcacatca gcgcggtattcgtattctctttgatgtcgtgatgaaccacaccggctatgccacgctggc ggatatgcaggagtatcagtttggcgcgttatatctttctggtgacgaagtgaaaaaatc gctgggtgaacgctggagcgactggaaacctgccgccgggcaaacctggcatagctttaa cgattacattaatttcagcgacaaaacaggctgggataaatggtggggaaaaaactggat cagaacggatatcggcgattacgacaatcctggattcgacgatctcactatgtcgctagc ctttttgccggatatcaaaaccgaatcaactaccgcttctggtctgccggtgttctataa aaacaaaatggatacccacgccaaagccattgacggctatacgccgcgcgattacttaac ccactggttaagtcagtgggtccgcgactatgggattgatggttttcgggtcgataccgc caaacatgttgagttgcccgcctggcagcaactgaaaaccgaagccagcgccgcgcttcg cgaatggaaaaaagctaaccccgacaaagcattagatgacaaacctttctggatgaccgg tgaagcctggggccacggcgtgatgcaaagtgactactatcgccacggcttcgatgcgat gatcaatttcgattatcaggagcaggcggcgaaagcagtcgactgtctggcgcagatgga tacgacctggcagcaaatggcggagaaattgcagggtttcaacgtgttgagctacctctc gtcgcatgatacccgcctgttccgtgaagggggcgacaaagcagcagagttattactatt agcgccaggcgcggtacaaatcttttatggtgatgaatcctcgcgtccgttcggtcctac aggttctgatccgctgcaaggtacacgttcggatatgaactggcaggatgttagcggtaa atctgccgccagcgtcgcgcactggcagaaaatcagccagttccgcgcccgccatcccgc aattggcgcgggcaaacaaacgacacttttgctgaagcagggctacggctttgttcgtga gcatggcgacgataaagtgctggtcgtctgggcagggcaacagggtactagtagcg
gccgctgcag

bglX using primers f1/r1 (colony 1)

• Assigned code <partinfo>BBa_K523002</partinfo>
• Prefix and suffix in blue.
• Pre-coding sequence in CAPITALS and contains native RBS.
• BglII site in bold.
• Double stop codon is present.
• The sequence as it stands has a PstI site (red).
• This has been sequenced and looks good. A silent mutation from the expected sequence is indicated as a red capital T.

gaattcgcggccgcttctagagatctGCCACGTCGGGCAACAAAGGAAGAAAAATCCATatgaaatggctatgttcagtaggaatcgcggtgagtctggc cctgcagccagcactggcggatgatttattcggcaaccatccattaacgcccgaagcgcgggatgcgttcgtcaccgaactgcttaagaaaatgacagtt gatgagaaaattggtcagctgcgcttaatcagcgtcggcccggataacccgaaagaggcgatccgcgagatgatcaaagacggtcaggttggggcgattt tcaacaccgtaacccgtcaggatatccgcgccatgcaggatcaggtgatggaattaagccgcctgaaaattcctcttttctttgcttacgacgtgctgca cggtcagcgcacggtgttcccgattagcctcggtctggcctcgtcttttaacctcgatgcagtgaaaacggtcggacgtgtctctgcttatgaagcggca gatgatggcctgaatatgacctgggcaccgatggtcgatgtctcgcgcgatccgcgctggggacgtgcttccgaaggttttggcgaagatacgtatctca cctcaacaatgggtaaaaccatggtggaagcgatgcagggtaaaagcccggcagatcgctactcggtgatgaccagcgtcaaacactttgccgcatacgg cgcggtagaaggcggtaaagagtacaacaccgtcgatatgagtccgcagcgcctgtttaatgattatatgccgccgtacaaagcggggctggacgcaggc agcggcgcggtgatggtggcgctgaactcgctgaacggcacgccagccacctccgattcctggctgctgaaagatgttctgcgcgaccagtggggcttta aaggcatcaccgtttccgatcacggtgcaatcaaagagctgattaaacatggcacggcggcagacccggaagatgcggtgcgcgtggcgctgaaatccgg aatcaacatgagcatgagcgacgagtactactcgaagtatctgcctgggttgattaaatccggcaaagtgacgatggcagagctggacgatgctgcccgc catgtactgaacgttaaatatgatatggggttgtttaacgacccatacagccatttggggccgaaagagtctgacccggtggataccaatgccgaaagcc gcctgcaccgtaaagaagcgcgtgaagtggcgcgcgaaagcttggtgttgctgaaaaaccgtctcgaaacgttaccgctgaaaaaatcggccaccattgc ggtggttgggccactggcggacagtaaacgtgacgtgatgggcagctggtccgcagccggtgttgccgatcaatccgtgaccgtactgaccgggattaaa aatgccgtcggtgaaaacggtaaagtgctgtatgccaaaggggcgaacgttaccagtgacaaaggcattatcgatttcctgaatcagtatgaagaagcgg tcaaagtcgatccgcgttcgccgcaagagatgattgatgaagcggtgcagacggcgaaacaatctgatgtggtggtggctgtagtcggtgaagcacaggg gatggcgcacgaagcctccagccggaccgatatcactattccgcaaagccaacgtgacttgattgcggcgctgaaagccaccggtaaaccgctggtgctg gtgctgatgaacgggcgtccgctggcgctggtgaaagaagatcagcaggctgatgcgattctggaaacctggtttgcggggactgaaggcggtaatgcaa ttgccgatgtattgtttggcgattacaacccgtccggcaagctgccaatgtccttcccgcgttctgtcgggcagatcccggtgtactacagccatctgaa taccggtcgcccgtataatgccgacaagccgaacaaatacacttcgcgttattttgatgaagctaacggggcgttgtatccgttcggctatgggctgagc tacaccactttcaccgtctctgatgtgaaactttctgcgccgaccatgaagcgtgacggcaaagtgactgccagcgtgcaggtgacgaacaccggtaagc gcgagggtgccacggtagtgcagatgtacttgcaggatgtgacTgcttccatgagtcgccctgtgaaacagctgaaaggctttgagaaaatcaccctgaa accgggcgaaactcagactgtcagcttcccgatcgatattgaggcgctgaagttctggaatcaacagatgaaatatgacgccgagcctggcaagttcaat gtctttatcggcactgattccgcacgcgttaagaaaggcgagtttgagttgctgtaataatactagtagcggccgctgcag

bglX using primers f2/r2 (colony 1)

• This is essentially as above but starting at the start codon, and with no stop codon, and adding two bases at the end of the BioBrick, which (together with the T at the start of the suffix) code for a glycine when using BioSandwich assembly.
• This has been sequenced and looks good. A silent mutation from the expected sequence is indicated as a red capital T.

gaattcgcggccgcttctagagatctatgaaatggctatgttcagtaggaatcgcggtgagtctggc cctgcagccagcactggcggatgatttattcggcaaccatccattaacgcccgaagcgcgggatgcgttcgtcaccgaactgcttaagaaaatgacagtt gatgagaaaattggtcagctgcgcttaatcagcgtcggcccggataacccgaaagaggcgatccgcgagatgatcaaagacggtcaggttggggcgattt tcaacaccgtaacccgtcaggatatccgcgccatgcaggatcaggtgatggaattaagccgcctgaaaattcctcttttctttgcttacgacgtgctgca cggtcagcgcacggtgttcccgattagcctcggtctggcctcgtcttttaacctcgatgcagtgaaaacggtcggacgtgtctctgcttatgaagcggca gatgatggcctgaatatgacctgggcaccgatggtcgatgtctcgcgcgatccgcgctggggacgtgcttccgaaggttttggcgaagatacgtatctca cctcaacaatgggtaaaaccatggtggaagcgatgcagggtaaaagcccggcagatcgctactcggtgatgaccagcgtcaaacactttgccgcatacgg cgcggtagaaggcggtaaagagtacaacaccgtcgatatgagtccgcagcgcctgtttaatgattatatgccgccgtacaaagcggggctggacgcaggc agcggcgcggtgatggtggcgctgaactcgctgaacggcacgccagccacctccgattcctggctgctgaaagatgttctgcgcgaccagtggggcttta aaggcatcaccgtttccgatcacggtgcaatcaaagagctgattaaacatggcacggcggcagacccggaagatgcggtgcgcgtggcgctgaaatccgg aatcaacatgagcatgagcgacgagtactactcgaagtatctgcctgggttgattaaatccggcaaagtgacgatggcagagctggacgatgctgcccgc catgtactgaacgttaaatatgatatggggttgtttaacgacccatacagccatttggggccgaaagagtctgacccggtggataccaatgccgaaagcc gcctgcaccgtaaagaagcgcgtgaagtggcgcgcgaaagcttggtgttgctgaaaaaccgtctcgaaacgttaccgctgaaaaaatcggccaccattgc ggtggttgggccactggcggacagtaaacgtgacgtgatgggcagctggtccgcagccggtgttgccgatcaatccgtgaccgtactgaccgggattaaa aatgccgtcggtgaaaacggtaaagtgctgtatgccaaaggggcgaacgttaccagtgacaaaggcattatcgatttcctgaatcagtatgaagaagcgg tcaaagtcgatccgcgttcgccgcaagagatgattgatgaagcggtgcagacggcgaaacaatctgatgtggtggtggctgtagtcggtgaagcacaggg gatggcgcacgaagcctccagccggaccgatatcactattccgcaaagccaacgtgacttgattgcggcgctgaaagccaccggtaaaccgctggtgctg gtgctgatgaacgggcgtccgctggcgctggtgaaagaagatcagcaggctgatgcgattctggaaacctggtttgcggggactgaaggcggtaatgcaa ttgccgatgtattgtttggcgattacaacccgtccggcaagctgccaatgtccttcccgcgttctgtcgggcagatcccggtgtactacagccatctgaa taccggtcgcccgtataatgccgacaagccgaacaaatacacttcgcgttattttgatgaagctaacggggcgttgtatccgttcggctatgggctgagc tacaccactttcaccgtctctgatgtgaaactttctgcgccgaccatgaagcgtgacggcaaagtgactgccagcgtgcaggtgacgaacaccggtaagc gcgagggtgccacggtagtgcagatgtacttgcaggatgtgacTgcttccatgagtcgccctgtgaaacagctgaaaggctttgagaaaatcaccctgaa accgggcgaaactcagactgtcagcttcccgatcgatattgaggcgctgaagttctggaatcaacagatgaaatatgacgccgagcctggcaagttcaat gtctttatcggcactgattccgcacgcgttaagaaaggcgagtttgagttgctgggtactagtagcggccgctgcag

pVIII

• Blue is the leader sequence...

atgaaaaagtctttagtcctcaaagcctctgtagccgttgctaccctcgttccgatgctgtctttcgctgctgagggtgacgatcccgcaaaagcggcct ttaactccctgcaagcctcagcgaccgaatatatcggttatgcgtgggcgatggttgttgtcattgtcggcgcaactatcggtatcaagctgtttaagaa
attcacctcgaaagcaagctga