Difference between revisions of "Part:BBa K2363001"

Latest revision as of 06:49, 1 November 2017

PCBA4/5 upstream region of Dehalococcoides mccartyi

This part contains the upstream region (160 base pairs) of the PCBA4/5 gene, found originally in d.mycarti (Wang et all. 2014). The sequence contains the promoter region, which we plan to manipulate in the future for further characterization. We originally planned to extract the upstream regions from all four of the PCBA1, 4, 5, but discovered that the upstream region of 4 and 5 were nearly identical in sequence. To pick an adequate number of base pairs upstream from the coding region to form our geneblock, we used the Neural Network Promoter Prediction software with BDGP with all three sequences, locating the base pair position of all predicted promoters, and designing our upstream-region geneblock around the average distance the predicted promoters were from the start codon.

Wang S, Chng KR, Wilm A, et al. Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(33):12103-12108. doi:10.1073/pnas.1404845111.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

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 <partinfo>BBa_K2363001 short</partinfo>
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+This part contains the upstream region (160 base pairs) of the PCBA4/5 gene, found originally in d.mycarti (Wang et all. 2014). The sequence contains the promoter region, which we plan to manipulate in the future for further characterization. We originally planned to extract the upstream regions from all four of the PCBA1, 4, 5, but discovered that the upstream region of 4 and 5 were nearly identical in sequence. To pick an adequate number of base pairs upstream from the coding region to form our geneblock, we used the Neural Network Promoter Prediction software with BDGP with all three sequences, locating the base pair position of all predicted promoters, and designing our upstream-region geneblock around the average distance the predicted promoters were from the start codon.
+Wang S, Chng KR, Wilm A, et al. Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(33):12103-12108. doi:10.1073/pnas.1404845111.
 <!-- Add more about the biology of this part here