Difference between revisions of "Part:BBa K2282003"

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===Usage and Biology===
 
===Usage and Biology===
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The UP element is believed to stimulate the transcription of the CspA gene at a cold temperature, although some reports conclude the opposite (Phadtare et al., 2005). This promoter plays a role in transcription, though does not relate to the translation regulation (DSbox, 5’UTR). The CspA promoter is considered to be a strong promoter (Mitta et al., 1997).
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===Source of this part===
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Go to: https://www.ncbi.nlm.nih.gov/gene/948070  and in the 5'UTR. The Up element is an "AT-rich sequence (-47 to -38) upstream of the CspA -35 region. If you look at the Cold-shock protein A gene on this region, you will find the sequence. If you take the CspA gene, you can then go to nucleotide number 3719890 (ACGGTT) to have the beginning of the 5'UTR. Then you need to go further to 3719843 (AAAATAATTG). You will notice that the sequence is indeed located from -47 to -38 from the 5'UTR beginning and is AT rich.
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===Design consideration===
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Finding the UP element and the promoter was tricky and we needed certain amount of time to make sure we did not miss the sequence in the NCBI GenBank. 
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===References===
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Phadtare S, Severinov K. Extended −10 Motif Is Critical for Activity of the cspA Promoter but Does Not Contribute to Low-Temperature Transcription. Journal of Bacteriology. 2005;187(18):6584-6589. doi:10.1128/JB.187.18.6584-6589.2005.
  
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K2282003 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K2282003 SequenceAndFeatures</partinfo>

Latest revision as of 11:37, 25 October 2017

The UP element followed by the CspA promoter


Usage and Biology

The UP element is believed to stimulate the transcription of the CspA gene at a cold temperature, although some reports conclude the opposite (Phadtare et al., 2005). This promoter plays a role in transcription, though does not relate to the translation regulation (DSbox, 5’UTR). The CspA promoter is considered to be a strong promoter (Mitta et al., 1997).

Source of this part

Go to: https://www.ncbi.nlm.nih.gov/gene/948070 and in the 5'UTR. The Up element is an "AT-rich sequence (-47 to -38) upstream of the CspA -35 region. If you look at the Cold-shock protein A gene on this region, you will find the sequence. If you take the CspA gene, you can then go to nucleotide number 3719890 (ACGGTT) to have the beginning of the 5'UTR. Then you need to go further to 3719843 (AAAATAATTG). You will notice that the sequence is indeed located from -47 to -38 from the 5'UTR beginning and is AT rich.

Design consideration

Finding the UP element and the promoter was tricky and we needed certain amount of time to make sure we did not miss the sequence in the NCBI GenBank.

References

Phadtare S, Severinov K. Extended −10 Motif Is Critical for Activity of the cspA Promoter but Does Not Contribute to Low-Temperature Transcription. Journal of Bacteriology. 2005;187(18):6584-6589. doi:10.1128/JB.187.18.6584-6589.2005.

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]