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As this question is a first post it is probably just a basic question question about protein synthesis, which @Sean Johnson has answered adequately. However I’m not quite sure. And as I used to work in protein synthesis (but am a rather out of touch now) I decided to look at the recent literature a little to address some more esoteric or obscure questions it ...


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Whether or not there are multiple start and stop codons depends on what you mean by "start codon" and "stop codon". The start codon has the sequence "AUG", and the stop codon has the sequence "UAG", "UAA", or "UGA". Both the pre-mRNA and the mature-mRNA can, and usually do, contain multiple instances of all of these sequences. However, only one "AUG" ...


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Generally speaking for RNA-seq data, you don't want to correct for GC content or other gene level effects (e.g. length) because you compare expression values between conditions WITHIN a gene. For this reason, it is recommended to use raw counts and not normalized values such as FPKM. See Section 2.7 of the edgeR user manual. This recent benchmark comparing ...


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Normalization of expression data is a big topic with new methods being published regularly. When approaching something like this you generally want look at people who have done similar things to what you've done, and then once you understand why they did what they did, you can ask what you need to do to answer your questions. Always keep your biological ...


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From Nature: A TATA box is a DNA sequence that indicates where a genetic sequence can be read and decoded. It is a type of promoter sequence, which specifies to other molecules where transcription begins. [...]. The TATA box is named for its conserved DNA sequence, which is most commonly TATAAA. Many eukaryotic genes have a conserved TATA box ...


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TATA box serves as a binding site for the TATA-binding protein (TBP; and its associated factors, together comprising the TFIID). TATA-box is one of the basic promoters present in many genes and therefore TBP is a general transcription factor i.e. TATA-box and TBP do not have specific roles. TATA-box is like a minimal promoter.


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TATA box simply is a type of promoter sequence, which specifies to Transcription Factors where transcription begins - which is usually 30bp downstream of TATA Box. Transcription factors can bind to the TATA box and recruit the RNA polymerase enzyme to synthesize RNA.


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I think the presence of a single terminator is related to the high processivity of T7 RNA polymerase. T7 RNA polymerase will transcribe a circular plasmid repeatedly before dissociating. The T7 terminator after ORF2 ensures that the transcript terminates efficiently. Based on your schematic, these are the potential mRNA transcripts from that construct: ...



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