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In the paper on CRISPRs, the following figure is shown: enter image description here

I added the light-green boxes.

What do the red arrows and the line with a filled circle on the far left mean? What does the arrow in the middle mean (also just infront of cas9)? Is the purple square to be understood as the RNA section in the B plot (blue arrow)?

Taken from here.

The caption is (cited):

The type II-A system from S. pyogenes is shown as an example. (A) The cas gene operon with tracrRNA and the CRISPR array. (B) The natural pathway of antiviral defense involves association of Cas9 with the antirepeat-repeat RNA (tracrRNA:crRNA) duplexes, RNA co-processing by ribonuclease III, further trimming, R-loop formation, and target DNA cleavage. (C) Details of the natural DNA cleavage with the duplex tracrRNA:crRNA.

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The arrow direction denote transcription direction and its location denotes the transcription start site. The circle is probably the transcription terminator (I cannot access this article at the moment, but this is what it should mean).

The purple boxes refer to the protospacers which are derived from foreign DNA. These elements help in recognizing and cleaving foreign DNA. These are transcribed as RNA which in turn guide the Cas complex to the target DNA. In a way, these protospacers provide some kind of immunological memory to the bacteria. See the below figure (From Nuñez et al. 2015 ):

enter image description here

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  • $\begingroup$ "They are the protospacers": What exactly do you mean by "they"? $\endgroup$ – TMOTTM Sep 13 '15 at 11:56
  • $\begingroup$ @TMOTTM the purple boxes.. I'll edit the answer $\endgroup$ – WYSIWYG Sep 13 '15 at 17:30

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