I've been looking at this structure diagram of the 16S rRNA and have been wondering why some parts of the diagrams have labelled base pairs while other parts are just lines and dots. I'm new to this field of science and am an undergraduate biologist just getting into reading this sort of scientific literature out of pure curiosity.
The diagram is a composite of all 16S RNA structures.
It has a summary with it that explains all.
"16S rRNA secondary structure, showing conserved parts for Prokaryotes (IUPAC letters) and amongst Archea/Bacteria (asterisks) all others as dots. Adapted (in SVG!) from Woese Bacterial evolution 1987"
The base pairs that are marked with A,U,C,G are present in all Prokaryotes studied so far.
The lines are base pair links (A-U and C-G)
There are a couple of lines that are pointers from the reference numbers e.g at 700 and 750