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Table 5 Attributes for the "RNA Structure Query System." The 5' and 3' ends of helices and loops are based on the global orientation determined from the 5' and 3' ends of the entire RNA molecule.

From: The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

RNA Types 5S rRNA, 16S rRNA, 23S rRNA, Group I intron
Phylogenetic Groups / Cell Locations Bacteria (nucleus), Archaea (nucleus), Eucarya (nucleus, mitochondria, and chloroplast)
number/type of nucleotides structural element short name brief explanation (if necessary)
single nuc total  
  paired (helix) paired positions
  unpaired (loop) unpaired positions
  5' helix end 5' end of helix
  3' helix end 3' end of helix
  5' loop end 5' end of loop
  3' loop end 3' end of loop
  helix center in helix but not at the 5' or 3' ends
  loop center in loop but not at the 5' or 3' ends
  unpaired/paired ratio of 'unpaired' / 'paired'
adjacent nucs total  
  in helix paired positions
  in loop unpaired positions
  3'helix 5'loop junction: 3' end ofhelix/5' end of loop
  3'loop 5'helix junction: 3' end ofloop/5' end of helix
  in loop/in helix ratio 'in loop' / 'in helix'
base pairs total  
  5'helix end at the 5' end of a helix
  3'helix end at the 3' end of a helix
  helix center in helix, but not at the 5' or 3' ends
three nucs total  
  000, 111,001,011,010, 100, 101,110 0 = unpaired, 1 = paired; patterns of three consecutive nucleotides
  5'-(A:C)B base pair with an unpaired nucleotide 3' to one paired position
  5'-A(B:C) base pair with an unpaired nucleotide 3' to one paired position
four nucs total  
  0000,1111,0001, 1110,0010, 1101,0011,1100,0100, 1011, 0101,1010,0110, 1001, 1000, 0111 0 = unpaired, 1 = paired; patterns of four consecutive nucleotides
  double pair@5end two consecutive base pairs at the 5' end of helices
  double pair@mid two consecutive base pairs not at the 5' or 3'ends of helices
  double pair@3end two consecutive base pairs at the 3' end of helices
  5-(A:D)BC base pair with two consecutive unpaired nucleotides 3' to one paired position
  lonepair base pair with unpaired nucleotides 5' and 3' to one unpaired position
  5-AB(C:D) base pair with two consecutive unpaired nucleotides 5' to one paired position
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