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.
| 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 | |