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RNA World
Informatics Phylogeny Database |
NON-CANONICAL BASE PAIR DATABASE : Summary Note: the duplicated entries (with different data available) are grouped together in the table.
# Base Pair Type Sequence Context Structure Details 
1
5' 3'
3' 5'2 AC reverse Hoogsteen
5' 3'
A-A,amino-N7
C-A
A-A,amino-N3,symmetric
3' 5'Structure of the 30S ribosomal subunit 3 AC reverse Hoogsteen
5' 3'
A-U,reverse Hoogsteen
A-C
G-C,Watson-Crick
3' 5'Structure of the 30S ribosomal subunit 4 AC reverse Hoogsteen
5' 3'
C A,*
A-C
C U,*
3' 5'Structure of the 30S ribosomal subunit 5 AC reverse Hoogsteen
5' 3'
C C,*
A-C
C A,*
3' 5'Atomic structure of the large ribosomal subunit 6 AC reverse Hoogsteen
5' 3'
C C,*
A-C
U U,*
3' 5'Atomic structure of the large ribosomal subunit 7 AC reverse Hoogsteen
5' 3'
C G,*
A-U
A C,*
3' 5'tRNA (Val) 8 AC reverse Hoogsteen
5' 3'
C-A,amino-N1
A-C
A-U,reverse Hoogsteen
3' 5'Structure of the 30S ribosomal subunit 9 AC reverse Hoogsteen
5' 3'
C-A,carbonyl-amino (1 bond)
A-C
G-G,amino-carbonyl (1 bond)
3' 5'4.5S RNA, domain IV, loopA 10 AC reverse Hoogsteen
5' 3'
C-A,carbonyl-amino(1bond)
A-C
G-G,carbonyl-amino(1 bond)
3' 5'dodecamer 11 AC reverse Hoogsteen
5' 3'
C-A,carbonyl-amino
A-C
G-G,carbonyl-amino
3' 5'SRP19 12 AC reverse Hoogsteen
5' 3'
C-A,Carbonyl-amino
A-C
G-G,Carbonyl-amino
3' 5'Ribonucleoprotein core of the SRP 13 AC reverse Hoogsteen
5' 3'
G A,*
A-C
A-A,amino-N1,N7-amino
3' 5'Atomic structure of the large ribosomal subunit 14 AC reverse Hoogsteen
5' 3'
G-A,sheared
A-C
G-G,amino-carbonyl(1 bond)
3' 5'Atomic structure of the large ribosomal subunit 15 AC reverse Hoogsteen
5' 3'
U C,*
C-A
A G,*
3' 5'Structure of the 30S ribosomal subunit 16 AC reverse Hoogsteen
5' 3'
U G,*
A-C
A U,*
3' 5'Atomic structure of the large ribosomal subunit 17 AC reverse Hoogsteen
5' 3'
U-A,reverse Hoogsteen
A-C
A-A,N7-amino
3' 5'Structure of the 30S ribosomal subunit 18 AC wobble
5' 3'
A U,*
A-C
U-A,Watson-Crick
3' 5'Anticodon loop of tRNA (Lys) 19 AC wobble
5' 3'
A-G, sheared
A-C
G-C,Watson-Crick
3' 5'Secondary structure of VSm1 substrate hairpin analog 20 AC wobble
5' 3'
A-G,Sheared
A-C
G-C,Watson-Crick
3' 5'Loop B of hairpin ribozyme from tobacco ringspot virus 21 AC wobble
5' 3'
A-G,sheared
A-C
G-C,Watson-Crick
3' 5'VS ribozyme substarte RNA 22 AC wobble
5' 3'
A-U,Watson-Crick
A-C
U-A,Watson-Crick
3' 5'(GCAGACUUAAAUCUGC)2-duplex 23 AC wobble
5' 3'
A-U,Watson-Crick
C-A
U t6A, *
3' 5'tRNA Lys3 UUU anticodon stem/loop(ASL lys3 UUU) 24 AC wobble
5' 3'
C-A,Wobble
A-C
G-C,Watson-Crick
3' 5'RNA internal loop with tandem C-A+ mismatches 25 AC wobble
5' 3'
C-G, Watson-Crick
A-C
A-U, Watson-Crick
3' 5'Natural guanine responsive riboswitch complexed with hypoxanthine 26 AC wobble
5' 3'
C-G, Watson-Crick
A-C
A-U, Watson-Crick
3' 5'Bacillus subtilis xpt G-Riboswitch G complex 27 AC wobble
5' 3'
C-G,Watson-Crick
A-C
C-G,Watson-Crick
3' 5'Acceptor helix model of tRNA (Ala) 28 AC wobble
5' 3'
C-G,Watson-Crick
C-A
U-G,Wobble
3' 5'RNA helix recognized by zinc-finger protein 29 AC wobble
5' 3'
C-U,*
C-A
C-G,Watson-Crick
3' 5'U6 stem loop RNA 30 AC wobble
5' 3'
G G,*
A-C
G-C,Watson-Crick
3' 5'Leadzyme RNA 31 AC wobble
5' 3'
G U,*
A-C
U-A,4-carbonyl-amino (1 bond)
3' 5'Dienococcus Radiodurans 23S RNA 32 AC wobble
5' 3'
G-C, Watson-Crick
A-C
A-G, imino
3' 5'Group I Intron 33 AC wobble
5' 3'
G-C, Watson-Crick
A-C
U C,*
3' 5'U6 RNA 34 AC wobble
5' 3'
G-C,Watson-Crick
A-C
A-C,Wobble
3' 5'SRP 19 splicing domain 35 AC wobble
5' 3'
G-C,Watson-Crick
A-C
A-U,Watson-Crick
3' 5'RNA helix recognized by zinc-finger protein 36 AC wobble
5' 3'
G-C,Watson-Crick
A-C
C-A,wobble
3' 5'SRP 19 splicing domain 37 AC wobble
5' 3'
G-C,Watson-Crick
A-C
C-A,Wobble
3' 5'Helix 6 of human SRP 38 AC wobble
5' 3'
G-C,Watson-Crick
A-C
U-A,Watson-Crick
3' 5'RNA hairpin loop 39 AC wobble
5' 3'
U-A,Watson-Crick
A-C
C-G,Watson-Crick
3' 5'Theophylline binding RNA 40 AT reverse Hoogsteen
5' 3'
A Y,*
A-T
U G,*
3' 5'Yeast tRNA (Asp) 41 AT reverse Hoogsteen
5' 3'
A PSU,*
A-T
A G,*
3' 5'Methionyl-tRNAFMET formyltransferase 42 AT reverse Hoogsteen
5' 3'
G Y,*
A-T
C G,*
3' 5'tRNA (Cys) 43 AT reverse Hoogsteen
5' 3'
G Y,*
A-T
U G,*
3' 5'Yeast tRNA (Phe) AT reverse Hoogsteen
5' 3'
G Y,*
A-T
U G,*
3' 5'Yeast tRNA (Phe) more info... 44 AU reverse Hoogsteen
5' 3'
* C,*
A-U
G-A,sheared
3' 5'Group II intron branch site AU reverse Hoogsteen
5' 3'
* C,*
A-U
G-A,sheared
3' 5'Group II intron branch site more info... 45 AU reverse Hoogsteen
5' 3'
A C,*
A-U
A C,*
3' 5'Atomic structure of the large ribosomal subunit AU reverse Hoogsteen
5' 3'
A C,*
A-U
A C,*
3' 5'Atomic structure of the large ribosomal subunit more info... 46 AU reverse Hoogsteen
5' 3'
A C,*
A-U
A G,*
3' 5'Dienococcus Radiodurans 23S RNA 47 AU reverse Hoogsteen
5' 3'
A C,*
A-U
A-G,N7-amino
3' 5'Atomic structure of the large ribosomal subunit 48 AU reverse Hoogsteen
5' 3'
A G,*
A-U
A G,*
3' 5'Dienococcus Radiodurans 23S RNA 49 AU reverse Hoogsteen
5' 3'
A G,*
A-U
A-C,amino-N3
3' 5'Structure of the 30S ribosomal subunit 50 AU reverse Hoogsteen
5' 3'
A G,*
A-U
C U,*
3' 5'Atomic structure of the large ribosomal subunit 51 AU reverse Hoogsteen
5' 3'
A U,*
A-U
A G,*
3' 5'tRNA (tyr) 52 AU reverse Hoogsteen
5' 3'
A U,*
A-U
G A,*
3' 5'Atomic structure of the large ribosomal subunit 53 AU reverse Hoogsteen
5' 3'
A U,*
A-U
G C,*
3' 5'Atomic structure of the large ribosomal subunit 54 AU reverse Hoogsteen
5' 3'
A U,*
A-U
G G,*
3' 5'tRNA (Ile) 55 AU reverse Hoogsteen
5' 3'
A U,*
A-U
G G,*
3' 5'tRNA (Val) 56 AU reverse Hoogsteen
5' 3'
A U,*
A-U
G-C,Watson-Crick
3' 5'Group I intron ribozyme 57 AU reverse Hoogsteen
5' 3'
A-A,N3-amino(1 bond)
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit 58 AU reverse Hoogsteen
5' 3'
A-A,N7-amino
A-U
G C,*
3' 5'Atomic structure of the large ribosomal subunit 59 AU reverse Hoogsteen
5' 3'
A-A,N7-amino
A-U
G-A,Sheared
3' 5'SRL of 28S rRNA 60 AU reverse Hoogsteen
5' 3'
A-G,sheared
A-U
A-A,N3-amino
3' 5'Structure of the 30S ribosomal subunit 61 AU reverse Hoogsteen
5' 3'
A-U,amino-2-carbonyl(1 bond)
A-U
C G,*
3' 5'HCV-IRES RNA tertiary domain 62 AU reverse Hoogsteen
5' 3'
C A,*
A-U
A C,*
3' 5'Atomic structure of the large ribosomal subunit 63 AU reverse Hoogsteen
5' 3'
C A,*
A-U
G G,*
3' 5'Prolyl-tRNA Synthetase form Thermus Thermophilus 64 AU reverse Hoogsteen
5' 3'
C A,*
A-U
G U,*
3' 5'Yeast tRNA (Phe) 65 AU reverse Hoogsteen
5' 3'
C C,*
A-U
G-A,sheared
3' 5'Atomic structure of the large ribosomal subunit 66 AU reverse Hoogsteen
5' 3'
C G,*
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit 67 AU reverse Hoogsteen
5' 3'
C-A,reverse Hoogsteen
A-U
A-C,reverse Hoogsteen
3' 5'Structure of the 30S ribosomal subunit 68 AU reverse Hoogsteen
5' 3'
C-C,carbonyl-amino
A-U
A-G,sheared
3' 5'Atomic structure of the large ribosomal subunit 69 AU reverse Hoogsteen
5' 3'
C-G,Watson-Crick
G-U
G-C,Watson-Crick
3' 5'Dienococcus Radiodurans 23S RNA 70 AU reverse Hoogsteen
5' 3'
G A,*
A-U
A A,*
3' 5'Specificity domain of RNAse P 71 AU reverse Hoogsteen
5' 3'
G A,*
A-U
A C,*
3' 5'Dienococcus Radiodurans 23S RNA AU reverse Hoogsteen
5' 3'
G A,*
A-U
A C,*
3' 5'Dienococcus Radiodurans 23S RNA more info... 72 AU reverse Hoogsteen
5' 3'
G A,*
A-U
A C,*
3' 5'Atomic structure of the large ribosomal subunit 73 AU reverse Hoogsteen
5' 3'
G A,*
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit 74 AU reverse Hoogsteen
5' 3'
G A,*
A-U
A-G,amino-N3
3' 5'Structure of the 30S ribosomal subunit 75 AU reverse Hoogsteen
5' 3'
G A,*
A-U
C-C,*
3' 5'57nt 16S ribosomal RNA 76 AU reverse Hoogsteen
5' 3'
G A,*
A-U
G A,*
3' 5'Dienococcus Radiodurans 23S RNA 77 AU reverse Hoogsteen
5' 3'
G A,*
A-U
G A,*
3' 5'Structure of the 30S ribosomal subunit 78 AU reverse Hoogsteen
5' 3'
G A,*
A-U
G U,*
3' 5'Atomic structure of the large ribosomal subunit 79 AU reverse Hoogsteen
5' 3'
G A,*
A-U
U C,*
3' 5'Dienococcus Radiodurans 23S RNA 80 AU reverse Hoogsteen
5' 3'
G A,*
A-U
U G,*
3' 5'Dienococcus Radiodurans 23S RNA 81 AU reverse Hoogsteen
5' 3'
G A,*
U-A
A-G,amino-N3,N7-amino
3' 5'Structure of the 30S ribosomal subunit 82 AU reverse Hoogsteen
5' 3'
G C,*
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit AU reverse Hoogsteen
5' 3'
G C,*
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit more info... 83 AU reverse Hoogsteen
5' 3'
G C,*
A-U
A-A,amino-N1
3' 5'Atomic structure of the large ribosomal subunit 84 AU reverse Hoogsteen
5' 3'
G C,*
A-U
C A,*
3' 5'Structure of the 30S ribosomal subunit 85 AU reverse Hoogsteen
5' 3'
G C,*
A-U
C C,*
3' 5'Atomic structure of the large ribosomal subunit 86 AU reverse Hoogsteen
5' 3'
G G,*
5MU-1MA
PSU A,*
3' 5'Arginyl-tRNA Synthetase 87 AU reverse Hoogsteen
5' 3'
G G,*
A-U
A C,*
3' 5'Atomic structure of the large ribosomal subunit AU reverse Hoogsteen
5' 3'
G G,*
A-U
A C,*
3' 5'Atomic structure of the large ribosomal subunit more info... 88 AU reverse Hoogsteen
5' 3'
G G,*
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit 89 AU reverse Hoogsteen
5' 3'
G G,*
A-U
C C,*
3' 5'Structure of the 30S ribosomal subunit 90 AU reverse Hoogsteen
5' 3'
G G,*
A-U
C-G,amino-carbonyl
3' 5'Structure of the 30S ribosomal subunit 91 AU reverse Hoogsteen
5' 3'
G G,*
A-U
G G,*
3' 5'Atomic structure of the large ribosomal subunit 92 AU reverse Hoogsteen
5' 3'
G Y,*
A-D
C A,*
3' 5'tRNA (Thr) 93 AU reverse Hoogsteen
5' 3'
G U,*
A-U
A G,*
3' 5'tRNA (Glu) 94 AU reverse Hoogsteen
5' 3'
G U,*
A-U
A G,*
3' 5'tRNA apatamer 95 AU reverse Hoogsteen
5' 3'
G-A,amino-N7(1 bond)
A-U
A C,*
3' 5'Atomic structure of the large ribosomal subunit 96 AU reverse Hoogsteen
5' 3'
G-A,amino-N7(1 bond)
A-U
G A,*
3' 5'Dienococcus Radiodurans 23S RNA 97 AU reverse Hoogsteen
5' 3'
G-A,Sheared,
A-U
G-G,carbonyl-imino:amino
3' 5'5S rRNA loop E 98 AU reverse Hoogsteen
5' 3'
G-A,Sheared
A-U
A A,*
3' 5'FMN-binding RNA aptamer 99 AU reverse Hoogsteen
5' 3'
G-A,sheared
A-U
3' 5'Structure of the 30S ribosomal subunit 100 AU reverse Hoogsteen
5' 3'
G-A,sheared
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit 101 AU reverse Hoogsteen
5' 3'
G-A,Sheared
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit 102 AU reverse Hoogsteen
5' 3'
G-A,Sheared
A-U
A G,*
3' 5'Restrictocin-inhibitor complexes 103 AU reverse Hoogsteen
5' 3'
G-A,sheared
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit AU reverse Hoogsteen
5' 3'
G-A,sheared
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit more info... AU reverse Hoogsteen
5' 3'
G-A,sheared
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit more info... 104 AU reverse Hoogsteen
5' 3'
G-A,sheared
A-U
A G,*
3' 5'Dienococcus Radiodurans 23S RNA 105 AU reverse Hoogsteen
5' 3'
G-A,sheared
A-U
A G,*
3' 5'Atomic structure of the large ribosomal subunit (5S)