Changes in PDB files used for clustering

Release 1.15 has 232 PDB files, release 1.17 has 243 PDB files, 230 of them are identical.

1 equivalence classes changed representatives: 4NVV4QCN.

12 new structures in release 1.17: 1VWW, 1VX2, 1VX6, 3J7A, 4KZD, 4QIK, 4QK8, 4QK9, 4QLM, 4TS2, 4UN3, 4UN5.

Obsolete: 4NVV4V9R.

Help Every Motif Atlas release is based on a representative set of PDB files. When comparing two releases, it's important to know how the input data changed.

Representative sets are quite stable in time, but PDB files from the older releases can be replaced by newer PDB files or removed from the set altogether if the structure is obsoleted by PDB without replacement.

PDB files from the newer release either replace representatives in the existing equivalence classes or come from new equivalence classes.

Redistribution of motif instances

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Changes in motif groups

Release 1.15 has 304 motif groups, release 1.17 has 364 motif groups, 143 of them are identical.

58 motif groups were updated, 103 groups are present only in release 1.15, 163 groups are only in release 1.17.

Help The Sankey diagram shows redistribution of motif instances (loops) between two releases. The rectangles represent the motif groups and are colored as follows:

Added motif groups: green
Removed motif groups: grey
Updated motif groups: orange
Added motif instances: green
Removed motif instances: grey

Hover over the links connecting the motif groups to see which motif instances were exchanged.


Identical motif groups

#Motif idInstancesDescription
1IL_77263.26Kink-turn from U4
2IL_34363.35Kink-turn from 23S H42
3IL_39980.25
4IL_16166.5423S H91 IL
5IL_09530.34Double S-turn motif
6IL_39526.44
7IL_48918.34Kink-turn variant
8IL_83339.14
9IL_40892.23
10IL_82563.13Thi-box riboswitch T-loop
11IL_34628.23Kink-turn
12IL_70089.13
13IL_43946.13
14IL_94403.63LSU H77
15IL_28003.22
16IL_94744.12Sarcin-ricin motif with extra cWW GA pair
17IL_23414.12
18IL_46435.12
19IL_52940.12
20IL_16330.12
21IL_31707.12Vitamin B12 aptamer
22IL_39175.12
23IL_65137.12Kink-turn like motif in Group I Intron
24IL_76095.32Motif from Hairpin Ribozyme
25IL_98172.12
26IL_09882.12
27IL_33842.12
28IL_39439.12
29IL_06413.12LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
30IL_67024.12
31IL_21495.12
32IL_50521.12
33IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
34IL_92422.12
35IL_03362.12
36IL_40041.12
37IL_70401.12
38IL_87548.12
39IL_03808.11
40IL_06847.11Group II Intron IL
41IL_15205.11
42IL_22953.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
43IL_36006.11
44IL_40364.11
45IL_45432.11
46IL_52610.11
47IL_62296.11
48IL_70529.11
49IL_80505.11
50IL_85510.11
51IL_88367.11
52IL_02257.11
53IL_05221.11
54IL_07252.11
55IL_28644.11
56IL_37347.11
57IL_40527.11Kink-turn
58IL_63952.11
59IL_73656.11
60IL_80652.11
61IL_85805.11
62IL_89463.11
63IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
64IL_02835.11
65IL_05513.11
66IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
67IL_23639.11tWH-tHS-L-cWW
68IL_40845.11
69IL_47687.11
70IL_52958.11
71IL_75415.11Pseudo-knot forming internal loop
72IL_80714.11
73IL_86059.11
74IL_89794.11
75IL_97842.11
76IL_02897.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
77IL_06177.11cWW AG or UU
78IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
79IL_25420.11
80IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
81IL_39324.11
82IL_47702.11
83IL_55649.11
84IL_65681.11
85IL_86060.11
86IL_91044.11
87IL_02957.11
88IL_06306.11
89IL_21077.11
90IL_25926.11
91IL_41027.11
92IL_48036.11
93IL_57977.11
94IL_66744.11SSU Helix 21 (h21) IL2 E.coli
95IL_82601.11Tandem cWW water-inserted CU pairs
96IL_86336.11
97IL_91078.11
98IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
99IL_03110.11
100IL_11302.11
101IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
102IL_26868.11
103IL_41139.11
104IL_58270.11
105IL_77296.11
106IL_82650.11
107IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
108IL_91089.11
109IL_98924.11
110IL_03282.11
111IL_06468.1116S h40 3WJ E.c.
112IL_11778.11
113IL_26971.11
114IL_41516.11
115IL_59907.11
116IL_83250.1116S h40 3WJ T.th.
117IL_87523.11
118IL_99784.11
119IL_06808.11Double sheared (tSH-tSH) one bulged base.
120IL_12507.11
121IL_22909.11
122IL_27640.11
123IL_35267.11
124IL_51572.11
125IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
126IL_79910.11
127IL_99937.11

Updated motif groups

#Motif idInstancesDescription
1IL_41766.988Tandem cWW pairs (Not AU or GC)
2IL_39199.770Hoogsteen-edge Platform, Single bulged base
3IL_44540.762Sugar-edge, 1-base platform, consensus tHS
4IL_82444.442cWH basepair
5IL_13959.740Double Sheared (tSH-tHS)
6IL_93424.731tSH-inserted-tHW
7IL_73276.829C-loop
8IL_65553.1127Kink-turn
9IL_55938.727LSU Helix 89 (H89) IL2. cSH Platform.
10IL_85647.625Sarcin-ricin parent motif with 15 Nts
11IL_92027.62416S h21 S8 binding site
12IL_24982.821SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
13IL_37104.618Single sheared with bulged bases
14IL_49493.717Sarcin-ricin Parent Motif - bacterial LSU H95 IL
15IL_94430.81516S h32-h33-h34 3WJ
16IL_31555.713Tandem sheared with inserted, unpaired purine
17IL_11015.211tHS and base triple with flanking pair
18IL_02809.410REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
19IL_92114.410GAAA loop receptor "platform" motif
20IL_86357.69LSU Helix 61 IL2
21IL_53635.69LSU Helix 32 (H32) IL
22IL_70237.69
23IL_93568.59Triple Sheared (tSH-tHS-tHS) with wobble cWW.
24IL_72158.69LSU Helix 62 (H62) IL
25IL_73000.39cHS-cWS
26IL_13069.68LSU 3WJ H32-H33-H35A
27IL_74856.38LSU Helix 89 (H89) IL2
28IL_31066.57SSU Helix 44 (h44) extension
29IL_64847.27Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
30IL_08926.5723S H91 IL
31IL_82188.47LSU H68 IL from H.m.
32IL_28572.4716S h18 kink-turn like motif
33IL_95652.56SSU Helix 27 (h27) IL Sarcin-Ricin motif
34IL_02359.66
35IL_15123.36Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
36IL_32261.36LSU Helix 89 (H89) IL2
37IL_25230.56Bacterial 5S rRNA Loop E
38IL_98421.75SSU Helix 12 (h12) IL | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
39IL_04397.25
40IL_37053.35Kink-turn from 23S H58
41IL_55114.35Double S-turn motif | tHS tHH bulge with S-turn | Double S-turn motif
42IL_71229.25
43IL_74876.34Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
44IL_69536.44LSU Helix 96 (H96) IL2
45IL_77076.34
46IL_37197.34
47IL_12211.34
48IL_94519.24
49IL_62499.10323S H91 IL
50IL_90735.23
51IL_98073.23Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
52IL_45592.2323S H91 IL
53IL_17204.23
54IL_21639.23
55IL_80494.43LSU H58 IL2 H.m.
56IL_37914.23
57IL_59563.23Sarcin-ricin motif with syn G
58IL_07300.32

Removed motif groups

#Motif idInstancesDescription
1IL_97217.132981-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_83000.1260cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | cWW AG or water inserted cWW Y-Y. | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
3IL_56465.654Single, unpaired intercalated base, consensus A
4IL_87904.735Triple sheared (tSH-tHS-tHS) no inserted bases
5IL_04465.1311-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
6IL_67813.219cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | 16S h34 ILa : Part of larger motif | cWW AG or UU | cWW AG or water inserted cWW Y-Y. | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
7IL_46648.81623S H91 IL | Single-Base Intercalation Site
8IL_77277.11623S H73 ILa : Part of larger Motif | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
9IL_03128.1141-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 23S H41 IL and 16S h18 IL : Has large bulge on one side
10IL_21761.111Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
11IL_58291.510Recurrent Sub-motif found in junctions
12IL_25549.19cWW AG or UU | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
13IL_47444.39SRP Loop E-like motif
14IL_84950.19LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
15IL_65554.28cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. | Tandem sheared with inserted, unpaired purine. | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
16IL_24546.6723S H41 IL and 16S h18 IL : Has large bulge on one side
17IL_44067.67Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
18IL_96952.17Double sheared with wobble cWW.
19IL_97057.47
20IL_32987.17cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
21IL_90133.56
22IL_59745.16Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
23IL_59864.26
24IL_16029.26cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
25IL_48183.26tSH-tHW-bulge
26IL_87065.3523S H91 IL | Single-Base Intercalation Site
27IL_79083.45
28IL_01080.25
29IL_09698.1516S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL
30IL_21427.15tHS tHH bulge with S-turn | tSH-inserted-tHS
31IL_47758.35REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
32IL_49668.14
33IL_89252.24
34IL_19493.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | SSU Decoding Site -- Human. Bulge-cSW-tHS | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
35IL_30840.34
36IL_22658.14Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
37IL_98601.14
38IL_05723.23
39IL_68668.13
40IL_06211.33
41IL_45794.23
42IL_79955.23SSU Helix (23) h23 IL1
43IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
44IL_51247.13
45IL_81597.13SSU Decoding Site -- Human. Bulge-cSW-tHS | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. | tSH-tHW-bulge
46IL_03337.13tSH-inserted-tHS
47IL_12204.23
48IL_37171.13LSU H58 IL2 H.m.
49IL_72641.23cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
50IL_26910.1323S H91 IL
51IL_38328.13cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. | Tandem sheared with inserted, unpaired purine. | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
52IL_16415.32SSU Helix 23 (h23) Kink-turn T. thermophilus
53IL_49445.12Triple sheared (tSH-tHS-tHS) no inserted bases
54IL_56250.12tHS tHH bulge with S-turn
55IL_95908.22LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
56IL_00734.12
57IL_18783.12
58IL_30323.1216S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
59IL_69106.32Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
60IL_09587.12
61IL_19451.12
62IL_30381.12tHS tHH bulge with S-turn
63IL_03252.12
64IL_11751.12
65IL_25541.12Triple Sheared with unpaired, inserted A
66IL_90877.12
67IL_67128.12
68IL_92576.12
69IL_14901.12tHS tHH bulge with S-turn
70IL_38207.1223S H73 ILa : Part of larger Motif | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
71IL_97833.12
72IL_05641.12
73IL_60613.12
74IL_95150.72
75IL_23302.11
76IL_29989.11
77IL_43284.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
78IL_60649.11Kink-turn
79IL_78513.11
80IL_49527.11
81IL_61352.11
82IL_96920.11SSU Helix 12 (h12) IL
83IL_25082.11
84IL_57079.11
85IL_63133.11Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
86IL_71685.11Sarcin-like with an intercalated basepair
87IL_46151.11Triple Sheared with unpaired, inserted A
88IL_57359.1123S H91 IL
89IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
90IL_72293.11
91IL_81398.11
92IL_20775.11tSH-inserted
93IL_52509.11
94IL_72367.11
95IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
96IL_53988.11
97IL_26448.11
98IL_54450.11
99IL_73367.11
100IL_83920.11
101IL_92886.11cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
102IL_54696.11SSU Decoding Site -- Human. Bulge-cSW-tHS | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
103IL_68457.11tSH-inserted-tHS

Added motif groups

#Motif idInstancesDescription
1IL_48256.13601-3 bulged nucleotides
2IL_92602.1309Non-canonical cWW basepair
3IL_67828.16123S H91 IL | Single-Base Intercalation Site | Single, unpaired intercalated base, consensus A | 16S h32-h33-h34 3WJ
4IL_81965.144Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW.
5IL_82822.133One or more bulged bases
6IL_53587.122IL_53587.1 is a mixed group with either one cSW pair or an intercalated base
7IL_34098.119cWW with bulged base
8IL_68200.118One or more bulged nucleotides
9IL_37964.116Recurrent Sub-motif found in junctions
10IL_19986.115Pair and triple
11IL_67038.11523S H91 IL | Single-Base Intercalation Site
12IL_58261.114SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
13IL_49203.114Double sheared with wobble cWW.
14IL_27005.112Non-canonical cWW
15IL_89033.11223S H41 IL and 16S h18 IL : Has large bulge on one side
16IL_18271.112Single, unpaired intercalated base, consensus A | 23S H91 IL
17IL_86933.111Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
18IL_65542.110SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
19IL_92122.110
20IL_38078.19
21IL_51342.18Non-canonical cWW with inserted stacked base.
22IL_32902.18Stacked cWW-cWH pairs
23IL_12849.18
24IL_39212.18
25IL_98016.17One or more bulged nucleotides
26IL_18916.17One or more bulged nucleotides
27IL_10743.16
28IL_31772.16SRP Loop E-like motif | SSU Helix (23) h23 IL1
29IL_51439.16
30IL_67399.16REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
31IL_60760.16
32IL_77920.16
33IL_01551.16
34IL_40053.16
35IL_37688.15Stacked bases not quite making a basepair.
36IL_85010.1523S H91 IL | Single-Base Intercalation Site
37IL_15702.15
38IL_59276.15
39IL_99363.15
40IL_52024.15
41IL_72062.15
42IL_86694.15SSU Helix 8 (h8) IL E.c. and Yeast
43IL_10554.15SSU Helix 23 (h23) Kink-turn T. thermophilus
44IL_26321.14LSU H58 IL2 H.m.
45IL_32508.1423S H91 IL
46IL_45593.14
47IL_00520.14
48IL_61513.14One or more bulged nucleotides
49IL_73281.14Sarcin-like with an intercalated basepair
50IL_13023.14
51IL_43727.14tSH-inserted-tHS | tHS tHH bulge with S-turn | tSH-inserted-tHS
52IL_62615.14cWS plus stacked base
53IL_50787.14tSH-tHW-bulge
54IL_87899.14SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
55IL_63917.13
56IL_22025.13
57IL_48070.13C-loop
58IL_82600.13cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
59IL_62504.13Triple Sheared with unpaired, inserted A
60IL_79398.13cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
61IL_91102.13
62IL_14081.13Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted
63IL_74163.13cWS making long-range triple
64IL_01827.13Base triple, intercalated pair, and bulged bases making long-range interactions.
65IL_19268.13
66IL_24955.13
67IL_06527.12
68IL_44977.12LSU H58 IL2 H.m. | SSU Helix (23) h23 IL1
69IL_74462.12
70IL_92205.12cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
71IL_06675.12Triple Sheared with unpaired, inserted A
72IL_88416.12
73IL_06692.12
74IL_21062.12Sarcin-ricin motif with cWW UU instead of tSH basepair.
75IL_51576.12
76IL_64894.1223S H91 IL | Single-Base Intercalation Site
77IL_68034.12
78IL_86033.12
79IL_00697.12
80IL_28028.12
81IL_38488.12
82IL_43363.12
83IL_94799.12tHS tHH bulge with S-turn
84IL_10119.12
85IL_28058.12
86IL_68945.12
87IL_73348.12Triple sheared (tSH-tHS-tHS) no inserted bases
88IL_24583.12
89IL_44092.12
90IL_79636.12Kink-turn
91IL_91942.12
92IL_35558.12
93IL_44847.12
94IL_67005.12
95IL_69668.12
96IL_15219.11
97IL_25808.11
98IL_40987.1123S H91 IL | Single-Base Intercalation Site
99IL_63366.11
100IL_70069.11tHS tHH bulge with S-turn
101IL_81512.11
102IL_88263.11
103IL_00346.11
104IL_11268.11
105IL_20608.11
106IL_41215.11
107IL_63723.11
108IL_70102.11
109IL_76024.11
110IL_81587.11
111IL_85707.11
112IL_00519.11Triple sheared (tSH-tHS-tHS) no inserted bases
113IL_11529.11
114IL_15813.11
115IL_37970.11tHS tHH bulge with S-turn | tSH-inserted-tHS
116IL_41371.11
117IL_45617.11
118IL_72055.11
119IL_77862.11
120IL_81956.11
121IL_85975.11
122IL_92957.11
123IL_08588.11
124IL_11989.11
125IL_15884.11
126IL_27713.11
127IL_33217.11
128IL_41920.11
129IL_90633.11
130IL_92986.11
131IL_09430.11
132IL_22601.11
133IL_62008.11
134IL_78984.11
135IL_91061.11
136IL_18506.11
137IL_22731.11
138IL_34548.11
139IL_48268.11
140IL_55210.111-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
141IL_66407.11
142IL_94958.11
143IL_01562.11
144IL_29058.11
145IL_34816.11
146IL_39296.11
147IL_57334.11
148IL_66775.11
149IL_69482.11
150IL_84276.11
151IL_87168.11
152IL_96591.11
153IL_10628.11
154IL_14240.11
155IL_31160.11
156IL_57625.11
157IL_62617.11
158IL_74400.11
159IL_81280.11
160IL_84995.11
161IL_97803.11