Motif Atlas Releases 1.15 and 1.17
Changes in PDB files used for clustering
Release 1.15 has 233 PDB files, release 1.17 has 244 PDB files, 231 of them are identical.
1 equivalence classes changed representatives: 4NVV → 4QCN.
12 new structures in release 1.17: 1VWW, 1VX2, 1VX6, 3J7A, 4KZD, 4QIK, 4QK8, 4QK9, 4QLM, 4TS2, 4UN3, 4UN5.
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
Loading the Sankey diagram...
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 id | Instances | Description |
|---|---|---|---|
| 1 | IL_77263.2 | 6 | Kink-turn from U4 |
| 2 | IL_34363.3 | 5 | Kink-turn from 23S H42 |
| 3 | IL_39980.2 | 5 | |
| 4 | IL_16166.5 | 4 | 23S H91 IL |
| 5 | IL_39526.4 | 4 | |
| 6 | IL_83339.1 | 4 | |
| 7 | IL_09530.3 | 4 | Double S-turn motif |
| 8 | IL_48918.3 | 4 | Kink-turn variant |
| 9 | IL_43946.1 | 3 | |
| 10 | IL_94403.6 | 3 | LSU H77 |
| 11 | IL_70089.1 | 3 | |
| 12 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 13 | IL_40892.2 | 3 | |
| 14 | IL_34628.2 | 3 | Kink-turn |
| 15 | IL_06413.1 | 2 | LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1 |
| 16 | IL_09882.1 | 2 | |
| 17 | IL_28003.2 | 2 | |
| 18 | IL_40041.1 | 2 | |
| 19 | IL_50521.1 | 2 | |
| 20 | IL_67024.1 | 2 | |
| 21 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 22 | IL_92422.1 | 2 | |
| 23 | IL_03362.1 | 2 | |
| 24 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 25 | IL_21495.1 | 2 | |
| 26 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 27 | IL_39175.1 | 2 | |
| 28 | IL_46435.1 | 2 | |
| 29 | IL_52940.1 | 2 | |
| 30 | IL_70401.1 | 2 | |
| 31 | IL_96446.1 | 2 | |
| 32 | IL_33842.1 | 2 | |
| 33 | IL_39439.1 | 2 | |
| 34 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 35 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 36 | IL_16330.1 | 2 | |
| 37 | IL_23414.1 | 2 | |
| 38 | IL_98172.1 | 2 | |
| 39 | IL_87548.1 | 2 | |
| 40 | IL_03110.1 | 1 | |
| 41 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 42 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 43 | IL_35267.1 | 1 | |
| 44 | IL_42891.1 | 1 | |
| 45 | IL_58270.1 | 1 | |
| 46 | IL_80652.1 | 1 | |
| 47 | IL_85805.1 | 1 | |
| 48 | IL_88367.1 | 1 | |
| 49 | IL_98924.1 | 1 | |
| 50 | IL_03282.1 | 1 | |
| 51 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 52 | IL_11302.1 | 1 | |
| 53 | IL_21077.1 | 1 | |
| 54 | IL_25420.1 | 1 | |
| 55 | IL_28644.1 | 1 | |
| 56 | IL_36006.1 | 1 | |
| 57 | IL_40364.1 | 1 | |
| 58 | IL_51572.1 | 1 | |
| 59 | IL_59907.1 | 1 | |
| 60 | IL_68827.1 | 1 | Reverse Kink-Turn |
| 61 | IL_76263.1 | 1 | |
| 62 | IL_80714.1 | 1 | |
| 63 | IL_86059.1 | 1 | |
| 64 | IL_88865.1 | 1 | |
| 65 | IL_99784.1 | 1 | |
| 66 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 67 | IL_11778.1 | 1 | |
| 68 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 69 | IL_25926.1 | 1 | |
| 70 | IL_31006.1 | 1 | tSH-tHW-L-bif-cWW |
| 71 | IL_37347.1 | 1 | |
| 72 | IL_40527.1 | 1 | Kink-turn |
| 73 | IL_45432.1 | 1 | |
| 74 | IL_52610.1 | 1 | |
| 75 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
| 76 | IL_77014.1 | 1 | |
| 77 | IL_86060.1 | 1 | |
| 78 | IL_89463.1 | 1 | |
| 79 | IL_99937.1 | 1 | |
| 80 | IL_03808.1 | 1 | |
| 81 | IL_06847.1 | 1 | Group II Intron IL |
| 82 | IL_12507.1 | 1 | |
| 83 | IL_26868.1 | 1 | |
| 84 | IL_40845.1 | 1 | |
| 85 | IL_62296.1 | 1 | |
| 86 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 87 | IL_86336.1 | 1 | |
| 88 | IL_89794.1 | 1 | |
| 89 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 90 | IL_02257.1 | 1 | |
| 91 | IL_05221.1 | 1 | |
| 92 | IL_07252.1 | 1 | |
| 93 | IL_15205.1 | 1 | |
| 94 | IL_22909.1 | 1 | |
| 95 | IL_26971.1 | 1 | |
| 96 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 97 | IL_39324.1 | 1 | |
| 98 | IL_47687.1 | 1 | |
| 99 | IL_52958.1 | 1 | |
| 100 | IL_63952.1 | 1 | |
| 101 | IL_70529.1 | 1 | |
| 102 | IL_77296.1 | 1 | |
| 103 | IL_82650.1 | 1 | |
| 104 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 105 | IL_91044.1 | 1 | |
| 106 | IL_02835.1 | 1 | |
| 107 | IL_05513.1 | 1 | |
| 108 | IL_08114.1 | 1 | |
| 109 | IL_22953.1 | 1 | 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) |
| 110 | IL_27243.1 | 1 | |
| 111 | IL_41027.1 | 1 | |
| 112 | IL_47702.1 | 1 | |
| 113 | IL_55649.1 | 1 | |
| 114 | IL_73656.1 | 1 | |
| 115 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 116 | IL_87394.1 | 1 | |
| 117 | IL_91078.1 | 1 | |
| 118 | IL_97842.1 | 1 | |
| 119 | IL_02897.1 | 1 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th. |
| 120 | IL_06177.1 | 1 | cWW AG or UU |
| 121 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 122 | IL_27640.1 | 1 | |
| 123 | IL_41139.1 | 1 | |
| 124 | IL_48036.1 | 1 | |
| 125 | IL_57285.1 | 1 | |
| 126 | IL_65681.1 | 1 | |
| 127 | IL_75328.1 | 1 | |
| 128 | IL_79910.1 | 1 | |
| 129 | IL_87523.1 | 1 | |
| 130 | IL_91089.1 | 1 | |
| 131 | IL_02957.1 | 1 | |
| 132 | IL_06306.1 | 1 | |
| 133 | IL_16921.1 | 1 | |
| 134 | IL_23448.1 | 1 | |
| 135 | IL_27668.1 | 1 | |
| 136 | IL_41516.1 | 1 | |
| 137 | IL_57977.1 | 1 | |
| 138 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 139 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 140 | IL_80505.1 | 1 | |
| 141 | IL_85510.1 | 1 | |
| 142 | IL_91379.1 | 1 | |
| 143 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_41766.9 | 88 | Tandem cWW pairs (Not AU or GC) |
| 2 | IL_39199.7 | 70 | Hoogsteen-edge Platform, Single bulged base |
| 3 | IL_44540.7 | 62 | Sugar-edge, 1-base platform, consensus tHS |
| 4 | IL_82444.4 | 42 | cWH basepair |
| 5 | IL_13959.7 | 40 | Double Sheared (tSH-tHS) |
| 6 | IL_93424.7 | 31 | tSH-inserted-tHW |
| 7 | IL_73276.8 | 29 | C-loop |
| 8 | IL_55938.7 | 27 | LSU Helix 89 (H89) IL2. cSH Platform. |
| 9 | IL_65553.11 | 27 | Kink-turn |
| 10 | IL_85647.6 | 25 | Sarcin-ricin parent motif with 15 Nts |
| 11 | IL_92027.6 | 24 | 16S h21 S8 binding site |
| 12 | IL_24982.8 | 21 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 13 | IL_37104.6 | 18 | Single sheared with bulged bases |
| 14 | IL_49493.7 | 17 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 15 | IL_94430.8 | 15 | 16S h32-h33-h34 3WJ |
| 16 | IL_31555.7 | 13 | Tandem sheared with inserted, unpaired purine |
| 17 | IL_11015.2 | 11 | tHS and base triple with flanking pair |
| 18 | IL_02809.4 | 10 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 19 | IL_92114.4 | 10 | GAAA loop receptor "platform" motif |
| 20 | IL_93568.5 | 9 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 21 | IL_72158.6 | 9 | LSU Helix 62 (H62) IL |
| 22 | IL_73000.3 | 9 | cHS-cWS |
| 23 | IL_86357.6 | 9 | LSU Helix 61 IL2 |
| 24 | IL_53635.6 | 9 | LSU Helix 32 (H32) IL |
| 25 | IL_70237.6 | 9 | |
| 26 | IL_13069.6 | 8 | LSU 3WJ H32-H33-H35A |
| 27 | IL_74856.3 | 8 | LSU Helix 89 (H89) IL2 |
| 28 | IL_08926.5 | 7 | 23S H91 IL |
| 29 | IL_82188.4 | 7 | LSU H68 IL from H.m. |
| 30 | IL_28572.4 | 7 | 16S h18 kink-turn like motif |
| 31 | IL_31066.5 | 7 | SSU Helix 44 (h44) extension |
| 32 | IL_64847.2 | 7 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 33 | IL_25230.5 | 6 | Bacterial 5S rRNA Loop E |
| 34 | IL_95652.5 | 6 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 35 | IL_02359.6 | 6 | |
| 36 | IL_15123.3 | 6 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th. |
| 37 | IL_32261.3 | 6 | LSU Helix 89 (H89) IL2 |
| 38 | IL_55114.3 | 5 | Double S-turn motif | tHS tHH bulge with S-turn | Double S-turn motif |
| 39 | IL_71229.2 | 5 | |
| 40 | IL_98421.7 | 5 | SSU Helix 12 (h12) IL | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1 |
| 41 | IL_04397.2 | 5 | |
| 42 | IL_37053.3 | 5 | Kink-turn from 23S H58 |
| 43 | IL_37197.3 | 4 | |
| 44 | IL_12211.3 | 4 | |
| 45 | IL_94519.2 | 4 | |
| 46 | IL_74876.3 | 4 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 47 | IL_69536.4 | 4 | LSU Helix 96 (H96) IL2 |
| 48 | IL_77076.3 | 4 | |
| 49 | IL_37914.2 | 3 | |
| 50 | IL_59563.2 | 3 | Sarcin-ricin motif with syn G |
| 51 | IL_62499.10 | 3 | 23S H91 IL |
| 52 | IL_90735.2 | 3 | |
| 53 | IL_98073.2 | 3 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 54 | IL_45592.2 | 3 | 23S H91 IL |
| 55 | IL_17204.2 | 3 | |
| 56 | IL_21639.2 | 3 | |
| 57 | IL_80494.4 | 3 | LSU H58 IL2 H.m. |
| 58 | IL_07300.3 | 2 |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_97217.13 | 298 | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_83000.1 | 260 | 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) | 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 |
| 3 | IL_56465.6 | 54 | Single, unpaired intercalated base, consensus A |
| 4 | IL_87904.7 | 35 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 5 | IL_04465.1 | 31 | 1-3 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 |
| 6 | IL_67813.2 | 19 | 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 | 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 |
| 7 | IL_77277.1 | 16 | 23S 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. |
| 8 | IL_46648.8 | 16 | 23S H91 IL | Single-Base Intercalation Site |
| 9 | IL_03128.1 | 14 | 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 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 10 | IL_21761.1 | 11 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 11 | IL_58291.5 | 10 | Recurrent Sub-motif found in junctions |
| 12 | IL_25549.1 | 9 | cWW 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) |
| 13 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 14 | IL_84950.1 | 9 | 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 | 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 |
| 15 | IL_65554.2 | 8 | cHS-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. |
| 16 | IL_24546.6 | 7 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 17 | IL_44067.6 | 7 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 18 | IL_96952.1 | 7 | Double sheared with wobble cWW. |
| 19 | IL_97057.4 | 7 | |
| 20 | IL_32987.1 | 7 | 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) | 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) |
| 21 | IL_59745.1 | 6 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 22 | IL_59864.2 | 6 | |
| 23 | IL_16029.2 | 6 | 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 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 24 | IL_48183.2 | 6 | tSH-tHW-bulge |
| 25 | IL_90133.5 | 6 | |
| 26 | IL_21427.1 | 5 | tHS tHH bulge with S-turn | tSH-inserted-tHS |
| 27 | IL_47758.3 | 5 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 28 | IL_87065.3 | 5 | 23S H91 IL | Single-Base Intercalation Site |
| 29 | IL_79083.4 | 5 | |
| 30 | IL_01080.2 | 5 | |
| 31 | IL_09698.1 | 5 | 16S 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 |
| 32 | IL_22658.1 | 4 | Single 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) |
| 33 | IL_98601.1 | 4 | |
| 34 | IL_49668.1 | 4 | |
| 35 | IL_89252.2 | 4 | |
| 36 | IL_19493.1 | 4 | Leadzyme 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. |
| 37 | IL_30840.3 | 4 | |
| 38 | IL_03337.1 | 3 | tSH-inserted-tHS |
| 39 | IL_12204.2 | 3 | |
| 40 | IL_37171.1 | 3 | LSU H58 IL2 H.m. |
| 41 | IL_72641.2 | 3 | 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 |
| 42 | IL_26910.1 | 3 | 23S H91 IL |
| 43 | IL_38328.1 | 3 | cHS-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. |
| 44 | IL_05723.2 | 3 | |
| 45 | IL_68668.1 | 3 | |
| 46 | IL_06211.3 | 3 | |
| 47 | IL_45794.2 | 3 | |
| 48 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 49 | IL_25271.2 | 3 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 50 | IL_51247.1 | 3 | |
| 51 | IL_81597.1 | 3 | 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. | tSH-tHW-bulge |
| 52 | IL_67128.1 | 2 | |
| 53 | IL_92576.1 | 2 | |
| 54 | IL_14901.1 | 2 | tHS tHH bulge with S-turn |
| 55 | IL_38207.1 | 2 | 23S 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) |
| 56 | IL_97833.1 | 2 | |
| 57 | IL_05641.1 | 2 | |
| 58 | IL_60613.1 | 2 | |
| 59 | IL_95150.7 | 2 | |
| 60 | IL_16415.3 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 61 | IL_49445.1 | 2 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 62 | IL_56250.1 | 2 | tHS tHH bulge with S-turn |
| 63 | IL_95908.2 | 2 | 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 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 64 | IL_00734.1 | 2 | |
| 65 | IL_18783.1 | 2 | |
| 66 | IL_30323.1 | 2 | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 67 | IL_69106.3 | 2 | Leadzyme 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. |
| 68 | IL_09587.1 | 2 | |
| 69 | IL_19451.1 | 2 | |
| 70 | IL_30381.1 | 2 | tHS tHH bulge with S-turn |
| 71 | IL_03252.1 | 2 | |
| 72 | IL_11751.1 | 2 | |
| 73 | IL_25541.1 | 2 | Triple Sheared with unpaired, inserted A |
| 74 | IL_90877.1 | 2 | |
| 75 | IL_53988.1 | 1 | |
| 76 | IL_26448.1 | 1 | |
| 77 | IL_54450.1 | 1 | |
| 78 | IL_73367.1 | 1 | |
| 79 | IL_83920.1 | 1 | |
| 80 | IL_92886.1 | 1 | 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 |
| 81 | IL_54696.1 | 1 | 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. |
| 82 | IL_68457.1 | 1 | tSH-inserted-tHS |
| 83 | IL_23302.1 | 1 | |
| 84 | IL_29989.1 | 1 | |
| 85 | IL_43284.1 | 1 | 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) |
| 86 | IL_60649.1 | 1 | Kink-turn |
| 87 | IL_78513.1 | 1 | |
| 88 | IL_49527.1 | 1 | |
| 89 | IL_61352.1 | 1 | |
| 90 | IL_96920.1 | 1 | SSU Helix 12 (h12) IL |
| 91 | IL_25082.1 | 1 | |
| 92 | IL_57079.1 | 1 | |
| 93 | IL_63133.1 | 1 | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 94 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 95 | IL_46151.1 | 1 | Triple Sheared with unpaired, inserted A |
| 96 | IL_57359.1 | 1 | 23S H91 IL |
| 97 | IL_63253.1 | 1 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 98 | IL_72293.1 | 1 | |
| 99 | IL_81398.1 | 1 | |
| 100 | IL_20775.1 | 1 | tSH-inserted |
| 101 | IL_52509.1 | 1 | |
| 102 | IL_72367.1 | 1 | |
| 103 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_48256.1 | 360 | 1-3 bulged nucleotides |
| 2 | IL_92602.1 | 309 | Non-canonical cWW basepair |
| 3 | IL_67828.1 | 61 | 23S H91 IL | Single-Base Intercalation Site | Single, unpaired intercalated base, consensus A | 16S h32-h33-h34 3WJ |
| 4 | IL_81965.1 | 44 | Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW. |
| 5 | IL_82822.1 | 33 | One or more bulged bases |
| 6 | IL_53587.1 | 22 | IL_53587.1 is a mixed group with either one cSW pair or an intercalated base |
| 7 | IL_34098.1 | 19 | cWW with bulged base |
| 8 | IL_68200.1 | 18 | One or more bulged nucleotides |
| 9 | IL_37964.1 | 16 | Recurrent Sub-motif found in junctions |
| 10 | IL_19986.1 | 15 | Pair and triple |
| 11 | IL_67038.1 | 15 | 23S H91 IL | Single-Base Intercalation Site |
| 12 | IL_49203.1 | 14 | Double sheared with wobble cWW. |
| 13 | IL_58261.1 | 14 | SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 14 | IL_18271.1 | 12 | Single, unpaired intercalated base, consensus A | 23S H91 IL |
| 15 | IL_27005.1 | 12 | Non-canonical cWW |
| 16 | IL_89033.1 | 12 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 17 | IL_86933.1 | 11 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 18 | IL_65542.1 | 10 | SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 19 | IL_92122.1 | 10 | |
| 20 | IL_38078.1 | 9 | |
| 21 | IL_12849.1 | 8 | |
| 22 | IL_39212.1 | 8 | |
| 23 | IL_51342.1 | 8 | Non-canonical cWW with inserted stacked base. |
| 24 | IL_32902.1 | 8 | Stacked cWW-cWH pairs |
| 25 | IL_18916.1 | 7 | One or more bulged nucleotides |
| 26 | IL_98016.1 | 7 | One or more bulged nucleotides |
| 27 | IL_01551.1 | 6 | |
| 28 | IL_40053.1 | 6 | |
| 29 | IL_10743.1 | 6 | |
| 30 | IL_31772.1 | 6 | SRP Loop E-like motif | SSU Helix (23) h23 IL1 |
| 31 | IL_51439.1 | 6 | |
| 32 | IL_67399.1 | 6 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 33 | IL_60760.1 | 6 | |
| 34 | IL_77920.1 | 6 | |
| 35 | IL_86694.1 | 5 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 36 | IL_10554.1 | 5 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 37 | IL_37688.1 | 5 | Stacked bases not quite making a basepair. |
| 38 | IL_85010.1 | 5 | 23S H91 IL | Single-Base Intercalation Site |
| 39 | IL_15702.1 | 5 | |
| 40 | IL_59276.1 | 5 | |
| 41 | IL_99363.1 | 5 | |
| 42 | IL_52024.1 | 5 | |
| 43 | IL_72062.1 | 5 | |
| 44 | IL_73281.1 | 4 | Sarcin-like with an intercalated basepair |
| 45 | IL_13023.1 | 4 | |
| 46 | IL_43727.1 | 4 | tSH-inserted-tHS | tHS tHH bulge with S-turn | tSH-inserted-tHS |
| 47 | IL_62615.1 | 4 | cWS plus stacked base |
| 48 | IL_50787.1 | 4 | tSH-tHW-bulge |
| 49 | IL_87899.1 | 4 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 50 | IL_26321.1 | 4 | LSU H58 IL2 H.m. |
| 51 | IL_32508.1 | 4 | 23S H91 IL |
| 52 | IL_45593.1 | 4 | |
| 53 | IL_00520.1 | 4 | |
| 54 | IL_61513.1 | 4 | One or more bulged nucleotides |
| 55 | IL_82600.1 | 3 | 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 |
| 56 | IL_62504.1 | 3 | Triple Sheared with unpaired, inserted A |
| 57 | IL_79398.1 | 3 | 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 |
| 58 | IL_91102.1 | 3 | |
| 59 | IL_01827.1 | 3 | Base triple, intercalated pair, and bulged bases making long-range interactions. |
| 60 | IL_14081.1 | 3 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted |
| 61 | IL_74163.1 | 3 | cWS making long-range triple |
| 62 | IL_19268.1 | 3 | |
| 63 | IL_24955.1 | 3 | |
| 64 | IL_63917.1 | 3 | |
| 65 | IL_22025.1 | 3 | |
| 66 | IL_48070.1 | 3 | C-loop |
| 67 | IL_28028.1 | 2 | |
| 68 | IL_38488.1 | 2 | |
| 69 | IL_43363.1 | 2 | |
| 70 | IL_10119.1 | 2 | |
| 71 | IL_28058.1 | 2 | |
| 72 | IL_68945.1 | 2 | |
| 73 | IL_73348.1 | 2 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 74 | IL_94799.1 | 2 | tHS tHH bulge with S-turn |
| 75 | IL_24583.1 | 2 | |
| 76 | IL_44092.1 | 2 | |
| 77 | IL_79636.1 | 2 | Kink-turn |
| 78 | IL_91942.1 | 2 | |
| 79 | IL_35558.1 | 2 | |
| 80 | IL_44847.1 | 2 | |
| 81 | IL_67005.1 | 2 | |
| 82 | IL_69668.1 | 2 | |
| 83 | IL_06527.1 | 2 | |
| 84 | IL_44977.1 | 2 | LSU H58 IL2 H.m. | SSU Helix (23) h23 IL1 |
| 85 | IL_74462.1 | 2 | |
| 86 | IL_92205.1 | 2 | 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 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 87 | IL_06675.1 | 2 | Triple Sheared with unpaired, inserted A |
| 88 | IL_88416.1 | 2 | |
| 89 | IL_06692.1 | 2 | |
| 90 | IL_21062.1 | 2 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 91 | IL_51576.1 | 2 | |
| 92 | IL_00697.1 | 2 | |
| 93 | IL_64894.1 | 2 | 23S H91 IL | Single-Base Intercalation Site |
| 94 | IL_68034.1 | 2 | |
| 95 | IL_86033.1 | 2 | |
| 96 | IL_09430.1 | 1 | |
| 97 | IL_22601.1 | 1 | |
| 98 | IL_62008.1 | 1 | |
| 99 | IL_78984.1 | 1 | |
| 100 | IL_91061.1 | 1 | |
| 101 | IL_93855.1 | 1 | |
| 102 | IL_01562.1 | 1 | |
| 103 | IL_18506.1 | 1 | |
| 104 | IL_22731.1 | 1 | |
| 105 | IL_34548.1 | 1 | |
| 106 | IL_48268.1 | 1 | |
| 107 | IL_55210.1 | 1 | 1-3 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 |
| 108 | IL_66407.1 | 1 | |
| 109 | IL_29058.1 | 1 | |
| 110 | IL_34816.1 | 1 | |
| 111 | IL_39296.1 | 1 | |
| 112 | IL_57334.1 | 1 | |
| 113 | IL_66775.1 | 1 | |
| 114 | IL_69482.1 | 1 | |
| 115 | IL_84276.1 | 1 | |
| 116 | IL_87168.1 | 1 | |
| 117 | IL_94958.1 | 1 | |
| 118 | IL_03030.1 | 1 | tSH-inserted-tHS |
| 119 | IL_10628.1 | 1 | |
| 120 | IL_14240.1 | 1 | |
| 121 | IL_31160.1 | 1 | |
| 122 | IL_57625.1 | 1 | |
| 123 | IL_62617.1 | 1 | |
| 124 | IL_74400.1 | 1 | |
| 125 | IL_81280.1 | 1 | |
| 126 | IL_84995.1 | 1 | |
| 127 | IL_96591.1 | 1 | |
| 128 | IL_00346.1 | 1 | |
| 129 | IL_15219.1 | 1 | |
| 130 | IL_25808.1 | 1 | |
| 131 | IL_40987.1 | 1 | 23S H91 IL | Single-Base Intercalation Site |
| 132 | IL_63366.1 | 1 | |
| 133 | IL_70069.1 | 1 | tHS tHH bulge with S-turn |
| 134 | IL_81512.1 | 1 | |
| 135 | IL_88263.1 | 1 | |
| 136 | IL_97803.1 | 1 | |
| 137 | IL_00519.1 | 1 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 138 | IL_11268.1 | 1 | |
| 139 | IL_20608.1 | 1 | |
| 140 | IL_41215.1 | 1 | |
| 141 | IL_63723.1 | 1 | |
| 142 | IL_70102.1 | 1 | |
| 143 | IL_76024.1 | 1 | |
| 144 | IL_81587.1 | 1 | |
| 145 | IL_85707.1 | 1 | |
| 146 | IL_11529.1 | 1 | |
| 147 | IL_15813.1 | 1 | |
| 148 | IL_37970.1 | 1 | tHS tHH bulge with S-turn | tSH-inserted-tHS |
| 149 | IL_41371.1 | 1 | |
| 150 | IL_45617.1 | 1 | |
| 151 | IL_72055.1 | 1 | |
| 152 | IL_77862.1 | 1 | |
| 153 | IL_81956.1 | 1 | |
| 154 | IL_85975.1 | 1 | |
| 155 | IL_92957.1 | 1 | |
| 156 | IL_08588.1 | 1 | |
| 157 | IL_11989.1 | 1 | |
| 158 | IL_15884.1 | 1 | |
| 159 | IL_27713.1 | 1 | |
| 160 | IL_33217.1 | 1 | |
| 161 | IL_41920.1 | 1 | |
| 162 | IL_90633.1 | 1 | |
| 163 | IL_92986.1 | 1 |