RNA 3D Hub //

Motif HL_86880.1 Version HL_86880.1 of this group appears in releases 3.3 to 3.11

#SLoop idPDBDisc#Non-coreAnnotationChain(s)Standardized name 1 2 3 4 51-5
1 HL_4Y4O_1394Y4O0.249922A LSU rRNAG1492A1494A1495A1496C1498cWW
2 HL_5J7L_1705J7L0.19532Pseudoknot geometry with 3' bulgeDA LSU rRNAG1492A1494A1495A1496C1498cWW
3 HL_4V8P_1144V8P0.27942Pseudoknot geometry with 3' bulge (H)D1 LSU rRNAA1532C1534A1535A1536U1538cWW
4 HL_5TBW_0325TBW0.24782Pseudoknot geometry with 3' bulge1 LSU rRNAA1506C1508A1509G1510U1512cWW
5 HL_4Y4O_1354Y4O0.079622A LSU rRNAG1324U1326C1327G1328C1330cWW
6 HL_4IOA_0324IOA0.07662X LSU rRNAG1337U1339C1340G1341C1343cWW
7 HL_4WF9_0334WF90.00002Pseudoknot geometry with 3' bulgeX LSU rRNAG1361U1363C1364G1365C1367cWW
8 HL_5J7L_1665J7L0.26042Pseudoknot geometry with 3' bulgeDA LSU rRNAG1324U1326A1327A1328C1330cWW
9 HL_4V9F_0354V9F0.19232Pseudoknot geometry with 3' bulge0 LSU rRNAG1430U1432G1433A1434C1436cWW
10 HL_5VJ9_0035VJ90.49711Pseudoknot geometry with 3' bulgeCRNA (16-mer)G6A7C8G9C11cWW
11 HL_5NDH_0015NDH0.53591Pseudoknot geometry with 3' bulgeARNA (16-mer)G6A7C8G9C11cWW
12 HL_5NEP_0035NEP0.53601ARNA (18-mer)G7||||3_455A8||||3_455C9||||3_455G10||||3_455C12||||3_455cWW
13 HL_5NEP_0025NEP0.53601ARNA (18-mer)G7||||2_565A8||||2_565C9||||2_565G10||||2_565C12||||2_565cWW
14 HL_5NEP_0015NEP0.53601ARNA (18-mer)G7A8C9G10C12cWW
15 HL_5NDI_0025NDI0.53511Pseudoknot geometry with 3' bulgeBRNA (20-mer)G8A9C10G11C13cWW
16 HL_4Y4O_1434Y4O0.624712A LSU rRNAC1631A1631|||AA1632G1633G1635cWW
17 HL_4IOA_0404IOA0.57171X LSU rRNAU1647C1648A1649A1650G1652cWW

3D structures

Complete motif including flanking bases
SequenceCounts
GACGAC6
GCAAAUC2
GGUCGUC2
AGCAAUU1
AGCAGUU1
GCUCGUC1
GUUAAUC1
GCUGAUC1
CAAGAG1
UCAAUG1
Non-Watson-Crick part of the motif
SequenceCounts
ACGA6
CAAAU2
GUCGU2
GCAAU1
GCAGU1
CUCGU1
UUAAU1
CUGAU1
AAGA1
CAAU1

Release history

Release3.33.43.53.63.73.83.93.103.11
Date2018-03-082018-04-062018-05-042018-06-012018-06-292018-07-272018-08-242018-09-212018-10-19
StatusNew id, 1 parentExact matchExact matchExact matchExact matchExact matchExact matchExact matchExact match

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.
Annotations
  • (8)
  • Pseudoknot geometry with 3' bulge (8)
  • Pseudoknot geometry with 3' bulge (H) (1)
    • Basepair signature
    cWW-R-R
    Heat map statistics
    Min 0.06 | Avg 0.41 | Max 0.78
    Help

    Coloring options:

    HL_4Y4O_139:HL_4Y4O_139 = 0HL_4Y4O_139:HL_5J7L_170 = 0.1399HL_4Y4O_139:HL_4V8P_114 = 0.2252HL_4Y4O_139:HL_5TBW_032 = 0.2394HL_4Y4O_139:HL_4Y4O_135 = 0.2629HL_4Y4O_139:HL_4IOA_032 = 0.2585HL_4Y4O_139:HL_4WF9_033 = 0.2499HL_4Y4O_139:HL_5J7L_166 = 0.4315HL_4Y4O_139:HL_4V9F_035 = 0.3543HL_4Y4O_139:HL_5VJ9_003 = 0.5442HL_4Y4O_139:HL_5NDH_001 = 0.5656HL_4Y4O_139:HL_5NEP_003 = 0.5732HL_4Y4O_139:HL_5NEP_002 = 0.5732HL_4Y4O_139:HL_5NEP_001 = 0.5732HL_4Y4O_139:HL_5NDI_002 = 0.5876HL_4Y4O_139:HL_4Y4O_143 = 0.6835HL_4Y4O_139:HL_4IOA_040 = 0.6085HL_5J7L_170:HL_4Y4O_139 = 0.1399HL_5J7L_170:HL_5J7L_170 = 0HL_5J7L_170:HL_4V8P_114 = 0.1984HL_5J7L_170:HL_5TBW_032 = 0.2076HL_5J7L_170:HL_4Y4O_135 = 0.2107HL_5J7L_170:HL_4IOA_032 = 0.2019HL_5J7L_170:HL_4WF9_033 = 0.1953HL_5J7L_170:HL_5J7L_166 = 0.4003HL_5J7L_170:HL_4V9F_035 = 0.307HL_5J7L_170:HL_5VJ9_003 = 0.5235HL_5J7L_170:HL_5NDH_001 = 0.5469HL_5J7L_170:HL_5NEP_003 = 0.5549HL_5J7L_170:HL_5NEP_002 = 0.5549HL_5J7L_170:HL_5NEP_001 = 0.5549HL_5J7L_170:HL_5NDI_002 = 0.5672HL_5J7L_170:HL_4Y4O_143 = 0.6826HL_5J7L_170:HL_4IOA_040 = 0.5973HL_4V8P_114:HL_4Y4O_139 = 0.2252HL_4V8P_114:HL_5J7L_170 = 0.1984HL_4V8P_114:HL_4V8P_114 = 0HL_4V8P_114:HL_5TBW_032 = 0.2026HL_4V8P_114:HL_4Y4O_135 = 0.2682HL_4V8P_114:HL_4IOA_032 = 0.2717HL_4V8P_114:HL_4WF9_033 = 0.2794HL_4V8P_114:HL_5J7L_166 = 0.4546HL_4V8P_114:HL_4V9F_035 = 0.3619HL_4V8P_114:HL_5VJ9_003 = 0.5959HL_4V8P_114:HL_5NDH_001 = 0.6202HL_4V8P_114:HL_5NEP_003 = 0.6298HL_4V8P_114:HL_5NEP_002 = 0.6298HL_4V8P_114:HL_5NEP_001 = 0.6298HL_4V8P_114:HL_5NDI_002 = 0.6569HL_4V8P_114:HL_4Y4O_143 = 0.7732HL_4V8P_114:HL_4IOA_040 = 0.6815HL_5TBW_032:HL_4Y4O_139 = 0.2394HL_5TBW_032:HL_5J7L_170 = 0.2076HL_5TBW_032:HL_4V8P_114 = 0.2026HL_5TBW_032:HL_5TBW_032 = 0HL_5TBW_032:HL_4Y4O_135 = 0.2204HL_5TBW_032:HL_4IOA_032 = 0.2231HL_5TBW_032:HL_4WF9_033 = 0.2478HL_5TBW_032:HL_5J7L_166 = 0.4016HL_5TBW_032:HL_4V9F_035 = 0.3456HL_5TBW_032:HL_5VJ9_003 = 0.625HL_5TBW_032:HL_5NDH_001 = 0.6591HL_5TBW_032:HL_5NEP_003 = 0.6738HL_5TBW_032:HL_5NEP_002 = 0.6738HL_5TBW_032:HL_5NEP_001 = 0.6738HL_5TBW_032:HL_5NDI_002 = 0.6872HL_5TBW_032:HL_4Y4O_143 = 0.7815HL_5TBW_032:HL_4IOA_040 = 0.6629HL_4Y4O_135:HL_4Y4O_139 = 0.2629HL_4Y4O_135:HL_5J7L_170 = 0.2107HL_4Y4O_135:HL_4V8P_114 = 0.2682HL_4Y4O_135:HL_5TBW_032 = 0.2204HL_4Y4O_135:HL_4Y4O_135 = 0HL_4Y4O_135:HL_4IOA_032 = 0.0633HL_4Y4O_135:HL_4WF9_033 = 0.0796HL_4Y4O_135:HL_5J7L_166 = 0.2773HL_4Y4O_135:HL_4V9F_035 = 0.2371HL_4Y4O_135:HL_5VJ9_003 = 0.543HL_4Y4O_135:HL_5NDH_001 = 0.5804HL_4Y4O_135:HL_5NEP_003 = 0.5834HL_4Y4O_135:HL_5NEP_002 = 0.5834HL_4Y4O_135:HL_5NEP_001 = 0.5834HL_4Y4O_135:HL_5NDI_002 = 0.5817HL_4Y4O_135:HL_4Y4O_143 = 0.6772HL_4Y4O_135:HL_4IOA_040 = 0.6093HL_4IOA_032:HL_4Y4O_139 = 0.2585HL_4IOA_032:HL_5J7L_170 = 0.2019HL_4IOA_032:HL_4V8P_114 = 0.2717HL_4IOA_032:HL_5TBW_032 = 0.2231HL_4IOA_032:HL_4Y4O_135 = 0.0633HL_4IOA_032:HL_4IOA_032 = 0HL_4IOA_032:HL_4WF9_033 = 0.0766HL_4IOA_032:HL_5J7L_166 = 0.2681HL_4IOA_032:HL_4V9F_035 = 0.2366HL_4IOA_032:HL_5VJ9_003 = 0.5475HL_4IOA_032:HL_5NDH_001 = 0.5835HL_4IOA_032:HL_5NEP_003 = 0.5861HL_4IOA_032:HL_5NEP_002 = 0.5861HL_4IOA_032:HL_5NEP_001 = 0.5861HL_4IOA_032:HL_5NDI_002 = 0.5846HL_4IOA_032:HL_4Y4O_143 = 0.6705HL_4IOA_032:HL_4IOA_040 = 0.6017HL_4WF9_033:HL_4Y4O_139 = 0.2499HL_4WF9_033:HL_5J7L_170 = 0.1953HL_4WF9_033:HL_4V8P_114 = 0.2794HL_4WF9_033:HL_5TBW_032 = 0.2478HL_4WF9_033:HL_4Y4O_135 = 0.0796HL_4WF9_033:HL_4IOA_032 = 0.0766HL_4WF9_033:HL_4WF9_033 = 0HL_4WF9_033:HL_5J7L_166 = 0.2604HL_4WF9_033:HL_4V9F_035 = 0.1923HL_4WF9_033:HL_5VJ9_003 = 0.4971HL_4WF9_033:HL_5NDH_001 = 0.5359HL_4WF9_033:HL_5NEP_003 = 0.536HL_4WF9_033:HL_5NEP_002 = 0.536HL_4WF9_033:HL_5NEP_001 = 0.536HL_4WF9_033:HL_5NDI_002 = 0.5351HL_4WF9_033:HL_4Y4O_143 = 0.6247HL_4WF9_033:HL_4IOA_040 = 0.5717HL_5J7L_166:HL_4Y4O_139 = 0.4315HL_5J7L_166:HL_5J7L_170 = 0.4003HL_5J7L_166:HL_4V8P_114 = 0.4546HL_5J7L_166:HL_5TBW_032 = 0.4016HL_5J7L_166:HL_4Y4O_135 = 0.2773HL_5J7L_166:HL_4IOA_032 = 0.2681HL_5J7L_166:HL_4WF9_033 = 0.2604HL_5J7L_166:HL_5J7L_166 = 0HL_5J7L_166:HL_4V9F_035 = 0.2101HL_5J7L_166:HL_5VJ9_003 = 0.6056HL_5J7L_166:HL_5NDH_001 = 0.6705HL_5J7L_166:HL_5NEP_003 = 0.656HL_5J7L_166:HL_5NEP_002 = 0.656HL_5J7L_166:HL_5NEP_001 = 0.656HL_5J7L_166:HL_5NDI_002 = 0.6368HL_5J7L_166:HL_4Y4O_143 = 0.648HL_5J7L_166:HL_4IOA_040 = 0.6123HL_4V9F_035:HL_4Y4O_139 = 0.3543HL_4V9F_035:HL_5J7L_170 = 0.307HL_4V9F_035:HL_4V8P_114 = 0.3619HL_4V9F_035:HL_5TBW_032 = 0.3456HL_4V9F_035:HL_4Y4O_135 = 0.2371HL_4V9F_035:HL_4IOA_032 = 0.2366HL_4V9F_035:HL_4WF9_033 = 0.1923HL_4V9F_035:HL_5J7L_166 = 0.2101HL_4V9F_035:HL_4V9F_035 = 0HL_4V9F_035:HL_5VJ9_003 = 0.4443HL_4V9F_035:HL_5NDH_001 = 0.5114HL_4V9F_035:HL_5NEP_003 = 0.5027HL_4V9F_035:HL_5NEP_002 = 0.5027HL_4V9F_035:HL_5NEP_001 = 0.5027HL_4V9F_035:HL_5NDI_002 = 0.4976HL_4V9F_035:HL_4Y4O_143 = 0.5721HL_4V9F_035:HL_4IOA_040 = 0.551HL_5VJ9_003:HL_4Y4O_139 = 0.5442HL_5VJ9_003:HL_5J7L_170 = 0.5235HL_5VJ9_003:HL_4V8P_114 = 0.5959HL_5VJ9_003:HL_5TBW_032 = 0.625HL_5VJ9_003:HL_4Y4O_135 = 0.543HL_5VJ9_003:HL_4IOA_032 = 0.5475HL_5VJ9_003:HL_4WF9_033 = 0.4971HL_5VJ9_003:HL_5J7L_166 = 0.6056HL_5VJ9_003:HL_4V9F_035 = 0.4443HL_5VJ9_003:HL_5VJ9_003 = 0HL_5VJ9_003:HL_5NDH_001 = 0.1088HL_5VJ9_003:HL_5NEP_003 = 0.1096HL_5VJ9_003:HL_5NEP_002 = 0.1096HL_5VJ9_003:HL_5NEP_001 = 0.1096HL_5VJ9_003:HL_5NDI_002 = 0.1215HL_5VJ9_003:HL_4Y4O_143 = 0.4189HL_5VJ9_003:HL_4IOA_040 = 0.4745HL_5NDH_001:HL_4Y4O_139 = 0.5656HL_5NDH_001:HL_5J7L_170 = 0.5469HL_5NDH_001:HL_4V8P_114 = 0.6202HL_5NDH_001:HL_5TBW_032 = 0.6591HL_5NDH_001:HL_4Y4O_135 = 0.5804HL_5NDH_001:HL_4IOA_032 = 0.5835HL_5NDH_001:HL_4WF9_033 = 0.5359HL_5NDH_001:HL_5J7L_166 = 0.6705HL_5NDH_001:HL_4V9F_035 = 0.5114HL_5NDH_001:HL_5VJ9_003 = 0.1088HL_5NDH_001:HL_5NDH_001 = 0HL_5NDH_001:HL_5NEP_003 = 0.0658HL_5NDH_001:HL_5NEP_002 = 0.0658HL_5NDH_001:HL_5NEP_001 = 0.0658HL_5NDH_001:HL_5NDI_002 = 0.1226HL_5NDH_001:HL_4Y4O_143 = 0.4648HL_5NDH_001:HL_4IOA_040 = 0.5141HL_5NEP_003:HL_4Y4O_139 = 0.5732HL_5NEP_003:HL_5J7L_170 = 0.5549HL_5NEP_003:HL_4V8P_114 = 0.6298HL_5NEP_003:HL_5TBW_032 = 0.6738HL_5NEP_003:HL_4Y4O_135 = 0.5834HL_5NEP_003:HL_4IOA_032 = 0.5861HL_5NEP_003:HL_4WF9_033 = 0.536HL_5NEP_003:HL_5J7L_166 = 0.656HL_5NEP_003:HL_4V9F_035 = 0.5027HL_5NEP_003:HL_5VJ9_003 = 0.1096HL_5NEP_003:HL_5NDH_001 = 0.0658HL_5NEP_003:HL_5NEP_003 = 0HL_5NEP_003:HL_5NEP_002 = 0HL_5NEP_003:HL_5NEP_001 = 0HL_5NEP_003:HL_5NDI_002 = 0.0858HL_5NEP_003:HL_4Y4O_143 = 0.4358HL_5NEP_003:HL_4IOA_040 = 0.503HL_5NEP_002:HL_4Y4O_139 = 0.5732HL_5NEP_002:HL_5J7L_170 = 0.5549HL_5NEP_002:HL_4V8P_114 = 0.6298HL_5NEP_002:HL_5TBW_032 = 0.6738HL_5NEP_002:HL_4Y4O_135 = 0.5834HL_5NEP_002:HL_4IOA_032 = 0.5861HL_5NEP_002:HL_4WF9_033 = 0.536HL_5NEP_002:HL_5J7L_166 = 0.656HL_5NEP_002:HL_4V9F_035 = 0.5027HL_5NEP_002:HL_5VJ9_003 = 0.1096HL_5NEP_002:HL_5NDH_001 = 0.0658HL_5NEP_002:HL_5NEP_003 = 0HL_5NEP_002:HL_5NEP_002 = 0HL_5NEP_002:HL_5NEP_001 = 0HL_5NEP_002:HL_5NDI_002 = 0.0858HL_5NEP_002:HL_4Y4O_143 = 0.4358HL_5NEP_002:HL_4IOA_040 = 0.503HL_5NEP_001:HL_4Y4O_139 = 0.5732HL_5NEP_001:HL_5J7L_170 = 0.5549HL_5NEP_001:HL_4V8P_114 = 0.6298HL_5NEP_001:HL_5TBW_032 = 0.6738HL_5NEP_001:HL_4Y4O_135 = 0.5834HL_5NEP_001:HL_4IOA_032 = 0.5861HL_5NEP_001:HL_4WF9_033 = 0.536HL_5NEP_001:HL_5J7L_166 = 0.656HL_5NEP_001:HL_4V9F_035 = 0.5027HL_5NEP_001:HL_5VJ9_003 = 0.1096HL_5NEP_001:HL_5NDH_001 = 0.0658HL_5NEP_001:HL_5NEP_003 = 0HL_5NEP_001:HL_5NEP_002 = 0HL_5NEP_001:HL_5NEP_001 = 0HL_5NEP_001:HL_5NDI_002 = 0.0858HL_5NEP_001:HL_4Y4O_143 = 0.4358HL_5NEP_001:HL_4IOA_040 = 0.503HL_5NDI_002:HL_4Y4O_139 = 0.5876HL_5NDI_002:HL_5J7L_170 = 0.5672HL_5NDI_002:HL_4V8P_114 = 0.6569HL_5NDI_002:HL_5TBW_032 = 0.6872HL_5NDI_002:HL_4Y4O_135 = 0.5817HL_5NDI_002:HL_4IOA_032 = 0.5846HL_5NDI_002:HL_4WF9_033 = 0.5351HL_5NDI_002:HL_5J7L_166 = 0.6368HL_5NDI_002:HL_4V9F_035 = 0.4976HL_5NDI_002:HL_5VJ9_003 = 0.1215HL_5NDI_002:HL_5NDH_001 = 0.1226HL_5NDI_002:HL_5NEP_003 = 0.0858HL_5NDI_002:HL_5NEP_002 = 0.0858HL_5NDI_002:HL_5NEP_001 = 0.0858HL_5NDI_002:HL_5NDI_002 = 0HL_5NDI_002:HL_4Y4O_143 = 0.4008HL_5NDI_002:HL_4IOA_040 = 0.4852HL_4Y4O_143:HL_4Y4O_139 = 0.6835HL_4Y4O_143:HL_5J7L_170 = 0.6826HL_4Y4O_143:HL_4V8P_114 = 0.7732HL_4Y4O_143:HL_5TBW_032 = 0.7815HL_4Y4O_143:HL_4Y4O_135 = 0.6772HL_4Y4O_143:HL_4IOA_032 = 0.6705HL_4Y4O_143:HL_4WF9_033 = 0.6247HL_4Y4O_143:HL_5J7L_166 = 0.648HL_4Y4O_143:HL_4V9F_035 = 0.5721HL_4Y4O_143:HL_5VJ9_003 = 0.4189HL_4Y4O_143:HL_5NDH_001 = 0.4648HL_4Y4O_143:HL_5NEP_003 = 0.4358HL_4Y4O_143:HL_5NEP_002 = 0.4358HL_4Y4O_143:HL_5NEP_001 = 0.4358HL_4Y4O_143:HL_5NDI_002 = 0.4008HL_4Y4O_143:HL_4Y4O_143 = 0HL_4Y4O_143:HL_4IOA_040 = 0.3013HL_4IOA_040:HL_4Y4O_139 = 0.6085HL_4IOA_040:HL_5J7L_170 = 0.5973HL_4IOA_040:HL_4V8P_114 = 0.6815HL_4IOA_040:HL_5TBW_032 = 0.6629HL_4IOA_040:HL_4Y4O_135 = 0.6093HL_4IOA_040:HL_4IOA_032 = 0.6017HL_4IOA_040:HL_4WF9_033 = 0.5717HL_4IOA_040:HL_5J7L_166 = 0.6123HL_4IOA_040:HL_4V9F_035 = 0.551HL_4IOA_040:HL_5VJ9_003 = 0.4745HL_4IOA_040:HL_5NDH_001 = 0.5141HL_4IOA_040:HL_5NEP_003 = 0.503HL_4IOA_040:HL_5NEP_002 = 0.503HL_4IOA_040:HL_5NEP_001 = 0.503HL_4IOA_040:HL_5NDI_002 = 0.4852HL_4IOA_040:HL_4Y4O_143 = 0.3013HL_4IOA_040:HL_4IOA_040 = 0HL_4Y4O_139HL_5J7L_170HL_4V8P_114HL_5TBW_032HL_4Y4O_135HL_4IOA_032HL_4WF9_033HL_5J7L_166HL_4V9F_035HL_5VJ9_003HL_5NDH_001HL_5NEP_003HL_5NEP_002HL_5NEP_001HL_5NDI_002HL_4Y4O_143HL_4IOA_040Discrepancy0.000.200.400.60
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