#SLoop idPDBDisc#Non-coreAnnotationChain(s)Standardized name 1 2break 3 41-42-33-4
1 IL_1KXK_0011KXK0.00002Aai5g group II Self-splicing intronU8C11*G61G62cWWcWW
2 IL_1MJI_0011MJI0.23072C5S rRNA fragmentG51G54*C30C31cWWcWW
3 IL_2NZ4_0042NZ40.30791F+Qsubstrate strand RNA 13-mer + GlmS ribozymeC5G7*C52G53cWWcWW
4 IL_2QUX_0012QUX0.35311CRNA (25-MER)C20G21*C5G7cWWcWW
5 IL_1S72_0421S720.36311Single bulged G (H)0 LSU rRNAC1225G1226*U1136G1138cWWcWW
6 IL_2QUX_0022QUX0.35451Single bulged AFRNA (25-MER)C20G21*C5G7cWWcWW
7 IL_3B31_0013B310.35981ARNA (29-MER)C6194G6195*C6181G6183cWWcWW
8 IL_1U9S_0061U9S0.36321Major groove intercalationARIBONUCLEASE PU158C160*G140G141ncWWcWW
9 IL_3G78_0043G780.40771AGroup II catalytic intron D1-D4-1A99A100*U82U84cWWcWW
10 IL_1U9S_0031U9S0.36402Major groove outside cWW, minor groove, intercalation pocketARIBONUCLEASE PC224A227*U116G117cWWcWW
11 IL_1FJG_0351FJG0.34311Single bulged A (H)A SSU rRNAG922A923*U1393C1395cWWcWW
12 IL_2QUX_0052QUX0.34291ORNA (25-MER)C20G21*C5G7cWWcWW
13 IL_1F7Y_0021F7Y0.37231B16S RIBOSOMAL RNA FRAGMENTG21G22*C46C48cWWcWW
14 IL_3D0U_0053D0U0.37681Single bulged GALysine Riboswitch RNAC81G82*U106G108ncWWcWW
15 IL_1S72_0961S720.51001Single bulged A (H)0 LSU rRNAG2860G2861*C2895C2897cWWcWW
16 IL_3DIR_0053DIR0.49921ARNA (174-MER)G84G85*U109C111cWWcWW
17 IL_1S72_0671S720.37632Major groove outside cWW, minor groove, intercalation pocket (H)0 LSU rRNAU1897G1898*U1939A1942cWWcWW
18 IL_1FJG_0051FJG0.34062Multiple bulged bases (H)A SSU rRNAC63G66*C103G104cWWcWW
19 IL_3F1H_0593F1H0.27901A23S RRNAU1489G1491*C1499G1500cWWcWW
20 IL_2NZ4_0072NZ40.32311G+Rsubstrate strand RNA 13-mer + GlmS ribozymeC5G7*C52G53cWWcWW
21 IL_1KXK_0031KXK0.82292Multiple bulged basesAai5g group II Self-splicing intronC42G45*U28G29cWWcWW
22 IL_3MUR_0043MUR0.75852RC92U mutant c-di-GMP riboswitchG56G57*U81C84cWWcWW
23 IL_3HHN_0013HHN0.75111CClass I ligase ribozyme, self-ligation productA112C113*G46U48cWWcWW
24 IL_3MEI_0013MEI0.71081Single bulged UA+BRNA (23-mer)C7G8*C15G17cWWcWW
25 IL_2ZY6_0022ZY60.59181Single bulged UAphenylalanyl transfer RNAG10G12*C24C25cWWcWW
26 IL_2QUX_0042QUX0.72191LRNA (25-MER)C5G7*C20G21cWWcWW
27 IL_1FUF_0031FUF0.72902Multiple bulged basesA+BRNA (14-mer)G9G10*U19C22cWWcWW
28 IL_1FUF_0021FUF0.69432Multiple bulged basesB+ARNA (14-mer)G23G24*U5C8cWWcWW
29 IL_3F1H_0323F1H0.70221A23S RRNAG880G881*U895C897cWWcWW
30 IL_2QUX_0062QUX0.69961RRNA (25-MER)C20G21*C5G7cWWcWW
31 IL_1FJG_0071FJG0.63902Multiple bulged bases (H)A SSU rRNAG231G232*U129C131cWWcWW
32 IL_2ZJR_0932ZJR0.62041X LSU rRNAC2570G2571*C2580G2582cWWcWW
33 IL_3F1H_0873F1H0.49591A23S RRNAU2401C2403*G2414G2415cWWcWW
34 IL_2PN4_0032PN40.53231B+ARNA (20-mer)G105G107*U61C62cWWcWW
35 IL_1ET4_0081ET40.56321DRNA APTAMER, 35-MERG526G528*C518C519cWWcWW
36 IL_2IPY_0032IPY0.55851Cferritin IRE RNAG18U20*A13C14cWWcWW
37 IL_2IPY_0062IPY0.55731Dferritin IRE RNAG18U20*A13C14cWWcWW
38 IL_3MUR_0033MUR0.57181RC92U mutant c-di-GMP riboswitchC52C54*G86G87cWWcWW
39 IL_1ET4_0021ET40.55241Major groove intercalationARNA APTAMER, 35-MERG226G228*C218C219cWWcWW
40 IL_1MJI_0031MJI0.59532Multiple bulged basesD5S rRNA fragmentG51G54*C30C31cWWcWW
41 IL_1GID_0051GID0.53621AP4-P6 RNA RIBOZYME DOMAING129U131*A192C193cWWcWW
42 IL_2PN4_0082PN40.51421D+CRNA (20-mer)G105G107*U61C62cWWcWW
43 IL_1S72_0101S720.53701Single bulged G (H)0 LSU rRNAG274G275*U374C376cWWcWW
44 IL_1ET4_0041ET40.61221BRNA APTAMER, 35-MERG326G328*C318C319cWWcWW
45 IL_1JZV_0021JZV0.81241Single bulged AB+ARNA (9-mer)U12C14*G4A5cWWcWW
46 IL_1S72_0881S720.820410 LSU rRNAC2626G2627*C2636G2638cWWcWW
47 IL_1FJG_0161FJG0.78411A SSU rRNAU375G376*U387A389cWWcWW
48 IL_1S72_0641S720.80721Single bulged A (H)0 LSU rRNAC1826G1827*C2021G2023cWWcWW
49 IL_2QUX_0032QUX0.66601IRNA (25-MER)C20G21*C5G7cWWcWW
50 IL_2ZJR_0312ZJR0.97401Single bulged C (H)X LSU rRNAU1170A1171*U1005A1007cWWncWWncWH
51 IL_1S72_0451S720.97972Bulged stacked bases (H)0 LSU rRNAA1286C1289*G1269U1270cWWcWW

3D structures

Complete motif including flanking bases
SequenceCounts
CG*CAG9
GUG*CC4
CAG*CG3
GUU*AC3
GAAG*CC2
CG*UGG2
GG*UGC2
GG*UUUC2
GUG*UC2
UAUC*GG1
UGC*GG1
AA*UGU1
CAAA*UG1
GA*UAC1
GG*CCC1
GG*CAC1
UG*UCAA1
CGUG*CG1
UAG*CG1
CACG*UG1
GG*UAGC1
AC*GCU1
CG*CUG1
GG*UAC1
GG*UGAC1
UCC*GG1
CUC*GG1
UAC*GA1
UG*UGA1
UA*UCA1
AAUC*GU1
Non-Watson-Crick part of the motif
SequenceCounts
*A12
U*10
*G6
A*5
AA*3
*C3
AU*2
*UU2
G*1
*CA1
GU*1
AC*1
*AG1
*U1
*GA1
C*1

Release history

Release0.3
Date2011-12-08
StatusNew id, 2 parents

Parent motifs

Parent motifCommon motif instancesOnly in IL_79986.1Only in the parent motif
IL_63653.1
Compare
IL_2PN4_008, IL_3F1H_087, IL_1ET4_004, IL_2QUX_002, IL_2NZ4_007, IL_2PN4_003, IL_2ZJR_031, IL_1FJG_005, IL_1FJG_007, IL_1MJI_001, IL_1MJI_003, IL_3G78_004, IL_1S72_088, IL_1S72_064, IL_1S72_067, IL_3F1H_032, IL_1S72_042, IL_3MEI_001, IL_1U9S_006, IL_3D0U_005, IL_1U9S_003, IL_3F1H_059, IL_2IPY_003, IL_2NZ4_004, IL_2IPY_006, IL_1KXK_003, IL_1FJG_035, IL_2QUX_004, IL_2QUX_005, IL_2QUX_006, IL_1JZV_002, IL_2QUX_001, IL_1ET4_008, IL_2QUX_003, IL_1GID_005, IL_1ET4_002, IL_3DIR_005, IL_1FUF_002, IL_1FUF_003, IL_1S72_096, IL_1FJG_016, IL_1S72_010, IL_3MUR_003, IL_3MUR_004, IL_2ZJR_093, IL_1F7Y_002, IL_3B31_001, IL_3HHN_001, IL_2ZY6_002IL_1S72_045, IL_1KXK_001IL_1S72_026, IL_2ZJR_011, IL_2ZJR_016, IL_2ZJR_015, IL_2C50_002, IL_2C50_001, IL_3D2V_004, IL_3D2V_001, IL_1S72_040, IL_3F1H_077, IL_3F1H_073, IL_2ZJR_065, IL_2IPY_002, IL_2IPY_001, IL_2IPY_004, IL_2IPY_005, IL_2ZJR_002, IL_3F1H_098, IL_1GID_009, IL_1GID_002, IL_1S72_014, IL_3F1H_066, IL_2ZJR_091, IL_2ZJR_098, IL_1DUQ_004, IL_2NOK_006, IL_1I9X_001, IL_2NOK_003, IL_1I9X_002, IL_2OZB_001, IL_2ZJR_034, IL_1FJG_040, IL_1FJG_043, IL_1GID_012, IL_2PLY_002, IL_1S72_104, IL_3F1H_018, IL_6MSF_001, IL_1U9S_001, IL_2OIU_003, IL_2OIU_001, IL_2ZJR_024, IL_2C4Z_002, IL_2C4Z_001, IL_1S72_077, IL_1S72_074, IL_1S72_070, IL_3F1H_002, IL_3OWZ_005, IL_3OWZ_001, IL_2BQ5_002, IL_2ZJR_056, IL_2BQ5_001, IL_2BU1_002, IL_2BU1_001, IL_1DUQ_002, IL_1S72_086, IL_1DUQ_006, IL_1DUQ_008, IL_3F1H_034, IL_3F1H_037, IL_2GIS_001, IL_1S72_002, IL_3D0U_001, IL_2IZN_002, IL_2IZN_001, IL_2IZM_001, IL_2IZM_002, IL_1S72_093, IL_3G78_015, IL_2PJP_001, IL_3DIR_001, IL_1S03_002, IL_1S03_001, IL_1S03_006, IL_1S03_005, IL_1R3E_001, IL_1R3E_002, IL_3F1H_103, IL_2IZ9_001, IL_2IZ9_002, IL_1FJG_001, IL_1FJG_002, IL_397D_001, IL_2VPL_005, IL_1S72_027, IL_1CSL_002, IL_2VPL_002, IL_1DQH_001, IL_1FJG_036, IL_1JZV_005, IL_1S72_030, IL_2PLY_001, IL_3F1H_019, IL_1FJG_014, IL_3F1H_046, IL_2ZJR_072, IL_3HHN_003, IL_2ZJR_076
IL_21500.1
Compare
IL_1KXK_001, IL_1S72_045IL_2PN4_008, IL_3F1H_087, IL_1ET4_004, IL_2QUX_002, IL_2NZ4_007, IL_2PN4_003, IL_2ZJR_031, IL_1FJG_005, IL_1FJG_007, IL_1MJI_001, IL_1MJI_003, IL_3G78_004, IL_1S72_088, IL_1S72_064, IL_1S72_067, IL_3F1H_032, IL_1S72_042, IL_3MEI_001, IL_1U9S_006, IL_3D0U_005, IL_1U9S_003, IL_3F1H_059, IL_2IPY_003, IL_2NZ4_004, IL_2IPY_006, IL_1KXK_003, IL_1FJG_035, IL_2QUX_004, IL_2QUX_005, IL_2QUX_006, IL_1JZV_002, IL_2QUX_001, IL_1ET4_008, IL_2QUX_003, IL_1GID_005, IL_1ET4_002, IL_3DIR_005, IL_1FUF_002, IL_1FUF_003, IL_1S72_096, IL_1FJG_016, IL_1S72_010, IL_3MUR_003, IL_3MUR_004, IL_2ZJR_093, IL_1F7Y_002, IL_3B31_001, IL_3HHN_001, IL_2ZY6_002

Children motifs

Child motifCommon motif instancesOnly in IL_79986.1Only in the child motif
IL_89723.1
Compare
IL_3F1H_087, IL_1S72_096, IL_1FJG_005, IL_1FJG_007, IL_1MJI_001, IL_1MJI_003, IL_3G78_004, IL_1S72_064, IL_1S72_067, IL_3F1H_032, IL_1S72_042, IL_1U9S_006, IL_3D0U_005, IL_1U9S_003, IL_3F1H_059, IL_2NZ4_007, IL_2NZ4_004, IL_1KXK_003, IL_2QUX_004, IL_1FJG_016, IL_2QUX_006, IL_2QUX_001, IL_2QUX_002, IL_2QUX_003, IL_3B31_001, IL_3DIR_005, IL_1FUF_002, IL_1FUF_003, IL_2QUX_005, IL_1S72_010, IL_3MUR_003, IL_3MUR_004IL_2PN4_008, IL_2IPY_003, IL_1S72_045, IL_2IPY_006, IL_3MEI_001, IL_1FJG_035, IL_1KXK_001, IL_2PN4_003, IL_2ZJR_031, IL_1F7Y_002, IL_2ZJR_093, IL_1JZV_002, IL_1ET4_008, IL_1GID_005, IL_1S72_088, IL_1ET4_002, IL_1ET4_004, IL_3HHN_001, IL_2ZY6_002IL_2OZB_001, IL_2IPY_001, IL_2IPY_004, IL_1S72_022
IL_96481.1
Compare
IL_2PN4_008, IL_1S72_045, IL_3MEI_001, IL_1KXK_001, IL_2PN4_003, IL_2ZJR_031, IL_1F7Y_002, IL_2ZJR_093, IL_1JZV_002, IL_1ET4_008, IL_1GID_005, IL_1S72_088, IL_1ET4_002, IL_1ET4_004, IL_2ZY6_002IL_3F1H_087, IL_1S72_096, IL_2IPY_003, IL_1FJG_005, IL_1FJG_007, IL_1MJI_001, IL_1MJI_003, IL_3G78_004, IL_1S72_064, IL_1S72_067, IL_3F1H_032, IL_1S72_042, IL_1U9S_006, IL_3D0U_005, IL_1U9S_003, IL_3F1H_059, IL_2NZ4_007, IL_2NZ4_004, IL_2IPY_006, IL_1KXK_003, IL_1FJG_035, IL_2QUX_004, IL_1FJG_016, IL_2QUX_006, IL_2QUX_001, IL_2QUX_002, IL_2QUX_003, IL_3B31_001, IL_3DIR_005, IL_1FUF_002, IL_1FUF_003, IL_2QUX_005, IL_1S72_010, IL_3MUR_003, IL_3MUR_004, IL_3HHN_001IL_1I9X_002, IL_2BU1_001, IL_1FJG_001, IL_1FJG_040, IL_2C50_002, IL_2C50_001, IL_3D2V_004, IL_3D2V_001, IL_3F1H_034, IL_2PLY_001, IL_2GIS_001, IL_2VPL_002, IL_1DQH_001, IL_1S03_006, IL_1FJG_036, IL_1JZV_005, IL_2C4Z_002, IL_1GID_009, IL_1S72_077, IL_3F1H_098, IL_1GID_002, IL_2PLY_002, IL_1S03_002, IL_1S72_104
IL_40289.2
Compare
IL_1FJG_035, IL_3HHN_001IL_2PN4_008, IL_3F1H_087, IL_1ET4_004, IL_2QUX_002, IL_2IPY_003, IL_2PN4_003, IL_2ZJR_031, IL_1FJG_005, IL_1FJG_007, IL_1MJI_001, IL_1MJI_003, IL_3G78_004, IL_1S72_088, IL_1S72_064, IL_1S72_067, IL_1S72_045, IL_3F1H_032, IL_1S72_042, IL_3MEI_001, IL_1U9S_006, IL_3D0U_005, IL_1U9S_003, IL_1ET4_008, IL_3F1H_059, IL_2NZ4_007, IL_2NZ4_004, IL_2IPY_006, IL_1KXK_003, IL_1KXK_001, IL_2QUX_004, IL_1FJG_016, IL_2QUX_006, IL_1JZV_002, IL_2QUX_001, IL_1S72_096, IL_2QUX_003, IL_1GID_005, IL_1ET4_002, IL_3DIR_005, IL_1FUF_002, IL_1FUF_003, IL_2QUX_005, IL_1S72_010, IL_3MUR_003, IL_3MUR_004, IL_2ZJR_093, IL_1F7Y_002, IL_3B31_001, IL_2ZY6_002IL_2ZJR_056, IL_1S72_014, IL_2ZJR_011, IL_2ZJR_016, IL_1DUQ_002, IL_1DUQ_004, IL_1FJG_002, IL_1DUQ_006, IL_1DUQ_008, IL_1GID_012, IL_3OWZ_005, IL_3F1H_037, IL_1S72_002, IL_1S72_027, IL_1S72_026, IL_1U9S_001, IL_2OIU_003, IL_3F1H_073, IL_2ZJR_065, IL_2IPY_002, IL_2OIU_001, IL_2ZJR_068, IL_2ZJR_024, IL_2IPY_005, IL_2ZJR_002, IL_2PJP_001, IL_1S72_099, IL_1S72_070, IL_3F1H_019, IL_3F1H_066, IL_3F1H_002, IL_3F1H_105, IL_3F1H_046, IL_1CSL_002, IL_2ZJR_072, IL_3HHN_003
IL_89429.1
Compare
IL_2IPY_003, IL_2IPY_006IL_2PN4_008, IL_3F1H_087, IL_1ET4_004, IL_2QUX_002, IL_2PN4_003, IL_2ZJR_031, IL_1FJG_005, IL_1FJG_007, IL_1MJI_001, IL_1MJI_003, IL_3G78_004, IL_1S72_088, IL_1S72_064, IL_1S72_067, IL_1S72_045, IL_3F1H_032, IL_1S72_042, IL_3MEI_001, IL_1U9S_006, IL_3D0U_005, IL_1U9S_003, IL_1ET4_008, IL_3F1H_059, IL_2NZ4_007, IL_2NZ4_004, IL_1KXK_003, IL_1KXK_001, IL_1FJG_035, IL_2QUX_004, IL_1FJG_016, IL_2QUX_006, IL_1JZV_002, IL_2QUX_001, IL_1S72_096, IL_2QUX_003, IL_1GID_005, IL_1ET4_002, IL_3DIR_005, IL_1FUF_002, IL_1FUF_003, IL_2QUX_005, IL_1S72_010, IL_3MUR_003, IL_3MUR_004, IL_2ZJR_093, IL_1F7Y_002, IL_3B31_001, IL_3HHN_001, IL_2ZY6_002IL_2BQ5_002, IL_2NOK_006, IL_2BQ5_001, IL_1I9X_001, IL_2NOK_003, IL_2BU1_002, IL_2ZJR_034, IL_2IZM_002, IL_2ZJR_015, IL_1S72_086, IL_397D_001, IL_1FJG_043, IL_1S72_040, IL_2VPL_005, IL_3D0U_001, IL_3F1H_077, IL_2IZN_002, IL_2IZN_001, IL_2IZM_001, IL_3F1H_095, IL_1S72_030, IL_1FJG_014, IL_3G78_015, IL_2C4Z_001, IL_3DIR_001, IL_1S72_074, IL_1S03_001, IL_1S03_005, IL_3F1H_018, IL_1R3E_001, IL_1R3E_002, IL_2ZJR_091, IL_1S72_093, IL_3OWZ_001, IL_6MSF_001, IL_2IZ9_001, IL_2IZ9_002, IL_2ZJR_076
Annotations
  • (29)
  • Multiple bulged bases (4)
  • Single bulged A (H) (3)
  • Major groove intercalation (2)
  • Multiple bulged bases (H) (2)
  • Single bulged A (2)
  • Single bulged G (H) (2)
  • Single bulged U (2)
  • Bulged stacked bases (H) (1)
  • Major groove outside cWW, minor groove, intercalation pocket (H) (1)
  • Major groove outside cWW, minor groove, intercalation pocket (1)
  • Single bulged C (H) (1)
  • Single bulged G (1)
  • Basepair signature
    Heat map statistics
    Min 0.04 | Avg 0.53 | Max 1.20
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