RNA 3D Hub

JAR3D Query RF02984-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF02984 DUF3800-X RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
((((((..............................................(((((((((.......((....((................(((((................))))).))....).).....)))))))))))))))
>URS0000D66C3C_12908_1-95
UUACAA-GUAAA----------------------------------------UCCCUUCCAGAAA---G---GAGA---CCUCUCACGAGGCACUUCACCGCCAUGU-GUAGUGGAGUAUCGUUA--CGAGUAUGGAAGGUAUUGUAA
>URS0000D6C323_12908_1-69
GUAUGA-GUAAG-----------------------------------------U-CGCAAUGAAA---GAAUGAUG----------------UCUCA------GGA-------UGAGA-UUAGGA--CGAGUAAUUACG-GUUCAUAC
>URS0000D68BF5_12908_1-72
AUGCGU-GUAAG-----------------------------------------ACCUGCCCGAAG---CAAUGAAG----------------GCCGA-----GGAG-------UCGGU-ACGGGAG-UGUGUAGGGCAGGC-UCGCAA
>URS0000D65D1C_12908_1-72
ACGCGC-AUAAG-----------------------------------------ACCUGUCCGAGG---CUAUGAUG----------------CCCAU-----GGAC-------UUGGG-AUGGGAG-CGAGUAGGACAGGC-ACGCAC
>URS0000D66678_12908_1-77
UUGCGA-GUAAG-----------------------------------------UCCCUUCCGAAGUAUAAAUGGGUG---------------GCACC-----UUGA-------GGCGA-CCGCGAC-GCAGUAGGAAGGGGUUCGCAA
>URS0000D6A211_12908_1-72
UAGUGA-GUAAG-----------------------------------------UCCCGUUCGAAC---CUAUGAUG----------------CCUGU-----GUUU-------UCAGG-AUGGGA--GAAGUAGAGCGGGGAUCACGG
>URS0000D67D2B_589924_1-93
AGGCGG-GUAAGGUC------GGGGC-------CUACUAU-------GCCCCCCUCCGUCCGAAA---CGAUGAGG----------------CCUCC-----UUGA-------GGAGG-GUGGGAU-GGAGUAGGACGGGG-CCGCCG
>URS0000D6593E_387631_1-71
UAUGGG-GUAAG-----------------------------------------UCCCAC-CGAAA---CGAUGAGG----------------CCUCC-----UUGA-------GGAGG-GUGGGAU-GGAGUAG-GUGGGGUCCCGUU
>URS0000D6CDB1_12908_1-86
-GGGGAGGUAAGGUC------GGCGA---------------------UAGCCCCUCCGGCCGAAA---CGAUGAGG----------------CUCAC-----GUAA-------GUGGG-GUGGGAU-GGAGUAGGCCGGGGCUCCCC-
>URS0000D6CDD9_12908_1-86
UAGGGG-GUAAGGUC------GGC---------GAUA------------GCCCCUCCGUCCGAAA---CGAUGAGG----------------CCCGC-----GUAA-------GCGGG-GUGGGAU-GGAGUAGGAUGGGG-CCCCUU
>URS0000D6728D_12908_1-86
UAGGGG-GUAAGGUC------GGCGA---------------------UAGCCCCUCCGUCCGAAA---CGAUGAGG----------------CCCGC-----GUAA-------GCGGG-GUGGGAU-GGAGUAGGACGGGG-CCCCUU
>URS0000D68278_12908_1-72
CUGCGA-GUAAG-----------------------------------------GCCCGUCCGAGG---CUGUGAUG----------------CCUGC-----GGCU-------GCGGG-AUGGGA--GCAAUAGGACGGGGUUCGCAC
>URS0000D669D9_12908_1-73
UUGCGU-GUAAA----------------------------------------GACCCACCCGAGG---CAAUGAUG----------------CCUGC-----GUAU-------GUAGG-AUGAGG--GUAAUAGGGUGGGCAACGCAA
>URS0000D6AB0D_12908_1-73
AUGCGU-GUAAA----------------------------------------GACCCAUCCGAGG---CAGUGAUG----------------CUCGC-----GUAU-------GCGGG-AUGGGA--GUAAUAGGGUGGGCAACGCAC
>URS0000D68EB1_12908_1-78
UGGUGG-UUAAACCACUAGAA-------------------------------CUCCGCCCC-AAA---GGAUGAUG----------------CCCGU-----GGAU-------GCGGG-AUGGGAC--GA--AGGGGAGGA-CCACCA
>URS0000D69E33_12908_1-78
UUGUGG-UUAAACCACUGGAA-------------------------------CUCCGCCCC-AAA---GGAUGAUG----------------UCCGU-----GGAU-------ACGGA-AUGGGAC-GA---AGGGGAGGA-UCACAU
>URS0000D69D98_12908_1-96
GGGCGG-UUAAA------------CGUCGCGUGCUAUUUUCGCGCGACG----GCCCGC-CGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CUGGGAG-CGAGUAG-GCGGGUGCCGCCC
>URS0000D6BC09_12908_1-96
GGGCGG-UUAAA------------CGUCGCGUGCUAUUUUCGCGCGACG----GCCCGC-CGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CCGGGAG-CGAGUAG-GCGGGUGCCGCCC
>URS0000D66F69_12908_1-84
GGGCGG-UUAAAC--------GUCGC---------------------GCGACGGCCCGCUCGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CCGGGAG-CGAGUAG-GCGGGUGCCGCCC
>URS0000D6BDFE_12908_1-83
GGGCGG-UUAAAC--------GUCGC---------------------GCGACGGCCC-GCCGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CCGGGAA-CGAGUAGGC-GGGUGCCGCCC
>URS0000D68FCE_12908_1-83
GGGCGG-UUAAAC--------GUCGC---------------------GCGACGGCCC-GCCGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CCGGGAG-CGAGUAGGC-GGGUGCCGCCC
>URS0000D69C8F_12908_1-71
UAGUGA-GUAAG-----------------------------------------UCCUGU-UGAAC---GAAUGACG----------------CCUCA-----GGAAU------GGAGG-UCAGGA--CAAGUAA-ACAGGGUUCACUU
>URS0000D678ED_12908_1-70
UAACGA-GUAAG-----------------------------------------UCCUGC-UGAAA---GGAUGACG----------------GCUCA-----GGAU-------UGAGC-UCAGGA--CCAGUAA-GCAGGGUUCGUUU
>URS0000D67FFC_12908_1-70
CAACGA-GUAAG-----------------------------------------UCCUGC-UGAAA---GGAUGACG----------------GCUCA-----GGAU-------UGAGC-UCAGGA--CCAGUAA-GCAGGGUUCGUUC
>URS0000D66005_12908_1-70
UAACGA-GUAAG-----------------------------------------UCCU-ACUGAAC---GAAUGACG----------------GCUCA-----GGAU-------UGAGC-UCAGGA--CCAGUAAGUAGGG-GUCGUUA
>URS0000D6631F_12908_1-89
GGGUGG-GUAACC--------GCGGG-------AAUA----------CCCGCCUCCUCCCCGAAA---GGGUGAGG----------------CCGCU-----GGAU-------GGCGG-ACCAGAG-CGAGUAGGGGAGGGGCCACCU
>URS0000D6BEEA_12908_1-89
GGGUGG-GUAACC--------GCGGG-------GAUA----------CCCGCCUCCUCCCCGAAA---GGGUGAGG----------------CCGCC-----GGAU-------GGCGG-ACCAGAG-CGAGUAGGGGAGGGGCCACCU
>URS0000D6A83A_12908_1-89
GGGUGG-GUAACC--------GCGGG-------GAUA----------CCCGCCUCCUCCCCGAAA---GGGUGAGG----------------CCGCC-----GGAC-------GGCGG-ACCAGAG-CGAGUAGGGGAGGGGCCACCU
>URS0000D67063_12908_1-104
GGGUGG-GUAACU--------GCGGG--CCCGGCGCACG-CCGGGAACCUGCCUCCUCCCCGAAA---GUAUGAGG----------------CCGCC-----GGAC-------GGCGG-ACCGGAGGCGAGUAGGGGAGGGGCCACCU
>URS0000D65BFA_12908_1-102
-GGUGG-GUAACU--------GCGGG--CCCGGCGCACA-CCGGGAACCUGCCUCCUCCCCGAAA---GUAUGAGG----------------CCGCC-----GGAC-------GGCGG-ACCGGAGGCGAGUAGGGGAGGGGCCACC-
>URS0000D6B860_12908_1-97
GGGCGA--UAAU---------UGCGCCCGGU--GCGG-----AGCGGGCGCAUCCCGCCCCGAAA---GUAUGAGG----------------CCGCC-----GGAC-------GGCGG-UCCGGAGGCGAGUAGGGGCGGU-UCGCCC
>URS0000D6A8FE_12908_1-90
GGGCGG-GUAAA----------GCGGA------GGAA---------UCCGCUUCCCUCCCCGAAA---GUAUGAGG----------------CCGCC-----GGAG-------GGCGG-UCCGGAGCCGAGUAGGGGAGGUCCCGCCC
>URS0000D6D1B9_12908_1-72
UAGUGA-AUAAA-----------------------------------------UCCUGUUCGAAA---UGAUGAUG----------------CCUGC-----AUUA-------GUGGG-UUAGGA--AAAGUAGAACAGGUAUCACAG
>URS0000D668EC_12908_1-73
CAGUGA-GUAAG-----------------------------------------UCCCUCUUGAAAA--GAAUGAGG----------------CUAC------UUUGGU------GUGG--UGUGAC-GAAGUAAAGAGGGCUUCACUC
>URS0000D65A59_12908_1-84
AGGUGA-CUAAUG--------CCC---------AUAA------------GGGGUCUUUCCCGAAA---GAAUGAUG----------------CCCGU-----GGAU-------GCGGG-AUGGGA--CAAGUAGGGGGAGAUUCACCA
>URS0000D6A2DC_12908_1-84
AGGUGA-CUAAUG--------CCC---------AUAA------------GGGGUCUUUCCCGAAA---GAAUGAUG----------------CCCGU-----GGAU-------GUGGG-AUGGGA--CAAGUAGGGGGAGAUUCACCA
>URS0000D675F0_12908_1-84
AGGUGA-CUAAUG--------CCC---------AUCAA-----------GGGGUCUUUCCCGAAA---GAAUGAUG----------------CCCGU-----GGAU-------GCGGG-AUGGGA--CAAGUAGGGGA-GAUUCACCA
>URS0000D6B36B_12908_1-85
AGGUGA-CUAAUG--------CCC---------AUCAA-----------GGGGUCUUUCCCGAAA---GAAUGAUG----------------CCCGU-----GGAU-------GCGGG-AUGGGA--CAAGUAGGGGGAGAUUCACCA
>URS0000D68B80_12908_1-72
UGGUGA-GUAAG-----------------------------------------GCUC-CCAGAAA---GAAUGAUG----------------UCCGU-----GGAC-------GCGGG-AUGGGAU-CAAGUAAGGGGAGGUUCACCA
>URS0000D6CEA6_868131_1-71
AAGUGA-GUAAG-----------------------------------------UCCC-CCAGAAA---GGAUGAUG----------------UCCAC-----GUAU-------GUGGA-GUGGGA--CGAGUACGGUGGGGUUCACUU
>URS0000D67A2C_12908_1-80
AGGUGA-GUAAG-----------------------------------------UCCU-CCCGAAA---UAAUGAUGAUG-------------CCAUGAC---UAAUU----GACAGGG-GUGGGAG-CAAGUAGGGGAGGGUUCAGCU
>URS0000D6C25E_12908_1-72
UGGUGA-GUAAG-----------------------------------------UCCU-CCCGAAA---GGAUGAUG----------------CCAUG-----UUGA-------CAUGG-GUGGGAG-CGAGUAGGGAAGGGUUCACCA
>URS0000D69A07_12908_1-75
UAGUGUUGUAAG-----------------------------------------ACCCUUCUGAAAA--GGAUGAUG----------------CCACC-----GAUU-------GGUGG-ACGUGAC-GAAGUAAGGAGGGGUUCACUA
>URS0000D66B3A_12908_1-75
UAGUGUUGUAAG-----------------------------------------ACCCUCCUGAAAA--GGAUGAUG----------------CCACC-----CAUU-------GGUGG-ACGUGAC-GAAGUAUGGAGGGGGUCACUA
>URS0000D66553_12908_1-75
UAGUGUUGUAAG-----------------------------------------UCCCUUCCGAAAA--GGAUGAUG----------------CCACC-----AAUU-------GGUGG-ACGUGAC-GAAGUACGAAGGGGUUCACUA
>URS0000D6B639_12908_1-78
UAGUGUUGUAAGAGU--------------------------------------UCCCUCCUGAAAA--GGAUGAUG----------------CUGCC-----UAUU-------GGCAG-GCGUGAC-GAAGUAGGGUGGGGUUCACUA
>URS0000D667A3_12908_1-74
UCGUGG-GUAAG-----------------------------------------UCCUUUCCGAAAC--GGAUGAGG----------------CCACC-----GUGA-------GGUGG-GUGGGAC-AAAGUAGGAGAGGGGCCACUU
>URS0000D68C85_12908_1-74
UGGUGA-AUAAG-----------------------------------------UCCUUUCCGAAAC--GGAUGAGG----------------CCACC-----UUGA-------GGUGG-GUGGGAC-AAAGUAGGAAAGGGAUCACAA
>URS0000D6ABC4_12908_1-74
UAGUGA-GUAAG-----------------------------------------UCCUUUCCGAAAC--GGAUGAGG----------------CCACC-----AUGA-------GGUGG-GUGGGAC-AAAGUAGGAAAGGGUUCACUU
>URS0000D67076_12908_1-74
UAGUGA-GUAAG-----------------------------------------ACCUUUCUGAAAC--GGAUGAGG----------------CCACC-----UUGA-------GGUGG-GCGGGAC-AAAGUAGGAAAGGGUUCACGU
>URS0000D69096_12908_1-74
CUGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAC--GGAUGAGG----------------CUACC-----UUGA-------GGUAG-AUGGGAC-AAAGUAGGGAAGGGUUCACAC
>URS0000D6CA26_368407_1-74
UAGUGA-GUAAA-----------------------------------------UCCUUCCUGAAAA--GGAUGAGG----------------CCGCC-----UUGA-------GGCGG-GUGGGAC-AAAGUAAGGAAGGGGUCACUA
>URS0000D658E7_12908_1-74
UUGUGA-GUAAA-----------------------------------------UCCUUCCCGAAAA--GGAUGAGG----------------CCGCC-----UUGA-------GGCGG-GUGGGAC-AAAGUAGGGAAGGGGUCACGU
>URS0000D6CDCF_12908_1-75
UAGUGUUGUAAG-----------------------------------------UCCUUCCUGAAAA--GGAUGAGG----------------CCGCC-----CUGA-------GGCGG-AUGGGAC-GAAGUAAGGAAGGGUUCACUA
>URS0000D6B65C_12908_1-75
UAGUGUUGUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAGG----------------CCGCC-----CUGA-------GGCGG-AUGGGAC-GAAGUAAGGAAGGGUUCACUA
>URS0000D668F4_12908_1-75
UAGUGCUGUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAGG----------------CCGCC-----CUGA-------GGCGG-AUGGGAC-GAAGUAGGGAAGGGUUCACUA
>URS0000D6C134_28892_1-74
CAGCGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUG----------------CCACC-----GUAA-------GGUGG-GUGGGAC-GAAGUAGGGAAGGGUUCACUG
>URS0000D67465_12908_1-74
UAGUGA-GUAAG-----------------------------------------UCCUUCCC-AAAAA-GGAUGAUG----------------CCACC-----UUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGUUCACUG
>URS0000D68B04_12908_1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAC--GGAUGAUG----------------CCACC-----CUGA-------GGUGG-AUGGGAC-AAAGUAGGGAAGGGUUCACUG
>URS0000D6D3FC_12908_1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUA----------------CCACC-----CUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGUUCACGU
>URS0000D6C442_12908_1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUG----------------CCACC-----CUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGGUCACUA
>URS0000D66EEE_12908_1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUG----------------CCACC-----CUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGUUCACUU
>URS0000D6BF74_12908_1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUG----------------CCACC-----CUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGUUCACUA
>URS0000D6A168_12908_1-74
ACGUGA-GUAAG-----------------------------------------UCCUUUCCGAAAC--GAAUGAUG----------------CUACC-----UUGA-------GGUAG-GUGGGAC-AAAGUAGGGAAGGGGUCACAU
>URS0000D68283_12908_1-72
GAGCGA-GUAAG-----------------------------------------UCCCUCUCGAAA---GGAUGAUG----------------CUGCU-----CAUG-------AGCAG-GUGGGA--CGAUUAGAGAGGGGUUCACCA
>URS0000D66BE9_12908_1-72
GAGUGA-GUAAG-----------------------------------------UCCCUCUCGAAA---GGAUGAUG----------------CUGCU-----CAUG-------AGCAG-GUGGGA--CGAUUAGAGAGGGGUUCACCA
>URS0000D67888_12908_1-72
UAGUGA-GUAAG-----------------------------------------UCCCUCUCGAAA---GGAUGAUG----------------CUGCU-----UAUU-------AGCAG-GUGGGA--CAAUUAGAGAGGGGUUCACUA
>URS0000D69DB6_12908_1-72
AAGUGA-GUAAG-----------------------------------------UCCCUCUCGAAA---GGAUGAUG----------------CUGCU-----UAUU-------AGCAG-GUGGGA--CAAUUAGAGAGGGGUUCACUA
>URS0000D6AECF_12908_1-73
AGGUGA-GUAAG-----------------------------------------UCCCUCUCGAAAA--GAAUGAGG----------------CCGCC-----AAUU-------GGCGG--GGGGAC-GAAGUAGAGAGGGGUUCACUA
>URS0000D67AAD_12908_1-75
UAGUGCUGUAAG-----------------------------------------UCCCUCUCGAAAA--GAAUGAGG----------------CCGCC-----AAUU-------GGCGG-GUGGGAC-GAAGUAGAGAGGGGUUCGCUA
>URS0000D6909D_12908_1-74
GAGUGA-GUAAG-----------------------------------------UCCCUCUCGAAAA--GGAUGAGG----------------CCGCC-----AAUU-------AGCGG-GUGGGAC-GAAGUAGAGAGGGGGUCGCUA
>URS0000D67DE1_12908_1-74
UGGUAA-GUAAG-----------------------------------------ACCUGCCCGAAAA--GAAUGAGG----------------CCUAU-----GGAA-------GUAGG-AUGGAAG-CGAGUAGGGCAGGGUUUACCA
>URS0000D6B01C_12908_1-73
UGGUAA-GUAAG-----------------------------------------ACCUGCCCGAAA---GAAUGAGG----------------CCUAC-----GGAA-------GUAGG-AUGGGAG-CGAGUAGGGCAGGGUUUACCA
>URS0000D6C3DB_12908_1-73
UGGUAA-GUAAG-----------------------------------------ACCUGCCCGAAA---GAAUGAGG----------------CCUAU-----GGAA-------GUAGG-AUGGGAG-CGAGUAGGGCAGGAUUUACCA
>URS0000D6892D_12908_1-72
UGGUGA-GUAAG-----------------------------------------UCCU-UCUGAAA---GGAUGAUG----------------UCCAC-----GUAG-------GUGGA-AUGGGAG-CGAGUAGGAAAGGGUUCACCA
>URS0000D67E45_12908_1-72
UGGUGA-GUAAG-----------------------------------------UCCU-UCCGAAA---GGAUGAUG----------------CCUGC-----GGAC-------GCAGG-AUGGGAG-CGAGUAGGAAAGGGUUCACCA
>URS0000D66E2B_12908_1-72
UGGUGA-GUAAG-----------------------------------------UCCU-UCCGAAA---GGAUGAUG----------------CCUGU-----GGAC-------GCAGG-AUGGGAG-CGAGUAGGAAAGGGUUCACCA
>URS0000D6CFB4_12908_1-72
UGGUGA-GUAAG-----------------------------------------UCCU-UCCGAAA---GGAUGAUG----------------CCUGU-----GGAC-------GCAGG-AUGGGAG-CGAGUAGGAAAGGGUUCACCG
>URS0000D69350_12908_1-73
UGGUGA-GUAAG-----------------------------------------UCUUGCCCGAAA---GGAUGAGG----------------CCUGU-----GGAG-------ACAGG-AUGGGAG-CGAGUAGGGCAAGGUUCACCA
>URS0000D6D265_868131_1-71
CAGUGA-GUAAG-----------------------------------------UCCU-UUCGAAA---GAAUGAGG----------------CCCGU-----GGAC-------ACGGG-GUGGGA--CAAGUAGGAAUGGGUUCACCU
>URS0000D6ABC6_12908_1-71
AGGUGA-GUAAG-----------------------------------------UCCU-UCUGAAA---GAAUGAGG----------------CCCGU-----GGAU-------ACGGG-GUGGGA--UGAGUAAGAAAGGGUUCACCU
>URS0000D681B1_12908_1-72
AAGUGA-GUAAG-----------------------------------------UCCUCCCUGAAA---GAAUGAGG----------------CUGCC-----GGAU-------GGUGG-AUGGGA--CAAGUAAGAGAGGGUUCACGA
>URS0000D69953_323259_1-72
AAGUGA-GUAAG-----------------------------------------UCCUCCCUGAAA---GAAUGAGG----------------CUGCC-----GGAU-------GGUGG-AUGGAA--CAAGUAAGAGAGGGUUCACGA
>URS0000D6CD98_12908_1-72
CUGCGA-GUAAG-----------------------------------------UCCUAUCCGAGG---CAAUGAUG---------------CCCGC------ACUU--------GUGGAAUGGGA--GUACUAUGAUAGGGGUCGCAG
>URS0000D6D0E7_12908_1-72
UUGCGA-GUAAG-----------------------------------------UCCUAUCCGAGG---CAAUGAUG----------------CCCGC-----GCUU-------GUGGG-AUGGGA--GUAUUAGAAUAGGGAUCGCGA
>URS0000D670E1_12908_1-72
UCUCGA-GUAAG-----------------------------------------UCCUAUCCGAGG---CAAUAAUG----------------CCCGC-----GCUU-------GUGGG-AUGGGA--GCAUUAGGAUAGGGGUCGCGU
>URS0000D6C2BA_12908_1-72
CAGCGA-GUAAG-----------------------------------------UCCUAUUCGAAC---CAAUGAUG----------------CCUGC-----AUUA-------GUGGG-AUGGGA--GAACUAGGGUAGGGGUCGCUU
>URS0000D6BC49_12908_1-72
UAGCGA-GUAAA-----------------------------------------GCCUAUCCGAAA---CAAUGAUG----------------CCUGC-----AUUA-------GUGGG-UUAGGA--GGAUUAGGAUAGGGGUCGCUU

There are no chains in PDB that we map to Rfam family RF02984.

Jump to results for:

  • Loop 1IL Column numbers: 6-53, 142-143
  • Loop 2IL Column numbers: 61-69, 128-134
  • Loop 3IL Column numbers: 69-70, 126-128
  • Loop 4IL Column numbers: 70-75, 121-126
  • Loop 5IL Column numbers: 76-93, 118-120
  • Loop 6HL Column numbers: 97-114

Loop 1 Internal loop

Column numbers: 6-53, 142-143 
    Scored sequences and counts

    
    A-GUAAG-----------------------------------------*UU   37

    
    A-GUAAG-----------------------------------------*GU    7

    
    UUGUAAG-----------------------------------------*UU    4

    
    G-UUAAAC--------GUCGC---------------------GCGACG*GC    3

    
    A-GUAAA-----------------------------------------*GU    3

    
    G-UUAAA------------CGUCGCGUGCUAUUUUCGCGCGACG----*GC    2

    
    G-GUAACC--------GCGGG-------GAUA----------CCCGCC*GC    2

    
    A-CUAAUG--------CCC---------AUCAA-----------GGGG*UU    2

    
    A-CUAAUG--------CCC---------AUAA------------GGGG*UU    2

    
    CUGUAAG-----------------------------------------*UU    2

    
    U-GUAAA----------------------------------------G*AA    2

    
    A-GUAAG-----------------------------------------*AU    2

    
    G-GUAACU--------GCGGG--CCCGGCGCACA-CCGGGAACCUGCC*GC    1

    
    G-GUAACU--------GCGGG--CCCGGCGCACG-CCGGGAACCUGCC*GC    1

    
    G-GUAAA----------GCGGA------GGAA---------UCCGCUU*CC    1

    
    G-GUAACC--------GCGGG-------AAUA----------CCCGCC*GC    1

    
    AGGUAAGGUC------GGCGA---------------------UAGCCC*CU    1

    
    UUGUAAGAGU--------------------------------------*UU    1

    
    A-GUAAA----------------------------------------U*AU    1

    
    UUGUAAG-----------------------------------------*GU    1

    
    A-AUAAA-----------------------------------------*AU    1

    
    A-AUAAG-----------------------------------------*AU    1

    
    G-GUAAG-----------------------------------------*GC    1

    
    G-GUAAG-----------------------------------------*UC    1

    
    Omitted sequenced and counts

    
    A--UAAU---------UGCGCCCGGU--GCGG-----AGCGGGCGCAU*-U    1

    
    G-GUAAGGUC------GGGGC-------CUACUAU-------GCCCCC*-C    1

    
    G-GUAAGGUC------GGC---------GAUA------------GCCC*-C    1

    
    G-GUAAGGUC------GGCGA---------------------UAGCCC*-C    1

    
    G-UUAAACCACUAGAA-------------------------------C*-C    1

    
    G-UUAAACCACUGGAA-------------------------------C*-U    1

    
    C-AUAAG-----------------------------------------*-A    1

    
    U-GUAAG-----------------------------------------*-U    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_38186.6

Basepair signature:
cWW-L-cWW-L-L-R

68.75 -1213.73 4 1

2

Motif group IL_87211.1

Basepair signature:
cWW-cSW-L-cWW-L

50.00 -1593.77 4 3

3

Motif group IL_46086.1

Basepair signature:
cWW-L-cWW-L-L-R

1.25 -1111.13 4.5 4

4

Motif group IL_25412.1

Basepair signature:
cWW-L-cWW-L-L

1.25 -1400.95 6 3

Major groove intercalation

5

Motif group IL_25573.1

Basepair signature:
cWW-tSW-L-cWW-L-L

1.25 -1659.74 5 2

Loop 2 Internal loop

Column numbers: 61-69, 128-134 
    Scored sequences and counts

    
    CGAAA---G*CGAGUAG   19

    
    CGAAAA--G*GAAGUAG    9

    
    CGAAAC--G*AAAGUAG    6

    
    CGAAA---C*GGAGUAG    5

    
    CGAAA---G*CAAGUAG    5

    
    UGAAAA--G*GAAGUAA    3

    
    CGAAA---G*CAAUUAG    2

    
    CGAAA---G*CGAUUAG    2

    
    CGAGG---C*GUAAUAG    2

    
    UGAAA---G*CAAGUAA    2

    
    UGAAA---G*CCAGUAA    2

    
    CGAAGUAUA*GCAGUAG    1

    
    C-AAAAA-G*GAAGUAG    1

    
    CGAAAA--G*AAAGUAG    1

    
    CGAAAA--G*CGAGUAG    1

    
    CGAAAA--G*GAAGUAA    1

    
    CGAAAA--G*GAAGUAC    1

    
    UGAAAA--G*AAAGUAA    1

    
    UGAAAA--G*GAAGUAG    1

    
    UGAAAA--G*GAAGUAU    1

    
    UGAAAC--G*AAAGUAG    1

    
    AGAAA---G*CAAGUAA    1

    
    AGAAA---G*CGAGUAC    1

    
    AGAAA---G*CGAGUAU    1

    
    CGAAA---C*GGAUUAG    1

    
    CGAAA---U*AAAGUAG    1

    
    CGAAA---U*CAAGUAG    1

    
    CGAAC---C*GAACUAG    1

    
    CGAAC---C*GAAGUAG    1

    
    CGAAG---C*UGUGUAG    1

    
    CGAGG---C*CGAGUAG    1

    
    CGAGG---C*GCAAUAG    1

    
    CGAGG---C*GCAUUAG    1

    
    CGAGG---C*GUACUAU    1

    
    CGAGG---C*GUAUUAG    1

    
    UGAAA---G*CGAGUAA    1

    
    UGAAA---G*CGAGUAG    1

    
    UGAAA---G*UGAGUAA    1

    
    UGAAC---G*CAAGUAA    1

    
    UGAAC---G*CCAGUAA    1

    
    C-AAA---G*-GA--AG    1

    
    C-AAA---G*GA---AG    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_26307.2

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW

84.09 47.54 3 1

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_29198.2

Basepair signature:
cWW-cWW-L-R-cSH-R-tWH-tHS-cWW

81.82 7.95 4 3

7x7 Sarcin-Ricin with intercalated A; G-bulge

3

Motif group IL_24254.1

Basepair signature:
cWW-cWW-tHH-cSH-tWH-tHS-cWW

60.23 10.55 6 2.5

7x6 Sarcin-Ricin with UU cWW pair; G-bulge

4

Motif group IL_61286.1

Basepair signature:
cWW-L-R-L-R-L-tWH-L-tHS-cWW

57.95 -1.60 6 3

8x6 Sarcin-Ricin with inserted A; G-bulge

5

Motif group IL_47346.2

Basepair signature:
cWW-tSH-L-R-tHH-tHS-cWW

56.82 -12.67 4 2.5

tSH-tSH-tHH-tHS

6

Motif group IL_41756.4

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW-L

53.41 -4.53 5 2

8x6 Sarcin-Ricin with inserted Y; G-bulge

7

Motif group IL_16458.4

Basepair signature:
cWW-L-R-L-R-cSH-tWH-tHS-cWW

51.14 -22.18 6 3

Sarcin-Ricin target in LSU H95; G-bulge

8

Motif group IL_02349.4

Basepair signature:
cWW-tSH-tWH-cSH-tWH-tHS-cWW

50.00 -12.92 5 3

8x6 Sarcin-Ricin with bulged A; G-bulge

9

Motif group IL_04346.10

Basepair signature:
cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW

50.00 -15.35 4 2

8x7 Sarcin-Ricin; G-bulge

10

Motif group IL_88269.4

Basepair signature:
cWW-tWW-cSH-tWH-tHS-cWW

14.77 -33.52 5 3

6x5 Sarcin-Ricin; G-bulge

Loop 3 Internal loop

Column numbers: 69-70, 126-128 
    Scored sequences and counts

    
    GG*C-G   15

    
    GG*G-C   13

    
    GG*C-A    8

    
    CG*U-G    5

    
    GU*GGC    3

    
    GA*C-G    3

    
    GA*G-C    3

    
    GU*GCC    1

    
    AA*C-G    1

    
    CA*G-U    1

    
    CU*G-C    1

    
    GA*C-A    1

    
    GA*U-C    1

    
    GG*A-C    1

    
    UA*G-C    1

    
    Omitted sequenced and counts

    
    GA*--C   10

    
    CA*--G    7

    
    GG*--C    7

    
    CU*--G    2

    
    GA*--U    1

    
    GG*C--    1

    
    UG*--A    1

    
    G-*--C    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_84476.1

Basepair signature:
cWW-cWW

31.03 -10.92 2 2

Multiple bulged bases

2

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

27.59 0.29 3 1

Major groove platform

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

17.24 -16.22 3 1

Multiple bulged bases

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

17.24 -17.19 4 1

Intercalated cWS

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

17.24 -17.46 3 1

6

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

17.24 -17.97 1 1

Major groove intercalation

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

17.24 -21.93 2 1

8

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

17.24 -23.39 1 1

Single bulged G

9

Motif group IL_31462.6

Basepair signature:
cWW-L-cWW

10.34 -42.83 2 1

Single bulged A

10

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

8.62 -24.23 3 1

Loop 4 Internal loop

Column numbers: 70-75, 121-126 
    Scored sequences and counts

    
    GAUGAG*UGGGAC   10

    
    GAUGAU*UGGGAC    9

    
    AAUGAU*UGGGA-    7

    
    GAUGAG*UGGGAU    5

    
    GAUGAU*UGGGAG    5

    
    GAUGAU*UGGGA-    5

    
    GAUGAU*CGUGAC    4

    
    UAUGAG*CCGGAG    4

    
    GAUGAG*CGGGAG    3

    
    GGUGAG*CCAGAG    3

    
    AAUGAG*UGGGA-    3

    
    AAUGAG*UGGGAG    2

    
    GAUGAG*UGGGAG    2

    
    AAUGAC*CAGGA-    2

    
    AAUGAU*UAGGA-    2

    
    GAUGAC*CAGGA-    2

    
    AAUGAA*CGGGAG    1

    
    AAUGAG*GGGGAC    1

    
    AAUGAG*UGGAAG    1

    
    AAUGAG*UGGGAC    1

    
    AAUGAG*UGUGAC    1

    
    AAUGAU*UGGGAC    1

    
    AAUGAU*UGGGAG    1

    
    AAUGAU*UGGGAU    1

    
    AAUGGG*CGCGAC    1

    
    GAUGAG*CGGGAA    1

    
    GAUGAG*CGGGAC    1

    
    UAUGAU*UGGGAG    1

    
    AAUAAU*UGGGA-    1

    
    AAUGAG*UGGAA-    1

    
    AAUGAU*UGAGG-    1

    
    AGUGAU*UGGGA-    1

    
    GAUGAU*UAGGA-    1

    
    UAUGAU*UGGGA-    1

    
    UGUGAU*UGGGA-    1

    
    ---GAG*CGUUA-    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_94351.1

Basepair signature:
cWW-L-R-L-R-L-tHS-cWW

20.45 -11.58 6 3

2

Motif group IL_21667.1

Basepair signature:
cWW-tSH-L-R-L-cWW

2.27 -33.15 5 3

3

Motif group IL_42778.1

Basepair signature:
cWW-L-R-L-R-L-R-L-cWW

1.14 -26.18 7 4

4

Motif group IL_32016.1

Basepair signature:
cWW-tSH-tSH-tSS-tHS-L-R-cWW

1.14 -66.80 6 3

Kink-turn

5

Motif group IL_95570.1

Basepair signature:
cWW-cWH-R-L-cWW

1.14 -296.83 7 5

Loop 5 Internal loop

Column numbers: 76-93, 118-120 
    Scored sequences and counts

    
    G----------------C*G-A   39

    
    G----------------C*G-G   23

    
    C----------------C*G-C    5

    
    G----------------C*G-U    5

    
    G----------------G*C-U    3

    
    G----------------U*A-A    2

    
    A---CCUCUCACGAGGCA*UAU    1

    
    GAUG-------------C*G-G    1

    
    G---------------CC*GAA    1

    
    UG---------------G*A-C    1

    
    A----------------C*G-A    1

    
    G----------------G*U-A    1

    
    G----------------U*A-G    1

    
    G----------------U*A-U    1

    
    G----------------U*G-A    1

    
    Omitted sequenced and counts

    
    G----------------C*G--    2
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

67.44 -96.94 4 1

Major groove platform

2

Motif group IL_84476.1

Basepair signature:
cWW-cWW

65.12 -130.54 3 2

Multiple bulged bases

3

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

11.63 -149.39 1 1

Single bulged G

4

Motif group IL_42771.1

Basepair signature:
cWW-cWW

10.47 -140.73 4 1

Multiple bulged bases

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

9.30 -140.22 2 1

6

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

3.49 -141.16 4 1

Intercalated cWS

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

1.16 -142.79 2 1

Major groove intercalation

8

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

1.16 -152.07 4 1

9

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

1.16 -156.70 2 1

Stack and bulge

10

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

1.16 -198.17 4 2

Isolated non-canonical cWW pair

Loop 6 Hairpin loop

Column numbers: 97-114 
    Scored sequences and counts

    
    C-----GGAC-------G   10

    
    C-----UUGA-------G   10

    
    C-----CUGA-------G    8

    
    U-----GGAU-------G    6

    
    C-----GUAA-------G    4

    
    A-----GGAU-------U    3

    
    C-----AAUU-------G    3

    
    C-----AUUA-------G    3

    
    C-----GGAU-------G    3

    
    C-----GUAU-------G    3

    
    U-----GGAC-------G    3

    
    C-----GCUU-------G    2

    
    U-----CAUG-------A    2

    
    U-----GGAA-------G    2

    
    U-----GGAU-------A    2

    
    U-----UAUU-------A    2

    
    CACCGCCAUGU-GUAGUG    1

    
    GAC---UAAUU----GAC    1

    
    A-----GGAAU------G    1

    
    ------UUUGGU------    1

    
    A-----GGAG-------U    1

    
    C-----AAUU-------A    1

    
    C-----AUGA-------G    1

    
    C-----CAUU-------G    1

    
    C-----GAUU-------G    1

    
    C-----GGAA-------G    1

    
    C-----GGAG-------G    1

    
    C-----GGCU-------G    1

    
    C-----GUAG-------G    1

    
    C-----GUGA-------G    1

    
    C-----UAUU-------G    1

    
    G-----UUGA-------C    1

    
    U-----GGAC-------A    1

    
    U-----GGAC-------U    1

    
    U-----GGAG-------A    1

    
    U-----GUUU-------U    1

    
    A------GGA-------U    1

    
    ------ACUU--------    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_56334.1

Basepair signature:
cWW-F

89.77 -212.07 2 1

Mini UNCG

2

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

84.09 -105.08 2 2

3

Motif group HL_93535.1

Basepair signature:
cWW-F-F-F-F

81.82 -111.76 2 2

4

Motif group HL_56131.2

Basepair signature:
cWW-F-F

78.41 -111.96 3 2

5

Motif group HL_48417.5

Basepair signature:
cWW-F-F

63.64 -2.33 2 2

6

Motif group HL_57875.1

Basepair signature:
cWW-F-F

63.64 -110.73 2 2

7

Motif group HL_75660.5

Basepair signature:
cWW-F

63.64 -113.67 2 2

8

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

63.64 -121.64 3 2

tRNA D-loop

9

Motif group HL_13963.3

Basepair signature:
cWW-F-F

62.50 -122.18 4 2

10

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

60.23 -9.21 2 2

Coloring options: