Examples

Structures with pseudoknots | 16s rRNA (Large structures with over 1500 bases)

Tetrahymena  Group I Intron (RNA, 10: 1730-1739, 2004; Structure data from XRNA)
Tetrahymena Group I Intron #Tetrahymena Group I Intron
1
UAAAUAGCAAUAUUUACCUUUGGAGGGAAAAGUUAUCAGGCAUGCACCUG
GUAGCUAGUCUUUAAACCAAUAGAUUGCAUCGGUUUAAAAGGCAAGACCG
UCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGG
AAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUG
GUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUG
GAUGCAGUUCACAGACUAAAUGUCGGUCGGGGAAGAUGUAUUCUUCUCAU
AAGAUAUAGUCGGACCUCUCCUUAAUGGGAGCUAGCGGAUGAAGUGAUGC
AACACUGGAGCCGCUGGGAACUAAUUUGUAUGCGAAAGUAUAUUGAUUAG
UUUUGGAGUACUCGUAAGGUA

((((..............))))(((((...((((((((((......))))
)))))).((((((((((((((.......)))))))))).))))..(((((
(((...((((((....(((......((((.(((((((((((((((((((.
...)))))))))))(((.....)))....)))....).))))))))....
.)))...)).))))(((..((((...((((((((.....))))))))..)
)))..)))...[.[[[[[..))))))))((((((((.....)))))))).
......]]]]]]((...(((((....)))))(((((((....((((....
..))))....))))))).(((((((((((((((....)))))))))))))
)).........))........

#exon
1
/CUCUC
/)))))

C.botulinum tmRNA intron (Nucleic Acids Res. 30 (1): 179-182, 2002)
C.botulinum tmRNA intron Sequence
agggguucgaUUCAAAAGAGUCGCCUUAUGAAGUGAUUCAUAAGUGAAAA
CUUGGCUUUAUCGGUGAAACCGAAACGUAAAGACGUCGGCAAUACCGAGU
GGUAUGUGGGGAAACCCAAACAGCCGUGUUCGACUCAUAGGUUUCUUAAC
CUUAAGAAAUGAAAUUUUCUUAAGUAAGAAAUCUAGGAUAGAAGUUUUAA
ACUAUAAUAUAGCUUCUAUAACAUGCCAAGGUACUUAAAACUUAUAAGUU
UUAAGCACGAGAUAUAGUCAGUGCCAUUAGAGAUAAUGGAAUAGCAUGuc
cccu

Structure data
((((...((((((....)))))).((((((((....))))))))......
((((((....((((((...((((..(((....)))))))...))))))((
(((...((((....))))....)))))..[.[[[[..(((((((((....
(((((((((......)))))))))..)))))))))..(((((((((.((.
.......)).))))))))).....))))))((.(((((((((....))))
))))).)).......]]]]](((((((((....)))))).....)))...
))))

DiGIR1 (Nucleic Acids Res. 28 (10): 2194-2200, 2000)
DiGIR1 Sequence
GGGUUGGGAAGUAUCAUGGCUAAUCACCAUGAUGCAAUCGGGUUGAACAC
UUAAUUGGGUUAAAACGGUGGGGGACGAUCCCGUAACAUCCGUCCUAACG
GCGACAGACUGCACGGCCCUGCCUCUUAGGUGUGUUCAAUGAACAGUCGU
UCCGAAAGGAAGCAUCCGGUAUCCCAAGACAAUC

Structure data
...((((((.(((((((((.......))))))))).(((((((.((((((
......(((((...((((((((((....))))....)).))))((....)
)...[.[[[[[...))))).((((...))))))))))......]]]]]](
(((....))))..))))))).)))))).......

E.coli  tmRNA (tmRDB; http://psyche.uthct.edu/dbs/tmRDB/rna/tmrna.html)
E.coli tmRNA Sequence
GGGGCUGAUUCUGGAUUCCACGGGAUUUGCGAAACCCAAGGUGCAUGCCG
AGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGA
AAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAG
CCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCG
CGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUU
UGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACU
AAGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUGCAACGCCC
GCCAGCUCCACCA

Structure data
(((((((.............((((((((.....((((..(((((((((((
(((.[[[[[[..))))).....]]]]]]......................
.......((((((((((.........)))).))))))(((((((((((..
(((...[[[[[)))..))))....)))))))..........]]]]]...(
(((...((((..[[[[[[))))...))))..........]]]]]]..(((
(((((((.(((.[[[.[[[))).)))))))))).........]]].]]].
..)))))...))))..))))....))))))))...(((((.......)))
)))))))))....

HCV_IRES (Nucleic Acids Res. 29 (12): 2535-2541, 2001)
HCV_IRES Sequence
GCCAGCCCCCGAUUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGA
GGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG
UGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUG
CGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUG
GAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGC
UAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGG
GUGCUUGCGAGUGCCCCGGGAGGUCUGGUAGACCGUGCACCAUGAGCACG
AAUCCUAAACCUCAAAGAAAAACCAAACGUAAC

Structure data
....((((((....)))))).......................((((.((
((............((((((...((((((.......))))))....))))
))........))))))))......(((((((((((.((((((((((((((
(((..((((((....))))))((((.(((((..((.(((((.........
.....))))).))....))))).)))).(((....))))))).)))))))
))((((..(.(((......))).).))))....)))).))(((......)
))((.[[[[[[.))))))))))).]]]]]]((.(((((.......)))))
..)).............................

Odontoglossum  ringspot virus (PseudoBase; http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html)
odontoglossum ringspot virus Sequence
UUCCUAAUCAUAUUUAGGAAAAUAACGUUGAUAGUGUUGAACUAUCCGUG
GUGCAUACGAUAAUGCAUAGUGGUUAUCCCUCCACUUAAAUCGAAGGGUU
UUUCACUGCGGAUAUGUAGGUUUCCUCGGUGAAUAUAAAACUUAUAUCCC
GUUGUGUACACGAUAGUACAUAGUGUUUAUCCCUCCACUUGAAUCGAAGG
GUUUUGUGUCAGACGCGUGUAAGGAGUGGUCAACCUUACGACACAUUUAA
AUAAUGCGUCCGUGGUGCAUACGAUAAUGCAUAGUGUUUGUCCCUCCACU
UAAAUCGAAGGGUUGUGUAUAUGGAUCAUGCGGAUAAAGUUAUACUGGUG
CAGUAUAACCCGUUAUACACAUAAAAUUAUGAGGGAUUCGAAUUCCCCCU
UACCUCGGGUAGAGGCCCA

Structure data
(((((((......)))))))..((((((.[[[[))))))...]]]](((.
[[[[[[)))...]]]]]]((((.....[[[[[))))......].]]]]..
.(((((....[[[[((.(((...))))))))))...........]]]].(
((.[[[[[[)))...]]]]]]((((.....[[[[[))))......].]]]
]...(((((...[[[[.(((((((.........)))))))))))).....
....]]]]..(((.[[[[[[)))...]]]]]]((((.....[[[[[))))
......].]]]].((((((((....[[[[((((.....((((((((....
.)))))))))))))))))))).......]]]]((((.......))))(((
..[[[[)))..]]]]....

td group I intron of bacteriophage T4 (Nucleic Acids Res. 27 (12): 2494-2502, 1999)
td group I intron of bacteriophage T4 Sequence
uuggguUAAUUGAGGCCUGAGUAUAAGGUGACUUAUACUUGUGAAUCUAU
CUAAACGGGGAACCUCUCUAGUAGACAAUCCCGUGCUAAAUUGUAGGACU
GCCCGGGUUCUACAUAAAUGCCUAACGACUAUCCCUUUGGGGAGUAGGGU
CAAGUGACUCGAAACGAUAGACAACUUGCUUUAACAAGUUGGAGAUAUAG
UCUGCUCUGCAUGGUGACAUGCAGCUGGAUAUAAUUCCGGGGUAAGAUUA
ACGACCUUAUCUGAACAUAAUGcauc

Structure data
(((((((......)))))))(((((((....))))))).......(((((
(...((((((....(((.....)))...))))))((.....(((((((((
.....))))))))).....))...[.[[[[[.(((....)))(.((((((
(....))))))))..))))))(((((((......)))))))......]]]
]]]...(((((((....)))))))(.(((......))))(((((((....
.....)))))))..............

Cyanophora paradoxa cyanelle  tmRNA (http://www.bioinf.au.dk/tmRDB/rna/tmrna.html)
cyanophora paradoxa cyanelle tmRNA Sequence
GGGGCUGUUUAGGUUUCGACGUUUUUUUCUAAUUAUGUUUGUUAAGCAAG
UCGAGGAUUUGUUCUAUCUCGAAAACUAAGAACUCUCAAAAUUUAAACGC
AACUAAUAUUGUACGUUUUAACCGUAAAGCAGCUUUCGCUGUUUAAUAAU
UACUUUUAAUUUAAAAACCUAAUUUUUUUAGGAAUUUAUUUAUUUAUUGU
UUAUCCUGCUUAAUGAAUUAAAAAAAGCUAUACUUGUGAAUAAACGCAUA
AUUUAAAAAAACGGACGUGGGUUCAAAUCCCACCAGCUCC

Structure data
(((((((............((((((((...((((((((...((...((((
((((((..[[.[[...)))))......]].]]..................
..................................................
..................................................
...............................))))).....))..)))))
)))..))))))))...(((((.......))))))))))))

satellite tobacco mosaic virus (J. Gen. Virol., 75: 2851-2856, 1994)
satellite	tobacco mosaic virus Sequence
UGAACCUCGACAUAAGCCUUUUGGAUCGAAGGUUAAACGAUCCGCUCCUC
GCUUGAGCUUGAGGCGGCGUAUCUCUUAUGUCAACAGAGACCACUUUGGU
CUAUGGUUGUAUAACAAUAGAUAGACUCCCGUUUGCAAGAUUACAAUUGG
GAGAUCUUGCCGUUAGUCUGGUUAGCGCGUAACCGGCCUUGAUUUAUGGA
AUAGAUCCAUUGUCCAAUGGCUUUGCCAAUGGAACGCCGACGUGGCUGUA
UAAUACGUCGUUGACAAGUACGAAAUCUUGUUAGUGUUUUUCCCUCCACU
UAAAUCGAAGGGUUUUGUUUUGGUCUUCCCGAACGCAUACGUUAGUGUGA
CUACCGUUGUUCGAAACAAGUAAAACAGGAAGGGGGUUCGAAUCCCUCCC
UAACCGCGGGUAAGCGGCCCA

Structure data
..............((((((..[[[[[[))))))...]]]]]]((((.[[
[[[[))))...]]]]]]((((.[[[[)))).....]]]]........(((
((((.(((((...)))))..))))))).......((((((((........
..)))))))).(((((.(((((((.....)))))))..)))))..(((((
.....)))))..((((.((((...)))).))))..(((.[[[[)))....
....]]]](((.[[[[[[.)))....]]]]]]((((.....[[[[[))))
......].]]]].(((((((....[[[[[((((((...(((.(((.....
))).)))))))))))))))).......]]]]]((((.......))))(((
...[[[[)))...]]]]....

satellite tobacco necrosis virus 1 (PseudoBase; http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html)
satellite tobacco necrosis virus 1 Sequence
UAAUCCCAGAGGUUCACAAUGUUAGUGAUGGGGCGCUGAAAGAUGCGUAG
CUACCCUUCUGGAGCCACUUCCUGGUGGUAAGCAGAAAUCCAAGGGUACG
GUGGUACGGUGGAAAGCAGUCCCAGCUCUGCAUUGGGAACCGGCUUACAC
CCAGCUUAGGGCUAAAGUGUACUACUUGCUCAUUUGUAGUCUAAAUGAGA
CGUUGGCCUCGACGUGUCGAGGUGGCCUAAGGGAUUGGAACCCCUGAUGG
UC

Structure data
............(((..................(((.........((((.
.((((((..(((((((((......))))).........))))))))))..
....))))))))))(((..[[[[[)))......]]]]]....(((....[
[[)))...]]].........(((((...[[[[[[[)))))..]]]]]]](
(((..[[[[[[))))..]]]]]]((((..((((........))))...))
))

tobacco mosaic virus (Pseudobase; http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html)
tobacco mosaic virus Sequence
UGCAACUUGAGGUAGUCAAGAUGCAUAAUAAAUAACGGAUUGUGUCCGUA
AUCACACGUGGUGCGUACGAUAACGCAUAGUGUUUUUCCCUCCACUUAAA
UCGAAGGGUUGUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAU
ACAUCCGCAGGCACGUAAUAAAGCGAGGGGUUCGAAUCCCCCCGUUACCC
CCGGUAGGGGCCCA

Structure data
((((.(((((.....))))).)))).........(((((.[[[[))))).
..]]]](((.[[[[[[)))...]]]]]]((((.....[[[[[))))....
..].]]]].(((((((....[[[[((((.....((((((((.....))))
))))))))))))))).......]]]]((((.......))))(((...[[[
[)))..]]]]....

turnip yellow mosaic virus (PseudoBase; http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html)
turnip yellow mosaic virus Sequence
UUAGCUCGCCAGUUAGCGAGGUCUGUCCCCACACGACAGAUAAUCGGGUG
CAACUCCCGCCCCUUUUCCGAGGGUCAUCGGAACCA

Structure data
....(((((......))))).((((((.......))))))....((((..
.....))))(((...[[[[[[)))...]]]]]]...

Coxsackie (Seminars in Virology 8: 166-175, 1997)
Coxsackie Sequence
UUUUAGAUUAgAGACAAUUUGAAAUAAUUUAGAUUGGCUUAACCCUACUG
UGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCG
GUGCGGAAAAAAAA

Structure data
((((....(.(((.(((((((((....))))))))).))).)((((((((
((((.[[[[[[.........)))))))))))).....((.(((((.]]]]
]]))))).))))))

E. coli  Cysteiny1-tRNA (Structure Fold Des. 7: 143-156, 1999)
E. coli Cysteiny1-tRNA Sequence
GGCGCGUUAACAAAGCGGUUAUGUAGCGGAUUGCAAAUCCGUCUAGUCCG
GTUCGACUCCGGAACGCGCCUCCA

Structure data
((((.((.(.[.)..(.(....]..(...............)....[[[[
[..)..).]]]]])).))))....

Hepatitis delta  virus
(Pseudobase; http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html and PNAS. 97: 6515-6520, 2000)
Hepatitis delta virus Sequence
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCC
GAGGGGACCGUCCCCUCGGUAAUGGCGAAUGGGACCCACAAAUCUCUCUA
GAUUCCGAUAGAGAAUCGAGAGAAAAGUGGCUCUCCCUUAGCCAUCCGAG
UGGACGUGCGUCCUCCUUCGGAUGCCCAGGUCGGACCGCGAGGAGGUGGA
GAUGCCAUGCCGACCC

Structure data
.(((((((..[[[[[[[(((.[[.....))))))))))]]....((((((
(((((((...))))))))).)))).....]]]]]]]......((((((..
(((((.......)))))))))))....(((((.......)))))((((((
.((((....))))...))))))......((((((..........((((..
..))))...)))))).

E. coli  alpha operon mRNA
(Pseudobase; http://biology.leidenuniv.nl/~batenburg/PKBase/PKB00071.html)
E. coli mRNA Sequence
UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACG
UACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAAC
AUUCCUGA

Structure data
(((((((.(((((........[[[[....[[[[....{{{{.))))))))
))))..........................]]]].....]]]].......
....}}}}