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| # STOCKHOLM 1.0 | ||
|
|
||
| #=GF ID ANYA | ||
| #=GF DE ANYA tetraloop | ||
| #=GF AU Gardner PP | ||
| #=GF SE Published; PMID:19528080 | ||
| #=GF SS Published; PMID:19528080 | ||
| #=GF GA 20.00 | ||
| #=GF DR URL;http://scor.berkeley.edu/structure.jsp?parse=makeListWithElement&dagId=ANYADAGCODE1465974881 | ||
| #=GF DR URL;http://en.wikipedia.org/wiki/Tetraloop | ||
| #=GF RN [1] | ||
| #=GF RM 9461079 | ||
| #=GF RT Crystal structure of an RNA aptamer-protein complex at 2.8 A | ||
| #=GF RT resolution. | ||
| #=GF RA Convery MA, Rowsell S, Stonehouse NJ, Ellington AD, Hirao I, | ||
| #=GF RA Murray JB, Peabody DS, Phillips SE, Stockley PG | ||
| #=GF RL Nat Struct Biol. 1998;5:133–139. | ||
| #=GF RN [2] | ||
| #=GF RM 9808042 | ||
| #=GF RT Crystal structures of a series of RNA aptamers complexed to the | ||
| #=GF RT same protein target. | ||
| #=GF RA Rowsell S, Stonehouse NJ, Convery MA, Adams CJ, Ellington AD, | ||
| #=GF RA Hirao I, Peabody DS, Stockley PG, Phillips SE. | ||
| #=GF RL Nat Struct Biol. 1998;5(11):970-975. | ||
| #=GF RN [3] | ||
| #=GF RM 15121895 | ||
| #=GF RT Three-dimensional motifs from the SCOR, structural classification | ||
| #=GF RT of RNA database: extruded strands, base triples, tetraloops and | ||
| #=GF RT U-turns. | ||
| #=GF RA Klosterman PS, Hendrix DK, Tamura M, Holbrook SR, Brenner SE. | ||
| #=GF RL Nucleic Acids Res. 2004;32(8):2342-2352. | ||
|
|
||
| 1aq3_R ACAUGAGGAUUACCCAUGU | ||
| #=GR 1aq3_R SS (((((.((....))))))) | ||
| 1zdk_R ACAUGAGGAUCACCCAUGU | ||
| #=GR 1zdk_R SS (((((.((....))))))) | ||
| 1zdh_R ACAUGAGGAUCACCCAUGU | ||
| #=GR 1zdh_R SS (((((.((....))))))) | ||
| 1zdj_R ------GGAUCACC----- | ||
| #=GR 1zdj_R SS -----.........----- | ||
| 2iz8_R ACAUGAGGCUCACCCAUGU | ||
| #=GR 2iz8_R SS (((((.((....))))))) | ||
| 2izn_R ACAUCGCGAUUACGGAUGU | ||
| #=GR 2izn_R SS (((((.((....))))))) | ||
| 2c4z_R ACAUGAGGAUUACCCAUGU | ||
| #=GR 2c4z_R SS (((((.((....))))))) | ||
| 2iz9_R ACAUGAGGAUUACCCAUGU | ||
| #=GR 2iz9_R SS (((((.((....))))))) | ||
| 2c4y_R ACAUGAGGAUUACCCAUGU | ||
| #=GR 2c4y_R SS (((((.((....))))))) | ||
| 2c50_R ACAUGAGGAUAACCCAUGU | ||
| #=GR 2c50_R SS (((((.((....))))))) | ||
| 2izm_R ACAUGCGGAUCACCCAUGU | ||
| #=GR 2izm_R SS (((((.((....))))))) | ||
| #=GC SS_cons (((((.((....))))))) | ||
| // | ||
|
|
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| License | ||
|
|
||
| Creative Commons Attribution 3.0 Unported License | ||
|
|
||
| RMfam is a free and open-source project, you are free to download, | ||
| modify and use RMfam software and data. The contents of RMfam are | ||
| copyright (c) 2011 by Paul P. Gardner (PPG), University of Canterbury | ||
| (UC) and The Royal Society of New Zealand (RSNZ). The software and | ||
| information contents are distributed under the terms of the Creative | ||
| Commons Attribution 3.0 Unported License, which grants parties the | ||
| non-exclusive right to use, distribute and create derivative works | ||
| based on RMfam, provided that the software and information is | ||
| correctly attributed to PPG, UC and RSNZ. | ||
|
|
||
| More details about the Creative Commons License is available here: | ||
| http://creativecommons.org/licenses/by/3.0/ | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,199 @@ | ||
| # STOCKHOLM 1.0 | ||
|
|
||
| #=GF ID T-loop | ||
| #=GF DE T-loop | ||
| #=GF AU Gardner PP | ||
| #=GF SE Published; PMID:19528080 | ||
| #=GF SS Published; PMID:19528080 | ||
| #=GF GA 9.20 | ||
| #=GF DR URL;http://rna.bgsu.edu/FR3D/MotifLibrary/Hairpins/LIB70005_HL_T_Loop.html | ||
| #=GF DR URL;http://rnafrabase.cs.put.poznan.pl/?act=pdbdetails&id=2J01 | ||
| #=GF DR RFAM:RF00005 | ||
| #=GF RN [1] | ||
| #=GF RM 17694311 | ||
| #=GF RT FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. | ||
| #=GF RA Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB | ||
| #=GF RL J Math Biol. 2008;56:215-52. | ||
| #=GF RN [2] | ||
| #=GF RM 19528080 | ||
| #=GF RT Classification and energetics of the base-phosphate interactions in RNA. | ||
| #=GF RA Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB | ||
| #=GF RL Nucleic Acids Res. 2009;37:4898-918. | ||
| #=GF RN [3] | ||
| #=GF RM 12358430 | ||
| #=GF RT Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs. | ||
| #=GF RA Nagaswamy U, Fox GE | ||
| #=GF RL RNA. 2002;8:1112-9. | ||
| #=GF RN [4] | ||
| #=GF RM 12756321 | ||
| #=GF RT On the occurrence of the T-loop RNA folding motif in large RNA molecules. | ||
| #=GF RA Krasilnikov AS, Mondrag�n A | ||
| #=GF RL RNA. 2003;9:640-3. | ||
| #=GF RN [5] | ||
| #=GF RM 17940098 | ||
| #=GF RT Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin. | ||
| #=GF RA Zhuang Z, Jaeger L, Shea JE | ||
| #=GF RL Nucleic Acids Res. 2007;35:6995-7002. | ||
|
|
||
| #=GS thi-Box SE PubMed:16962976 | ||
|
|
||
| 1C04/42-49 .........GAAA..G....C.GUA.AUA.G...CU....C.......... | ||
| #=GR 1C04/42-49 SS .........(..(..(....(.........)...))....).......... | ||
| 1E8O/110-117 ...GG.G..C..G..C....G.GUG.GCG.C...GC....G..C..CU... | ||
| 1GAX/952-960 ......G..U..A..G....G.UUC.AAGUC...CU....A..C....... | ||
| #=GR 1GAX/952-960 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1H3E/31-39 ....G.A..C..G..G....U.CUG.UAAAA...CC....G..U..U.... | ||
| #=GR 1H3E/31-39 SS ....(.(..(..(..(....(.........)...))....)..)..).... | ||
| 1J1U/532-540 ......G..C..G..G....A.CUG.UAGAU...CC....G..C....... | ||
| #=GR 1J1U/532-540 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1J1U/554-562 ......G..C..U..G....G.UUC.AAAUC...CG....G..C....... | ||
| #=GR 1J1U/554-562 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1J2B/932-940 ..GACGC..C..G..C....C.CUU.ACGAG...GC....G..GAGGUC.. | ||
| #=GR 1J2B/932-940 SS ..(((....(..(..(....(.........)...))....).....))).. | ||
| 1J2B/954-962 ......C..G..G..G....G.UUC.AAGUC...CC....C..G....... | ||
| 1J5E/259-267 ..UUG.G..U..G..G....G.GUA.AUGGC...CC....A..C..CAA.. | ||
| #=GR 1J5E/259-267 SS ..(((.(..(..(..(....(.........)...))....)..)..))).. | ||
| 1J5E/80-89 GGCCG.C..G..G..G....G.UUU.UA..C...UC....C..G..UGGUC | ||
| #=GR 1J5E/80-89 SS (((((.(..(..(..(....(.........)...))....)..)..))))) | ||
| 1MJI/38-44 ..CUG.A....CC..C....C.AUG.CC..G...AA....C..U..CAG.. | ||
| #=GR 1MJI/38-44 SS ..(((.(.............(.........)............)..))).. | ||
| 1MMS/1092-1099 .........G..AGUG....C.GUA.ACA.G...CU....C.......... | ||
| #=GR 1MMS/1092-1099 SS .........(.....(....(.........)...).....).......... | ||
| 1N78/531-539 ......C..G..G..C....C.CUC.UCAAG...GC....C..G....... | ||
| #=GR 1N78/531-539 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1N78/553-561 ......G..G..G..G....G.UUC.GAUUC...CC....C..C....... | ||
| 1NBS/118-125 ....G.C..A..G..U....C.UUU.AGA.G...GC....U..GA.C.... | ||
| #=GR 1NBS/118-125 SS ....(.(..(..(..(....(.........)...))....)..)..).... | ||
| 1QA6/142-149 .........GAAA..G....C.GUA.AUA.G...CU....C.......... | ||
| #=GR 1QA6/142-149 SS .........(..(..(....(.........)...))....).......... | ||
| 1QTQ/953-961 ......C..G..A..G....G.UUC.GAAUC...CU....C..G....... | ||
| #=GR 1QTQ/953-961 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1QU2/53-61 ......G..G..U..G....G.UUC.AAGUC...CA....C..U....... | ||
| #=GR 1QU2/53-61 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1S72/1196-1203 ............A..G....C.GUA.ACA.G...CU............... | ||
| #=GR 1S72/1196-1203 SS ............(..(....(.........)...))............... | ||
| 1S72/1274-1282 ...CG.U..A..C..C....A.CUC.AUACU...GG....U..AAUCG... | ||
| #=GR 1S72/1274-1282 SS ...((.(..(..(..(....(.........)...))....)..)..))... | ||
| 1S72/1705-1713 ....................C.GGC.GA.AG.................... | ||
| 1S72/1990-1998 ............G..G....C.GGC.GAAAG...CC............... | ||
| #=GR 1S72/1990-1998 SS ............(..(....(.........)...))............... | ||
| 1S72/312-319 ......G.UC..U..C....U.UGG.AAC.A...GA....G..C....... | ||
| #=GR 1S72/312-319 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1S72/37-43 ......C..C..G..U.ACCC.AUC.CC..GAACAC....G..G....... | ||
| #=GR 1S72/37-43 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1U0B/31-39 ......G..C..G..G....A.UUG.CAAAU...CC....G..U....... | ||
| #=GR 1U0B/31-39 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1U0B/53-61 ......U..C..C..G....G.UUC.GACUC...CG....G..A....... | ||
| #=GR 1U0B/53-61 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1U9S/181-189 ......G..G.CG..G....G.GUA.AGAGC...CCA...C..C....... | ||
| #=GR 1U9S/181-189 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1VFG/53-61 ......G..G..C..G....G.UUC.GAUUC...CG....C..C....... | ||
| #=GR 1VFG/53-61 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1WZ2/965-973 ......C..G..G..G....G.UUC.GAAUC...CC....C..G....... | ||
| #=GR 1WZ2/965-973 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1Y0Q/224-234 ...GG.A..U..A..G....GAGUAACGAAC...CU....A..U..CC... | ||
| #=GR 1Y0Q/224-234 SS ...((.(..(..(..(....(.........)...))....)..)..))... | ||
| 1Y69/1103-1110 .........G..A..G....UGCGUAAUA.G...CU....C.......... | ||
| #=GR 1Y69/1103-1110 SS .........(..(..(....(.........)...))....).......... | ||
| 1Y69/1855-1862 .........G..C..G....G.UGC.AA.GC...UG....C.......... | ||
| #=GR 1Y69/1855-1862 SS .........(..(..(....(.........)...))....).......... | ||
| 1Y69/1932-1940 ......G..U..C..G....G.GUA.AGUUC...CG....A..C....... | ||
| #=GR 1Y69/1932-1940 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 1Y69/2227-2235 ............G..A....C.UGG.GGCGG...UC............... | ||
| 1Y69/2334-2341 ............G..A....C.UGA.CA.CG...UC............... | ||
| 1Y69/2794-2802 ......C..C..C..G....G.AAG.ACCAC...CG....G..G....... | ||
| 1Y69/316-323 ......G..U..G..G....C.UGG.AA.AG...CU....A..C....... | ||
| 1Y69/575-584 ...............C...CU.AUUGAAGCAU..G................ | ||
| 1Y69/725-732 ......C..C..C..C....C.GUG.AC.AG...GG....G..G....... | ||
| #=GR 1Y69/725-732 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2A2E/156-164 ......G..U..G..G....G.GUA.AGAGC...CC....A..C....... | ||
| #=GR 2A2E/156-164 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2A64/69-76 ......C..G..G.UG....C.UGA.GA.UG...CC....C..G....... | ||
| #=GR 2A64/69-76 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2AVY/259-267 ..UAG.G..U..G..G....G.GUA.ACGGC...UC....A..C..CUA.. | ||
| #=GR 2AVY/259-267 SS ..(((.(..(..(..(....(.........)...))....)..)..))).. | ||
| 2AVY/689-698 ..AGG.U.GU.AG..C....G.GUG.AA.AU...GCGUAGAG.A..UCU.. | ||
| #=GR 2AVY/689-698 SS ..(((.(..(..(..(....(.........)...))....)..)..))).. | ||
| 2AVY/786-796 .........C..A..G....GAUUAGAUACC...CU....G.......... | ||
| #=GR 2AVY/786-796 SS .........(..(..(....(.........)...))....).......... | ||
| 2AW4/1092-1099 .........GAAA..G....C.GUA.AU.AG...CU....C.......... | ||
| #=GR 2AW4/1092-1099 SS .........(..(..(....(.........)...))....).......... | ||
| 2AW4/1949-1957 ......G..U..C..G....G.GUA.AGUUC...CG....A..C....... | ||
| #=GR 2AW4/1949-1957 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2AW4/2248-2256 ............G..A....C.UGG.GGCGG...UC............... | ||
| 2AW4/2819-2827 ......C..G..U..U....G.AAG.ACGAC...GA....C..G....... | ||
| #=GR 2AW4/2819-2827 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2AW4/305-312 ......G..C..G..U....C.UGG.AA.AG...GC....G..C....... | ||
| #=GR 2AW4/305-312 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2AW4/38-44 ......C..U..G..A.CCCC.AUG.CC..GAACUC....A..G....... | ||
| #=GR 2AW4/38-44 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2AW4/712-719 ....G.G..U..U..G....G.GUA.AC.AC...UA....A..C..U.... | ||
| #=GR 2AW4/712-719 SS ....(.(..(..(..(....(.........)...))....)..)..).... | ||
| 2AZX/531-539 ......U..C..U..G....A.CUC.CAGAU...CA....G..A....... | ||
| #=GR 2AZX/531-539 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2AZX/553-561 ......G..C..G..U....G.UUC.GAAUC...AC....G..U....... | ||
| #=GR 2AZX/553-561 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2BH2/1949-1957 ......G..U..C..G....G.GUA.AGUUC...CG....A..C....... | ||
| #=GR 2BH2/1949-1957 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2BTE/53-61 ......G..C..G..G....G.UUC.AAGUC...CC....G..C....... | ||
| #=GR 2BTE/53-61 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2CT8/53-61 ......G..G..A..G....G.UUC.GAGUC...CU....C..C....... | ||
| #=GR 2CT8/53-61 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2D6F/953-961 ......A..G..C..G....G.UUC.GACUC...CG....C..U....... | ||
| #=GR 2D6F/953-961 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2DER/31-39 ......C..C..G..C....C.CUU.UCACG...GC....G..G....... | ||
| #=GR 2DER/31-39 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2DER/53-61 .........G..G..G....G.UUC.GAAUC...CC....C.......... | ||
| #=GR 2DER/53-61 SS .........(..(..(....(.........)...))....).......... | ||
| 2DET/31-39 ......C..C..G..C....C.CUU.UCACG...GC....G..G....... | ||
| #=GR 2DET/31-39 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2DET/53-61 ............G..G....G.UUC.GAAUC...CC............... | ||
| #=GR 2DET/53-61 SS ............(..(....(.........)...))............... | ||
| 2DEU/31-39 ......C..C..G..C....C.CUU.UCACG...GC....G..G....... | ||
| #=GR 2DEU/31-39 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2DEU/53-61 .........G..G..G....G.UUC.GAAUC...CCC...U.......... | ||
| #=GR 2DEU/53-61 SS .........(..(..(....(.........)...))....).......... | ||
| 2DR2/31-39 ......U..C..U..G....A.CUC.CAGAU...CA....G..A....... | ||
| #=GR 2DR2/31-39 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2DR2/53-61 ......G..C..G..U....G.UUC.GAAUC...AC....G..U....... | ||
| #=GR 2DR2/53-61 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2G9C/46-53 ....C.G..G..G..C....A.CCG.UAAAU...GU....C..C..G.... | ||
| #=GR 2G9C/46-53 SS ....(.(..(..(..(....(.........)...))....)..)..).... | ||
| 2HOP/65-74 ......C..C..U..GaUUGG.AUA.AU.CCAGGU.....A..G..G.... | ||
| #=GR 2HOP/65-74 SS ......(..(..(..(....(.........)...).....)..)..).... | ||
| thi-Box ..CCU.GAUC..U..G....G.AUA.AUG.C...CA....GCGU..AGG.. | ||
| #=GR thi-Box SS ..(((.(..(..(..(....(.........)...))....)..)..))).. | ||
| 2IL9/6118-6124 .........G..G..A....G.CGA.AA.GC...UC....C.......... | ||
| #=GR 2IL9/6118-6124 SS .........(..(..(....(.........)...))....).......... | ||
| 2IY5/31-39 ......U..G..C..G....A.CUG.AAAAU...CG....C..A....... | ||
| #=GR 2IY5/31-39 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2J01/1949-1957 ......G..G..C..C....G.UGAAGAUGC...GG....C..C....... | ||
| #=GR 2J01/1949-1957 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2J01/2355-2362 ...............G....C.GUC.CACAG...C................ | ||
| 2J01/2551-2557 .CGGU.G..G.UC..C....C.GUGUGGAAG...GG....C..C..AUCG. | ||
| #=GR 2J01/2551-2557 SS .((((.(..(..(..(....(.........)...))....)..)..)))). | ||
| 2J01/2819-2827 ......C..C..G..G....G.AAG.ACCAC...CC....G..G....... | ||
| #=GR 2J01/2819-2827 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2J01/305-312 ......G..C..U..G....U.UGG.GA.AG...CA....G..C....... | ||
| #=GR 2J01/305-312 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2J01/566-575 ............C..C....U.AUUGAAGCA...UG............... | ||
| 2J01/712-719 ....G.C..U..G..G....G.GUG.AG.AC...CC....A..G..U.... | ||
| #=GR 2J01/712-719 SS ....(.(..(..(..(....(.........)...))....)..)..).... | ||
| 2DU3/952-960 ......C..C..C..G....G.UUC.GAAUC...CG....G..G....... | ||
| #=GR 2DU3/952-960 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2FK6/53-61 ......A..G..C..G....G.UUC.GAGCC...CG....C..U....... | ||
| #=GR 2FK6/53-61 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2NQP/53-61 .........C..G..G....G.UUC.AAGUC...CC....G.......... | ||
| #=GR 2NQP/53-61 SS .........(..(..(....(.........)...))....).......... | ||
| 2NR0/53-61 ......A..C..G..G....G.UUC.AAGUC...CC....G..U....... | ||
| #=GR 2NR0/53-61 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2NRE/53-61 ......A..C..G..G....G.UUC.AAGUC...CC....G..U....... | ||
| #=GR 2NRE/53-61 SS ......(..(..(..(....(.........)...))....)..)....... | ||
| 2R8S/166-174 ...............C....C.UUG.CAAAG...G................ | ||
| #=GR 2R8S/166-174 SS ...............(....(.........)...)................ | ||
| 387D/4-13 .........u..C..C....G.AAGUGCAAC...GGGA..A.......... | ||
| #=GR 387D/4-13 SS .........(..(..(....(.........)...))....).......... | ||
| 3B31/6184-6193 gGUUA.U..U..C.AG....A.UUAGGUAGU...CG....A..A..UGACC | ||
| #=GR 3B31/6184-6193 SS (((((.(..(..(..(....(.........)...))....)..)..))))) | ||
| #=GC SS_cons (((((.(..(..(..(....(.........)...))....)..)..))))) | ||
| // |
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