RF00001
5S_rRNA
   [1]
   11752286
   5S Ribosomal RNA Database.
  Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J;
   Nucleic Acids Res 2002;30:176-178.
   [2]
   11283358
   Crystal structure of the ribosome at 5.5 A resolution.
  Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH,
  Noller HF;
   Science 2001;292:883-896.
   [3]
   10926492
   The role of the central zinc fingers of transcription factor IIIA in
   binding to 5 S RNA.
  Searles MA, Lu D, Klug A;
   J Mol Biol 2000;301:47-60.
RF00002
5_8S_rRNA
   [1]
   11125083
   The European Large Subunit Ribosomal RNA Database.
  Wuyts J, De Rijk P, Van de Peer Y, Winkelmans T, De Wachter R;
   Nucleic Acids Res 2001;29:175-177.
   [2]
   9108162
   Role of the 5.8S rRNA in ribosome translocation.
  Abou Elela S, Nazar RN;
   Nucleic Acids Res 1997;25:1788-1794.
   [3]
   9154813
   Cytoplasmic p53 polypeptide is associated with ribosomes.
  Fontoura BM, Atienza CA, Sorokina EA, Morimoto T, Carroll RB;
   Mol Cell Biol 1997;17:3146-3154.
RF00003
U1
   [1]
   9016512
   The uRNA database.
  Zwieb C;
   Nucleic Acids Res 1997;25:102-103.
   [2]
   2405391
   Saccharomyces cerevisiae U1 small nuclear RNA secondary structure
   contains both universal and yeast-specific domains.
  Kretzner L, Krol A, Rosbash M;
   Proc Natl Acad Sci U S A 1990;87:851-855.
   [3]
   7984237
   Crystal structure at 1.92 A resolution of the RNA-binding domain of
   the U1A spliceosomal protein complexed with an RNA hairpin.
  Oubridge C, Ito N, Evans PR, Teo CH, Nagai K;
   Nature 1994;372:432-438.
   [4]
   11297556
   Two functionally distinct steps mediate high affinity binding of U1A
   protein to U1 hairpin II RNA.
  Katsamba PS, Myszka DG, Laird-Offringa IA;
   J Biol Chem 2001;276:21476-21481.
RF00004
U2
   [1]
   9016512
   The uRNA database.
  Zwieb C;
   Nucleic Acids Res 1997;25:102-103.
   [2]
   11424937
   A conserved pseudouridine modification in eukaryotic U2 snRNA induces
   a change in branch-site architecture.
  Newby MI, Greenbaum NL;
   RNA 2001;7:833-845.
   [3]
   11350032
   Crystal structure of a model branchpoint-U2 snRNA duplex containing
   bulged adenosines.
  Berglund JA, Rosbash M, Schultz SC;
   RNA 2001;7:682-691.
   [4]
   2339054
   The spliceosomal snRNAs of Caenorhabditis elegans.
  Thomas J, Lea K, Zucker-Aprison E, Blumenthal T;
   Nucleic Acids Res 1990;18:2633-2642.
RF00005
tRNA
   [1]
   8256282
   The tertiary structure of tRNA and the development of the genetic
   code.
  Hou YM;
   Trends Biochem Sci 1993;18:362-364.
   [2]
   9023104
   tRNAscan-SE: a program for improved detection of transfer RNA genes
   in genomic sequence.
  Lowe TM, Eddy SR;
   Nucleic Acids Res 1997;25:955-964.
RF00008
Hammerhead_3
   [1]
   7969422
   Three-dimensional structure of a hammerhead ribozyme.
  Pley HW, Flaherty KM, McKay DB;
   Nature 1994;372:68-74.
   [2]
   9506521
   The structural basis of hammerhead ribozyme self-cleavage.
  Murray JB, Terwey DP, Maloney L, Karpeisky A, Usman N, Beigelman L,
  Scott WG;
   Cell 1998;92:665-673.
   [3]
   10899150
   Distribution of hammerhead and hammerhead-like RNA motifs through the
   GenBank.
  Ferbeyre G, Bourdeau V, Pageau M, Miramontes P, Cedergren R;
   Genome Res 2000;10:1011-1019.
RF00011
RNaseP_bact_b
   [1]
   9759486
   Ribonuclease P: unity and diversity in a tRNA processing ribozyme.
  Frank DN, Pace NR;
   Annu Rev Biochem 1998;67:153-180.
   [2]
   9847214
   The Ribonuclease P Database.
  Brown JW;
   Nucleic Acids Res 1999;27:314.
RF00012
U3
   [1]
   9016512
   The uRNA database.
  Zwieb C;
   Nucleic Acids Res 1997;25:102-103.
   [2]
   10567566
   Nuclear retention elements of U3 small nucleolar RNA.
  Speckmann W, Narayanan A, Terns R, Terns MP;
   Mol Cell Biol 1999;19:8412-8421.
RF00015
U4
   [1]
   9016512
   The uRNA database.
  Zwieb C;
   Nucleic Acids Res 1997;25:102-103.
   [2]
   11163207
   Crystal structure of the spliceosomal 15.5kD protein bound to a U4
   snRNA fragment.
  Vidovic I, Nottrott S, Hartmuth K, Luhrmann R, Ficner R;
   Mol Cell 2000;6:1331-1342.
   [3]
   9452384
   A spliceosomal recycling factor that reanneals U4 and U6 small
   nuclear ribonucleoprotein particles.
  Raghunathan PL, Guthrie C;
   Science 1998;279:857-860.
   [4]
   2339054
   The spliceosomal snRNAs of Caenorhabditis elegans.
  Thomas J, Lea K, Zucker-Aprison E, Blumenthal T;
   Nucleic Acids Res 1990;18:2633-2642.
RF00017
SRP_euk_arch
   [1]
   11839493
   Towards the structure of the mammalian signal recognition particle.
  Wild K, Weichenrieder O, Strub K, Sinning I, Cusack S;
   Curr Opin Struct Biol 2002;12:72-81.
   [2]
   10678824
   Crystal structure of the ribonucleoprotein core of the signal
   recognition particle.
  Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA;
   Science 2000;287:1232-1239.
   [3]
   11243816
   Structural and energetic analysis of RNA recognition by a universally
   conserved protein from the signal recognition particle.
  Batey RT, Sagar MB, Doudna JA;
   J Mol Biol 2001;307:229-246.
   [4]
   12520023
   SRPDB: Signal Recognition Particle Database.
  Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T;
   Nucleic Acids Res 2003;31:363-364.
   [5]
   12140321
   Prediction of signal recognition particle RNA genes.
  Regalia M, Rosenblad MA, Samuelsson T;
   Nucleic Acids Res 2002;30:3368-3377.
RF00019
Y
   [1]
   10606662
   Conserved features of Y RNAs: a comparison of experimentally derived
   secondary structures.
  Teunissen SW, Kruithof MJ, Farris AD, Harley JB, Venrooij WJ, Pruijn
  GJ;
   Nucleic Acids Res 2000;28:610-619.
   [2]
   7489501
   Caenorhabditis elegans embryos contain only one major species of Ro
   RNP.
  Van Horn DJ, Eisenberg D, O'Brien CA, Wolin SL;
   RNA 1995;1:293-303.
   [3]
   10766734
   Ro ribonucleoproteins contribute to the resistance of Deinococcus
   radiodurans to ultraviolet irradiation.
  Chen X, Quinn AM, Wolin SL;
   Genes Dev 2000;14:777-782.
RF00023
tmRNA
   [1]
   8972778
   Phylogenetic analysis of tmRNA secondary structure.
  Williams KP, Bartel DP;
   RNA 1996;2:1306-1310.
   [2]
   8990402
   Probing the structure of the Escherichia coli 10Sa RNA (tmRNA).
  Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF;
   RNA 1997;3:89-103.
   [3]
   11752287
   The tmRNA Website: invasion by an intron.
  Williams KP;
   Nucleic Acids Res 2002;30:179-182.
   [4]
   12140330
   BRUCE: a program for the detection of transfer-messenger RNA genes in
   nucleotide sequences.
  Laslett D, Canback B, Andersson S;
   Nucleic Acids Res 2002;30:3449-3453.
RF00024
Telomerase-vert
   [1]
   10721988
   Secondary structure of vertebrate telomerase RNA.
  Chen JL, Blasco MA, Greider CW;
   Cell 2000;100:503-514.
   [2]
   11842102
   Analysis of the structure of human telomerase RNA in vivo.
  Antal M, Boros E, Solymosy F, Kiss T;
   Nucleic Acids Res 2002;30:912-920.
RF00025
Telomerase-cil
   [1]
   7739888
   Ciliate telomerase RNA structural features.
  McCormick-Graham M, Romero DP;
   Nucleic Acids Res 1995;23:1091-1097.
   [2]
   7958872
   Telomerase RNAs of different ciliates have a common secondary
   structure and a permuted template.
  Lingner J, Hendrick LL, Cech TR;
   Genes Dev 1994;8:1984-1998.
RF00031
SECIS
   [1]
   8634917
   A novel RNA structural motif in the selenocysteine insertion element
   of eukaryotic selenoprotein mRNAs.
  Walczak R, Westhof E, Carbon P, Krol A;
   RNA 1996;2:367-379.
   [2]
   12458087
   A survey of metazoan selenocysteine insertion sequences.
  Lambert A, Lescure A, Gautheret D;
   Biochimie 2002;84:953-959.
RF00037
IRE
   [1]
   8710843
   Molecular control of vertebrate iron metabolism: mRNA-based
   regulatory circuits operated by iron, nitric oxide, and oxidative
   stress.
  Hentze MW, Kuhn LC;
   Proc Natl Acad Sci U S A 1996;93:8175-8182.
RF00050
RFN
   [1]
   12136096
   Regulation of riboflavin biosynthesis and transport genes in bacteria
   by transcriptional and translational attenuation.
  Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS;
   Nucleic Acids Res 2002;30:3141-3151.
   [2]
   10529804
   A conserved RNA structure element involved in the regulation of
   bacterial riboflavin synthesis genes.
  Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA;
   Trends Genet 1999;15:439-442.
   [3]
   12456892
   An mRNA structure that controls gene expression by binding FMN.
  Winkler WC, Cohen-Chalamish S, Breaker RR;
   Proc Natl Acad Sci U S A 2002;99:15908-15913.
RF00162
S_box
   [1]
   10094622
   The S box regulon: a new global transcription termination control
   system for methionine and cysteine biosynthesis genes in
   gram-positive bacteria.
  Grundy FJ, Henkin TM;
   Mol Microbiol 1998;30:737-749.
   [2]
   12910260
   An mRNA structure that controls gene expression by binding
   S-adenosylmethionine.
  Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR;
   Nat Struct Biol 2003;10:701-707.
   [3]
   12702767
   The riboswitch-mediated control of sulfur metabolism in bacteria.
  Epshtein V, Mironov AS, Nudler E;
   Proc Natl Acad Sci U S A 2003;100:5052-5056.
   [4]
   15215334
   Comparative genomics of the methionine metabolism in Gram-positive
   bacteria: a variety of regulatory systems.
  Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS;
   Nucleic Acids Res 2004;32:3340-3353.
RF00164
s2m
   [1]
   9568965
   A common RNA motif in the 3' end of the genomes of astroviruses,
   avian infectious bronchitis virus and an equine rhinovirus.
  Jonassen CM, Jonassen TO, Grinde B;
   J Gen Virol 1998;79:715-718.
   [2]
   15630477
   The structure of a rigorously conserved RNA element within the SARS
   virus genome.
  Robertson MP, Igel H, Baertsch R, Haussler D, Ares M Jr, Scott WG;
   PLoS Biol 2005;3:e5.
RF00167
Purine
   [1]
   12787499
   Riboswitches Control Fundamental Biochemical Pathways in Bacillus
   subtilis and Other Bacteria.
  Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR;
   Cell 2003;113:577-586.
   [2]
   14718920
   Adenine riboswitches and gene activation by disruption of a
   transcription terminator.
  Mandal M, Breaker RR;
   Nat Struct Mol Biol 2004;11:29-35.
RF00168
Lysine
   [1]
   12787499
   Riboswitches Control Fundamental Biochemical Pathways in Bacillus
   subtilis and Other Bacteria.
  Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR;
   Cell 2003;113:577-586.
   [2]
   14523230
   The L box regulon: Lysine sensing by leader RNAs of bacterial lysine
   biosynthesis genes.
  Grundy FJ, Lehman SC, Henkin TM;
   Proc Natl Acad Sci U S A 2003;100:12057-12062.
   [3]
   14597663
   An mRNA structure in bacteria that controls gene expression by
   binding lysine.
  Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR;
   Genes Dev 2003;17:2688-2697.
   [4]
   14627808
   Regulation of lysine biosynthesis and transport genes in bacteria:
   yet another RNA riboswitch?.
  Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS;
   Nucleic Acids Res 2003;31:6748-6757.
RF00169
SRP_bact
   [1]
   12520023
   SRPDB: Signal Recognition Particle Database.
  Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T;
   Nucleic Acids Res 2003;31:363-364.
   [2]
   12140321
   Prediction of signal recognition particle RNA genes.
  Regalia M, Rosenblad MA, Samuelsson T;
   Nucleic Acids Res 2002;30:3368-3377.
RF00181
sno_14q_I_II
   [1]
   12045206
   Identification of tandemly-repeated C/D snoRNA genes at the imprinted
   human 14q32 domain reminiscent of those at the Prader-Willi/Angelman
   syndrome region.
  Cavaille J, Seitz H, Paulsen M, Ferguson-Smith AC, Bachellerie JP;
   Hum Mol Genet 2002;11:1527-1538.
RF00233
Tymo_tRNA-like
   [1]
   15033563
   The tRNA-like structure of Turnip yellow mosaic virus RNA is a
   3'-translational enhancer.
  Matsuda D, Dreher TW;
   Virology 2004;321:36-46.
RF00236
ctRNA_pGA1
   [1]
   12670963
   Control of rep gene expression in plasmid pGA1 from Corynebacterium
   glutamicum.
  Venkova-Canova T, Patek M, Nesvera J;
   J Bacteriol 2003;185:2402-2409.
RF00436
UnaL2
   [1]
   15273327
   Solution structure of an RNA stem-loop derived from the 3' conserved
   region of eel LINE UnaL2.
  Baba S, Kajikawa M, Okada N, Kawai G;
   RNA 2004;10:1380-1387.