Nucleic Acids Research, 2005, Vol. 33, Database issue D139-D140
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
Compilation of tRNA sequences and sequences of tRNA genes
Laboratorium für Biochemie, Universität Bayreuth, 95440 Bayreuth, Germany and 1 Institute of Protein Research, Russian Academy of Sciences, 142290 Puschchino, Moscow Region, Russia
* To whom correspondence should be addressed. Tel: +49 921 552420; Fax: +49 921 552432; Email: Mathias.Sprinzl{at}uni-bayreuth.de
Received September 15, 2004; Accepted September 15, 2004
Maintained at the Universität Bayreuth, Bayreuth, Germany, the Compilation of tRNA Sequences and Sequences of tRNA Genes is accessible at the URL http://www.tRNA.uni-bayreuth.de with mirror site located at the Institute of Protein Research, Pushchino, Russia (http://alpha.protres.ru/trnadbase). The compilation is a searchable, periodically updated database of currently available tRNA sequences. The present version of the database contains a new Genomic tRNA Compilation including the sequences of tRNA genes from genomic sequences published up to July 2003. It consists of about 5800 tRNA gene sequences from 111 organisms covering archaea, bacteria, higher and lower eukarya. The former Compilation of tRNA Genes (up to the end of 1998) and the updated Compilation tRNA Sequences (561 entries) are also supported by the new software. The database can be explored by using multiple search criteria and sequence templates. The database provides a service that allows to obtain statistical information on the occurrences of certain bases at given positions of the tRNA sequences. This allows phylogenic studies and search for identity elements in respect to interactions of tRNAs with various enzymes.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  F. A.P. Vendeix, A. M. Munoz, and P. F. Agris Free energy calculation of modified base-pair formation in explicit solvent: A predictive model RNA, December 1, 2009; 15(12): 2278 - 2287. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Huang, E. V. Koonin, D. J. Lipman, and T. M. Przytycka Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage Nucleic Acids Res., November 1, 2009; 37(20): 6799 - 6810. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Jaric, S. Bilokapic, S. Lesjak, A. Crnkovic, N. Ban, and I. Weygand-Durasevic Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition J. Biol. Chem., October 30, 2009; 284(44): 30643 - 30651. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. El Yacoubi, B. Lyons, Y. Cruz, R. Reddy, B. Nordin, F. Agnelli, J. R. Williamson, P. Schimmel, M. A. Swairjo, and V. de Crecy-Lagard The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA Nucleic Acids Res., May 1, 2009; 37(9): 2894 - 2909. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Muller, A. Urban, A. Hecker, F. Leclerc, C. Branlant, and Y. Motorin Deficiency of the tRNATyr:{Psi}35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery Nucleic Acids Res., March 1, 2009; 37(4): 1308 - 1322. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Urban, I. Behm-Ansmant, C. Branlant, and Y. Motorin RNA Sequence and Two-dimensional Structure Features Required for Efficient Substrate Modification by the Saccharomyces cerevisiae RNA:{Psi}-Synthase Pus7p J. Biol. Chem., February 27, 2009; 284(9): 5845 - 5858. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Schaefer, T. Pollex, K. Hanna, and F. Lyko RNA cytosine methylation analysis by bisulfite sequencing Nucleic Acids Res., February 1, 2009; 37(2): e12 - e12. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. P. Chan and T. M. Lowe GtRNAdb: a database of transfer RNA genes detected in genomic sequence Nucleic Acids Res., January 1, 2009; 37(suppl_1): D93 - D97. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Abe, T. Ikemura, Y. Ohara, H. Uehara, M. Kinouchi, S. Kanaya, Y. Yamada, A. Muto, and H. Inokuchi tRNADB-CE: tRNA gene database curated manually by experts Nucleic Acids Res., January 1, 2009; 37(suppl_1): D163 - D168. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Czerwoniec, S. Dunin-Horkawicz, E. Purta, K. H. Kaminska, J. M. Kasprzak, J. M. Bujnicki, H. Grosjean, and K. Rother MODOMICS: a database of RNA modification pathways. 2008 update Nucleic Acids Res., January 1, 2009; 37(suppl_1): D118 - D121. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Juhling, M. Morl, R. K. Hartmann, M. Sprinzl, P. F. Stadler, and J. Putz tRNAdb 2009: compilation of tRNA sequences and tRNA genes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D159 - D162. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Gurha and R. Gupta Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA RNA, December 1, 2008; 14(12): 2521 - 2527. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Sugahara, K. Kikuta, K. Fujishima, N. Yachie, M. Tomita, and A. Kanai Comprehensive Analysis of Archaeal tRNA Genes Reveals Rapid Increase of tRNA Introns in the Order Thermoproteales Mol. Biol. Evol., December 1, 2008; 25(12): 2709 - 2716. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Lusic, E. M. Gustilo, F. A.P. Vendeix, R. Kaiser, M. O. Delaney, W. D. Graham, V. A. Moye, W. A. Cantara, P. F. Agris, and A. Deiters Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNAMet Nucleic Acids Res., November 1, 2008; 36(20): 6548 - 6557. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. T. Rubio, J. J. Rinehart, B. Krett, S. Duvezin-Caubet, A. S. Reichert, D. Soll, and J. D. Alfonzo Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import PNAS, July 8, 2008; 105(27): 9186 - 9191. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Targanski and V. Cherkasova Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon-codon hydrogen bonds as a major determinant of tRNA compositional variations RNA, June 1, 2008; 14(6): 1095 - 1109. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Roovers, K. H. Kaminska, K. L. Tkaczuk, D. Gigot, L. Droogmans, and J. M. Bujnicki The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK) Nucleic Acids Res., June 1, 2008; 36(10): 3252 - 3262. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. A. Decatur and M. N. Schnare Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs Mol. Cell. Biol., May 15, 2008; 28(10): 3089 - 3100. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Alian, T. T. Lee, S. L. Griner, R. M. Stroud, and J. Finer-Moore Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases PNAS, May 13, 2008; 105(19): 6876 - 6881. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Kondo and E. Westhof The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates Nucleic Acids Res., May 1, 2008; 36(8): 2654 - 2666. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. J. Paukstelis and A. M. Lambowitz Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity PNAS, April 22, 2008; 105(16): 6010 - 6015. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Bonnefond, C. Florentz, R. Giege, and J. Rudinger-Thirion Decreased aminoacylation in pathology-related mutants of mitochondrial tRNATyr is associated with structural perturbations in tRNA architecture RNA, April 1, 2008; 14(4): 641 - 648. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Lloyd, A. M. Gilbey, A. M. Blewett, G. De Pascale, A. El Zoeiby, R. C. Levesque, A. C. Catherwood, A. Tomasz, T. D. H. Bugg, D. I. Roper, et al. Characterization of tRNA-dependent Peptide Bond Formation by MurM in the Synthesis of Streptococcus pneumoniae Peptidoglycan J. Biol. Chem., March 7, 2008; 283(10): 6402 - 6417. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Montanari, C. Besagni, C. De Luca, V. Morea, R. Oliva, A. Tramontano, M. Bolotin-Fukuhara, L. Frontali, and S. Francisci Yeast as a model of human mitochondrial tRNA base substitutions: Investigation of the molecular basis of respiratory defects RNA, February 1, 2008; 14(2): 275 - 283. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. J. Nasvall, P. Chen, and G. R. Bjork The wobble hypothesis revisited: Uridine-5-oxyacetic acid is critical for reading of G-ending codons RNA, December 1, 2007; 13(12): 2151 - 2164. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. W. Gaston, M. A. T. Rubio, J. L. Spears, I. Pastar, F. N. Papavasiliou, and J. D. Alfonzo C to U editing at position 32 of the anticodon loop precedes tRNA 5' leader removal in trypanosomatids Nucleic Acids Res., November 29, 2007; 35(20): 6740 - 6749. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Abergel, J. Rudinger-Thirion, R. Giege, and J.-M. Claverie Virus-Encoded Aminoacyl-tRNA Synthetases: Structural and Functional Characterization of Mimivirus TyrRS and MetRS J. Virol., November 15, 2007; 81(22): 12406 - 12417. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Soma, A. Onodera, J. Sugahara, A. Kanai, N. Yachie, M. Tomita, F. Kawamura, and Y. Sekine Permuted tRNA Genes Expressed via a Circular RNA Intermediate in Cyanidioschyzon merolae Science, October 19, 2007; 318(5849): 450 - 453. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Oliva, A. Tramontano, and L. Cavallo Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs RNA, September 1, 2007; 13(9): 1427 - 1436. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Leger, D. Dulude, S. V. Steinberg, and L. Brakier-Gingras The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift Nucleic Acids Res., August 17, 2007; (2007) gkm578v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Putz, B. Dupuis, M. Sissler, and C. Florentz Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures RNA, August 1, 2007; 13(8): 1184 - 1190. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Taquist, Y. Cui, and D. H. Ardell TFAM 1.0: an online tRNA function classifier Nucleic Acids Res., July 13, 2007; 35(suppl_2): W350 - W353. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Walbott, C. Husson, S. Auxilien, and B. Golinelli-Pimpaneau Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase RNA, July 1, 2007; 13(7): 967 - 973. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Auxilien, F. El Khadali, A. Rasmussen, S. Douthwaite, and H. Grosjean Archease from Pyrococcus abyssi Improves Substrate Specificity and Solubility of a tRNA m5C Methyltransferase J. Biol. Chem., June 29, 2007; 282(26): 18711 - 18721. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. L. S. Ng and S. K. Mishra De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures Bioinformatics, June 1, 2007; 23(11): 1321 - 1330. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Roy, H. D. Becker, M.-H. Mazauric, and D. Kern Structural elements defining elongation factor Tu mediated suppression of codon ambiguity Nucleic Acids Res., May 11, 2007; 35(10): 3420 - 3430. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. T. Rubio, I. Pastar, K. W. Gaston, F. L. Ragone, C. J. Janzen, G. A. M. Cross, F. N. Papavasiliou, and J. D. Alfonzo An adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U deamination of DNA PNAS, May 8, 2007; 104(19): 7821 - 7826. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Wang, B. W. Sobral, and K. P. Williams Loss of a Universal tRNA Feature J. Bacteriol., March 1, 2007; 189(5): 1954 - 1962. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. NG Kwang Loong and S. K. Mishra Unique folding of precursor microRNAs: Quantitative evidence and implications for de novo identification RNA, February 1, 2007; 13(2): 170 - 187. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hossain and P. A. Limbach Mass spectrometry-based detection of transfer RNAs by their signature endonuclease digestion products RNA, February 1, 2007; 13(2): 295 - 303. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Goodenbour and T. Pan Diversity of tRNA genes in eukaryotes Nucleic Acids Res., December 4, 2006; 34(21): 6137 - 6146. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. E. McCrate, M. E. Varner, K. I. Kim, and M. C. Nagan Molecular dynamics simulations of human Formula: the role of modified bases in mRNA recognition Nucleic Acids Res., November 14, 2006; 34(19): 5361 - 5368. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. J. Silva, E. Belda, and S. E. Talens Differential annotation of tRNA genes with anticodon CAT in bacterial genomes Nucleic Acids Res., November 6, 2006; 34(20): 6015 - 6022. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Arita, T. Suematsu, A. Osanai, T. Inaba, H. Kamiya, K. Kita, M. Sisido, Y.-i. Watanabe, and T. Ohtsuki An evolutionary 'intermediate state' of mitochondrial translation systems found in Trichinella species of parasitic nematodes: co-evolution of tRNA and EF-Tu Nucleic Acids Res., October 6, 2006; 34(18): 5291 - 5299. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Rosen, B. S. Brooks, E. Guth, C. S. Francklyn, and K. Musier-Forsyth Evolutionary conservation of a functionally important backbone phosphate group critical for aminoacylation of histidine tRNAs RNA, July 1, 2006; 12(7): 1315 - 1322. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Fender, C. Sauter, M. Messmer, J. Putz, R. Giege, C. Florentz, and M. Sissler Loss of a Primordial Identity Element for a Mammalian Mitochondrial Aminoacylation System J. Biol. Chem., June 9, 2006; 281(23): 15980 - 15986. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. N. Suhasini and R. Sirdeshmukh Transfer RNA Cleavages by Onconase Reveal Unusual Cleavage Sites J. Biol. Chem., May 5, 2006; 281(18): 12201 - 12209. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. D. Kapp, S. E. Kolitz, and J. R. Lorsch Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation RNA, May 1, 2006; 12(5): 751 - 764. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. Cridge, L. L. Major, A. A. Mahagaonkar, E. S. Poole, L. A. Isaksson, and W. P. Tate Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms Nucleic Acids Res., April 13, 2006; 34(7): 1959 - 1973. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Sabina and D. Soll The RNA-binding PUA Domain of Archaeal tRNA-Guanine Transglycosylase Is Not Required for Archaeosine Formation J. Biol. Chem., March 17, 2006; 281(11): 6993 - 7001. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. DING Statistical and Bayesian approaches to RNA secondary structure prediction. RNA, March 1, 2006; 12(3): 323 - 331. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Freyhult, V. Moulton, and D. H. Ardell Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos Nucleic Acids Res., February 9, 2006; 34(3): 905 - 916. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Oliva, L. Cavallo, and A. Tramontano Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions Nucleic Acids Res., February 6, 2006; 34(3): 865 - 879. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Helm Post-transcriptional nucleotide modification and alternative folding of RNA Nucleic Acids Res., February 1, 2006; 34(2): 721 - 733. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Shigi, T. Suzuki, T. Terada, M. Shirouzu, S. Yokoyama, and K. Watanabe Temperature-dependent Biosynthesis of 2-Thioribothymidine of Thermus thermophilus tRNA J. Biol. Chem., January 27, 2006; 281(4): 2104 - 2113. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. G. Goll, F. Kirpekar, K. A. Maggert, J. A. Yoder, C.-L. Hsieh, X. Zhang, K. G. Golic, S. E. Jacobsen, and T. H. Bestor Methylation of tRNAAsp by the DNA Methyltransferase Homolog Dnmt2 Science, January 20, 2006; 311(5759): 395 - 398. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. T. Rubio, F. L. Ragone, K. W. Gaston, M. Ibba, and J. D. Alfonzo C to U Editing Stimulates A to I Editing in the Anticodon Loop of a Cytoplasmic Threonyl tRNA in Trypanosoma brucei J. Biol. Chem., January 6, 2006; 281(1): 115 - 120. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Marck, R. Kachouri-Lafond, I. Lafontaine, E. Westhof, B. Dujon, and H. Grosjean The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res., January 1, 2006; 34(6): 1816 - 1835. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Dunin-Horkawicz, A. Czerwoniec, M. J. Gajda, M. Feder, H. Grosjean, and J. M. Bujnicki MODOMICS: a database of RNA modification pathways Nucleic Acids Res., January 1, 2006; 34(suppl_1): D145 - D149. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Suematsu, A. Sato, M. Sakurai, K. Watanabe, and T. Ohtsuki A unique tRNA recognition mechanism of Caenorhabditis elegans mitochondrial EF-Tu2 Nucleic Acids Res., August 19, 2005; 33(15): 4683 - 4691. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. OZANICK, A. KRECIC, J. ANDERSLAND, and J. T. ANDERSON The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans RNA, August 1, 2005; 11(8): 1281 - 1290. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Urbonavicius, S. Skouloubris, H. Myllykallio, and H. Grosjean Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria--evolutionary implications Nucleic Acids Res., July 18, 2005; 33(13): 3955 - 3964. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. BONNEFOND, M. FRUGIER, R. GIEGE, and J. RUDINGER-THIRION Human mitochondrial TyrRS disobeys the tyrosine identity rules RNA, May 1, 2005; 11(5): 558 - 562. [Abstract] [Full Text] [PDF]
|
|