G~tRNA~db: The Genomic tRNA Database

tRNAscan-SE analysis of complete genomes
 

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Introduction

This genomic tRNA database contains tRNA identifications made by the program tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964, 1997) on complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been inspected for agreement with published literature.

Inevitably with automated sequence analysis, we find exceptions to general identification rules, isoacceptor type predictions (esp. due to variable post-transcriptional anticodon modification), and questionable tRNA identifications (due to pseudogenes, SINES, or other tRNA-derived elements). We attempt to document all cases we come across, and welcome feedback (lowe @soe.ucsc.edu) on new or unrecognized discrepancies. For a more detailed description of information in tables and the tRNA search algorithm, see the [Legend].

Genomes
[Eukarya] [Archaea] [Bacteria]


Eukarya

Anopheles gambiae Aspergillus fumigatus Arabidopsis thaliana (Feb 2004)
Bos taurus (cow) (Baylor release Btau_4.0 Oct 2007) Candida glabrata CBS138 Caenorhabditis brenneri (Jan 2007)
Caenorhabditis briggsae (cb3 Jan 2007) Caenorhabditis elegans (Jan 2007) Canis familiaris (dog) (May 2005)
Caenorhabditis remanei (Mar 2006) Cryptococcus neoformans var JEC21 Debaryomyces hansenii CBS767
Drosophila melanogaster (Release 5 Apr 2006) Danio rerio (Zebrafish) (danRer5 July 2007) Equus caballus (horse) (Jan 2007)
Encephalitozoon cuniculi Eremothecium gossypii Felis catus (cat) (Broad Release 3 May 2005)
Takifugu rubripes (fr2 Oct 2004) Gallus gallus (galGal3 May 2006) Glycine max (soybean) (Glyma0 preliminary release)
Homo sapiens (Hg18 Mar 2006) Kluyveromyces lactis NRRL Y-1140 Macaca mulatta (Rhesus Jan 2006)
Mus musculus (mm9 July 2007) Medicago truncatula (Aug 2007 Version 2.0) Oryza sativa
Plasmodium falciparum (Oct 2007) Pongo pygmaeus abelii (orangutan) (July 2007) Pan troglodytes (chimp) (Mar 2006)
Rattus norvegicus (rn4 Nov 2004) Saccharomyces cerevisiae Schizosaccharomyces pombe
Strongylocentrotus purpuratus (Sea urchin) (Version 2.1) Yarrowia lipolytica CLIB99
Number of Genomes: 35

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Archaea

Aeropyrum pernix Archaeoglobus fulgidus Caldivirga maquilingensis IC-167
Candidatus Korarchaeum cryptofilum OPF8 Candidatus Methanoregula boonei 6A8 Cenarchaeum symbiosum
Ferroplasma acidarmanus Fer1 Haloarcula marismortui ATCC 43049 Halobacterium salinarum R1
Halobacterium sp Haloferax volcanii DS2 Haloquadratum walsbyi
Hyperthermus butylicus Ignicoccus hospitalis KIN4 I Metallosphaera sedula DSM 5348
Methanosarcina acetivorans Methanococcus aeolicus Nankai-3 Methanosarcina barkeri fusaro
Methanococcoides burtonii DSM 6242 Methanospirillum hungatei JF-1 Methanococcus jannaschii
Methanopyrus kandleri Methanocorpusculum labreanum Z Methanococcus maripaludis C5
Methanococcus maripaludis C6 Methanococcus maripaludis C7 Methanoculleus marisnigri JR1
Methanococcus maripaludis S2 Methanosarcina mazei Methanobrevibacter smithii ATCC 35061
Methanosphaera stadtmanae Methanobacterium thermoautotrophicum Methanosaeta thermophila PT
Methanococcus vannielii SB Nanoarchaeum equitans Natronomonas pharaonis
Nitrosopumilus maritimus SCM1 Picrophilus torridus DSM 9790 Pyrococcus abyssi
Pyrobaculum aerophilum Pyrobaculum arsenaticum DSM 13514 Pyrobaculum calidifontis JCM 11548
Pyrococcus furiosus Pyrococcus horikoshii Pyrobaculum islandicum DSM 4184
Staphylothermus marinus F1 Sulfolobus acidocaldarius DSM 639 Sulfolobus solfataricus
Sulfolobus tokodaii Thermoplasma acidophilum Thermococcus kodakaraensis KOD1
Thermoproteus neutrophilus V24Sta Thermofilum pendens Hrk 5 Thermoplasma volcanium
uncultured methanogenic archaeon RC-I
Number of Genomes: 55

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Bacteria

Acidovorax JS42 Acidovorax avenae citrulli AAC00-1 Acidobacteria bacterium Ellin345
Acidothermus cellulolyticus 11B Acidiphilium cryptum JF-5 Acinetobacter sp ADP1
Actinobacillus pleuropneumoniae L20 Aeromonas hydrophila ATCC 7966 Agrobacterium tumefaciens C58 Cereon
Agrobacterium tumefaciens C58 UWash Alcanivorax borkumensis SK2 Alkalilimnicola ehrlichei MLHE-1
Alkaliphilus metalliredigens QYMF Anabaena variabilis ATCC 29413 Anaeromyxobacter dehalogenans 2CP-C
Anaplasma marginale St Maries Anaplasma phagocytophilum HZ Aquifex aeolicus
Arthrobacter FB24 Aster yellows witches-broom phytoplasma AYWB Azoarcus sp EbN1
Azorhizobium caulinodans ORS 571 Bacillus anthracis A2012 Bacillus anthracis Ames
Bacillus anthracis Ames 0581 Bacillus anthracis str Sterne Bacillus cereus ATCC14579
Bacillus cereus ATCC 10987 Bacillus cereus ZK Bacillus clausii KSM-K16
Bacillus halodurans Bacillus licheniformis ATCC 14580 Bacillus licheniformis DSM 13
Bacillus subtilis Bacillus thuringiensis konkukian Bacteroides fragilis NCTC 9434
Bacteroides fragilis YCH46 Bacteroides thetaiotaomicron VPI-5482 Bartonella henselae Houston-1
Bartonella quintana Toulouse Baumannia cicadellinicola Homalodisca coagulata Bdellovibrio bacteriovorus
Bifidobacterium longum Blochmannia floridanus Bordetella bronchiseptica
Bordetella parapertussis Bordetella pertussis Borrelia afzelii PKo
Borrelia burgdorferi Borrelia garinii PBi Bradyrhizobium japonicum
Brucella abortus 9-941 Brucella melitensis Brucella melitensis biovar Abortus
Brucella suis 1330 Buchnera aphidicola Buchnera aphidicola Sg
Buchnera sp Burkholderia 383 Burkholderia cenocepacia AU 1054
Burkholderia cenocepacia HI2424 Burkholderia cepacia AMMD Burkholderia mallei ATCC 23344
Burkholderia pseudomallei 1106a Burkholderia pseudomallei 1710b Burkholderia pseudomallei K96243
Burkholderia thailandensis E264 Burkholderia vietnamiensis G4 Burkholderia xenovorans LB400
Caldicellulosiruptor saccharolyticus DSM 8903 Campylobacter fetus 82-40 Campylobacter jejuni
Campylobacter jejuni 81-176 Campylobacter jejuni RM1221 Candidatus Blochmannia floridanus
Candidatus Blochmannia pennsylvanicus BPEN Candidatus Carsonella ruddii Candidatus Pelagibacter ubique HTCC1062
Carboxydothermus hydrogenoformans Z-2901 Caulobacter crescentus Chlamydophila abortus S26 3
Chlamydophila caviae Chlamydophila felis Fe C-56 Chlamydia muridarum
Chlamydophila pneumoniae AR39 Chlamydophila pneumoniae CWL029 Chlamydophila pneumoniae J138
Chlamydophila pneumoniae TW 183 Chlamydia trachomatis Chlamydia trachomatis A HAR-13
Chlorobium chlorochromatii CaD3 Chlorobium tepidum TLS Chromohalobacter salexigens DSM 3043
Chromobacterium violaceum Clavibacter michiganensis NCPPB 382 Clostridium acetobutylicum
Clostridium difficile QCD-32g58 Clostridium perfringens Clostridium perfringens ATCC 13124
Clostridium perfringens SM101 Clostridium tetani E88 Colwellia psychrerythraea 34H
Corynebacterium diphtheriae Corynebacterium efficiens YS-314 Corynebacterium glutamicum
Corynebacterium glutamicum ATCC 13032 Bielefeld Corynebacterium glutamicum ATCC 13032 Kitasato Corynebacterium jeikeium K411
Coxiella burnetii Crocosphaera watsonii WH8501 Cyanobacteria bacterium Yellowstone A-Prime
Cyanobacteria bacterium Yellowstone B-Prime Cytophaga hutchinsonii ATCC 33406 Dechloromonas aromatica RCB
Dehalococcoides CBDB1 Dehalococcoides ethenogenes 195 Deinococcus geothermalis DSM 11300
Deinococcus radiodurans Desulfovibrio desulfuricans G20 Desulfitobacterium hafniense Y51
Desulfotalea psychrophila LSv54 Desulfotomaculum reducens MI-1 Desulfovibrio vulgaris Hildenborough
Dichelobacter nodosus VCS1703A Ehrlichia canis Jake Ehrlichia chaffeensis Arkansas
Ehrlichia ruminantium Gardel Ehrlichia ruminantium Welgevonden Ehrlichia ruminantium str. Welgevonden
Enterobacter 638 Enterococcus faecalis V583 Erwinia carotovora atroseptica SCRI1043
Erythrobacter litoralis HTCC2594 Escherichia coli 536 Escherichia coli APEC O1
Escherichia coli CFT073 Escherichia coli K12 Escherichia coli O157H7
Escherichia coli O157H7 EDL933 Escherichia coli UTI89 Escherichia coli W3110
Flavobacterium johnsoniae UW101 Flavobacterium psychrophilum JIP02 86 Frankia CcI3
Frankia alni ACN14a Francisella tularensis FSC 198 Francisella tularensis holarctica
Francisella tularensis tularensis Fusobacterium nucleatum Geobacter bemidjiensis
Geobacillus kaustophilus HTA426 Geobacter lovleyi Geobacter metallireducens GS-15
Geobacter sp FRC32 Geobacter sulfurreducens Geobacillus thermodenitrificans NG80-2
Geobacter uraniumreducens Rf4 Gloeobacter violaceus Gluconobacter oxydans 621H
Gramella forsetii KT0803 Granulobacter bethesdensis CGDNIH1 Haemophilus ducreyi 35000HP
Haemophilus influenzae Haemophilus influenzae 86 028NP Haemophilus somnus 129PT
Hahella chejuensis KCTC 2396 Halorhodospira halophila SL1 Helicobacter acinonychis Sheeba
Helicobacter hepaticus Helicobacter pylori 26695 Helicobacter pylori G27
Helicobacter pylori HPAG1 Helicobacter pylori J99 Herminiimonas arsenicoxydans
Hyphomonas neptunium ATCC 15444 Idiomarina loihiensis L2TR Jannaschia CCS1
Lactobacillus acidophilus NCFM Lactobacillus delbrueckii bulgaricus Lactobacillus delbrueckii bulgaricus ATCC BAA-365
Lactobacillus johnsonii NCC 533 Lactococcus lactis Lactobacillus plantarum
Lactobacillus sakei 23K Lactobacillus salivarius UCC118 Lawsonia intracellularis PHE MN1-00
Legionella pneumophila Lens Legionella pneumophila Paris Legionella pneumophila Philadelphia 1
Leifsonia xyli xyli CTCB0 Leptospira interrogans Leptospira interrogans serovar Copenhageni
Leptospira interrogans serovar Lai Leuconostoc mesenteroides ATCC 8293 Listeria innocua
Listeria monocytogenes Listeria monocytogenes 4b F2365 Magnetococcus MC-1
Magnetospirillum magneticum AMB-1 Mannheimia succiniciproducens MBEL55E Marinobacter aquaeolei VT8
Maricaulis maris MCS10 Mesorhizobium BNC1 Mesoplasma florum L1
Mesorhizobium loti Methylococcus capsulatus Bath Methylobacillus flagellatus KT
Methylibium petroleiphilum PM1 Moorella thermoacetica ATCC 39073 Mycobacterium MCS
Mycobacterium avium paratuberculosis Mycobacterium bovis Mycoplasma capricolum ATCC 27343
Mycoplasma gallisepticum Mycoplasma genitalium Mycoplasma hyopneumoniae 232
Mycoplasma hyopneumoniae 7448 Mycoplasma hyopneumoniae J Mycobacterium leprae
Mycoplasma mobile 163K Mycoplasma mycoides Mycoplasma penetrans
Mycoplasma pneumoniae Mycoplasma pulmonis Mycoplasma synoviae 53
Mycobacterium tuberculosis CDC1551 Mycobacterium tuberculosis H37Rv Myxococcus xanthus DK 1622
Neisseria gonorrhoeae FA 1090 Neisseria meningitidis FAM18 Neisseria meningitidis MC58
Neisseria meningitidis Z2491 Neorickettsia sennetsu Miyayama Nitrosomonas europaea
Nitrobacter hamburgensis X14 Nitrosospira multiformis ATCC 25196 Nitrosococcus oceani ATCC 19707
Nitrobacter winogradskyi Nb-255 Nocardioides JS614 Nocardia farcinica IFM10152
Nostoc sp Novosphingobium aromaticivorans DSM 12444 Oceanobacillus iheyensis
Oenococcus oeni PSU-1 Onion yellows phytoplasma Orientia tsutsugamushi Boryong
Paracoccus denitrificans PD1222 Parachlamydia sp UWE25 Pasteurella multocida
Pediococcus pentosaceus ATCC 25745 Pelobacter carbinolicus Pelodictyon luteolum DSM 273
Pelobacter propionicus DSM 2379 Pelotomaculum thermopropionicum SI Photorhabdus luminescens
Photobacterium profundum SS9 Pirellula sp Polaromonas JS666
Polynucleobacter QLW-P1DMWA-1 Porphyromonas gingivalis W83 Prochlorococcus marinus CCMP1375
Prochlorococcus marinus MED4 Prochlorococcus marinus MIT9313 Prochlorococcus marinus MIT 9312
Prochlorococcus marinus NATL2A Propionibacterium acnes KPA171202 Pseudomonas aeruginosa
Pseudoalteromonas atlantica T6c Pseudomonas entomophila L48 Pseudomonas fluorescens Pf-5
Pseudomonas fluorescens PfO-1 Pseudoalteromonas haloplanktis TAC125 Pseudomonas putida KT2440
Pseudomonas syringae phaseolicola 1448A Pseudomonas syringae pv B728a Pseudomonas syringae tomato DC3000
Psychrobacter arcticum 273-4 Psychrobacter cryohalolentis K5 Psychromonas ingrahamii 37
Ralstonia eutropha H16 Ralstonia eutropha JMP134 Ralstonia metallidurans CH34
Ralstonia solanacearum Rhizobium etli CFN 42 Rhodococcus RHA1
Rhodoferax ferrireducens DSM 15236 Rhodoferax ferrireducens T118 Rhodopseudomonas palustris BisB18
Rhodopseudomonas palustris BisB5 Rhodopseudomonas palustris CGA009 Rhodopseudomonas palustris HaA2
Rhodospirillum rubrum ATCC 11170 Rhodobacter sphaeroides 2 4 1 Rickettsia bellii RML369-C
Rickettsia conorii Rickettsia felis URRWXCal2 Rickettsia prowazekii
Rickettsia typhi wilmington Roseobacter denitrificans OCh 114 Rubrobacter xylanophilus DSM 9941
Saccharophagus degradans 2-40 Saccharopolyspora erythraea NRRL 2338 Salinibacter ruber DSM 13855
Salinispora tropica CNB-440 Salmonella enterica Choleraesuis Salmonella enterica Paratypi ATCC 9150
Salmonella typhi Salmonella typhimurium LT2 Salmonella typhi Ty2
Shewanella ANA-3 Shewanella MR-4 Shewanella MR-7
Shewanella W3-18-1 Shewanella amazonensis SB2B Shewanella baltica OS155
Shewanella denitrificans OS217 Shewanella frigidimarina NCIMB 400 Shewanella halifaxensis HAW EB4
Shewanella loihica PV-4 Shewanella oneidensis Shewanella pealeana ATCC 700345
Shewanella putrefaciens CN-32 Shewanella sediminis HAW-EB3 Shewanella woodyi ATCC 51908
Shigella boydii Sb227 Shigella dysenteriae Shigella flexneri 2a
Shigella flexneri 2a 2457T Shigella flexneri 5 8401 Shigella sonnei Ss046
Silicibacter TM1040 Silicibacter pomeroyi DSS-3 Sinorhizobium meliloti
Sodalis glossinidius morsitans Solibacter usitatus Ellin6076 Sphingopyxis alaskensis RB2256
Staphylococcus aureus COL Staphylococcus aureus MW2 Staphylococcus aureus Mu50
Staphylococcus aureus N315 Staphylococcus aureus NCTC 8325 Staphylococcus aureus RF122
Staphylococcus aureus USA300 Staphylococcus aureus aureus MRSA252 Staphylococcus aureus aureus MSSA476
Staphylococcus epidermidis ATCC 12228 Staphylococcus epidermidis RP62A Staphylococcus haemolyticus
Staphylococcus saprophyticus Streptococcus agalactiae 2603 Streptococcus agalactiae A909
Streptococcus agalactiae NEM316 Streptomyces avermitilis Streptomyces coelicolor
Streptococcus mutans Streptococcus pneumoniae R6 Streptococcus pneumoniae TIGR4
Streptococcus pyogenes M1 GAS Streptococcus pyogenes MGAS10270 Streptococcus pyogenes MGAS10394
Streptococcus pyogenes MGAS10750 Streptococcus pyogenes MGAS2096 Streptococcus pyogenes MGAS315
Streptococcus pyogenes MGAS5005 Streptococcus pyogenes MGAS6180 Streptococcus pyogenes MGAS8232
Streptococcus pyogenes MGAS9429 Streptococcus pyogenes SSI-1 Streptococcus thermophilus CNRZ1066
Streptococcus thermophilus LMG 18311 Symbiobacterium thermophilum IAM14863 Synechococcus CC9605
Synechococcus CC9902 Synechocystis PCC6803 Synechococcus elongatus PCC 6301
Synechococcus elongatus PCC 7942 Synechococcus sp WH8102 Syntrophus aciditrophicus SB
Syntrophobacter fumaroxidans MPOB Syntrophomonas wolfei Goettingen Thermosynechococcus elongatus
Thermobifida fusca YX Thermotoga maritima Thermotoga petrophila RKU-1
Thermoanaerobacter tengcongensis Thermus thermophilus HB27 Thermus thermophilus HB8
Thiomicrospira crunogena XCL-2 Thiobacillus denitrificans ATCC 25259 Thiomicrospira denitrificans ATCC 33889
Treponema denticola ATCC 35405 Treponema pallidum Trichodesmium erythraeum IMS101
Tropheryma whipplei TW08 27 Tropheryma whipplei Twist Ureaplasma urealyticum
Verminephrobacter eiseniae EF01-2 Vibrio cholerae Vibrio cholerae MO10
Vibrio cholerae O395 Vibrio fischeri ES114 Vibrio parahaemolyticus
Vibrio vulnificus CMCP6 Vibrio vulnificus YJ016 Wigglesworthia brevipalpis
Wolbachia endosymbiont of Brugia malayi TRS Wolbachia endosymbiont of Drosophila melanogaster Wolinella succinogenes
Xanthomonas campestris Xanthomonas campestris 8004 Xanthomonas campestris vesicatoria 85-10
Xanthomonas citri Xanthomonas oryzae KACC10331 Xanthomonas oryzae MAFF 311018
Xylella fastidiosa Xylella fastidiosa Temecula1 Yersinia pestis Antiqua
Yersinia pestis CO92 Yersinia pestis KIM Yersinia pestis Nepal516
Yersinia pestis biovar Mediaevails Yersinia pseudotuberculosis IP32953 Yersinia pseudotuberculosis IP 31758
Zymomonas mobilis ZM4
Number of Genomes: 424

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The Genomic tRNA Database is curated by Todd Lowe and Patricia Chan. Please email lowe @soe.ucsc.edu with any questions, comments, or corrections.

Last updated Sun Jul 20 08:26:45 2008