G~tRNA~db: The Genomic tRNA Database

tRNAscan-SE analysis of complete genomes
 

[Citation] [Legend]
[GtRNAdb Home] [tRNAscan-SE Server] [Lowe Lab] [Other Links]

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

Bacteria

Acinetobacter sp ADP1
Agrobacterium tumefaciens C58 Cereon
Agrobacterium tumefaciens C58 UWash
Anabaena variabilis ATCC 29413
Anaplasma marginale St Maries
Aquifex aeolicus
Azoarcus sp EbN1
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
Bdellovibrio bacteriovorus
Bifidobacterium longum
Blochmannia floridanus
Bordetella bronchiseptica
Bordetella parapertussis
Bordetella pertussis
Borrelia burgdorferi
Borrelia garinii PBi
Bradyrhizobium japonicum
Brucella abortus 9-941
Brucella melitensis
Brucella suis 1330
Buchnera aphidicola
Buchnera aphidicola Sg
Buchnera sp
Burkholderia mallei ATCC 23344
Burkholderia pseudomallei K96243
Campylobacter jejuni
Campylobacter jejuni RM1221
Candidatus Blochmannia pennsylvanicus BPEN
Candidatus Pelagibacter ubique HTCC1062
Caulobacter crescentus
Chlamydophila abortus S26 3
Chlamydophila caviae
Chlamydia muridarum
Chlamydophila pneumoniae AR39
Chlamydophila pneumoniae CWL029
Chlamydophila pneumoniae J138
Chlamydophila pneumoniae TW 183
Chlamydia trachomatis
Chlamydia trachomatis A HAR-13
Chlorobium tepidum TLS
Chromobacterium violaceum
Clostridium acetobutylicum
Clostridium perfringens
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
Dechloromonas aromatica RCB
Dehalococcoides ethenogenes 195
Deinococcus radiodurans
Desulfotalea psychrophila LSv54
Desulfovibrio vulgaris Hildenborough
Ehrlichia canis Jake
Ehrlichia ruminantium Gardel
Ehrlichia ruminantium Welgevonden
Ehrlichia ruminantium str. Welgevonden
Enterococcus faecalis V583
Erwinia carotovora atroseptica SCRI1043
Escherichia coli CFT073
Escherichia coli K12
Escherichia coli O157H7
Escherichia coli O157H7 EDL933
Francisella tularensis tularensis
Fusobacterium nucleatum
Geobacillus kaustophilus HTA426
Geobacter sulfurreducens
Gloeobacter violaceus
Gluconobacter oxydans 621H
Haemophilus ducreyi 35000HP
Haemophilus influenzae
Haemophilus influenzae 86 028NP
Helicobacter hepaticus
Helicobacter pylori 26695
Helicobacter pylori J99
Idiomarina loihiensis L2TR
Lactobacillus acidophilus NCFM
Lactobacillus johnsonii NCC 533
Lactococcus lactis
Lactobacillus plantarum
Legionella pneumophila Lens
Legionella pneumophila Paris
Legionella pneumophila Philadelphia 1
Leifsonia xyli xyli CTCB0
Leptospira interrogans
Leptospira interrogans serovar Copenhageni
Leptospira interrogans serovar Lai
Listeria innocua
Listeria monocytogenes
Listeria monocytogenes 4b F2365
Mannheimia succiniciproducens MBEL55E
Mesoplasma florum L1
Mesorhizobium loti
Methylococcus capsulatus Bath
Mycobacterium avium paratuberculosis
Mycobacterium bovis
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
Neisseria gonorrhoeae FA 1090
Neisseria meningitidis MC58
Neisseria meningitidis Z2491
Nitrosomonas europaea
Nitrosococcus oceani ATCC 19707
Nitrobacter winogradskyi Nb-255
Nocardia farcinica IFM10152
Nostoc sp
Oceanobacillus iheyensis
Onion yellows phytoplasma
Parachlamydia sp UWE25
Pasteurella multocida
Photorhabdus luminescens
Photobacterium profundum SS9
Pirellula sp
Porphyromonas gingivalis W83
Prochlorococcus marinus CCMP1375
Prochlorococcus marinus MED4
Prochlorococcus marinus MIT9313
Prochlorococcus marinus NATL2A
Propionibacterium acnes KPA171202
Pseudomonas aeruginosa
Pseudomonas fluorescens Pf-5
Pseudomonas fluorescens PfO-1
Pseudoalteromonas haloplanktis TAC125
Pseudomonas putida KT2440
Pseudomonas syringae
Pseudomonas syringae phaseolicola 1448A
Pseudomonas syringae pv B728a
Ralstonia eutropha JMP134
Ralstonia solanacearum
Rhodopseudomonas palustris CGA009
Rhodobacter sphaeroides 2 4 1
Rickettsia conorii
Rickettsia felis URRWXCal2
Rickettsia prowazekii
Rickettsia typhi wilmington
Salmonella enterica Choleraesuis
Salmonella enterica Paratypi ATCC 9150
Salmonella typhi
Salmonella typhimurium LT2
Salmonella typhi Ty2
Shewanella oneidensis
Shigella flexneri 2a
Shigella flexneri 2a 2457T
Shigella sonnei Ss046
Silicibacter pomeroyi DSS-3
Sinorhizobium meliloti
Staphylococcus aureus COL
Staphylococcus aureus MW2
Staphylococcus aureus Mu50
Staphylococcus aureus N315
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
Streptococcus pyogenes M1 GAS
Streptococcus pyogenes M49 591
Streptococcus pyogenes MGAS10394
Streptococcus pyogenes MGAS315
Streptococcus pyogenes MGAS5005
Streptococcus pyogenes MGAS6180
Streptococcus pyogenes MGAS8232
Streptococcus pyogenes SSI-1
Streptococcus thermophilus CNRZ1066
Streptococcus thermophilus LMG 18311
Symbiobacterium thermophilum IAM14863
Synechocystis PCC6803
Synechococcus elongatus PCC 6301
Synechococcus sp WH8102
Thermosynechococcus elongatus
Thermobifida fusca YX
Thermotoga maritima
Thermoanaerobacter tengcongensis
Thermus thermophilus HB27
Thermus thermophilus HB8
Thiobacillus denitrificans ATCC 25259
Treponema denticola ATCC 35405
Treponema pallidum
Tropheryma whipplei TW08 27
Tropheryma whipplei Twist
Ureaplasma urealyticum
Vibrio cholerae
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 citri
Xanthomonas oryzae KACC10331
Xylella fastidiosa
Xylella fastidiosa Temecula1
Yersinia pestis CO92
Yersinia pestis KIM
Yersinia pestis biovar Mediaevails
Yersinia pseudotuberculosis IP32953
Zymomonas mobilis ZM4

Eukarya

Aspergillus fumigatus
Arabidopsis thaliana (Feb 2004)
Candida glabrata CBS138
Caenorhabditis briggsae (cb25.agp8 July 2002)
Caenorhabditis elegans (May 2003)
Canis familiaris (dog) (canFam1 July 2004)
Cryptococcus neoformans var JEC21
Debaryomyces hansenii CBS767
Drosophila melanogaster (Release 4, March 2004)
Danio rerio (Zebrafish) (Zv4 assembly June 2004)
Encephalitozoon cuniculi
Eremothecium gossypii
Takifugu rubripes (v.3.0 Aug. 2002)
Gallus gallus (galGal2 Feb 2004)
Homo sapiens (Hg17 May 2004)
Kluyveromyces lactis NRRL Y-1140
Mus musculus (mm6 March 2005)
Plasmodium falciparum (Oct 2002)
Pan troglodytes (chimp) (Nov 2003)
Rattus norvegicus (rn3 June 2003)
Saccharomyces cerevisiae (Nov 2002)
Schizosaccharomyces pombe (July 2004)
Strongylocentrotus purpuratus (Sea urchin) (April 2005)
Yarrowia lipolytica CLIB99

Archaea

Aeropyrum pernix
Archaeoglobus fulgidus
Ferroplasma acidarmanus
Haloarcula marismortui ATCC 43049
Halobacterium sp
Methanosarcina acetivorans
Methanosarcina barkeri fusaro
Methanococcoides burtonii
Methanococcus jannaschii
Methanopyrus kandleri
Methanococcus maripaludis S2
Methanosarcina mazei
Methanobacterium thermoautotrophicum
Nanoarchaeum equitans
Natronomonas pharaonis
Picrophilus torridus DSM 9790
Pyrococcus abyssi
Pyrobaculum aerophilum
Pyrococcus furiosus
Pyrococcus horikoshii
Sulfolobus acidocaldarius DSM 639
Sulfolobus solfataricus
Sulfolobus tokodaii
Thermoplasma acidophilum
Thermococcus kodakaraensis KOD1
Thermoplasma volcanium




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

Last updated Mon Apr 22 16:44:36 2019