GtRNAdb

tRNAscan-SE Analysis of Desulfovibrio vulgaris Hildenborough

>> Main Overview
>> tRNAs by Isotype
>> tRNAs by Locus
>> Secondary Structures
>> tRNA Alignments
>> FASTA Seqs
>> Run Options/Stats
>> Analysis Notes
>> UCSC Genome Browser
>> Genome DB
>> Genome Seq
Structurally Aligned tRNAs (by Isotype & Anticodon)

Structural alignments are generated by aligning tRNA sequences against domain-specific tRNA covariance models with the use of COVE.


[Ala] [Arg] [Asn] [Asp] [Cys] [Gln] [Glu] [Gly] [His] [Ile] [Leu] [Lys] [Met] [Phe] [Pro] [Ser] [Thr] [Trp] [Tyr] [Val]
[Suppressor] [Selenocysteine]


Ala tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGGCTGTAGCTCAGTTGGGAGAGCGCTTGAATGGCATTCAAGAG...........GtCAGGAGTTCAATTCTCCTCAGCTCCACCA chr.trna2-AlaGGC Sc: 86.96 GGGGCTGTAGCTCAGTTGGGAGAGCGCTTGAATGGCATTCAAGAG...........GtCAGGAGTTCAATTCTCCTCAGCTCCACCA chr.trna1-AlaGGC Sc: 86.96 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGGATGTAGCTCAGCTGGGAGAGCGCAGCGTTCGCAATGCTGAA...........GtCAGGGGTTCAATCCCCCTCATCTCCACCA chr.trna23-AlaCGC Sc: 82.51 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGGGCGTAGCTCAGCTGGGAGAGCACCTGCCTTGCACGCAGGGG...........GtCAACGGTTCAATCCCGTTCGCCTCCACCA chr.trna6-AlaTGC Sc: 93.18 GGGGGCGTAGCTCAGCTGGGAGAGCACCTGCCTTGCACGCAGGGG...........GtCAACGGTTCAATCCCGTTCGCCTCCACCA chr.trna47-AlaTGC Sc: 93.18 GGGGGCGTAGCTCAGCTGGGAGAGCACCTGCCTTGCACGCAGGGG...........GtCAACGGTTCAATCCCGTTCGCCTCCACCA chr.trna43-AlaTGC Sc: 93.18 GGGGGCGTAGCTCAGCTGGGAGAGCACCTGCCTTGCACGCAGGGG...........GtCAACGGTTCAATCCCGTTCGCCTCCACCA chr.trna4-AlaTGC Sc: 93.18 GGGGGCGTAGCTCAGCTGGGAGAGCACCTGCCTTGCACGCAGGGG...........GtCAACGGTTCAATCCCGTTCGCCTCCACCA chr.trna39-AlaTGC Sc: 93.18

Arg tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGCCGGTAGCTCAGTTGGAtAGAGCAACAGGCTACGAACCTGTAG...........GtCGGAGGTTCGAATCCTTCCCGGCGCACCA chr.trna53-ArgACG Sc: 94.32 GCGCTGGTAGCTCAGTTGGAtAGAGCAACAGGCTACGAACCTGTAG...........GtCGGAGGTTCGAATCCTTCCCAGCGCGCCA chr.trna55-ArgACG Sc: 89.92 >>>>>>>..>>.>.........<.<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGCCGGTAGCCCAGCTGGAtAGAGCAACAGGCTACGAACCTGTAG...........GtCGGAGGTTCGAATCCTTCCCGGCGCGCCA chr.trna54-ArgACG Sc: 84.77 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCAATTAGCTCAGATGGAtAGAGCGTTGGCCTCCGGAGCCAAAG...........GcCGCAAGTTCGAATCTTGCATTGCCCACCA chr.trna35-ArgCCG Sc: 84.91 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGCCTGTAGCTCAGTTGGAtAGAGCGAGCGCCTCCTAAGCGCTAG...........GcCACAAGTTCGATTCTTGTCAGGCGCACCA chr.trna15-ArgCCT Sc: 88.33 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGCCCGTAGCTCAGTTGGAaAGAGCAGGAGCCTTCTAAGCTCTTG...........GcCGGGGGTTCGAATCCTCCCGGGCGCGCCA chr.trna40-ArgTCT Sc: 85.08

Asn tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... TCCCCGGTGGCTCAATCGGCAGAGCGGGTGACTGTTAATCACTAG...........GtTGGCGGTTCAAGTCCGTCCCGGGGAGCCA chr.trna25-AsnGTT Sc: 81.86 TCCCCGGTGGCTCAATCGGCAGAGCGGGTGACTGTTAATCACTAG...........GtTGGCGGTTCAAGTCCGTCCCGGGGAGCCA chr.trna24-AsnGTT Sc: 81.86

Asp tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGAGCGGTAGTTAAGACGGTtATAACGCCGGCCTGTCACGCCGGAG...........GcCGAGGGTTCGAGTCCCTTCCGCTCCGCCA chr.trna9-AspGTC Sc: 84.81 GGAGCCGTAGTTAAGACGGTtATAACGCCGGCCTGTCACGCCGGAG...........GcCGAGGGTTCGAGTCCCTTCGGCTCCGCCA chr.trna8-AspGTC Sc: 84.72

Cys tRNAs

>>>>>>>..>>>..........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGCGGCGTAGCCAAGTGGTA.AGGCAGAGGTCTGCAAAACCTCCA...........TtCTCCGGTTCAAATCCGGACGCCGCCTCCA chr.trna19-CysGCA Sc: 78.64

Gln tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... TGGGCTGTCGTTCAATTGGCAGGACGACGGATTCTGGCTCCGTTA...........A.TCTAGGTTCGAGTCCTAGCAGCCCAGCCA chr.trna31-GlnCTG Sc: 62.75 >>>>>>>..>>>..........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... TGGGGTGTCGCCAAGTTGGTAAGGCAACGGGTTTTGGTCCCGTCA...........TtCGAGGGTTCGAGTCCTTCCGCCCCAGCCA chr.trna52-GlnTTG Sc: 73.71

Glu tRNAs

>>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<.... GTTCCCATCGTCTAGCC.GGCctAGGACAACGGCCTTTCACGCCGTCG...........ACAGGGGTTCGAATCCCCTTGGGAACGCCA chr.trna63-GluTTC Sc: 66.39 GTTCCCATCGTCTAGCC.GGCctAGGACAACGGCCTTTCACGCCGTCG...........ACAGGGGTTCGAATCCCCTTGGGAACGCCA chr.trna11-GluTTC Sc: 66.39 GTCCCTATCGTCTAGCCcGGCccAGGACAACGGCCTTTCACGCCGTCG...........ACAGGGGTTCAAATCCCCTTGGGGACGCCA chr.trna32-GluTTC Sc: 59.47

Gly tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGGAGTAACTCAGT.GGT.A.GAGTGCAACCTTGCCAAGGTTGAA...........GtCGCGGGTTCAAATCCCGTCTCCCGCTCCA chr.trna22-GlyGCC Sc: 85.83 GCGGGAGTAACTCAGT.GGT.A.GAGTGCAACCTTGCCAAGGTTGAA...........GtCGCGGGTTCAAATCCCGTCTCCCGCTCCA chr.trna20-GlyGCC Sc: 85.83 GCGGGAGTAACTCAGT.GGT.A.GAGTGCAACCTTGCCAAGGTTGAA...........GtCGCGGGTTCAAATCCCGTCTCCCGCTCCA chr.trna18-GlyGCC Sc: 85.83 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGGAATAACTCAGC.GGT.A.GAGTGTCAGCTTCCCAAGCTGAAG...........GtCGCGGGTTCAAATCCCGTTTCCCGCTCCA chr.trna21-GlyCCC Sc: 87.68 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGGAATAGCTCAAGTGGCtA.GAGCATCAGCCTTCCAAGCTGAGG...........GtTGCGAGTTCGAGTCTCGTTTCCCGCTCCA chr.trna28-GlyTCC Sc: 88.91

His tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGATGTAGCTCAGCAGGTAGAGCACCTGGTTGTGGCCCAGGTG...........GcCGTGGGTTCAAGTCCCATCATTCGCCCCA chr.trna34-HisGTG Sc: 79.40

Ile tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCTGTAGCTCAGGTGGCtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAAGTTCAAGTCTTCCCAGGCCCACCA chr.trna5-IleGAT Sc: 94.70 GGGCCTGTAGCTCAGGTGGCtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAAGTTCAAGTCTTCCCAGGCCCACCA chr.trna46-IleGAT Sc: 94.70 GGGCCTGTAGCTCAGGTGGCtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAAGTTCAAGTCTTCCCAGGCCCACCA chr.trna42-IleGAT Sc: 94.70 GGGCCTGTAGCTCAGGTGGCtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAAGTTCAAGTCTTCCCAGGCCCACCA chr.trna38-IleGAT Sc: 94.70 GGGCCTGTAGCTCAGGTGGCtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAAGTTCAAGTCTTCCCAGGCCCACCA chr.trna3-IleGAT Sc: 94.70

Leu tRNAs

>>>>>>>..>>>...........<<<.>>>>>.......<<<<<..>>>>............<<<<...>>>>>.......<<<<<.<<<<<<<.... GCCGAGGTGGTGGAATTGGTaGACACGCTATCTTGAGGGGGTAGT.GGGA..GAAA......TCCCG.TGAGGGTTCGAGTCCCTC.CCTCGGCACCA chr.trna41-LeuGAG Sc: 65.36 GCCGAGGTGGTGGAATTGGTaGACACGCTATCTTGAGGGGGTAGT.GGGA..GAAA......TCCCG.TGAGGGTTCGAGTCCCTC.CTTCGGCACCA chr.trna49-LeuGAG Sc: 59.40 >>>>>>>..>>>...........<<<.>>>>>.......<<<<<..>>>>>..........<<<<<...>>>>>.......<<<<<.<<<<<<<.... GCCGAAGTGGTGGAATTGGTaGACACGCTAGGTTCAGGGTCTAGT.TGGGGT........TCCCCAG.TGGGAGTTCGAGTCTCCC.CTTCGGCACCA chr.trna64-LeuCAG Sc: 61.99 GCCGAAGTGGTGGAATTGGTaGACACGCTAGGTTCAGGGTCTAGT.TGGGGT........TCCCCAG.TGGGAGTTCGAGTCTCCC.CTTCGGCACCA chr.trna44-LeuCAG Sc: 61.99 >>>>>>>..>>>...........<<<.>>>>>.......<<<<<..>>................<<...>>>>>.......<<<<<.<<<<<<<.... GCGAGAGTGGCGGAATAGGTaGACGCACTGGACTTAGAATCCAGC.GCC...TTTG.......TGCG.TGGGAGTTCGAGTCTCCC.CTCTCGCACCA chr.trna14-LeuTAG Sc: 71.86 >>>>>>>..>>>...........<<<.>>>>>.......<<<<<..>>>..............<<<...>>>>>.......<<<<<.<<<<<<<.... GCCGGAATGGTGGAATTGGTaGACGCAGCGGACTCAAAATCCGCCGGTG...GCAA.......CACCtTGTCAGTTCGAGTCTGAC.TTCCGGTACCA chr.trna16-LeuCAA Sc: 72.18 >>>>>>>..>>>...........<<<.>>>>>.......<<<<<..>>>>............<<<<...>>>>>.......<<<<<.<<<<<<<.... GCCCGGATGGCGGAACTGGCaGACGCAAGGGACTTAAAATCCCTC.GGCC..TTCG......GGCTG.TACGAGTTCAATCCTCGT.TCCGGGTACCA chr.trna68-LeuTAA Sc: 67.67

Lys tRNAs

>>>>>>>..>>>>............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGTCATTAGCTCAATTGGT.A...GAGCAGCTGACTCTTAATCAGTTG...........GtTCGGGGTTCGAGTCCCTGATGGCCCACCA chr.trna60-LysCTT Sc: 90.63 GGGTCATTAGCTCAATTGGT.A...GAGCAGCTGACTCTTAATCAGTTG...........GtTCGGGGTTCGAGTCCCTGATGGCCCACCA chr.trna59-LysCTT Sc: 90.63 >>>>>>>..>>>>............<<<<..>>>>.......<<<<.................>>>>>.......<<<<<<<<<<<<.... GGGTCGTTAACTCAGTCGGT.A...GAGTACCTGCCTTTTAAGCAGAGA...........GtCGCAGGTTCGAATCCTGCACGACCCACCA chr.trna66-LysTTT Sc: 88.53 >...>.>...>>..............<<..>..>>.......<<..<................>>>>>.......<<<<<<.<...<.... GTTACTTTACCG...T.GTTcA...TCGCGTGGGCCTTTTAAGCAGAGA...........GtCGCAGGTTCGAATCCTGCACGACCCACCA chr.trna67-LysTTT Sc: 22.50 Pseudo

Met tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGCGAGGTAGCTCAGTT.GGTcAGAGCATGCGGCTCATATCCGCAGT...........GtCGGGGGTTCAATTCCCTCCCTCGCTACCA chr.trna50-MetCAT Sc: 86.53 >>>>>>>..>>>>..........<<<<..>>>>.......<<<<.................>>>>>.......<<<<<<<<<<<<.... GGGCCCATAGCTCAATT.GGC.AGAGCCCTCGGCTCATAACCGATTT...........GtTGCAGGTTCGAGTCCTGCTGGGCCCACCA chr.trna57-MetCAT Sc: 84.60 .>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<..... CGCGGGGTGGAGCAGCAcGGT.AGCTCGTCGGGCTCATAACCCGAAG...........GtCGTAGGTTCAAATCCTGCCCCCGCAACCA chr.trna48-MetCAT Sc: 83.17 CGCGGGGTGGAGCAGCAcGGT.AGCTCGTCGGGCTCATAACCCGAAG...........GtCGTAGGTTCAAATCCTGCCCCCGCAACCA chr.trna10-MetCAT Sc: 83.17

Phe tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGAGGTAGCTCAGTTGGTAGAGCAGGGGACTGAAAATCCCCGT...........GtCGGGAGTTCAATTCTCTCCCTCGGCACCA chr.trna36-PheGAA Sc: 91.09

Pro tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CGGGATGTAGCGCAGCCtGGG.AGCGCACTTGAATGGGGTTCAAGGG...........GtCGAAGGTTCAAATCCTTTCATCCCGACCA chr.trna33-ProGGG Sc: 80.67 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CGGGATGTGGCTCAGTTtGGCtAGAGCGCAGCGTTCGGGACGCTGAG...........GcCGGAGGTTCGAATCCTCTCATCCCGACCA chr.trna17-ProCGG Sc: 85.31 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CGGAACGTAGCGCAGCCtGGT.AGCGCACCTGCCTTGGGAGCAGGGG...........GtCGCTGGTTCGAATCCAGTCGTTCCGACCA chr.trna51-ProTGG Sc: 91.26

SeC tRNAs

.>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<..>>>>>>>....<<<<<<<.>>>>>.......<<<<<.<<<<<<<.... gGAAGCGTTTTCTATCCGGTgA.TAGGCCCGGTCTTCAAAACCGGTGGTAGGTCGAGAGGTCTACGGTAGGTTCGACTCCTAT.ACGCTTCC... chr.trna58-SeC(p)TCA Sc: 47.58

Ser tRNAs

>>>>>>>..>>>..............<<<.>>>>>.......<<<<<.>>>>>..........<<<<<.>>>>>.......<<<<<..<<<<<<<.... GGAGAGGTGTCCGAGAT.GGCcg.AAGGAGCACGATTGGAAATCGTGTGTACCC..TAAC.CCGGTACCGAGAGTTCGAATCTCTC..CCTCTCCGCCA chr.trna62-SerGGA Sc: 58.88 >>>>>>>..>>>..............<<<.>>>>>.......<<<<<.>>>>>>>......<<<<<<<.>>>>>.......<<<<<..<<<<<<<.... GGAGAGGTAGCGAAGCT.GGCcgtAACGCGCTCGACTCGAAATCGAGTTACGGGT.TAATaGCCCGTACGTGGGTTCGAATCCCAC..CCTCTCCGCCA chr.trna56-SerCGA Sc: 78.97 >>>>>>>..>>>>............<<<<.>>>>>.......<<<<<.>>>>>>........<<<<<<.>>>>>.......<<<<<..<<<<<<<.... GGAAGGGTGGCAGAGTCcGGTtt.ATTGCGGCGGTCTTGAAAACCGTTGTGGGG..GGAA..CCCCACCGGGGGTTCGAATCCCTC..CCCTTCCGCCA chr.trna12-SerTGA Sc: 67.95 >>>>>>>..>>>..............<<<.>>>>>.......<<<<<.>>>>>>>......<<<<<<<.>>>>>.......<<<<<..<<<<<<<.... GGAGAGGTGTCCGAGTC.GGCcg.AAGGAGCTCGCCTGCTAAGCGGGTATAGGGGcATAAaCCTCTATCGAGGGTTCGAATCCCTC..CCTCTCCGCCA chr.trna61-SerGCT Sc: 63.71

Sup tRNAs

Thr tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCCATGTGGCTCAGTCGGTAGAGCACATCCTTGGTAAGGATGAG...........GtCAGCAGTTCAATTCTGCTCATGGGCTCCA chr.trna65-ThrGGT Sc: 88.87 GCCCACATAGCTCAGGCGGTAGAGCACTTCCTTGGTAAGGAAGAG...........GtCATGAGTTCAAGTCTCATTGTGGGCTCCA chr.trna29-ThrGGT Sc: 86.35 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCAGCTTAGCTCAGATGGTAGAGCAACTGATTCGTAATCAGTAG...........GtCGGGAGTTCAATTCTCCCAGCTGGCTCCA chr.trna13-ThrCGT Sc: 88.64 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>.>>>.......<<<.<<<<<<<<.... GCTGGCGTAGCTCAACTGGCAGAGCAGCTGATTTGTAATCAGCCG...........GtTGCGGGTTCGAGTCCCATCGCCAGCTCCA chr.trna26-ThrTGT Sc: 85.30

Trp tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... AGGGCAGTAGCTCTAACGGCtAGAGCGCCGGTCTCCAAAACCGGAT...........GtTGGGGGTTCGAATCCCTCCTGCCCTGCCA chr.trna30-TrpCCA Sc: 76.66

Tyr tRNAs

>>>>>>>..>>>............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<.... GGTGGGGTTCCCGAGTGGCcaA.AGGGAACAGACTGTAAATCTGTCGTCGTAA....GACTtCGGTGGTTCAAATCCACC.CCCCACCACCA chr.trna27-TyrGTA Sc: 74.54

Val tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... AGGCGCGTAGCTCAGG.GGGA.GAGCACTTCCTTGACACGGAAGGG...........GtCAGCAGTTCAAATCTGCTCGTGCCTACCA chr.trna45-ValGAC Sc: 77.70 >>>>.>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<.<<<<.... GGGCAGTTAGCTCAGCTGGAA.GAGCACCGCCTTCACACGGCGGGG...........GtCGCAGGTTCGAGCCCTGCACCGCCCACCA chr.trna7-ValCAC Sc: 89.80 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCGGTTAGCTCAGCTGGTA.GAGCGTCGGCCTTACAAGCCGAAT...........GcCGGGGGTTCGATCCCCTCACCGCCCACCA chr.trna37-ValTAC Sc: 92.36

The Genomic tRNA Database is curated by Todd Lowe and Patricia Chan. Please email lowe@soe.ucsc.edu with any questions and comments. To submit corrections, please use our Bug and Request Tracking System.