GtRNAdb

tRNAscan-SE Analysis of Leptothrix cholodnii SP 6

>> Main Overview
>> tRNAs by Isotype
>> tRNAs by Locus
>> Secondary Structures
>> tRNA Alignments
>> FASTA Seqs
>> Run Options/Stats
>> Analysis Notes
>> 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

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGGGTATAGCTCAGCTGGGAGAGCGCTTGCATGGCATGCAAGAG...........GtCAGCGGTTCGATCCCGCTTACCTCCACCA chr.trna11-AlaGGC Sc: 86.46 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGGGGGTAGCTCAGCTGGGAGAGCGTCGCGTTCGCAATGCGAAG...........GtCGGGAGTTCGATCCTCCTCCTCTCCACCA chr.trna20-AlaCGC Sc: 80.39 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>.>>>.......<<<.<<<<<<<<.... GGGGGATTAGCTCAGCTGGGAGAGCACCTGCTTTGCAAGCAGGGG...........GtCGTCGGTTCGATCCCGTCATCCTCCACCA chr.trna7-AlaTGC Sc: 90.93 GGGGGATTAGCTCAGCTGGGAGAGCACCTGCTTTGCAAGCAGGGG...........GtCGTCGGTTCGATCCCGTCATCCTCCACCA chr.trna2-AlaTGC Sc: 90.93

Arg tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGCTGTAGCTCAGCTGGAtA.GAGTACTTGGCTACGAACCAAGGG...........GtCGTGGGTTCGATTCCTGCCAGCCGCACCA chr.trna4-ArgACG Sc: 86.82 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGCCCGTAGCTCAGT.GGAtA.GAGTATTGGCCTCCGAAGCCAAGG...........GcCGCTGGTTCGATCCCAGCCGGGCGCACCA chr.trna8-ArgCCG Sc: 83.28 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CTCGCCGTAGTTCAAT.GGAtA.GAACGGCCGCCTCCTAAGCGGCAA...........A.TACAGGTTCGATTCCTGTCGGCGGGACCA chr.trna21-ArgCCT Sc: 72.31 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CTGCCCGTAGCTCAACTGGAtA.GAGCACCGCCCTTCTAAGGCGGGG...........GtTGGGGGTTCGATCCCCTCCGGGCAGGCCA chr.trna40-ArgTCT Sc: 84.41

Asn tRNAs

>>>>>>>..>>>>........<<<<..>>>>.......<<<<.................>>>>>.......<<<<<<<<<<<<.... TCCCCGATAGCTCAGTCGGTAGAGCGACGGACTGTTAATCCGCAG...........GtCCCAGGTTCGAGCCCTGGTCGGGGAGCCA chr.trna18-AsnGTT Sc: 85.92

Asp tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGAGTGGTAGTTCAGTTGGTtAGAATACCGGCCTGTCACGCCGGGG...........GtCGCGGGTTCGAGTCCCGTCCACTCCGCCA chr.trna15-AspGTC Sc: 94.55 GGAGTGGTAGTTCAGTTGGTtAGAATACCGGCCTGTCACGCCGGGG...........GtCGCGGGTTCGAGTCCCGTCCACTCCGCCA chr.trna13-AspGTC Sc: 94.55

Cys tRNAs

>>>>>>>..>>>..........<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<.... GGCGCGGTAGCAAAGCGGTT.ATGCAGCGGATTGCAAATCCGTTT...........AGGGTGGTTCGACTCCACTCCGCGCCTCCA chr.trna35-CysGCA Sc: 61.70

Gln tRNAs

>>>>>>>..>>>...........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... AGGGGAGTCGCCAAGTTGGTcAAGGCATCGGATTTTGATTCCGACA...........TgCGAGGGTTCGAGTCCTTCCTCCCCTGCCA chr.trna24-GlnTTG Sc: 71.61

Glu tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<.... GACTCCTTCGTCTAGAGGCctA.GGACACGACCCTTTCACGGTCGTT...........ACAGGGGTTCGAATCCCCTAGGAGTCGCCA chr.trna14-GluTTC Sc: 56.22 GACTCCTTCGTCTAGAGGCctA.GGACACGACCCTTTCACGGTCGTT...........ACAGGGGTTCGAATCCCCTAGGAGTCGCCA chr.trna12-GluTTC Sc: 56.22

Gly tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGGATTAGCTCAGTTGGTA.GAGCGATACCTTGCCAAGGTATAG...........GtCGAGAGTTCGAGTCTCTTATCCCGCTCCA chr.trna36-GlyGCC Sc: 92.52 GCGGGATTAGCTCAGTTGGTA.GAGCGATACCTTGCCAAGGTATAG...........GtCGAGAGTTCGAGTCTCTTATCCCGCTCCA chr.trna34-GlyGCC Sc: 92.52 GCGGGATTAGCTCAGTTGGTA.GAGCGATACCTTGCCAAGGTATAG...........GtCGAGAGTTCGAGTCTCTTATCCCGCTCCA chr.trna26-GlyGCC Sc: 92.52 >>>>>>>..>>>>.........<<<<.>.>>>.......<<<.<................>>>>>.......<<<<<<<<<<<<.... GCGGGTGTAGTTCAAT.GGTA.GAACGGCAGCTTCCCAAGCTTCAT...........A.CGTGGGTTCGATTCCCATCACCCGCTCCA chr.trna46-GlyCCC Sc: 73.33 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGGAGTAGTTCAAT.GGTA.GAACTTCAGCCTTCCAAGCTGATA...........G.CGCGGGTTCGATTCCCGCCTCCCGCTCCA chr.trna28-GlyTCC Sc: 84.59

His tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GTGGCTGTAGCTCAGTTGGTAGAGTCCCAGATTGTGATTCTGGTT...........GtCGTGGGTTCGAGTCCCATCAGCCACCCCA chr.trna45-HisGTG Sc: 81.76

Ile tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGTCTGTAGCTCAGTCGGTtAGAGCACCGTCTTGATAAGGCGGGG...........GtCGTTGGTTCGAATCCAACCAGACCCACCA chr.trna6-IleGAT Sc: 93.29 GGGTCTGTAGCTCAGTCGGTtAGAGCACCGTCTTGATAAGGCGGGG...........GtCGTTGGTTCGAATCCAACCAGACCCACCA chr.trna1-IleGAT Sc: 93.29

Leu tRNAs

>>>>>>>..>>>...........<<<.>>>>>.......<<<<<.>>>..........<<<..>>>>>.......<<<<<.<<<<<<<.... GCCGACGTGGTGAAATTGGTaGACACGCTATCTTGAGGGGGTAGTGGC..GAAA....GCTGTGCGAGTTCGAGTCTCGC.CGTCGGCACCA chr.trna9-LeuGAG Sc: 63.68 >>>>>>>..>>>...........<<<.>>>>>.......<<<<<.>>>..........<<<..>>>>>.......<<<<<.<<<<<<<.... GCCCAGGTGGCGGAATTGGTaGACGCACTAGTTTCAGGTACTAGCGGG..TAAC....TCCGTGGAGGTTCGAGTCCTCT.CCTGGGCACCA chr.trna19-LeuCAG Sc: 71.43 >>>>>>>..>>>...........<<<..>>>>.......<<<<..>>>>........<<<<..>>>>>.......<<<<<.<<<<<<<.... GCGCGGGTGGCGAAATTGGTaGACGCACCAGGTTTAGGTCCTGACGCCT.TCAC...GGGCGTGCCGGTTCGAGTCCGGC.CCCGCGCACCA chr.trna33-LeuTAG Sc: 73.86 >>>>>>>..>>>...........<<<.>>>>>.......<<<<<.>>>..........<<<..>>>>>.......<<<<<.<<<<<<<.... GCCGGAGTGGCGAAATCGGTaGACGCAGGGGACTCAAAATCCCCCGCC..GCAA....GGCGTGCCGGTTCGAGTCCGGC.CTCCGGCACCA chr.trna3-LeuCAA Sc: 81.24 >>>>>>>..>>>...........<<<.>>>>>.......<<<<<.>>>>>......<<<<<..>>>>>.......<<<<<.<<<<<<<.... GCCTGGGTGGTGGAACTGGTaGACACAGCGGACTTAAAATCCGCCGATTGGAAA..CGATCGTACGGGTTCGATTCCCGT.CCTGGGCACCA chr.trna37-LeuTAA Sc: 71.13

Lys tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCTCTTAGCTCAGTTGGTAGAGCAGCGGACTCTTAATCCGTAG...........GtCGAGTGTTCGAGTCACTCAGGGCCCACCA chr.trna43-LysCTT Sc: 90.18 GGGCTCTTAGCTCAGTTGGTAGAGCAGCGGACTCTTAATCCGTAG...........GtCGAGTGTTCGAGTCACTCAGGGCCCACCA chr.trna42-LysCTT Sc: 90.18 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>.>>.......<<.<<<<<<<<<.... GGGTTGTTAGCTCAGTTGGTAGAGCAGCGGACTTTTAATCCGTAG...........GtCGCAGGTTCGAGTCCCGCACAACCCACCA chr.trna41-LysTTT Sc: 94.35

Met tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCGTTAGCTCAGTT.GGTcAGAGCAGAGGACTCATAATCCTTTG...........GtCGTTGGTTCAAGTCCAACACGGCCTACCA chr.trna23-MetCAT Sc: 90.97 >>>>>>>..>>>>..........<<<<..>>>>.......<<<<.................>>>>>.......<<<<<<<<<<<<.... GGCGCTTTAGCTCAGCC.GGTtAGAGCGACGGAATCATAATCCGCAG...........GtCCGGGGTTCGAATCCCTGAAGCGCCACCA chr.trna50-MetCAT Sc: 88.43 .>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<..... CGCGGAGTGGAGCAGTCtGGT.AGCTCGTTGGGCTCATAACCCAAAG...........GtCGCAGGTTCAAATCCTGCCTCCGCAACCA chr.trna31-MetCAT Sc: 88.10

Phe tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGCCTGGTAGCTCAGTTGGTAGAGCAGCGGATTGAAAATCCGCGT...........GtCGGTGGTTCGATTCCGCCCCAGGCCACCA chr.trna25-PheGAA Sc: 90.96

Pro tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>.>.......<.<<<<<<<<<<.... CGGGGCGTAGCGCAGCCaGGTAGCGCACTTGCATGGGGTGCAAGGG...........GtCGTGAGTTCGAATCCCACCGTCCCGACCA chr.trna16-ProGGG Sc: 71.09 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CGGGGTGTAGCTTAGCCtGGTAGAGCGCTACGTTCGGGACGTAGAG...........GcCGGAGGTTCGAATCCTCTCACCCCGACCA chr.trna22-ProCGG Sc: 81.43 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CGGGGCGTAGCGCAGCTtGGTAGCGCATCTGGTTTGGGACCAGAGG...........GtCGCACGTTCGAATCGTGTCGCCCCGACCA chr.trna39-ProTGG Sc: 87.76

SeC tRNAs

Ser tRNAs

>>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>>>........<<<<<..>>>>>.......<<<<<..<<<<<<<.... GGAGAGGTGGATGAGCGGTttA.AGTCGCACGCCTGGAAAGCGTGT.GTGGGTTAAT..CCCCAC.CGCGGGTTCGAATCCCGC..CCTCTCCGCCA chr.trna32-SerGGA Sc: 73.88 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<..>>>>..........<<<<..>>>>>.......<<<<<..<<<<<<<.... GGAGAGGTGGCAGAGTGGTcgA.TTGTACCTGACTCGAAATCAGGCGTACC..GCAA....GGTACCGTGGGTTCGAATCCCAC..CCTCTCCGCCA chr.trna49-SerCGA Sc: 67.83 >>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>>>>......<<<<<<..>>>>>.......<<<<<..<<<<<<<.... GGAGAGCTGGCCGAGCGGTttA.AGGCAGCAGTCTTGAAAACTGCC.GACGGTGGAA..GCCGTC.CGTGGGTTCGAATCCCAC..GCTCTCCGCCA chr.trna38-SerTGA Sc: 74.34 >>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>>>>......<<<<<<..>>>>>.......<<<<<..<<<<<<<.... GGAGACGTGACCGAGTGGCcgA.AGGTGCTCCCCTGCTAAGGGAGT.ATGTGCCAAAa.GCGCAT.CGAGGGTTCGAATCCCTC..CGTCTCCGCCA chr.trna10-SerGCT Sc: 62.37

Sup tRNAs

Thr tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCCATGTGGCTCAGT.GGTA.GAGCACTCCCTTGGTAAGGGAGAG...........GtCGCGCGTTCGATCCGCGCCATGGGCACCA chr.trna29-ThrGGT Sc: 87.68 >>>>>.>..>>>>.........<<<<..>>>>.......<<<<.................>>>>>.......<<<<<<.<<<<<.... GCCGGTGTAGCTCAGTTGGTA.GAGCAGCTCATTCGTAATGAGAAG...........GtCGAGGGTTCGATTCCTTTCTCCGGCACCA chr.trna47-ThrCGT Sc: 87.58 >>>>>>>..>>>>.........<<<<..>>>>.......<<<<.................>>>>>.......<<<<<<<<<<<<.... GCCGGCTTAGCTCAGCTGGTA.GAGCACCCGCCTTGTAAGCGGAAG...........GtCGTCCGTTCGATTCGGACAGCCGGCACCA chr.trna5-ThrTGT Sc: 90.33

Trp tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... AGGGGTATAGCTCAATTGGCAGAGCGTCGGTCTCCAAAACCGAAG...........GtTGGGGGTTCGATTCCCTCTGCCCCTGCCA chr.trna30-TrpCCA Sc: 85.70

Tyr tRNAs

>>>>>>>..>>>............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<.... GGAGGGGTGCCCGAGTGGCtaA.AGGGGGCAGACTGTAAATCTGTTGGCTTAC....GCCTaCGCTGGTTCGAATCCAGC.CTCCTCCACCA chr.trna27-TyrGTA Sc: 68.13

Val tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... AGGCGCGTAGCTCAGCTGGTtA.GAGCACCACCTTGACATGGTGGGG...........GtCGTTGGTTCGAGTCCAATCGCGCCTACCA chr.trna17-ValGAC Sc: 93.06 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCGGTTAGCTCAGC.GGT.A.GAGCACTGCCTTCACACGGCAGGG...........GtCGCAGGTTCGAACCCTGCACCGCCCACCA chr.trna48-ValCAC Sc: 93.97 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGTGCTTAGCTCAGTTGGT.A.GAGCGGCGCCCTTACAAGGCGTAG...........GtCGGGGGTTCGAGCCCCTCAGCACCCACCA chr.trna44-ValTAC Sc: 95.84

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.