GtRNAdb

tRNAscan-SE Analysis of Aeropyrum pernix

>> 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

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCGGTAGCTCAGCCtGGAAGAGCGCCCGGTTGGCATCCGGGAG...........GcCCCGGGTTCAAATCCCGGCCGGTCCACCA chr.trna39-AlaGGC Sc: 88.60 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCGGTAGCTCAGCCtGGAAGAGCGCCGCCCTCGCACGGCGGAG...........GcCCCGGGTTCAAATCCCGGCCGGTCCACCA chr.trna3-AlaCGC Sc: 93.45 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCGGTAGCTCAGCCtGGAAGAGCGCCCGGCTTGCACCCGGGAG...........GcCCCGGGTTCAAATCCCGGCCGGTCCACCA chr.trna27-AlaTGC Sc: 93.25

Arg tRNAs

>>>>>>>..>>>>..................<<<<.>>>>>...................................................<<<<<................>>>>>.......<<<<<.<<<<<<<.... GGGCCCGTAGCTCAGCCaGGAcc..A.....GAGCGCCGGCCTGCGG............................................AGCCGGAG...........GtCCCGGGTTCAAATCCCGG.CGGGCCCGCCA chr.trna9-ArgGCG Sc: 92.86 >>>>>>>..>>>>..................<<<<.>>>>>...................................................<<<<<................>>>>>.......<<<<<.<<<<<<<.... GGGCCCGTAGCTCAGCCaGGAt...A.....GAGCGCCGGCCTCCGG............................................AGCCGGAG...........GtCCCGGGTTCAAATCCCGG.CGGGCCCGCCA chr.trna1-ArgCCG Sc: 92.70 .>...>>..>........................<.>>>.>...................................................<.<<<................>>>>>.......<<<<<.<<...<..... TGCAACGT.GAGTATT....T....A.....TAGCGTCGTTCTCCGG............................................AGCCGGAG...........GtCCCGGGTTCAAATCCCGG.CGGGCCCGCCA chr.trna2-ArgCCG Sc: 24.36 Pseudo .....>>...>......................<..>.>>>...................................................<<<.<................>>>>>.......<<<<<.<<......... ATAAATGCAACACA....GGTatttA.....TAGAGCGGGTCTCCGG............................................AGCCGGAG...........GtCCCGGGTTCAAATCCCGG.CGGGCCCGCCA chr.trna18-ArgCCG Sc: 20.48 Pseudo >>>>>>>..>>>>..................<<<<.>>>>>...................................................<<<<<................>>>>>.......<<<<<.<<<<<<<.... GGGCCCGTAGCTCAGCCaGGAcc..A.....GAGCGCCGGCCTTCGG............................................AGCCGGCG...........GtCCCGGGTTCAAATCCCGG.CGGGCCCGCCA chr.trna17-ArgTCG Sc: 92.38 >>>>>>>..>>>>..................<<<<.>>>>>...................................................<<<<<................>>>>>.......<<<<<.<<<<<<<.... GGGCCCGTAGCTCAGCCaGGAt...A.....GAGCGCCGGCCTCCTA............................................AGCCGGTG...........GtCGGGGGTTCAAATCCCCC.CGGGCCCGCCA chr.trna26-ArgCCT Sc: 91.62 >>>>>>>..>>>>..................<<<<.>>>>>...................................................<<<<<................>>>>>.......<<<<<.<<<<<<<.... GGGCCCGTAGCTCAGCCaGGAc...A.....GAGCGCCGGCCTTCTAagcggggccgggaggcctcggccctacctcggctgcgcggggacAGCCGGTG...........GtCCCGGGTTCAAATCCCGG.CGGGCCCGCCA chr.trna12-ArgTCT Sc: 82.42

Asn tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGGGGTAGCTCAGCTaGGTAGAGCGCCGGGCTGTTAACCCGGTG...........GtCGGGGGTTCAAGTCCCCTCCCCGGCGCCA chr.trna41-AsnGTT Sc: 86.11

Asp tRNAs

>>>>>>>..>>>>...........<<<<.>>>>>................................................................................................................................<<<<<...............>>>>>.......<<<<<<<<<<<<.... GCCGCGGTAGTATAGCCtGGActAGTATGCGGGCCTGTCAagggccccgcctccgccccaccctcattctactacacgcttatcaggataaacagccgggcaaacgtttttaaccccgccgaaattcatactcttcccggggcggaggcgggcctgcggagAGCCCGTG...........ACCCGGGTTCAAATCCCGGCCGCGGCGCCA chr.trna4-AspGTC Sc: 54.79

Cys tRNAs

>>>>>>>..>>>............<<<.>>>>>.........................<<<<<.................>>>>>.......<<<<<<<<<<<<.... GCCGGGGTGGCCGAGCGGTctA.AGGCGGCGGGCTGCAGaggacctggcccgtagagACCCGTTA...........GttCCCGGGTTCGAATCCCGGCCCCGGCTCCA chr.trna23-CysGCA Sc: 65.01

Gln tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<.... AGCCGGGTCGTCTAGCGGCccA.GGATGCGGGGCTCTGGCCCCCGTG...........ACCGGGGTTCGAATCCCCGCCCGGCTACCA chr.trna20-GlnCTG Sc: 70.54 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<.... AGCCGGGTCGTCTAGCGGCccA.GGATGCGGGGTTTTGGCCCCCGTG...........ACCCGGGTTCGAATCCCGGCCCGGCTACCA chr.trna33-GlnTTG Sc: 71.26

Glu tRNAs

>>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<.... GCCGCGGTAGTATAGCCcGGCccAGTATGCGGGCCTCTCGAGCCCGTG...........ACCCGGGTTCAAATCCCGGCCGCGGCACCA chr.trna14-GluCTC Sc: 84.08 >>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<.... GCCGCGGTAGTATAGCCcGGCccAGTATGCGGGCCTTTCGAGCCCGTG...........ACCCGGGTTCAAATCCCGGCCGCGGCACCA chr.trna24-GluTTC Sc: 84.64

Gly tRNAs

>>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGCGGTCGTCTAGCCtGGActAGGACGCCGGCCTGCCAAGCCGGAG...........GtCCCGGGTTCAAATCCCGGCCGCCGCACCA chr.trna38-GlyGCC Sc: 91.07 >>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGCCGTCGTCTAGCCtGGActAGGACGCCGGCCTCCCAAGCCGGTG...........GtCCCGGGTTCAAATCCCGGCGGCCGCACCA chr.trna32-GlyCCC Sc: 90.77 >>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGCCGTCGTCTAGCCtGGActAGGACGCCGGCCTTCCAAGCCGGTG...........GtCCCGGGTTCAAATCCCGGCGGCCGCACCA chr.trna19-GlyTCC Sc: 91.33

His tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCCGGGTAGCTCAGCCtGGAtAGAGCGCCGGACTGTGGATCCGGAG...........GtCCCGGGTTCAAATCCCGGCCCGGGCCCCA chr.trna22-HisGTG Sc: 91.56

Ile tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCGTAGCTCAGCCtGGTAGAGCGCCCGGCTGATAACCGGGAG...........GtCGGGGGTTCGAATCCCCCCGGGCCCACCA chr.trna10-IleGAT Sc: 95.34

Leu tRNAs

>>>>>>>..>>>.............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<.... GCGGGGGTGCCCGAGCCtGGCcaAAGGGGTCGGGCTGAGGACCCGATGGCGTAG....GCCTgCGTGGGTTCAAATCCCAC.CCCCCGCACCA chr.trna28-LeuGAG Sc: 79.89 >>>>>>>..>>>.............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<.... GCGGGGGTGCCCGAGCCtGGCcaAAGGGGTCGGGCTCAGGACCCGATGGCGTAG....GCCTgCGTGGGTTCAAATCCCAC.CCCCCGCACCA chr.trna25-LeuCAG Sc: 79.97 >>>>>>>..>>>.............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<.... GCGGGGGTGCCCGAGCCtGGCcaAAGGGGTCGGGCTTAGGACCCGATGGCGTAG....GCCTgCGTGGGTTCAAATCCCAC.CCCCCGCACCA chr.trna42-LeuTAG Sc: 80.53 >>>>>>>..>>>.............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<.... GCGGGGGTGCCCGAGCCaGGGcgAAGGGGGCGGGCTCAAGACCCGTTGGCGTAG....GCCGgCGTGGGTTCAAATCCCAC.CCCCCGCACCA chr.trna6-LeuCAA Sc: 72.62 >>>>>>>..>>>.............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<.... GCGGGGGTGCCCGAGCCtGGCcaAAGGGGGCGGGCTTAAGACCCGTTGGCGTAG....GCCTgCGTGGGTTCAAATCCCAC.CCCCCGCACCA chr.trna36-LeuTAA Sc: 77.60

Lys tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.........................................<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCGTAGCTCAGCCtGGTAGAGCGGCGGGCTCTTAacccgtagaggggagtggaggggcttcgtcctggCCCCGCGGAA.........GtCCCGGGTTCAAATCCCGGCGGGCCCGCCA chr.trna49-LysCTT Sc: 93.13 >>>>>>>..>>>>.........<<<<.>>>>>.........................................<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCGTAGCTCAGCCcGGCAGAGCGGCGGGCTTTTAacccgtagaggggagttgaggggcctcgtcctggCCCCGCGGAA.........GtCCCGGGTTCAAATCCCGGCGGGCCCGCCA chr.trna15-LysTTT Sc: 91.48

Met tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......................................................<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGCCGTAGCTCAGCCtGGCAGAGCGCCGGACTCATAcggcccggctaaacacccacaggccgaagtcgcctgggggcctgggagATCCGGAG...........GtCCCGGGTTCGAATCCCGGCGGCGGCACCA chr.trna47-MetCAT Sc: 85.24 GGGCCCGTAGCTCAGCCaGGTAGAGCGCCCGGCTCATAccgccgggtctcgggttcgagacaagcccgcgtgagac..........ACCGGGTG...........GtCGGGGGTTCAAATCCCCCCGGGCCCACCA chr.trna5-MetCAT Sc: 82.11 AGCGGGGTAGGGTAGCCtGGCAGCCCGCGGGGCTCATA................................................ACCCCGAG...........GtCGGTGGTTCAAATCCACCCCCCGCTACCA chr.trna13-MetCAT Sc: 80.37

Phe tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGCCGTAGCTCAGCGGGA.GAGCGCCCGGCTGAAGACCGGGTG...........GtCCGGGGTTCGAATCCCCGCGGCGGCACCA chr.trna34-PheGAA Sc: 87.53

Pro tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>...................................................<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGGCCGTCGTCTAGCCtGGCtAGGATGCCAGCCTGGGGagcgtatccccacccccgcgctggggggcgcccggat.......CGCTGGTG...........GtCCCGGGTTCAAATCCCGGCGGCCCCACCA chr.trna30-ProGGG Sc: 71.31 >>>>>>>..>>>>..........<<<<.>>>>>...................................................<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCGTCGTCTAGCCtGGCtAGGATGCGGGGTACGGAgcagaaggtcccgctggagggcgggaggctccgcccgactcgggACCCCGTG...........GtCCGGGGTTCAAATCCCCGCGGGCCCACCA chr.trna51-ProCGG Sc: 84.43 >>>>>>>..>>>>..........<<<<.>>>>>...................................................<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGGCCGTCGTCTAGCCtGGCtAGGATGCGGGGCTTGGG............................................ACCCCGTG...........GtCCGGGGTTCAAATCCCCGCGGCCCCACCA chr.trna44-ProTGG Sc: 86.35

SeC tRNAs

Ser tRNAs

>>>>>>>..>>>..............<<<.>>>>>...........................................<<<<<..>>>>>.......<<<<<..>>>>>.......<<<<<.<<<<<<<.... GCCGGGGTGCCCGAGC..GGTccA.AGGGGACGGGCTGGAG....................................ACCCGTT.GCCCCGCGA...GGGGCGCGCGGGTTCGAATCCCGC.CCCCGGCGCCA chr.trna29-SerGGA Sc: 70.89 >>>>>>>..>>>..............<<<.>>>>>...........................................<<<<<..>>>>>.......<<<<<..>>>>>.......<<<<<.<<<<<<<.... GCCGGGGTGGCCGAGC..GGCccA.AGGCGGCGGGCTCGAGgtcggcaacaggggtttccgcgccgccgcacgagagACCCGTT.GCCCCGCGA...GGGGCGCGCGGGTTCGAATCCCGC.CCCCGGCGCCA chr.trna43-SerCGA Sc: 58.61 >>>>>>>..>>>..............<<<.>>>>>...........................................<<<<<..>>>>>.......<<<<<..>>>>>.......<<<<<.<<<<<<<.... GCCGGGGTGGCCGAGC..GGCccA.AGGCGGCGGGCTTGAG....................................ACCCGTT.GCCCCGCGA...GGGGCGCGCGGGTTCGAATCCCGC.CCCCGGCGCCA chr.trna35-SerTGA Sc: 70.62 >>>>>>>..>>>>............<<<<.>>>>>...........................................<<<<<..>>>...........<<<..>>>>>.......<<<<<.<<<<<<<.... GCCGCGGTCGCCTAGCCtGGCc.A.GGGCGCCGGCCTGCTA....................................AGCCGGTGGGG..GAGAc....CCCGCGCGGGTTCAAATCCCGC.CCGCGGCGCCA chr.trna50-SerGCT Sc: 81.64

Sup tRNAs

Thr tRNAs

>>>>>>>..>>>>............................<<<<.>>>>>........................................................<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGCCGTAGCTCAGCTGGCA....................GAGCGCCGCCCTGGTA.................................................AGGCGGAG...........GcCCCGGGTTCGAATCCCGGCGGCGGCTCCA chr.trna31-ThrGGT Sc: 88.81 >>>>>>>..>>>>............................<<<<.>>>>>........................................................<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGCCGTAGCTCAGC.GGTA....................GAGCGCCGGCCTCGTAcgggctagctccgaggtcgtccacccgccagaagtggagcccccgggacAGCCGGTG...........GtCGCGGGTTCGAATCCCGCCGGCGGCTCCA chr.trna52-ThrCGT Sc: 78.20 >>>>>>>..>>>..............................<<<.>>>>>........................................................<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGCCGTAGCTCAGCAGGCAgacccctgcgcggggccta.AAGCGCCGGCCTTGTA.................................................AGCCGGTG...........GtCGCGGGTTCGAATCCCGCCGGCGGCTCCA chr.trna48-ThrTGT Sc: 90.42 ...>>.>..>>>..............................<<<.>>>>>........................................................<<<<<................>>>>>.......<<<<<<.<<....... CACGCAGTAGCTAAGCTGACA....................CAGCGCCGCCCTTGTA.................................................AGGCGGAG...........GcCCCGGGTTTAAATCCCGGCGGCTCCA... chr.trna11-ThrTGT Sc: 55.39

Trp tRNAs

>>>>>>>..>>>>.........<<<<.>>>>...............................................<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCGTAGCTCAGCCaGGCAGAGCGGCGGACCCCGcataggcctccagagggtgcgggaggccgaggctccagA.CCCGTAG...........GtCGGGGGTTCAAATCCCCCCGGGCCCACCA chr.trna40-TrpCCA Sc: 88.00

Tyr tRNAs

>>>>>>>..>>>>........<<<<.>>>>>..............................................<<<<<................>>>>>.......<<<<<<<<<<<<.... CCCGCCGTAGCTCAGCGGCA.GAGCGCCCGGCTGTAGtgggacgcgggcggcgtaacccggtgtctccccgcagacACCGGGTG...........GtCCGGGGTTCGAATCCCCGCGGCGGGACCA chr.trna21-TyrGTA Sc: 71.65

Val tRNAs

>>>>>>>........>>>>..............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCG.TC.....GTCTAGCCtGGTt.A...GGACGCCGCCCTGACGCGGCGGAG...........GtCCGGGGTTCAAATCCCCGCGGGCCCACCA chr.trna16-ValGAC Sc: 87.94 >>>>>>>........>>>>..............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCG.TC.....GTCTAGCCtGGTt.A...GGACGCCGCCCTCACACGGCGGAG...........GtCCGGGGTTCAAATCCCCGCGGGCCCACCA chr.trna45-ValCAC Sc: 88.39 ...>>.>........>.>>..............<<.<..>>>>.......<<<<.................>>>>>.......<<<<<<.<<....... ATATCAG.TGat...ATGAAGCCaTGCatA...TCTTTGCGTTCTCACACGGCGGAG...........GtCCGGGGTTCAAATCCCCGCGGGCCCACCA chr.trna46-ValCAC Sc: 20.95 Pseudo >>>>>>>........>>>>..............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCG.TC.....GTCTAGCCtGGTt.A...GGACGCCGCCCTTACACGGCGGAG...........GtCCGGGGTTCAAATCCCCGCGGGCCCACCA chr.trna7-ValTAC Sc: 88.94 ..>>>>>........>>>>..............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<...... ACGCCTGcTAaacacGCCTACACc.........GGGCCCCGCCCTTACACGGCGGAG...........GtCCGGGGTTCAAATCCCCGCGGGCCCACCA chr.trna8-ValTAC Sc: 30.34 Pseudo

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.