GtRNAdb
>> tRNAscan-SE
>> Lowe Lab
 
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tRNAscan-SE Analysis of Ferroplasma acidarmanus Fer1

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>> tRNAs by Isotype
>> tRNAs by Locus
>> Secondary Structures
>> tRNA Alignments
>> FASTA Seqs
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>> 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





>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCTCATAGATCAGCGGTA.GATCGCTTCCTTGGCATGGAAGAG...........GgCAGGGGTTCAAATCCCCTTGAGTCCA... Contig164.trna44-AlaGGC Sc: 65.23  

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCCGGTAGATCAGCGGTA.GATCGCTTGCTTCGCAAGCAAGAG...........GgCTCGGGTCCAAATCCCGACCGGTCCA... Contig162.trna13-AlaCGC Sc: 72.98  

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCCGATAGATCAGCGGTA.GATCGCTTGCTTTGCAAGCAAGAG...........GgCTCGGGTCCAAATCCCGATCGGTCCA... Contig168.trna27-AlaTGC Sc: 71.42  





Arg tRNAs





>>>>>>>..>>>..............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.......................
GCCCGTGTGGGGTAATTtGGAt.A.TCCTGAAGGCCTGCGGAGCCTTAG...........A.TTCGGGTTCAAATCCCGGCGCGGGCG...................... Contig157.trna8-ArgGCG Sc: 59.20  

>>>>>>>..>>>..............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.......................
GGGCCCGTGGTGTAAC..GGAttA.TCATATAGGCCTCCGGAGCCTATA...........A.TCCGGGTTCGAATCCCGGCGGGCTCA...................... Contig155.trna45-ArgCCG Sc: 52.82  

>>>>>>>..>>>..............<<<..>>>>.......<<<<.................>>>>>.......<<<<<<<<<<<<.......................
GGATCCGTGGGGTAGTTaGGAt.A.TCCTGCTGGCCTTCGAAGCCGATG...........A.CCCGGGTTCAAATCCCGGCGGGTCCG...................... Contig167.trna32-ArgTCG Sc: 64.70  

>>>>>>>..>>>>............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.......................
GGGCACGTGGCCTAGCAtGGAt.A.GGGCAACAGCCTCCTAAGCTGTAA...........AtCAGGGGTCCAAATCCCCTCGTGCCCG...................... Contig169.trna16-ArgCCT Sc: 64.97  

>>>>>>>..>>>>............<<<<.>>>.>.......<.<<<................>>>>>.......<<<<<<<<<<<<.......................
GGGCTCGTGGCCTAGTAtGGAt.A.AGGCACCGTCCTTCTAAGTCGGTG...........AtCGTGGGTCCAAATCCCACCGAGCCCGCTAgaattctcttattcatagc Contig161.trna24-ArgTCT Sc: 68.14  





Asn tRNAs





>>>>.>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<.<<<<....
GCCGCCATAGCTCAGTTGGTAGAGCACTCGGCTGTTAACCGAGCG...........GtCGTCGGTTCAAGCCCGACTGACGGCG... Contig157.trna34-AsnGTT Sc: 64.52  





Asp tRNAs





>>>>>>>..>>>............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GCCCCGATAGTGTAGCGGCctA.TCATACAGGCCTGTCGAGCCTGTG...........ACACGGGTTCAAATCCCGTTCGGGGCG... Contig164.trna1-AspGTC Sc: 74.19  





Cys tRNAs










Gln tRNAs




>>>>>>>..>>>>..........<<<<..>>>>.......<<<<................>>>>>.......<<<<<<<<<<<<....
AGCTCCGTGGTGTAGTGGCcaA.GCATTACTGGCTCTGGACCAGCAG...........ACGGCAGTTCGAATCTGCCCGGAGCTA... Contig157.trna29-GlnCTG Sc: 55.62  

>>>>>>>..>>>>..........<<<<..>>>>.......<<<<................>>>>>.......<<<<<<<<<<<<....
AGCTCCGTGGTGTAGTGGAcaA.GCATTCCGGACTTTGGATCCGATG...........ACGGCAGTTCGAATCTGCCCGGAGCTG... Contig168.trna12-GlnTTG Sc: 55.37  





Glu tRNAs




>>>>>>>..>>>>...........<<<<..>>>>.......<<<<................>>>>>.......<<<<<<<<<<<<....
GCTCCGGTGGTGTAGCCaGGCcaAGCATTAGGGACTCTCAATCCCCCG...........ACTCGGGTCCAAATCCCGGCCGGAGCA... Contig166.trna14-GluCTC Sc: 65.08  

>>>>>>>..>>>>...........<<<<..>>>>.......<<<<................>>>>>.......<<<<<<<<<<<<....
GCTCCGATGGTGTAGTCaGGCcaAGCATTCCGGCCTTTCGAGCCGATG...........ACTCGGGTTCAAATCCCGGTCGGAGCA... Contig167.trna23-GluTTC Sc: 71.45  





Gly tRNAs





>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<.<<<<<<<....
GCGAGTGTGGTGTAGCCtGGCAACACGCGAGCTTGCCAAGCTCGT............GcCCCGGGTCCAAATCCCGG.CACTCGCA... Contig152.trna43-GlyGCC Sc: 66.00  

>>>>>>>..>>>...........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<.<<<<<<<....
GCGATTGTGGTGTAGCCtGGTATCACAGTGGCTTCCCAAGCCACTA...........A.CCCGGGTCCAAATCCCGG.CAATCGCA... Contig169.trna17-GlyCCC Sc: 66.64  

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<.<<<<<<<....
GCAGGTGTGGTGTAGCCtGGTAGCACGGAAGCCTTCCAAGCTTTCG...........A.CTCGGGTTCAAATCCCGG.CACCTGCA... Contig158.trna5-GlyTCC Sc: 71.55  





His tRNAs





>>>>>>>..>>>...........<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GCCGGGGTGGGGTAATGGAcA.TCCTTGGGGACTGTGGATCCCCGG...........ACCCGGGTTCGATTCCCGGTCCCGGCC... Contig163.trna4-HisGTG Sc: 50.24  





Ile tRNAs





>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGGTTGTAGCTTAGCTtGGTtGGAGCACCCGGCTGATAACCGGGAG...........GtCACCGGTTCAAATCCGGTCAGCCCCA... Contig150.trna39-IleGAT Sc: 74.79  






Leu tRNAs




>>>>>>>...>>.............<<..>>>>>.......<<<<<.>>>.............<<<...>>>>>.......<<<<<.<<<<<<<....
GCAGAGGTTACCGAGTTaGGAcaAAGGCGCTAGATTAAGGGTCTAGTCTC..GAAG.......GAGTtCGCGGGTTCAAATCCCGT.CCTCTGCA... Contig161.trna33-LeuAAG Sc: 45.65  


>>>>>>>..>>>.............<<<.>>>>>.......<<<<<.>>>.............<<<...>>>>>.......<<<<<.<<<<<<<....
GCGGAGATTGCCGAGCTaGGAcaAAGGCGATGGATTCAGGGTCCATTTCC..GCAG.......GGATtCGTGGGTTCAAATCCCAC.TCTCCGCA... Contig169.trna20-LeuCAG Sc: 58.91  

>>>>>>>..>>>.............<<<.>>>>>.......<<<<<.>>>.............<<<...>>>>>.......<<<<<.<<<<<<<....
GCGGAGATTGCCGAGCTaGGAa.AAGGCGATGGATTTAGGGTCCATTTCC..GTAG.......GGATtCGTGGGTTCAAATCCCAC.TCTCCGCA... Contig162.trna31-LeuTAG Sc: 62.17  

>>>>>>>..>>>.............<<<.>>>>>.......<<<<<.>>>.............<<<...>.>>>.......<<<.<.<<<<<<<....
GCGGAGGTTACCGAGTCaGGCtaAAGGTGATAGACTCAAAATCTATTCCCAA.........AGGGGTtCGCCGGTTCAAATCCGAC.CCTCCGCA... Contig169.trna18-LeuCAA Sc: 52.37  

>>>>>>>..>>>.............<<<.>>>>>.......<<<<<.>>>.............<<<...>>>>>.......<<<<<.<<<<<<<....
GCAAGGGTAACTAAGCTtGGCcaAAGGTGTAGGACTTAAGATTCTATCTC..GAAG.......GAGTtCGCGGGTTCAAATCCCGT.CCCTTGCA... Contig157.trna6-LeuTAA Sc: 52.75  





Lys tRNAs




>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<..........................
GGGTCCGTAGCTCAGCTaGGTAGAGCGATGGACTCTTAATCCATCG...........GtCAAGGGTTCAAATCCCTTCGGACCCG......................... Contig158.trna26-LysCTT Sc: 80.77  

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<..........................
GGGTCCGTAGCTCAGCTaGGTAGAGCGTCTGGCTTTTAACCAGGCG...........GtCAGGGGTTCAAACCCCCTCGGACCCGTttaggtgaaaatatgagtaaat.. Contig163.trna7-LysTTT Sc: 77.48  





Met tRNAs




>>>>>>>..>>>>..........<<<<.>>>>>.......................<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGGTTGTAGCTCAGCTaGGT.AGAGCGCCTGGCTCATA................ACCAGGTG...........GtCGTCGGTTCAAACCCGGCCAGCCCCA... Contig157.trna35-MetCAT Sc: 76.12  
GCCGGGGTGGCTCAGTT.GGT.AGAGCGTCGGACTCATAagtgaaaaactgagatATCCGAAG...........GcCTCGGGTTCAATCCCCGACCCCGGCA... Contig169.trna21-MetCAT Sc: 69.15  
>>>>>>>..>>>............<<<.>>>>>.......................<<<<<................>>>>>.......<<<<<<<<<<<<....
AGCGGGGTAGGGTAGTCaGGAgATCCCGACGGGCTCATA................ACCCGTAG...........AtCAATGGTTCAAATCCATTCCCCGCTA... Contig163.trna10-MetCAT Sc: 67.53  





Phe tRNAs





>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GCCGTGATAGCTCAGTTGGGAGAGCGCCAGACTGAAGATCTGGAG...........GtCGCTGGTTCAATCCCGGCTCACGGCA... Contig168.trna11-PheGAA Sc: 69.91  





Pro tRNAs





>>>>>>>..>>>...........<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GGGACCGTGGGGTAGCTtGGTATCCTACCAGCTTGGGGTGTTGGTG...........ACTCCGATTCAAATTCGGACGGTCCCA... Contig167.trna22-ProGGG Sc: 55.19  

>>>>>>>..>>>...........<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GGGTTTGTGGGGTAGCCtGGCATCCTTCCAGCTTCGGGAGTTGGAG...........ACTCCGGTCCAAATCCGGACAGACCCA... Contig147.trna42-ProCGG Sc: 55.94  

>>>>>>>..>>>...........<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GGGGCTGTGGGGTAGCTtGGCATCCTACGGGCTTTGGGAGCCTGAG...........ACTCCGATTCAAATTCGGGCAGCCCCA... Contig168.trna19-ProTGG Sc: 65.48  





SeC tRNAs









Ser tRNAs





>>>>>>>..>.>>..........<<.<.>>>>>.......<<<<<..>>>..........<<<...>>>>>.......<<<<<<<<<<<<....
GCTGGGATAGCCTAGCCtGGTA.AGACGCAGGTCTGGAAAACCTGTGCACGTAA......GTGCcCGGGAGTTCAAATCTCCCTCCCAGCG... Contig167.trna37-SerGGA Sc: 63.45  

>>>>>>>..>.>>..........<<.<.>>>>>.......<<<<<..>>>..........<<<...>>>>>.......<<<<<<<<<<<<....
GCTGGGATAGCCTAGCCcGGTA.AGACGGTAGATTCGAAATCTACTGCTAGAAA......TAGCtCGGGAGTTCAAATCTCCCTCCCAGCG... Contig155.trna36-SerCGA Sc: 52.72  

>>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>............<<...>>>>>.......<<<<<<<<<<<<....
GCCACGGTGGCCCAGT..GGTA.CGGCGCCAGCCTTGAGAGCTGGTTCCC.TTG......TGGAtCGGGTGTTCGAATCACCCCCGTGGCG... Contig169.trna25-SerTGA Sc: 64.52  


>>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>..........<<<...>>>>>.......<<<<<<<<<<<<....
GCGGGGATGGCCCAGT..GGTA.CGGCGGCAGCCTGCTAAGCTGTTTCTCGAAAt.....GAGAgCATGGGTTCAAATCCCATTCCCCGCG... Contig166.trna28-SerGCT Sc: 57.50  





Sup tRNAs










Thr tRNAs





>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.......................
GCCGTCGTAGCTCAGCCtGGTAGAGCGCGTGCTTGGTAAGCACGAG...........GtCGCGGGACCGAATCCCGTCGGCGGCT...................... Contig156.trna41-ThrGGT Sc: 73.12  

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.......................
GCCATCGTAGCTCAGCA.GGAAGAGTGGCTGATTCGTAATCAGCAG...........GtCGCGAGTTCAAATCTCGCCGATGGCT...................... Contig161.trna3-ThrCGT Sc: 70.37  

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.......................
GCCATCGTAGCTCAGCAtGGTAGAGCGGCTGATTTGTAATCAGCAG...........GtCGGGGGATCGAATCCCTCCGATGGCTTgctaaatataataataatCAt Contig158.trna9-ThrTGT Sc: 72.19  





Trp tRNAs




>>>>>>>..>>>...........<<<.>>>>>............................................................................<<<<<...............>>>>>.......<<<<<<<<<<<<....
GGAAGCATGGGGTAGTCaGGTATCCTAGAGGGCTCCAGtcagtttgtgattagctaaaggtcgtctgaatttatgatgaatgactggaacgatgaaacatggaagagACCCTTAG...........ATCTGGGTTCAAATCCCAGTGCTTCCA... Contig157.trna40-TrpCCA Sc: 47.61  





Tyr tRNAs





>>>>>>>..>>>>........<<<<.>>>>>..................................<<<<<................>>>>>.......<<<<<<<<<<<<....
CCCGGCTTAGCTCAGTTGGTAGAGCGATGGACTGTAGagtgatatactgccagaaaacgcagtcATCCATAG...........GtCTCTGGTTCGAATCCGGAAGCCGGGA... Contig157.trna38-TyrGTA Sc: 60.03  





Val tRNAs





>>>>>>>..>>>...........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCTCGTAGTCTAGTGGT.A.TGATGTCTCCCTGACACGGAGAAG...........GtCACCGGTCCGAATCCGGTCGGGCCCA... Contig169.trna2-ValGAC Sc: 67.67  

>>>>>>>..>>>...........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCTTGTGGTCCAGTGGTtA.TGACGCTTCCCTCACACGGAAGAA...........AtCGCCGGTTCAAATCCGGCCAGGCCCA... Contig167.trna15-ValCAC Sc: 67.20  

>>>>>>>..>>>...........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCTCGTAGTCTAGTGGTtA.TGATACCGCCCTTACAAGGCGGTG...........AtCACCGGTTCAAATCCGGTCGGGCCCA... Contig161.trna30-ValTAC Sc: 76.85  












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.