GtRNAdb
>> tRNAscan-SE
>> Lowe Lab
 
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tRNAscan-SE Analysis of Halobacterium salinarum R1

>> Main Overview
>> 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





>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCTCGTAGATCAGTGGTA.GATCATCCCCCTGGCACGGGGAAG...........GcCTCGGGTTCAAATCCCGACGAGTCCA... chr.trna7-AlaGGC Sc: 70.00  

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCTCGTAGATCAGCGGTA.GATCGCTTCCTTCGCAAGGAAGAG...........GcCCTGGGTTCAAATCCCAGCGAGTCCA... chr.trna26-AlaCGC Sc: 76.68  
GGGCTCGTAGATCAGCGGTA.GATCGCTTCCTTCGCAAGGAAGAG...........GcCCTGGGTTCAAATCCCAGCGAGTCCA... chr.trna24-AlaCGC Sc: 76.68  

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCCCATAGCTCAGTGGTA.GAGTGCCTCCTTTGCAAGGAGGAT...........GcCCTGGGTTCGAATCCCAGTGGGTCCA... chr.trna21-AlaTGC Sc: 79.40  





Arg tRNAs





>>>>>>>..>>>..............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GTCCGGATAGGGTAGT..GGActA.TCCTCTTGGCTTGCGGAGCCAGGG...........A.CCGGCGTTCAAATCGCCGTCCGGACG... chr.trna45-ArgGCG Sc: 50.23  

>>>>>>>..>>>>............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCGCGTAGCTCAGC..GGAc.A.GAGCACTTGGTTCCGGACCAAGAT...........GtCAGGGGTTCAAATCCCTTCGCGCCCG... chr.trna23-ArgCCG Sc: 70.66  

>>>>>>>..>>>>............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCGCTTAGCTCAGCTtGGAc.A.GAGCACTTGGCTTCGGACCAAGAT...........GcCGCGGGTTCAAATCCTGCAGCGCCCA... chr.trna6-ArgTCG Sc: 72.48  

>>>>>>>..>>>..............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCGTGTGGCCAAGC..GGAc.A.CGGCGAGAGGTTCCTAACCTCTAG...........AtCGCGGGTTCGAGTCCCGCCACGCCCG... chr.trna43-ArgCCT Sc: 66.43  

>>>>>>>..>>>>............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCGCGTAGCTCAGTCcGGAc.A.GAGCGTTCGGCTTCTAACCGAAAT...........GtCGGGGGTTCGAATCCCCTCGTGCCCG... chr.trna28-ArgTCT Sc: 73.82  





Asn tRNAs





>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GCCGCCATAGCTCAGTTGGTAGAGCACGTGGTTGTTACCCACGTT...........GtCCCAGGTTCGAGCCCTGGTGGCGGCG... chr.trna1-AsnGTT Sc: 63.25  





Asp tRNAs





>>>>>>>..>>>............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GCCCGGATGGTGTAGTGGCccA.TCATACAACCCTGTCACGGTTGTG...........ACGCGGGTTCAAATCCCGCTCCGGGCG... chr.trna25-AspGTC Sc: 67.24  





Cys tRNAs





>>>>>>>..>>...............<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GCCAAGGTGGCAGAGTTcGGCctAACGCGGCGGCCTGCAGAGCCGCTC...........AtCGCCGGTTCAAATCCGGCCCTTGGCT... chr.trna22-CysGCA Sc: 69.09  





Gln tRNAs




>>>>>>>..>>>............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
AGTCCCGTAGGGTAGTGGCcaA.TCCTGAAGCCTTCTGGGGGCTTCG...........ACGGAAGTTCGAATCTTCCCGGGACTA... chr.trna29-GlnCTG Sc: 50.49  

>>>>>>>..>>>............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
AGTCCCGTGGTGTAGTGGCcaA.TCATATGGGCCTTTGGAGCCCACG...........ACGGCGGTTCGAATCCGCCCGGGACTA... chr.trna5-GlnTTG Sc: 61.86  





Glu tRNAs




>>>>>>>..>>>.............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GCTCCGTTGGTGTAGTCcGGCcaATCATCTTGCCCTCTCACGGCAAGG...........ACTAGGGTTCAAATCCCTGACGGAGCA... chr.trna39-GluCTC Sc: 59.86  

>>>>>>>..>>>.............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GCTCGGTTGGTGTAGTCcGGCcaATCATGTTGGCCTTTCGAGCCGACG...........ACCAGGGTTCAAATCCCTGACCGAGCA... chr.trna13-GluTTC Sc: 68.73  





Gly tRNAs





>>>>>>>..>>>..........<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GCGCTGGTAGTGTAGTGGTA.TCACGTGACCTTGCCATGGTCACA...........ACCTGGGTTCAAATCCCAGCCAGCGCA... chr.trna33-GlyGCC Sc: 62.22  

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GCGCTGGTGGTCTAGTGGTA.GGACATGAGCTTCCCAAGCTCATA...........GCCCGGGTTCAATTCCCGGCCAGCGCA... chr.trna31-GlyCCC Sc: 65.26  

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GCGCCGGTAGTCTAGTGGTA.GGACCTGAGCCTTCCAAGCTCATG...........GCCCGGGTTCAAATCCCGGTCGGCGCA... chr.trna42-GlyTCC Sc: 72.10  





His tRNAs





>>>>>>>..>>>............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
TCCGGGGTAGGGTAGTGGActA.TCCTTCAGCCTTGTGGAGGCTGAG...........ACGCGGGTTCGATTCTCGCCCCTGGAC... chr.trna19-HisGTG Sc: 46.60  





Ile tRNAs





>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGTCAGTAGCTCAACTaGGTAGAGCGCCACTCTGATAAGGTGGAG...........GcTTGCGGTTCAAATCCGCACTGACCCA... chr.trna16-IleGAT Sc: 59.84  






Leu tRNAs





>>>>>>>..>>>..............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<....
GCGTGGGTAGCCGAGCTaGGTcaA.AGGCGCAGCGTTGAGGGCGCTGTCCTGTAG....AGGTtCGCCGGTTCGAATCCGGT.CCCACGCA... chr.trna36-LeuGAG Sc: 64.85  

>>>>>>>..>>>..............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<....
GCAGGGATAGCCAAGTTtGGCcaA.AGGCGCAGCGTTCAGGGCGCTGTCCCGTAG....GGGTtCGCAGGTTCAAATCCTGC.TCCCTGCA... chr.trna12-LeuCAG Sc: 64.42  

>>>>>>>..>>>..............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<....
GCGCGGGTAGCCAAGCCaGGAa.A.CGGCGTAGCGCTTAGGACGCTATCCCGTAG....GGGTcCGCCGGTTCAAATCCGGT.CCCGCGCA... chr.trna37-LeuTAG Sc: 71.46  

>>>>>>>..>>>..............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<....
GCGAGGGTAGCCAAGCTcGGCcaA.CGGCGACGGACTCAAGATCCGTTCTCGTAG....GAGTtCGAGGGTTCGAATCCCTT.CCCTCGCA... chr.trna38-LeuCAA Sc: 69.43  

>>>>>>>..>>>..............<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<....
GCGAGGGTGGCCGAGC..GGCcaA.AGGCGGCGGGCTTAAGACCCGCTCCCGTAG....GGGTtCGTGGGTTCGAATCCCAC.CTCTCGCA... chr.trna17-LeuTAA Sc: 69.84  





Lys tRNAs




>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCCGGTAGCTCAGTCtGGCAGAGCGACGGACTCTTAATCCGTCG...........GtCGCGTGTTCAAATCGCGCCCGGCCCG... chr.trna8-LysCTT Sc: 86.03  

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCCGATAGCTCAGCCcGGCAGAGCGTCTGGCTTTTAACCAGACG...........GtCGAGGGTTCAAATCCCTCTCGGCCCG... chr.trna27-LysTTT Sc: 85.16  





Met tRNAs




>>>>>>>..>>>.............<<<.>>>>>...........................................................................................<<<<<................>>>>>.......<<<<<<<<<<<<....
GCCCGGGTGGCTTAGCT.GGTc.ATAGCGCCGCACTCATAgggtatcgagcttcggtgcggcatcccactgccacgtggatgctcagcatgtccgcgaggcccgccgagcctcgaacctgggacATGCGGAG...........AtCGAGGGTTCAAAACCCTCCCCGGGCA... chr.trna34-MetCAT Sc: 65.69  
AGCGGGATGGGATAGCCaGGAg.ATTCCGCCGGGCTCATA....................................................................................ACCCGGAG...........AtCGGTAGTTCAAATCTACCTCCCGCTA... chr.trna44-MetCAT Sc: 63.10  
>>>>>>>..>>>>...........<<<<.>>>>>...........................................................................................<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGCCCTTAGCTTAGTCcGGTtcAAAGCCCCCGGCTCATAtcagtgccgtcgcatgcggcggcgctgtgggac...................................................ACCGGGTG...........AgCGGTGGTTCAAATCCGCCAGGGCCCA... chr.trna2-MetCAT Sc: 60.74  





Phe tRNAs





>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GCCGCCTTAGCTCAGACtGGGAGAGCACTCGACTGAAGATCGAGCT...........GtCCCTGGTTCAAATCCGGGAGGCGGCA... chr.trna47-PheGAA Sc: 74.29  





Pro tRNAs





>>>>>>>..>>>............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GGGACCGTGGGGTAGC..GGTA.TCCTCGGCGCATGGGGTGCGTCGG...........ACTCGAGTTCGAATCTCGACGGTCCCA... chr.trna15-ProGGG Sc: 47.58  

>>>>>>>..>>>............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GGGCCGGTGGGGTAGCTtGGTA.TCCTTCGGCCTTCGGGTGGCCGTA...........ACCGCGATTCGAATTCGCGCCGGCCCA... chr.trna32-ProCGG Sc: 59.60  

>>>>>>>..>>>............<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<....
GGGACTGTAGGGTAGCTtGGTA.TCCTTCGGGCCTTGGGTGCCCGTG...........ACCCCGATTCAAATTCGGGCGGTCCCA... chr.trna20-ProTGG Sc: 63.72  





SeC tRNAs









Ser tRNAs





>>>>>>>..>>................<<.>>>>>.......<<<<<..>>>..............<<<...>>>>>.......<<<<<.<<<<<<<....
GCCGGGATGGCCGAAT..GGC..A.AAGCGCACGCCTGGAAAGCGTGTCCCC..TTAC........GGGGtTCAGGGTTCAAATCCCTG.TCCCGGCG... chr.trna30-SerGGA Sc: 56.38  

>>>>>>>..>>>>............<<<<.>>>>>.......<<<<<..>>>..............<<<...>>>>>.......<<<<<.<<<<<<<....
GCCGAGGTAGCCTAGCCtGGCc.A.AGGCGGTTGCTTCGAGAGCAACTGTCCAC..........ACGGACtCAGGAGTTCAAATCTCCT.CCTCGGCG... chr.trna4-SerCGA Sc: 62.46  

>>>>>>>..>>>>............<<<<.>>>>>.......<<<<<..>>>..............<<<...>>>>>.......<<<<<.<<<<<<<....
GGTGAGGTGGCAGAGC..GGCctA.TTGCGCCGGTCTTGAAAACCGGT.GGC..GTCAc.......GCCT.CCTGGGTTCGAATCCCAG.CCTCACCG... chr.trna40-SerTGA Sc: 58.38  


>>>>>>>..>>>>............<<<<.>>>>>.......<<<<<..>>>..............<<<...>>>>>.......<<<<<.<<<<<<<....
GTCGTGGTAGCCTAGCCtGGTc.A.AGGCGCAGGGTTGCTAACTCTGT.GGC..GTAA........GCCT.CCGGGGTTCAAATCCCCG.CCACGACG... chr.trna11-SerGCT Sc: 69.78  





Sup tRNAs










Thr tRNAs





>>>>>>>..>>>>.............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GCCTGGGTAGCTT..AGCGGT..A..AAGCGCGTCCTTGGTAAGGACGAG...........AcCCCGGATTCAAATTCCGGCCTAGGCT... chr.trna18-ThrGGT Sc: 65.68  

>>>>>>>..>>>>.............<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GCCGGTGTAGCTC..AGCGGT..A..GAGCGATTCCTTCGTAAGGAATAG...........GcCGAGGGTTCAAATCCCTCCACCGGCT... chr.trna10-ThrCGT Sc: 74.36  

>>>>>>>..>>>...............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GCCAAGGGAGCTTgg.GTGGTccA...AGCACTCGATTTGTAATCGAGAG...........TtCGTGGGTTCAAATCCCACCCTTGGCT... chr.trna41-ThrTGT Sc: 50.88  





Trp tRNAs




>>>>>>>..>>>>.........<<<<.>>>>>.............................................................................................................<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGGCTGTGGCCAAGCCaGGCATGGCGACTGACTCCAGaggcccgcgcccgggacgacgctccagactggtataccgagcggccgactgatcatcggtccgctgtgacgaccctctggagttccgaggcgcaccggagatATCAGTCG...........AtCGGGGGTTCAAATCCCTCCGGCCCCA... chr.trna9-TrpCCA Sc: 56.31  





Tyr tRNAs





>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
CCGCCCTTAGCTCAGACtGGTAGAGCAGTCGACTGTAGATCGACTT...........GcCCCCCGTTCAAATCGGGGAGGGCGGA... chr.trna3-TyrGTA Sc: 64.55  





Val tRNAs





>>>>>>>..>>>............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGTTGGTGGTCTAGTCaGGCtATGACACCTCCTTGACATGGAGGAG...........GtCGGCGGTTCAAATCCGCCCCAACCCA... chr.trna14-ValGAC Sc: 69.70  

>>>>>>>..>>>............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGTCGGTGGTCTAGTCcGGTtATGACGGCTCCTTCACACGGAGCAG...........GtCGGCGGTTCAACTCCGCCCCGACCCA... chr.trna35-ValCAC Sc: 70.04  

>>>>>>>..>>>............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<....
GGGTTCGTGGTCTAGTC.GGTcATGACGCGGCCTTTACAAGGCCGAG...........GtCGGTGGTTCGAATCCGCCCGAACCCA... chr.trna46-ValTAC Sc: 74.98  












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.