GtRNAdb

tRNAscan-SE Analysis of Nitrosopumilus maritimus SCM1

>> 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

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCGGTCGTCTAGTCtGGTA.GGATAGGTGCATGGCATGCATCGG...........AtCAAGGGTTCAAATCCCTTCCGGTCCA... chr.trna6-AlaGGC Sc: 62.77 >>>>>>>..>>>............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCGGTGGTTTAGG..GGTA.TAATGCCTCGTTCGCAACGAGGAT...........GtCGAGGGTTCGATTCCCTCCCGGTCCA... chr.trna4-AlaCGC Sc: 70.62 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCGGTAGTATAGCCtGGTA.GTATACCCGCCTTGCACGCGGGGG...........GtCACGGATTCAAATTCCGTCCGGTCCA... chr.trna30-AlaTGC Sc: 73.24

Arg tRNAs

>>>>>>>..>>>>............................<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGACTCGTTGCATAG..................CTtGGAtAGTGCGAACGCTTGCGGAGCGTTAG...........GtCGCCGGTTCGAATCCGGTCGGGTCCG... chr.trna13-ArgGCG Sc: 62.07 >>.>>>>..>>>>............................<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<.<<.... GGACTCGTTGCACAG..................CCtGGAtAGTGCGGGCGGCTTCGAACCGCCAG...........GtCGAGGGATCGAAGCCCTCCGAGCCCT... chr.trna41-ArgTCG Sc: 54.05 >>>>>>>..>>>>............................<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCTTGTGGCGCAGagtcaatttgacgcgaaaCAtGGAtAGCGTGGTAGCCTCCTAAGTTACAG...........GtCGAGGGATCGAAGCCCTCCAAGCCCG... chr.trna25-ArgCCT Sc: 55.09 >>>>>>>..>>>>............................<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCATAGCTCAG..................CAtGGAtAGAGTGTTGGACTTCTAATCCAATG...........GtCAAGGGATCGAAGCCCTTTGGGCCCG... chr.trna23-ArgTCT Sc: 65.64

Asn tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGCCCTAGCTCAGCGtGGTAGAGCATCCGACTGTTAATCGGACG...........GtCGTCAGTTCAAGTCTGATGGGCGGCGCCA chr.trna34-AsnGTT Sc: 64.81

Asp tRNAs

>>>>>>>..>>.>...........<.<<.>>>>>.......<<<<<...............>>>.>.......<.<<<<<<<<<<.... GCCCTTGTAGTATAGCCcGGTctAGAATTCGGCCCTGTCACGGCTGAG...........ACGCGTGTTCAAATCCCGCCGAGGGCGCCA chr.trna7-AspGTC Sc: 64.16

Cys tRNAs

>>>>>>>..>>>..........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGTACTCTGGCAGAACGGTT.ATGCGTGGGCCTGCAAAGCCTATA...........CaAGGGGGTTCGACTCCCTCGGGTACCT... chr.trna19-CysGCA Sc: 25.47 Pseudo

Gln tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.........................<<<<<...............>>>>>.......<<<<<<<<<<<<.... AGCCCGATAGTCTAGCGGTcaA.GGATTCTGCCCTCTGGatctcacaaagtggatatAGGCGGAG...........ACGGCAGTTCGAATCTGCCTCGGGCTA... chr.trna38-GlnCTG Sc: 52.48 >>>>>>>..>>>>..........<<<<.>>>>>.........................<<<<<...............>>>>>.......<<<<<<<<<<<<.... AGCCCGATAGTGTAGAGGTcaA.GCATATGGGCCTTTGG..................AGCCCGTG...........ACGGCAGTTCGAATCTGCCTCGGGCTA... chr.trna42-GlnTTG Sc: 58.73

Glu tRNAs

>>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<................>>>>>.......................<<<<<<<<<<<<.... GCTCCCATAGTGTAGTCcGGTtaAGCATACAGCCCTCTCAAGGCTGTG...........A.CCCGGGTTCAAA................TCCCGGTGGGAGCACCA chr.trna36-GluCTC Sc: 77.67 >>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<................>>>>>.......................<<<<<<<<<<<<.... GTTCCAGTGGTGTAGACcGGTcaAGCATACTGCCCTTTCAAGGCAGTG...........AtCCCGGGTTCAAAatcaatcgatgaaaat.CCCGGCTGGAGCACCA chr.trna44-GluTTC Sc: 73.75

Gly tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCAGTTATAGTACAGTCtGGTtAGTACTCGTGCTTGCCAAGTACGTG...........A.CCCGGGTTCAAATCCCGGTAACTGCACCA chr.trna37-GlyGCC Sc: 65.50 >>>>>>>..>>>............<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGAGTTAGTTTAGTCtGGT.ATGATGTCAGCTTCCCAAGCTGAAG...........GcCGCGGGTTCAAATCCCGCACTCCGCA... chr.trna43-GlyCCC Sc: 73.68 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCAGTCATAGTATAGCCtGGTtAGTATTCGGGGTTTCCAACCCTGTG...........A.CGCGGGTTCGAATCCCGCTGACTGCA... chr.trna28-GlyTCC Sc: 70.32

His tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<...............>>>.>.......<.<<<<<<<<<<.... GCCTTCGTAGTACAGTGGTtA.GTATAGAGGATTGTGGATCCTCGG...........ACAGGAGTTCGATTCCCCTCGAGGGCC... chr.trna9-HisGTG Sc: 44.15

Ile tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCTCGTAGCTCAGCTtGGCtGGAGCGTTCGACTGATAATCGAAAG...........GtCATGAGTTCGAATCTCATCGGGCCCA... chr.trna21-IleGAT Sc: 72.57

Leu tRNAs

>>>>>>>..>>>..............<<<.>>>>>......................................................<<<<<..>>>...........<<<...>>>>>.......<<<<<.<<<<<<<.... GCGGGCGTCGCCCAGCCtGGCca.AAGGCGCTAGCTTGAGG...............................................GGCTAGT.CTCTCAG.......GAGTtCGTGGGTTCAAATCCCAT.CGCCCGCA... chr.trna10-LeuGAG Sc: 59.05 >>>>>>>..>>>..............<<<.>>>>>......................................................<<<<<..>>>...........<<<...>>>>>.......<<<<<.<<<<<<<.... GCGGGAGTCGCCCAGCCtGGTca.ACGGCGTAAGGTTCAGA...............................................TCCTTATCTTC.TAG.......GAGTtCGTGGGTTCAAATCCCAC.TTCCCGCA... chr.trna1-LeuCAG Sc: 53.62 >>>>>>>..>>>..............<<<.>>>>>......................................................<<<<<..>>>...........<<<...>>>>>.......<<<<<.<<<<<<<.... GCGGGAGTCGCCCAGCCtGGTca.AAGGCGTAGGGCTTAGG...............................................ACCCTAT.CTCTTAG.......GAGTtCGTGGGTTCAAATCCCAC.CTCCCGCACCA chr.trna40-LeuTAG Sc: 70.70 >>>>>>>..>>>..............<<<.>>>>>......................................................<<<<<..>>>...........<<<...>>>>>.......<<<<<.<<<<<<<.... GCAGAGATATCGAAGCCcGGTca.ACCGAGAGGGACTCAAGatcttccaaataggaa...............................ATCCCTT.CTCTCAG.......GAGTtCGTGGGTTCAAATCCCAC.TCTCTGCA... chr.trna12-LeuCAA Sc: 50.50 >>>>>>>...>................<..>..............................................................<......................>>>>>.......<<<<<.<<<<<<<.... GGAGGAGTAATCAAGCCtGGCcaaAGTAAGTACACTTTGTGcttttggacatgcaggacttaagatcaaataatgggtgatcctgtctCTCAGGAG.................TtCGTGGGTTCAAATCCCAC.CTCCTCCA... chr.trna29-LeuTAA Sc: 56.34

Lys tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>.>>>.......<<<.<<<<<<<<.... GGGTCTATGGCGCAGCCaGGTAGCGCACAGGACTCTTAATCCTGCT...........GtCGTGGGTTCGAATCCCTCTAGACCCG... chr.trna2-LysCTT Sc: 71.92 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGTCTATGGCGCAGCCaGGTAGCGCACCGGACTTTTAATCCGGTT...........GtCAAGGGTCCGAATCCCTTTAGACCCG... chr.trna39-LysTTT Sc: 70.65

Met tRNAs

>>>>>>>..>>>>..........<<<<.>>>>................................................<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGGGGTAGCTCAGCCtGGTtAGAGTGCCAGTTACTTGgtaaactctagcggttctccaactaaggcaatactcataATCTGGAG...........GtCGCGAGTTCGAAACTCGCCCCCGGCA... chr.trna18-MetCAT Sc: 80.94 >>>>>>>..>>>>..........<<<<.>>>>>..............................................<<<<<................>>>>>.......<<<<<<<<<<<<.... AGCGGGGTGGGGAAGCCaGGTcATCCCGGCGGGCTCATA.......................................ACCCGCAG...........TtCAGTAGTTCAAATCTACTCCCCGCTA... chr.trna24-MetCAT Sc: 66.66 GGGCCCGTAACTCAGCTtGGT.AGAGTAACCGGCTCATA.......................................ACCGGTGA...........GcCAAGGGATCGAAGCCCTTCGGGCCCA... chr.trna8-MetCAT Sc: 60.27

Phe tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>.>.......<.<<<<<<<<<<.... GCCGTGGTAGCTCAGCCtGGGAGAGCACTCGGCTGAAGACCGGGCT...........GtCGCGCGTTCAAATCCCGCCCGCGGCA... chr.trna33-PheGAA Sc: 73.70

Pro tRNAs

>>>>>>>..>>>...........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGATCGTCGTCTAGCTtGGTATGATACTAGTCTGGGGGACTAGTG...........GtCGCAGGTTCAAATCCTGCCGGTCCCA... chr.trna26-ProGGG Sc: 63.49 >>>>>>>..>>>...........<<<.>>>>>.......<<<<<................>>>.>.......<.<<<<<<<<<<.... GGGATCGTGGTCTAGCTtGGTATGATTCTGCGTTTGGGACGCAGAG...........GtCGCGCGTTCAAATCTCGCCGATCCCACCA chr.trna14-ProTGG Sc: 74.43

SeC tRNAs

Ser tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.....................<<<<<..>>>.........<<<...>>>>>.......<<<<<<<<<<<<.... GCCGGGGTCGCCTAGCCtGGTA.GGGCGCGCGCCTGGAAattgttaaccataaAGCGCGTTCTCGCAA.....GGGAaCGGGAGTTCAAATCTCCCTCCCGGCGCCA chr.trna11-SerGGA Sc: 59.06 >>>>>>>..>>>............<<<.>>>>>.....................<<<<<..>>>.........<<<...>>>>>.......<<<<<<<<<<<<.... GCCGGAATAGCCAAGT..GGTA.AGGCGGCCGTCTCGAA..............AACGGCTACGCGCAA.....GCGTgCGGGAGTTCGAATCTCTCTTCCGGCG... chr.trna15-SerCGA Sc: 55.73 >>>>>>>..>>>>..........<<<<.>>>>>.....................<<<<<..>>>.........<<<...>>>>>.......<<<<<<<<<<<<.... GCAGAGGTCGCCTAGCTcGGTA.GGGCGCGGGCCTTGAG..............AGCCTGTGTGCGCAA.....GCATaCGGGGGTTCAAATCCCTCTCTCTGCG... chr.trna5-SerTGA Sc: 65.85 >>>>>>>..>>>>..........<<<<.>>>>>.....................<<<<<....>.........<.....>>>>>.......<<<<<<<<<<<<.... GCGGGGATCGCCTAGCCtGGTA.GGGCGTGGGATTGCTA..............ATCCCATGTCCGCAAg....GACA.CGGGGGTTCAAATCCCCCTCCCCGCGCCA chr.trna32-SerGCT Sc: 70.89

Sup tRNAs

Thr tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCTTCGATAGCTCAGCCtGGT.AGAGCGTTACCTTGGTAAGGTAAAG...........GtCGCGGGTTCGGATCCCGTTCGAAGCT... chr.trna22-ThrGGT Sc: 69.19 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCTTGGTAGCTCAGCCtGGT.AGAGCGAACGCCTCGTAAGCGTTAG...........GtCGCGGGTTCAGATCCCGTCCGAGGCT... chr.trna31-ThrCGT Sc: 76.73 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCAATGTAGCTCAGCCtGGCtAGAGCATTCGCCTTGTAAGCGAAAG...........GtCATGGGTTCAGATCCCATCATTGGCT... chr.trna17-ThrTGT Sc: 68.33

Trp tRNAs

>>>>>>>..>>>>.........<<<<.>>.>.........................................................................................<.<<................>>>>>.......<<<<<<<<<<<<.... GGGGTCGTAGCCTAGCCtGGTAGGGCGACAGTGTCTACgaaaaagatcaccgctaagggctccagaggtaaactaagctaaactgactcacggatgatgtaagtttggagctgtagtgACCCGTAG...........GtCGTCGGTTCGATTCCGATCGGCCCCA... chr.trna20-TrpCCA Sc: 67.18

Tyr tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.........................................................<<<<<................>>>>>.......<<<<<<<<<<<<.... CCCGTGGTAGCTCAGCCtGGTAGAGCTTCCGGCTGTAGttgttggctttagatggctgaccgaataacagcatatcaggcatacagaaACCGGGTT...........GtCGGTGGTTCAACTCCGCCCCGCGGGACCA chr.trna35-TyrGTA Sc: 57.47

Val tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.............................<<<<<................>.>>>.......<<<.<<<<<<<<.... GGGCCGGTAGTCTAGCT.GGTtAGGATACCGCCTCGACA......................CGGCGGTG...........AtCGTGAGTTCGAATCTCTCTCGGCCCA... chr.trna27-ValGAC Sc: 60.87 >>>>>>>..>>>>..........<<<<...>>...............................<<..................>>>>>.......<<<<<<<<<<<<.... GGACCGGTCGTCTAGTTtGGTtTGGATGACGCACTCACActgcgtaagggaacaaaattctCCGCAAAG...........GtCGTGGGTTCAAATCCCATCCGGTCCA... chr.trna16-ValCAC Sc: 70.29 >>>>>>>..>>>............<<<.>>>>>.............................<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCCATAGTCCAGGTcGGTtATGACGTCGCCCTTACA......................CGGCGAAG...........AtCCGGGGTTCAAATCCCCGTGGGCCCA... chr.trna3-ValTAC Sc: 74.70

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.