Gene: tRNA-Lys-CTT-2-1

Overview
Organism Homo sapiens
Locus chr1:146039401-146039473 (+) View in Genome Browser
GtRNAdb Gene Symbol tRNA-Lys-CTT-2-1
HGNC Symbol TRK-CTT2-1
RNAcentral ID URS00001AD596_9606
tRNAscan-SE ID chr1.trna27
GtRNAdb 2009
Legacy Name and Score
chr1.trna119-LysCTT (80.47 bits)
Predicted tRNA Isotype / Anticodon Lys CTT
Top Scoring / Second Best Scoring Isotype Model Lys (122.7 bits) / Arg (88.9 bits)
Predicted Anticodon and Top Isotype Model Consistent
Rank of tRNA Isodecoder 2 out of 16
Upstream / Downstream Sequence AGAAGACGCCAGTAATCAGT / CTGTGTTTTTATTTAACCCT
Intron None
Possible Pseudogene No
Gene Score 87.8
Mature tRNA Score 87.8
HMM Score 68.80
Secondary Structure Score 19.00
Atypical Features None
Sequence
Genomic Sequence
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGtCGTGGGTTCGAGCCCCACGTTGGGCG
Secondary Structure (nested bp)
>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<.
Predicted Mature tRNA
GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG
Alignments
Lys tRNAs
>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<...<. GCCCGGCTAGCTCAGTCGGTAGAGCATGGGACTCTTAATCCCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG tRNA-Lys-CTT-1-1 Sc: 88.0 GCCCGGCTAGCTCAGTCGGTAGAGCATGGGACTCTTAATCCCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG tRNA-Lys-CTT-1-2 Sc: 88.0 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG tRNA-Lys-CTT-2-1 Sc: 87.8 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG tRNA-Lys-CTT-2-2 Sc: 87.8 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG tRNA-Lys-CTT-2-3 Sc: 87.8 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG tRNA-Lys-CTT-2-4 Sc: 87.8 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG tRNA-Lys-CTT-2-5 Sc: 87.8 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACCCTTAATCTCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG tRNA-Lys-CTT-3-1 Sc: 83.1 GCCCGGCTAGCTCAGTCGGTAGAGCATGGGACTCTTAATCTCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG tRNA-Lys-CTT-4-1 Sc: 82.3 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>.>.......<.<<<<<<<<<...<. GCCCGGCTAGCTCAGTCGATAGAGCATGAGACTCTTAATCTCAGG...........GtCGTGGGTTCGAGCCGCACGTTGGG...CG tRNA-Lys-CTT-5-1 Sc: 69.3 >>>.>>>..>>>>........<<<<.>>>>>.......<<<<<.................>>>>.......<<<<.<<<.<<...<. GCCCAGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGG...........GtCATGGGTTTGAGCCCCACGTTTGG...TG tRNA-Lys-CTT-7-1 Sc: 64.8 >>>>>>....>>>........<<<..>>>>>.......<<<<<................>>>>>.......<<<<<.<<<<<...<. GCCCGACTACCTCAGTCGGTGGAGCATGGGACTCTTCATCCCAGG...........GtTGTGGGTTCGAGCCCCACATTGGG...CA tRNA-Lys-CTT-9-1 Sc: 58.2 >>>>>>>..>>>..........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<...<. GCCTGGCTAGCTCAGTCGGCAAAGCATGAGACTCTTAATCTCAGG...........GtCGTGGGCTCGAGCTCCATGTTGGG...CG tRNA-Lys-CTT-8-1 Sc: 57.8 >..>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<.....<. G..CAGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGG...........GtCATGGGTTCGTGCCCCATGTTGGGtgcCA tRNA-Lys-CTT-11-1 Sc: 56.6 >>>>>>>..>>>>........<<<<.>.>>>.......<<<.<................>>>>.........<<<<<<<<<<...<. GCCCAGCTAGCTCAGTCGGTAGAGCATAAGACTCTTAATCTCAGG...........GtTGTGGATTCGTGCCCCATGCTGGG...TG tRNA-Lys-CTT-10-1 Sc: 54.8 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<...<. GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGG...........GtCGTGGGTTCGAGCCCCACGTTGGG...CG DK9991_CTT_HUMAN_CY >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<...<. GCCTGGATAGCTCAGTTGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTTCAGG...CA tRNA-Lys-TTT-1-1 Sc: 89.0 GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTTCGGG...CG tRNA-Lys-TTT-3-1 Sc: 87.8 GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTTCGGG...CG tRNA-Lys-TTT-3-2 Sc: 87.8 GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTTCGGG...CG tRNA-Lys-TTT-3-3 Sc: 87.8 GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTTCGGG...CG tRNA-Lys-TTT-3-4 Sc: 87.8 GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTTCGGG...CG tRNA-Lys-TTT-3-5 Sc: 87.8 GCCTGGATAGCTCAGTTGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTTCAGG...CG tRNA-Lys-TTT-2-1 Sc: 87.7 GCCTGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTTCAGG...CG tRNA-Lys-TTT-4-1 Sc: 86.8 GCCTGGGTAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTCCAGG...CG tRNA-Lys-TTT-6-1 Sc: 85.2 GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCGGGGTTCAAGTCCCTGTTCGGG...CG tRNA-Lys-TTT-5-1 Sc: 84.9 >>>>>>>..>.>>........<<.<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<...<. GCCTGGATAGCTCAGTTGGTAGAACATCAGACTTTTAATCTGACG...........GtGCAGGGTTCAAGTCCCTGTTCAGG...CG tRNA-Lys-TTT-7-1 Sc: 74.9 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.................>.>>.......<<.<.<<<<<<...<. ACCCAGATAGCTCAGTCAGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAAGGTTCATGTCCCTTTTTGGG...TG tRNA-Lys-TTT-11-1 Sc: 50.7 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<...<. GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGG...........GtCCAGGGTTCAAGTCCCTGTTCGGG...CG DK9990_TTT_HUMAN_CY
.......>...>.>>>.........>>>>..........................<<<<....>>>>>.........<<<<<.................>>>>>.......<<<<<.......<<<.<.<.... .......GA..CGAGC......T.AGCTCAG................TCGGT.A.GAGCA...TGGGACTCTTAA..TCCCAGG...........GtC.GTGGGTTTGAGCCCCAT.......GTTGGGCA... tRNA-Lys-CTT-6-1 Sc: 63.1 (filtered) best isotype model: Lys Sc: 93.7 .......>>..>>>>>.........>>>>..........................<<<<....>>>>>.........<<<<<.................>.>>>.......<<<.<.......<<<<<<<.... .......GC..CCGGA......G.AGCTCAG................T.GGGtA.GAGCA...TCAGACTTTTAA..TCTGAGG...........GtC.CAGGGTTCAAGTCCTCG.......TTCGGGCA... tRNA-Lys-TTT-8-1 Sc: 65.1 (filtered) best isotype model: Lys Sc: 85.6 .......>>..>>>>>.........>>>>..........................<<<<....>>.>>.........<<.<<.................>>>>>.......<<<<<.......<<<<<<<.... .......GC..CCGGA......T.AGTTCAG................TTGGT.A.GAGCA...TCAGACT..TAA..TCAGAGG...........GtC.CAGGGTTCAAGTCCCTG.......TTTGGGTG... tRNA-Sup-TTA-1-1 Sc: 57.1 (filtered) best isotype model: Lys Sc: 83.7 ........>..>>>>>.........>.>>..........................<<.<....>>>>>.........<<<<<.................>>>>>.......<<<<<.......<<<<<<..... .......AC..CTGGG......T.AGCTCAG................TAGGT.A.GAACA...TCAGACTTTTAA..TCTGAGG...........GtC.TAGGGTTCAAGTCCCTG.......TCCAGGCG... tRNA-Lys-TTT-9-1 Sc: 61.2 (filtered) best isotype model: Lys Sc: 82.7 ........>..>>>>..........>.>>..........................<<.<....>>>>>.........<<<<<.................>>>>>.......<<<<<........<<<<<..... .......CC..CCGGC......T.GGCTCAG................TCAGT.A.GATCA...TGAGACTCTTAA..TCTCAGG...........GtC.GTGGGTTCACGCCCCAC.......ACTGGGCG... tRX-Lys-NNN-1-1 Sc: 46.8 (filtered) best isotype model: Lys Sc: 80.2 .......>>..>.>>>.........>>>>..........................<<<<....>>>>...........<<<<.................>>>>>.......<<<<<.......<<<.<<<.... .......GC..CAGGA......T.AGTTCAG................GTGGT.A.GAGCA...TCAGACTTTTAA..CCTGAGG...........GtT.CAGGGTTCAAGTCTCTG.......TTTGGGCG... tRNA-Lys-TTT-10-1 Sc: 49.9 (filtered) best isotype model: Lys Sc: 76.6 .......>>..>>>>>.........>>>>..........................<<<<....>>>>>.........<<<<<.................>>>>.........<<<<.......<<<<<<<.... .......AC..CTGGG......T.AGCTTAG................TTGGT.A.GAGCA...TTGGACTTTTAA..TTTGAGG...........GcC.CAGGTTTCAAGTCCCTG.......TTTGGGTG... tRNA-Lys-TTT-12-1 Sc: 53.8 (filtered) best isotype model: Lys Sc: 73.3 .......>>..>>>>...........>>............................<<.....>>>>>.........<<<<<.................>>>>>.......<<<<<........<<<<<<.... .......GCcaCCAGCa.....T.GTCTCAG................TCGGT.A.TAGTG...TGAGACTCTTAA..TCTCAGG...........GtC.GTGGGTTCAAGCCCCACa.......TTGGGCG... tRNA-Lys-CTT-12-1 Sc: 48.3 (filtered) best isotype model: Lys Sc: 73.0 .......>>..>>>>>.........>>>>..........................<<<<....>>>.>.........<.<<<.................>>>>>.......<<<<<.......<<<<<<<.... .......GC..CTGGA......T.AGCTCCT................TCGGT.A.GAGCAtcaTCAGACTTTTAA..TGTGAGG...........GtC.CAGGGTTCAAGTTCCTG.......TTTGGGCG... tRX-Lys-NNN-2-1 Sc: 41.4 (filtered) best isotype model: Lys Sc: 72.2 .......>>..>>>>>.........>.>>..........................<<.<....>.>>>.........<<<.<..................>>>>.......<<<<........<<<<<<<.... .......GT..CTAGC......T.AGATCAG................TTGGT.A.GAGCA...TAAGACTCTTAA..TCTCAGG...........GtC.ATGGGTTTGAGCCCTAC.......GTTGGGCG... tRNA-Lys-CTT-13-1 Sc: 46.9 (filtered) best isotype model: Lys Sc: 69.8 .......>>...>>>>.........>>>>..........................<<<<......>>>.........<<<...................>>>>>.......<<<<<.......<<<<.<<.... .......GC..CCAGC......T.AGCTCAG................CCGGT.A.GAGCA...CAAGACTCTTAA..TCTCAGG...........GtC.GTGGGTTTGAGCCCTGT.......GTTGAGCA... tRNA-Lys-CTT-14-1 Sc: 48.5 (filtered) best isotype model: Lys Sc: 69.8 .......>>..>..>>.........>>>>..........................<<<<....>>>>>.........<<<<<.................>>>>>.......<<<<<.......<<..<<<.... .......TA..AACAAcccagaT.AGCTCAG................TTGAT.A.GAGCA...TCAGACTTTTAA..TCTGAGG...........GtC.CAGGGTTCATGTCCCTG.......TTCCTTAA... tRNA-Lys-TTT-14-1 Sc: 47.3 (filtered) best isotype model: Lys Sc: 68.3 .......>>...>.>>...........>>..........................<<......>>>>>.........<<<<<.................>>>>>.......<<<<<.......<<.<.<<.... .......GC..ACTGC......A.CAGTCAG................TCAGT.A.GAGCA...TGGGACTCTTAA..TCCCAGG...........GtC.GTGGGTTCAAGCCCCAC.......GTTGGGCG... tRX-Lys-NNN-3-1 Sc: 35.4 (filtered) best isotype model: Lys Sc: 65.8 ...........>>>>..........>>>>..........................<<<<....>>>>>.........<<<<<.................>>>>>.......<<<<<........<<<<...... .......AA..CCGAA......T.AGCTTAG................TTGAT.G.AAGCG...TGAGACTCTTAA..TCTCAGG...........GtA.GTGGGTTCAAGCCCCAC.......ATTGGACA... tRNA-Lys-CTT-15-1 Sc: 40.3 (filtered) best isotype model: Lys Sc: 64.7 .......>>...>>>...........>>>..........................<<<.....>>>>>.........<<<<<.................>>>>>.......<<<<<........<<<.<<.... .......GC..CTGGC......T.ACCTCAG................TTGGT.A.GAGCA...TGGGACTCTTAA..TCCCAGA...........GtCaGTGGGTTCAAGCCTCAC.......ATTGAGTG... tRNA-Lys-CTT-16-1 Sc: 35.8 (filtered) best isotype model: Lys Sc: 64.5 .......>>..>...>.........>>>............................<<<....>>>>>.........<<<<<.................>>>>>.......<<<<<.......<...<<<.... .......GG..CAGGC.........GCT.AG................TCAGT.A.GAGCA...TGAGACTCTTAA..TCTCAGG...........GtC.GTGGGTTCGAGCCCCAC..atc..GGGCGCCA... tRX-Lys-NNN-4-1 Sc: 34.5 (filtered) best isotype model: Lys Sc: 59.1 .......>>..>>.>>.........>>>>..........................<<<<....>>>>...........<<<<.................>>>>>.......<<<<<.......<<.<<<<.... .......GC..CTGGG......T.AGCTCAG................TCGGT.A.GAGCTa..TCAGACTTTTAG..CCTGAGG...........AtT.CAGGGTTCAATCCCTTG.......CTGGGGCG... tRNA-Lys-TTT-13-1 Sc: 46.0 (filtered) best isotype model: Lys Sc: 57.8 .......>>..>.>>>.........>>>>..........................<<<<.....>>>>.........<<<<..................>>.>>.......<<.<<.......<<<.<<<.... .......GT..TGGGG......T.AACTCAG................TTGGT.A.GAGTA...GCAGACTTTTCA..TCTGAGG...........GtC.CAGGGTTTAAGTCCATG.......TCCAGGCA... tRNA-Lys-TTT-15-1 Sc: 34.5 (filtered) best isotype model: Lys Sc: 51.9 .......>>..>>.>>.........>................................<....>>>>>.........<<<<<.................>>>>>.......<<<<<.......<<.<<<<.... gttttgtTT..CTTAT......TgGGGGAAG................TCGGT.A.GAACA...TGAGATTCTTAA..TCTCAGG...........GtC.CTGGGTTTAAGCCCCAG.......GTTGGGAGcca tRX-Lys-NNN-5-1 Sc: 31.1 (filtered) best isotype model: Lys Sc: 47.6 .......>>..>>>>>..........>>>..........................<<<.....>>>>>.........<<<<<.................>>.............<<.......<<<<<<<.... .......GC..CCAAC......T.GGTTCAG................TCGGT.A.GAGAA...TGAGACTCTTAA..TCTCAG............GtC.ATAGATTCATGTCACAT.......GTTGGGTG... tRX-Lys-NNN-6-1 Sc: 29.9 (filtered) best isotype model: Lys Sc: 40.8 .......>...>>>............>>>..........................<<<.....>>>.>.........<.<<<.................>>>>>.......<<<<<.........<<<.<.... .......GA..CTC........T.GTCTCAAaaaaaaaaaaaaaaaaT.GGTtA.GAGTG...TGGTGCTAATAA..CCCCAAG...........GtC.GCAGGTTTGATCCCTGT.......AGGGGCCA... tRX-Ile-NNN-4-1 Sc: 20.5 (filtered) best isotype model: Lys Sc: 14.9
Isotype-Specific Model Scores
AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSeCSerThrTrpTyrValiMet
54.188.983.426.153.633.721.938.837.782.821.4122.772.155.129.4No Hit11.972.059.642.147.1-26.3
mt-Alamt-Argmt-Asnmt-Aspmt-Cysmt-Glnmt-Glumt-Glymt-Hismt-Ilemt-LeuTAAmt-LeuTAGmt-Lysmt-Metmt-Phemt-Promt-SerGCTmt-SerTGAmt-Thrmt-Trpmt-Tyrmt-Val
No HitNo Hit-12.3No HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo Hit16.9No HitNo HitNo HitNo HitNo Hit-19.0No Hit

Top score2nd highest score3rd highest score
DNA Variants (25)
tRNA Position Genomic Position dbSNP ID Ref/Alt Allele Common SNP 1K Genome Effect
1 (5′ Acceptor Stem)chr1:146039401rs751259766G / TNoNobase pair mismatch
1 (5′ Acceptor Stem)chr1:146039401rs751259766G / CNoNobase pair mismatch
1 (5′ Acceptor Stem)chr1:146039401rs751259766G / ANoNobase pair mismatch
2 (5′ Acceptor Stem)chr1:146039402rs1008402380C / TNoNoGU base pair
11 (5′ D-arm)chr1:146039411rs961502848C / TNoNoGU base pair
19 (D-loop)chr1:146039419rs994630847G / ANoNouniversal base change
22 (3′ D-arm)chr1:146039422rs188130522G / CNoYesbase pair mismatch
27 (5′ Anticodon Stem)chr1:146039427rs1027014495T / GNoNobase pair mismatch
28 (5′ Anticodon Stem)chr1:146039428rs782201226G / CNoNobase pair mismatch
28 (5′ Anticodon Stem)chr1:146039428rs782201226G / TNoNobase pair mismatch
34 (Anticodon Loop)chr1:146039434rs782621401C / ANoNonon synonymous anticodon change
34 (Anticodon Loop)chr1:146039434rs782621401C / GNoNonon synonymous anticodon change
35 (Anticodon Loop)chr1:146039435rs990779210T / CNoNonon synonymous anticodon change
39 (3′ Anticodon Stem)chr1:146039439rs915865000T / GNoNobase pair mismatch
48 (Variable Loop)chr1:146039448rs970347236C / TNoNosubstitution in loop
53 (5′ T-arm)chr1:146039453rs928437256G / TNoNobase pair mismatch
56 (T-Psi-C Loop)chr1:146039456rs782373167C / ANoNouniversal base change
56 (T-Psi-C Loop)chr1:146039456rs782373167C / GNoNouniversal base change
60 (T-Psi-C Loop)chr1:146039460rs934496686C / TNoNosubstitution in loop
61 (3′ T-arm)chr1:146039461rs782673353C / ANoNobase pair mismatch
61 (3′ T-arm)chr1:146039461rs782673353C / GNoNobase pair mismatch
61 (3′ T-arm)chr1:146039461rs782673353C / TNoNoGU base pair
66 (3′ Acceptor Stem)chr1:146039466rs1052877759G / ANoNobase pair mismatch
70 (3′ Acceptor Stem)chr1:146039470rs763957479G / ANoNobase pair mismatch
72 (3′ Acceptor Stem)chr1:146039472rs947069057C / TNoNoGU base pair