Gene: tRNA-Lys-CTT-2-3

Overview
Organism Homo sapiens
Locus chr5:180648979-180649051 (-) View in Genome Browser
GtRNAdb Gene Symbol tRNA-Lys-CTT-2-3
HGNC Symbol TRK-CTT2-3
RNAcentral ID URS00001AD596_9606
tRNAscan-SE ID chr5.trna11
GtRNAdb 2009
Legacy Name and Score
chr5.trna11-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 GTTAGAATACAGACATGGCC / TAATTTCGCTTTTTGGAAAG
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
Genome Browser View with Related Data Tracks Zoomed in (750 bp flanking features)
Zoomed out (750 kbp flanking features)
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 (36)
tRNA Position Genomic Position dbSNP ID Ref/Alt Allele Common SNP 1K Genome Effect
1 (5′ Acceptor Stem)chr5:180649051rs141507780G / ANoYesbase pair mismatch
1 (5′ Acceptor Stem)chr5:180649051rs386695876CG / TANoNobulge in stem
2 (5′ Acceptor Stem)chr5:180649050rs562056967C / TNoNoGU base pair
4 (5′ Acceptor Stem)chr5:180649048rs575786894C / TNoYesGU base pair
5 (5′ Acceptor Stem)chr5:180649047rs558828599G / ANoYesrestore Watson-Crick base pair
11 (5′ D-arm)chr5:180649041rs148228042C / TNoYesGU base pair
13 (5′ D-arm)chr5:180649039rs758522113C / TNoNoGU base pair
17 (D-loop)chr5:180649035rs566657810C / TNoYessubstitution in loop
18 (D-loop)chr5:180649034rs113137878G / CYesNouniversal base change
19 (D-loop)chr5:180649033rs546846517G / ANoYesuniversal base change
20 (D-loop)chr5:180649032rs73814525T / CYesYessubstitution in loop
22 (3′ D-arm)chr5:180649030rs189956086G / ANoYesbase pair mismatch
23 (3′ D-arm)chr5:180649029rs550141680A / CNoYesbase pair mismatch
24 (3′ D-arm)chr5:180649028rs530568283G / CNoYesbase pair mismatch
25 (3′ D-arm)chr5:180649027rs187033204C / TNoYesGU base pair
26 (D-arm-Anticodon-linker)chr5:180649026rs552359762A / GNoYessubstitution in loop
27 (5′ Anticodon Stem)chr5:180649025rs796906093T / GNoNobase pair mismatch
28 (5′ Anticodon Stem)chr5:180649024rs773530115G / TNoNobase pair mismatch
28 (5′ Anticodon Stem)chr5:180649024rs773530115G / ANoNobase pair mismatch
32 (Anticodon Loop)chr5:180649020rs763938499C / TNoNosubstitution in loop
33 (Anticodon Loop)chr5:180649019rs143945094T / CNoYesuniversal base change
38 (Anticodon Loop)chr5:180649014rs149469060A / TNoYessubstitution in loop
38 (Anticodon Loop)chr5:180649014rs149469060A / GNoYessubstitution in loop
39 (3′ Anticodon Stem)chr5:180649013rs540886275T / CNoYesbase pair mismatch
41 (3′ Anticodon Stem)chr5:180649011rs762014572T / CNoNobase pair mismatch
43 (3′ Anticodon Stem)chr5:180649009rs367547861A / GNoYesGU base pair
45 (Variable Loop)chr5:180649007rs200353402G / ANoNosubstitution in loop
47 (Variable Loop)chr5:180649005rs746055778T / CNoNosubstitution in loop
53 (5′ T-arm)chr5:180648999rs561361304G / ANoYesbase pair mismatch
53 (5′ T-arm)chr5:180648999rs772145791G / -NoNobulge in stem
56 (T-Psi-C Loop)chr5:180648996rs776589662C / GNoNouniversal base change
57 (T-Psi-C Loop)chr5:180648995rs137884085G / ANoYessubstitution in loop
59 (T-Psi-C Loop)chr5:180648993rs770977751G / ANoNosubstitution in loop
62 (3′ T-arm)chr5:180648990rs745874321C / TNoNoGU base pair
66 (3′ Acceptor Stem)chr5:180648986rs575817892G / CNoYesbase pair mismatch
72 (3′ Acceptor Stem)chr5:180648980rs145195363C / TNoYesGU base pair
Expression Profiles