Gene: tRNA-Met-CAT-4-2

Overview
Organism Homo sapiens
Locus chr6:26743263-26743335 (+) View in Genome Browser
GtRNAdb Gene Symbol tRNA-Met-CAT-4-2
HGNC Symbol TRM-CAT4-2
RNAcentral ID URS0000703910_9606
tRNAscan-SE ID chr6.trna26
GtRNAdb 2009
Legacy Name and Score
chr6.trna162-MetCAT (75.76 bits)
Predicted tRNA Isotype / Anticodon Met CAT
Top Scoring / Second Best Scoring Isotype Model Met (108.2 bits) / Thr (83.4 bits)
Predicted Anticodon and Top Isotype Model Consistent
Rank of tRNA Isodecoder 4 out of 7
Upstream / Downstream Sequence GCGCGGCATTATACTTCGTC / GCTTTTGCAAGGAAAGCTTA
Intron None
Possible Pseudogene No
Gene Score 80.2
Mature tRNA Score 80.2
HMM Score 56.30
Secondary Structure Score 23.90
Atypical Features U31:U39
Sequence
Genomic Sequence
GCCCTCTTAGCGCAGCGGGcAGCGCGTCAGTCTCATAATCTGAAGGtCCTGAGTTCGAGCCTCAGAGAGGGCA
Secondary Structure (nested bp)
>>>>>>>..>>>>........<<<<.>>>>.........<<<<.....>>>>>.......<<<<<<<<<<<<.
Predicted Mature tRNA
GCCCUCUUAGCGCAGCGGGCAGCGCGUCAGUCUCAUAAUCUGAAGGUCCUGAGUUCGAGCCUCAGAGAGGGCA
Alignments
Met tRNAs
>>>>>>>..>>>>..........<<<<.>>>>.........<<<<................>>>>>.......<<<<<<<<<<<<.... GCCCTCTTAGCGCAGT.GGGcA.GCGCGTCAGTCTCATAATCTGAAG...........GtCCTGAGTTCGAGCCTCAGAGAGGGCA... tRNA-Met-CAT-2-1 Sc: 82.7 GCCTCGTTAGCGCAGTAGGT.A.GCGCGTCAGTCTCATAATCTGAAG...........GtCGTGAGTTCGATCCTCACACGGGGCA... tRNA-Met-CAT-1-1 Sc: 82.3 GCCCTCTTAGCGCAGC.GGGcA.GCGCGTCAGTCTCATAATCTGAAG...........GtCCTGAGTTCGAGCCTCAGAGAGGGCA... tRNA-Met-CAT-4-1 Sc: 80.2 GCCCTCTTAGCGCAGC.GGGcA.GCGCGTCAGTCTCATAATCTGAAG...........GtCCTGAGTTCGAGCCTCAGAGAGGGCA... tRNA-Met-CAT-4-2 Sc: 80.2 GCCCTCTTAGCGCAGC.GGGcA.GCGCGTCAGTCTCATAATCTGAAG...........GtCCTGAGTTCGAGCCTCAGAGAGGGCA... tRNA-Met-CAT-4-3 Sc: 80.2 GCCCTCTTAGCGCAGCTGGC.A.GCGCGTCAGTCTCATAATCTGAAG...........GtCCTGAGTTCAAGCCTCAGAGAGGGCA... tRNA-Met-CAT-5-1 Sc: 79.2 GCCCTCTTAGCGCAGCTGGC.A.GCGCGTCAGTCTCATAATCTGAAG...........GtCCTGAGTTCAAGCCTCAGAGAGGGCA... tRNA-Met-CAT-5-2 Sc: 79.2 GCCTCCTTAGCGCAGTAGGC.A.GCGCGTCAGTCTCATAATCTGAAG...........GtCCTGAGTTCGAACCTCAGAGGGGGCA... tRNA-Met-CAT-3-1 Sc: 77.4 GCCTCCTTAGCGCAGTAGGC.A.GCGCGTCAGTCTCATAATCTGAAG...........GtCCTGAGTTCGAACCTCAGAGGGGGCA... tRNA-Met-CAT-3-2 Sc: 77.4 GCCTCGTTAGCGCAGTAGGC.A.GCGCGTCAGTCTCATAATCTGAAG...........GtCGTGAGTTCGAGCCTCACACGGGGCA... tRNA-Met-CAT-6-1 Sc: 77.4 GCCCTCTTAGTGCAGCTGGC.A.GCGCGTCAGTTTCATAATCTGAAA...........GtCCTGAGTTCAAGCCTCAGAGAGGGCA... tRNA-Met-CAT-7-1 Sc: 66.2 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... AGCAGAGTGGCGCAGC.GGA.A.GCGTGCTGGGCCCATAACCCAGAG...........GtCGATGGATCGAAACCATCCTCTGCTA... DM9990_CAT_HUMAN_CY AGCAGAGTGGCGCAGC.GGA.A.GCGTGCTGGGCCCATAACCCAGAG...........GtCGATGGATCGAAACCATCCTCTGCTA... DX9990_CAT_HUMAN_CY AGCAGAGTGGCGCAGC.GGA.A.GCGTGCTGGGCCCATAACCCAGAG...........GtCGATGGATCTAAACCATCCTCTGCTA... DX9991_CAT_HUMAN_CY >>>>>>>..>>>>..........<<<<.>>>>.........<<<<................>>>>>.......<<<<<<<<<<<<.... GCCTCGTTAGCGCAGTAGGT.A.GCGCGTCAGTCTCATAATCTGAAG...........GtCGTGAGTTCGATCCTCACACGGGGCAcca RM9990_CAT_HUMAN_HELA-CELLS >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... AGCAGAGTGGCGCAGC.GGA.A.GCGTGCTGGGCCCATAACCCAGAG...........GtCGATGGATCGAAACCATCCTCTGCTAcca RX9990_CAT_HUMAN_PLACENTA
>>>>>.>..>>>>...........<<<<.>>>>.........<<<<................>>.>.>............<<.<<......<.<<<<<. GTCTTCTTAGCGCAGT.GAGcA..GCGCGTCAGTCTCATAATCTGAAG...........GtCCTGAtGTTCGAGC.....CTGAG......AAAAGGCA tRX-Met-NNN-2-1 Sc: 41.7 (filtered) best isotype model: Met Sc: 67.9 >>>>>>>..>..>...........<..<.>>>>.........<<<<................>.>>.>............<<<.<......<<<<<<<. GCCTTCTTAGCCCTGGAGGC.A..GCACATCAGTCTCATAATCTGAAG...........GtCCCGA.GCTTGAAC.....CTCAG......AGAGGGCA tRX-Met-NNN-1-1 Sc: 24.1 (filtered) best isotype model: Met Sc: 47.7 >>>>>>>..>>>>...........<<<<.>>.>.........<.<<................>>>>.>............<<<<<......<<<<<<<. GCAGCTGTGGCTCAGT.GGAaA..GAGCATCAGTCTGGGTATCAGAAG...........A.CCTAG.GT...........CCTAGccc...CAGCTGTA tRX-Pro-NNN-1-1 Sc: 24.8 (filtered) best isotype model: Met Sc: 25.7 >>>.>>>...>>>...........<<<...>>>>.......<<<<.................>>>>.>............<<<<<......<<<.<<<. GTGGATA..GCCCAGC.GGCtAt.GGGAGCCGGGCTCTCACTCTGAC............GtCCTGG.GTTCAAGT.....CCCAG......TGTGCACA tRNA-Glu-CTC-16-1 Sc: 27.3 (filtered) best isotype model: Met Sc: 6.8
Isotype-Specific Model Scores
AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSeCSerThrTrpTyrValiMet
42.769.364.541.252.647.330.838.450.778.319.779.4108.265.729.7No Hit14.783.452.433.575.0-9.1
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 HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo HitNo Hit

Top score2nd highest score3rd highest score
DNA Variants (23)
tRNA Position Genomic Position dbSNP ID Ref/Alt Allele Common SNP 1K Genome Effect
6 (5′ Acceptor Stem)chr6:26743268rs569449588C / GNoYesbase pair mismatch
22 (3′ D-arm)chr6:26743284rs559164168G / CNoYesbase pair mismatch
35 (Anticodon Loop)chr6:26743297rs539354662A / CNoYesnon synonymous anticodon change
35 (Anticodon Loop)chr6:26743297rs539354662A / TNoYesnon synonymous anticodon change
50 (5′ T-arm)chr6:26743312rs567110931T / ANoYesbase pair mismatch
50 (5′ T-arm)chr6:26743312rs567110931T / GNoYesbase pair mismatch
58 (T-Psi-C Loop)chr6:26743320rs546327726A / CNoYesuniversal base change
58 (T-Psi-C Loop)chr6:26743320rs546327726A / TNoYesuniversal base change
61 (3′ T-arm)chr6:26743323rs201808797C / TNoNoGU base pair
64 (3′ T-arm)chr6:26743326rs529685958A / GNoYesGU base pair
64 (3′ T-arm)chr6:26743326rs529685958A / TNoYesbase pair mismatch
65 (3′ T-arm)chr6:26743327rs114866759G / CNoYesbase pair mismatch
65 (3′ T-arm)chr6:26743327rs114866759G / TNoYesbase pair mismatch
67 (3′ Acceptor Stem)chr6:26743329rs200891726G / ANoNobase pair mismatch
68 (3′ Acceptor Stem)chr6:26743330rs550241867A / GNoYesGU base pair
68 (3′ Acceptor Stem)chr6:26743330rs550241867A / TNoYesbase pair mismatch
69 (3′ Acceptor Stem)chr6:26743331rs199598268G / CNoYesbase pair mismatch
69 (3′ Acceptor Stem)chr6:26743331rs199598268G / ANoYesbase pair mismatch
70 (3′ Acceptor Stem)chr6:26743332rs572920419G / ANoNobase pair mismatch
70 (3′ Acceptor Stem)chr6:26743332rs572920419G / CNoNobase pair mismatch
72 (3′ Acceptor Stem)chr6:26743334rs557716687C / ANoNobase pair mismatch
72 (3′ Acceptor Stem)chr6:26743334rs557716687C / GNoNobase pair mismatch
72 (3′ Acceptor Stem)chr6:26743334rs557716687C / TNoNoGU base pair