Gene: tRNA-Phe-GAA-1-2

Overview
Organism Homo sapiens
Locus chr6:28949449-28949521 (-) View in Genome Browser
GtRNAdb Gene Symbol tRNA-Phe-GAA-1-2
HGNC Symbol TRF-GAA1-2
RNAcentral ID URS000029CCC5_9606
tRNAscan-SE ID chr6.trna99
GtRNAdb 2009
Legacy Name and Score
chr6.trna96-PheGAA (84.19 bits)
Predicted tRNA Isotype / Anticodon Phe GAA
Top Scoring / Second Best Scoring Isotype Model Phe (124.5 bits) / Tyr (83.7 bits)
Predicted Anticodon and Top Isotype Model Consistent
Rank of tRNA Isodecoder 1 out of 12
Upstream / Downstream Sequence TTTTAAGTGGCGTGGGCGGA / TGAGAGCGCTCGGTTTTTTG
Intron None
Possible Pseudogene No
Gene Score 88.9
Mature tRNA Score 88.9
HMM Score 68.40
Secondary Structure Score 20.50
Atypical Features None
Known Modifications (Modomics) m2G10 m1A14 D16 D17 m2,2G26 Ψ27 Ψ28 Cm32 Gm34 o2yW37 Ψ39 m7G46 D47 m5C49 m5U54 Ψ55 m1A58
Genome Browser View with Related Data Tracks Zoomed in (750 bp flanking features)
Zoomed out (750 kbp flanking features)
Sequence
Genomic Sequence
GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGtCCCTGGTTCGATCCCGGGTTTCGGCA
Secondary Structure (nested bp)
>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<.
Predicted Mature tRNA
GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA
Alignments
Phe tRNAs
>>>>>>>..>>>>........<<<<.>>>>>.......<<<.<<.................>>>>>.......<<<<<<<<<<<<.... GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.AAAG...........Gt.CCCTGGTTCGATCCCGGGTTTCGGCA... tRNA-Phe-GAA-1-1 Sc: 88.9 GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.AAAG...........Gt.CCCTGGTTCGATCCCGGGTTTCGGCA... tRNA-Phe-GAA-1-2 Sc: 88.9 GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.AAAG...........Gt.CCCTGGTTCGATCCCGGGTTTCGGCA... tRNA-Phe-GAA-1-3 Sc: 88.9 GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.AAAG...........Gt.CCCTGGTTCGATCCCGGGTTTCGGCA... tRNA-Phe-GAA-1-4 Sc: 88.9 GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.AAAG...........Gt.CCCTGGTTCGATCCCGGGTTTCGGCA... tRNA-Phe-GAA-1-5 Sc: 88.9 GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.AAAG...........Gt.CCCTGGTTCGATCCCGGGTTTCGGCA... tRNA-Phe-GAA-1-6 Sc: 88.9 GCCGAGATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.AAAG...........Gt.CCCTGGTTCAATCCCGGGTTTCGGCA... tRNA-Phe-GAA-3-1 Sc: 88.3 GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.AAAG...........Gt.CCCTGGTTCAATCCCGGGTTTCGGCA... tRNA-Phe-GAA-2-1 Sc: 87.9 GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACCGAAGATCTtAAAG...........Gt.CCCTGGTTCAATCCCGGGTTTCGGCA... tRNA-Phe-GAA-4-1 Sc: 75.5 >>>>>>>..>>>>........<<<<.>.>>>.......<<<..<.................>>>>>.......<<<<<<<<<<<<.... GCTGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.TAAA...........GttCCCTGGTTCAACCCTGGGTTTCAGCC... tRNA-Phe-GAA-6-1 Sc: 58.8 >>>>>>>..>>>>........<<<<.>>>>>.......<<<.<<.................>>>>>.......<<<<<<<<<<<<.... GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCT.AAAG...........Gt.CCCTGGTTCGATCCCGGGTTTCGGCAcca RF9990_GAA_HUMAN_PLACENTA
>>>.>>>..>>>>........<<<<.>>>>>..........<<<<<................>>>>>.......<<<<<<<<.....<<<.... GCCAAAATTGCTCAGTTGGGAGAGCGTTAGACTGAAG...ATCTAAAG...........GtCCCTGGTTCGATCCCGGGTTTCaccaGGTT... tRNA-Phe-GAA-5-1 Sc: 65.8 (filtered) best isotype model: Phe Sc: 102.9 .>..>>>..>>>>........<<<<.>>>>>..........<<<<<................>>>>>.......<<<<<<<<......<..... GCCAAAATAGCTCAGCTGGGAGAGCATTAGACTGAAG...ATCTAAAG...........GtCTCTGGTTTGATCCTGGGTTTC....AGAA... tRNA-Phe-GAA-8-1 Sc: 45.5 (filtered) best isotype model: Phe Sc: 86.7 >.>>>>>..>>>>........<<<<..>>>>..........<<<<.................>>>>>.......<<<<<<<<<....<.<.... GCCGAAATAGCTCAATTGGGAGAGTGTTAGACTGAAGatcTTCTGCAG...........GtCTCTGGTTCAATTCCGGGTTTC....GACA... tRNA-Phe-GAA-7-1 Sc: 50.0 (filtered) best isotype model: Phe Sc: 78.5 >>>>>>>..>>>>........<<<<.>.>>............<<.<.................>>>>.......<<<<.<<<<....<<<.... GCTGAGATAGCTCGGTTGGGAGGGCATCAGCCTGAAG...ATCTAAAG...........GaGACTGGTTCAATTCTGGGTTTT....GGCA... tRNA-Phe-GAA-11-1 Sc: 33.3 (filtered) best isotype model: Phe Sc: 41.1 .>>.>>>..>>>>........<<<<.>>..>..........<..<<................>>>.>.......<.<<<<<<.....<<..... GCCAAAATAGCTCAGCTGGGAGAGTATTAGGTTGAAG...ATACAAAG...........TtCCTTGGCTCAATCCAGAGTTTG....GGGGact tRNA-Phe-GAA-12-1 Sc: 22.4 (filtered) best isotype model: Phe Sc: 29.1
Isotype-Specific Model Scores
AlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSeCSerThrTrpTyrValiMet
60.661.548.837.481.329.222.436.455.265.511.975.576.2124.539.5No Hit8.979.765.183.752.99.6
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 Hit-24.7No HitNo HitNo Hit38.5No HitNo HitNo HitNo HitNo Hit-13.8No Hit

Top score2nd highest score3rd highest score
DNA Variants (20)
tRNA Position Genomic Position dbSNP ID Ref/Alt Allele Common SNP 1K Genome Effect
3 (5′ Acceptor Stem)chr6:28949519rs561477312C / TNoYesGU base pair
3 (5′ Acceptor Stem)chr6:28949519rs561477312C / GNoYesbase pair mismatch
4 (5′ Acceptor Stem)chr6:28949518rs544885608G / TNoYesbase pair mismatch
6 (5′ Acceptor Stem)chr6:28949516rs368168256A / CNoNobase pair mismatch
8 (Acceptor-D-arm-linker)chr6:28949514rs180807346T / GNoYesuniversal base change
11 (5′ D-arm)chr6:28949511rs376016890C / TNoNoGU base pair
12 (5′ D-arm)chr6:28949510rs189309333T / CNoYesbase pair mismatch
21 (D-loop)chr6:28949501rs570175256- / TNoNouniversal base change
24 (3′ D-arm)chr6:28949498rs867649977G / CNoNobase pair mismatch
39 (3′ Anticodon Stem)chr6:28949483rs545108923T / ANoYesbase pair mismatch
41 (3′ Anticodon Stem)chr6:28949481rs146362461T / GNoYesbase pair mismatch
42 (3′ Anticodon Stem)chr6:28949480rs751116754A / GNoNoGU base pair
43 (3′ Anticodon Stem)chr6:28949479rs553235974A / TNoYesbase pair mismatch
45 (Variable Loop)chr6:28949477rs543108156G / CNoYessubstitution in loop
46 (Variable Loop)chr6:28949476rs556436812G / ANoYessubstitution in loop
61 (3′ T-arm)chr6:28949461rs762332734C / TNoNoGU base pair
66 (3′ Acceptor Stem)chr6:28949456rs142105459T / CNoYesbase pair mismatch
69 (3′ Acceptor Stem)chr6:28949453rs769701901C / TNoNoGU base pair
70 (3′ Acceptor Stem)chr6:28949452rs537718142G / ANoYesbase pair mismatch
71 (3′ Acceptor Stem)chr6:28949451rs184846255G / ANoYesbase pair mismatch
Expression Profiles