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ONTOLOGY REPORT - ANNOTATIONS


Term:tRNA modification
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Accession:GO:0006400 term browser browse the term
Definition:The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
Comment:The term 'RNA editing' (GO:0016547) was merged into 'RNA modification' (GO:0009451) on the basis of statements in the preface of Modification and Editing of RNA (ISBN:1555811337) that there is no clear distinction between modification and editing. Parallel changes were made for substrate (e.g. tRNA, rRNA, etc.) specific child terms of 'RNA editing'.
Synonyms:narrow_synonym: tRNA editing
 alt_id: GO:0016549


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tRNA modification term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07005588.1 RGD:1600115
G AABR07005618.1 RGD:13792537
G Aars alanyl-tRNA synthetase JBrowse link 19 43,193,264 43,215,281 RGD:1600115
RGD:13792537
RGD:1624291
G Aars2 alanyl-tRNA synthetase 2, mitochondrial JBrowse link 9 17,869,301 17,881,762 RGD:13792537
G Ankrd16 ankyrin repeat domain 16 JBrowse link 17 70,384,883 70,398,089 RGD:1600115
RGD:1624291
G Dtwd1 DTW domain containing 1 JBrowse link 3 118,427,790 118,443,003 RGD:1600115
RGD:1624291
G Dtwd2 DTW domain containing 2 JBrowse link 18 43,857,371 43,945,732 RGD:1624291
G Mettl1 methyltransferase like 1 JBrowse link 7 70,328,470 70,333,045 RGD:1624291
G Qtrt1 queuine tRNA-ribosyltransferase catalytic subunit 1 JBrowse link 8 22,447,057 22,454,328 RGD:13792537
G RGD1311345 similar to CG9752-PA JBrowse link 17 6,683,152 6,690,724 RGD:13792537
G Thg1l tRNA-histidine guanylyltransferase 1-like JBrowse link 10 31,043,647 31,052,092 RGD:1600115
G Trit1 tRNA isopentenyltransferase 1 JBrowse link 5 140,711,943 140,756,893 RGD:13792537
G Trub1 TruB pseudouridine synthase family member 1 JBrowse link 1 278,311,362 278,418,347 RGD:13792537
G Wdr4 WD repeat domain 4 JBrowse link 20 10,240,571 10,264,818 RGD:1624291
conversion of methionyl-tRNA to N-formyl-methionyl-tRNA term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Mtfmt mitochondrial methionyl-tRNA formyltransferase JBrowse link 8 70,952,209 70,986,393 RGD:13792537
mitochondrial tRNA methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Hsd17b10 hydroxysteroid (17-beta) dehydrogenase 10 JBrowse link X 21,696,796 21,699,241 RGD:1600115
RGD:1624291
G Trmt5 tRNA methyltransferase 5 JBrowse link 6 96,164,579 96,171,680 RGD:1624291
RGD:13792537
mitochondrial tRNA modification term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cdk5rap1 CDK5 regulatory subunit associated protein 1 JBrowse link 3 149,835,953 149,870,429 RGD:1624291
mitochondrial tRNA wobble uridine modification term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Mto1 mitochondrial tRNA translation optimization 1 JBrowse link 8 85,807,703 85,832,263 RGD:1624291
RGD:13792537
tRNA (guanine-N7)-methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Mettl1 methyltransferase like 1 JBrowse link 7 70,328,470 70,333,045 RGD:1600115
G Wdr4 WD repeat domain 4 JBrowse link 20 10,240,571 10,264,818 RGD:1600115
tRNA acetylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Nat10 N-acetyltransferase 10 JBrowse link 3 93,658,119 93,698,136 RGD:1600115
tRNA C5-cytosine methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Nsun6 NOP2/Sun RNA methyltransferase 6 JBrowse link 17 82,020,316 82,060,533 RGD:1624291
tRNA demethylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Alkbh1 alkB homolog 1, histone H2A dioxygenase JBrowse link 6 111,456,096 111,476,829 RGD:1624291
tRNA dihydrouridine synthesis term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dus1l dihydrouridine synthase 1-like JBrowse link 10 109,972,018 109,979,113 RGD:1600115
G Dus2 dihydrouridine synthase 2 JBrowse link 19 37,990,374 38,033,590 RGD:1624291
RGD:13792537
G Dus3l dihydrouridine synthase 3-like JBrowse link 9 10,289,440 10,294,213 RGD:1600115
G Dus4l dihydrouridine synthase 4-like JBrowse link 6 50,925,987 50,943,546 RGD:1600115
tRNA methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Alkbh8 alkB homolog 8, tRNA methyltransferase JBrowse link 6 18,877,885 18,952,773 RGD:1624291
G Bcdin3d BCDIN3 domain containing RNA methyltransferase JBrowse link 7 141,132,106 141,136,700 RGD:1600115
RGD:1624291
G Ftsj1 FtsJ RNA 2'-O-methyltransferase 1 JBrowse link X 14,993,685 15,006,010 RGD:13792537
G Gtpbp3 GTP binding protein 3 JBrowse link 16 19,897,135 19,902,226 RGD:13792537
G Lcmt2 leucine carboxyl methyltransferase 2 JBrowse link 3 113,089,646 113,091,770 RGD:13792537
G LOC103692719 tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A JBrowse link 6 136,244,466 136,250,496 RGD:13792537
G Mettl1 methyltransferase like 1 JBrowse link 7 70,328,470 70,333,045 RGD:13792537
G Mettl2 methyltransferase like 2 JBrowse link 10 93,353,944 93,367,769 RGD:1624291
G Mettl6 methyltransferase like 6 JBrowse link 16 7,559,964 7,588,841 RGD:1624291
G Mto1 mitochondrial tRNA translation optimization 1 JBrowse link 8 85,807,703 85,832,263 RGD:13792537
G Nsun2 NOP2/Sun RNA methyltransferase 2 JBrowse link 1 36,295,650 36,319,906 RGD:1624291
RGD:13792537
G Nsun6 NOP2/Sun RNA methyltransferase 6 JBrowse link 17 82,020,316 82,060,533 RGD:1624291
G Tarbp1 TAR (HIV-1) RNA binding protein 1 JBrowse link 19 59,331,399 59,384,807 RGD:13792537
G Thada THADA, armadillo repeat containing JBrowse link 6 7,423,555 7,741,431 RGD:13792537
G Thumpd2 THUMP domain containing 2 JBrowse link 6 3,743,080 3,794,512 RGD:13792537
G Thumpd3 THUMP domain containing 3 JBrowse link 4 144,985,850 145,010,164 RGD:13792537
G Trdmt1 tRNA aspartic acid methyltransferase 1 JBrowse link 17 80,824,652 80,859,585 RGD:1624291
RGD:1600115
G Trmo tRNA methyltransferase O JBrowse link 5 61,992,507 62,001,065 RGD:1624291
RGD:1600115
G Trmt10a tRNA methyltransferase 10A JBrowse link 2 243,422,811 243,437,533 RGD:1600115
RGD:1624291
G Trmt10b tRNA methyltransferase 10B JBrowse link 5 60,841,517 60,866,480 RGD:1600115
G Trmt10c tRNA methyltransferase 10C, mitochondrial RNase P subunit JBrowse link 11 47,047,342 47,052,420 RGD:1600115
G Trmt11 tRNA methyltransferase 11 homolog JBrowse link 1 29,432,109 29,576,079 RGD:1600115
G Trmt112 tRNA methyltransferase subunit 11-2 JBrowse link 1 222,167,927 222,168,780 RGD:13792537
G Trmt12 tRNA methyltransferase 12 JBrowse link 7 98,748,547 98,750,173 RGD:13792537
G Trmt13 tRNA methyltransferase 13 homolog JBrowse link 2 219,615,665 219,628,824 RGD:13792537
G Trmt44 tRNA methyltransferase 44 JBrowse link 14 80,361,490 80,379,408 RGD:13792537
G Trmt5 tRNA methyltransferase 5 JBrowse link 6 96,164,579 96,171,680 RGD:13792537
G Trmt6 tRNA methyltransferase 6 JBrowse link 3 125,458,692 125,470,413 RGD:1600115
G Trmt61a tRNA methyltransferase 61A JBrowse link 6 136,150,768 136,156,785 RGD:13792537
G Trmt9b tRNA methyltransferase 9B (putative) JBrowse link 16 59,316,145 59,368,559 RGD:1600115
G Tyw3 tRNA-yW synthesizing protein 3 homolog JBrowse link 2 260,861,825 260,884,270 RGD:13792537
tRNA methylthiolation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cdk5rap1 CDK5 regulatory subunit associated protein 1 JBrowse link 3 149,835,953 149,870,429 RGD:1600115
G Cdkal1 CDK5 regulatory subunit associated protein 1-like 1 JBrowse link 17 36,451,031 37,157,882 RGD:1624291
tRNA N1-guanine methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Trmt5 tRNA methyltransferase 5 JBrowse link 6 96,164,579 96,171,680 RGD:13792537
tRNA N2-guanine methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Trmt1 tRNA methyltransferase 1 JBrowse link 19 25,798,262 25,813,458 RGD:13792537
G Trmt1l tRNA methyltransferase 1-like JBrowse link 13 68,785,889 68,819,018 RGD:13792537
tRNA nucleoside ribose methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ftsj1 FtsJ RNA 2'-O-methyltransferase 1 JBrowse link X 14,993,685 15,006,010 RGD:1600115
tRNA pseudouridine synthesis term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Pus1 pseudouridine synthase 1 JBrowse link 12 51,936,721 51,945,930 RGD:1624291
RGD:13792537
G Pus10 pseudouridine synthase 10 JBrowse link 14 108,411,941 108,479,696 RGD:13792537
RGD:1624291
G Pus3 pseudouridine synthase 3 JBrowse link 8 36,760,874 36,769,167 RGD:1624291
RGD:13792537
G Pus7 pseudouridine synthase 7 JBrowse link 4 7,889,727 7,931,357 RGD:1624291
G Pusl1 pseudouridine synthase like 1 JBrowse link 5 173,326,755 173,339,934 RGD:13792537
tRNA thio-modification term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ctu1 cytosolic thiouridylase subunit 1 JBrowse link 1 99,599,608 99,605,412 RGD:1600115
G Ctu2 cytosolic thiouridylase subunit 2 JBrowse link 19 55,300,531 55,305,543 RGD:1600115
G Mocs3 molybdenum cofactor synthesis 3 JBrowse link 3 164,986,421 164,988,381 RGD:1624291
G Urm1 ubiquitin related modifier 1 JBrowse link 3 8,389,024 8,405,868 RGD:1624291
tRNA threonylcarbamoyladenosine modification term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Osgep O-sialoglycoprotein endopeptidase JBrowse link 15 27,842,447 27,849,866 RGD:1600115
RGD:1624291
G Osgepl1 O-sialoglycoprotein endopeptidase-like 1 JBrowse link 9 53,084,042 53,098,029 RGD:1600115
G Tprkb Tp53rk binding protein JBrowse link 4 117,589,527 117,604,481 RGD:1600115
RGD:1624291
tRNA wobble adenosine to inosine editing term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Adat2 adenosine deaminase, tRNA-specific 2 JBrowse link 1 7,726,447 7,743,112 RGD:13792537
G Adat3 adenosine deaminase, tRNA-specific 3 JBrowse link 7 11,977,285 11,981,814 RGD:13792537
tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Elp1 elongator complex protein 1 JBrowse link 5 73,503,406 73,552,798 RGD:13792537
G Elp3 elongator acetyltransferase complex subunit 3 JBrowse link 15 48,942,866 49,005,074 RGD:13792537
tRNA wobble base cytosine methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Nsun3 NOP2/Sun RNA methyltransferase 3 JBrowse link 11 38,535,971 38,590,274 RGD:1624291
tRNA wobble cytosine modification term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Alkbh1 alkB homolog 1, histone H2A dioxygenase JBrowse link 6 111,456,096 111,476,829 RGD:1624291
tRNA wobble position uridine thiolation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ctu1 cytosolic thiouridylase subunit 1 JBrowse link 1 99,599,608 99,605,412 RGD:13792537
G Ctu2 cytosolic thiouridylase subunit 2 JBrowse link 19 55,300,531 55,305,543 RGD:13792537
G Mocs3 molybdenum cofactor synthesis 3 JBrowse link 3 164,986,421 164,988,381 RGD:13792537
G Trmu tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase JBrowse link 7 126,756,140 126,772,749 RGD:13792537
G Urm1 ubiquitin related modifier 1 JBrowse link 3 8,389,024 8,405,868 RGD:13792537
tRNA wobble uridine modification term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07053185.1 RGD:1600115
G Alkbh8 alkB homolog 8, tRNA methyltransferase JBrowse link 6 18,877,885 18,952,773 RGD:1624291
G Ctu1 cytosolic thiouridylase subunit 1 JBrowse link 1 99,599,608 99,605,412 RGD:1600115
G Ctu2 cytosolic thiouridylase subunit 2 JBrowse link 19 55,300,531 55,305,543 RGD:1600115
G Dph3 diphthamide biosynthesis 3 JBrowse link 16 8,202,048 8,207,492 RGD:13792537
G Elp1 elongator complex protein 1 JBrowse link 5 73,503,406 73,552,798 RGD:1600115
G Elp2 elongator acetyltransferase complex subunit 2 JBrowse link 18 16,544,515 16,581,086 RGD:1600115
G Elp5 elongator acetyltransferase complex subunit 5 JBrowse link 10 56,578,980 56,590,706 RGD:1600115
G Elp6 elongator acetyltransferase complex subunit 6 JBrowse link 8 118,525,770 118,541,074 RGD:1600115
G Gtpbp3 GTP binding protein 3 JBrowse link 16 19,897,135 19,902,226 RGD:13792537
G Kti12 KTI12 chromatin associated homolog JBrowse link 5 128,464,035 128,465,557 RGD:13792537
G LOC365839 similar to elongation protein 4 homolog JBrowse link 2 186,630,203 186,631,703 RGD:1600115
G Mocs3 molybdenum cofactor synthesis 3 JBrowse link 3 164,986,421 164,988,381 RGD:1624291
G Mto1 mitochondrial tRNA translation optimization 1 JBrowse link 8 85,807,703 85,832,263 RGD:1624291
RGD:13792537
G Trmt9b tRNA methyltransferase 9B (putative) JBrowse link 16 59,316,145 59,368,559 RGD:13792537
G Urm1 ubiquitin related modifier 1 JBrowse link 3 8,389,024 8,405,868 RGD:1624291
tRNA-guanine transglycosylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Qtrt1 queuine tRNA-ribosyltransferase catalytic subunit 1 JBrowse link 8 22,447,057 22,454,328 RGD:1624291
RGD:1600115
G Qtrt2 queuine tRNA-ribosyltransferase accessory subunit 2 JBrowse link 11 61,748,822 61,779,631 RGD:1624291
RGD:13792537
G RGD1311345 similar to CG9752-PA JBrowse link 17 6,683,152 6,690,724 RGD:13792537
wybutosine biosynthetic process term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Lcmt2 leucine carboxyl methyltransferase 2 JBrowse link 3 113,089,646 113,091,770 RGD:13792537
G Trmt12 tRNA methyltransferase 12 JBrowse link 7 98,748,547 98,750,173 RGD:13792537
G Tyw1 tRNA-yW synthesizing protein 1 homolog JBrowse link 12 29,824,990 29,919,240 RGD:13792537
G Tyw3 tRNA-yW synthesizing protein 3 homolog JBrowse link 2 260,861,825 260,884,270 RGD:13792537
G Tyw5 tRNA-yW synthesizing protein 5 JBrowse link 9 64,077,841 64,096,265 RGD:1624291
RGD:13792537

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 19578
    metabolic process 11901
      organic substance metabolic process 11299
        macromolecule metabolic process 9767
          macromolecule modification 4081
            RNA modification 161
              tRNA modification 84
                2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine-tRNA biosynthesis 0
                archaeosine-tRNA biosynthetic process 0
                charged-tRNA amino acid modification + 1
                cyclic threonylcarbamoyladenosine biosynthetic process 0
                mitochondrial tRNA modification + 4
                tRNA acetylation 1
                tRNA adenosine deamination to inosine 0
                tRNA demethylation 1
                tRNA dihydrouridine synthesis 4
                tRNA methylation + 36
                tRNA methylthiolation 2
                tRNA pseudouridine synthesis + 5
                tRNA seleno-modification 0
                tRNA thio-modification + 5
                tRNA threonylcarbamoyladenosine modification + 3
                tRNA wobble base modification + 22
                tRNA-guanine transglycosylation 3
                wybutosine biosynthetic process 5
Path 2
Term Annotations click to browse term
  biological_process 19578
    metabolic process 11901
      cellular metabolic process 10737
        heterocycle metabolic process 5428
          nucleobase-containing compound metabolic process 5276
            nucleic acid metabolic process 4782
              RNA metabolic process 4290
                ncRNA metabolic process 489
                  ncRNA processing 390
                    tRNA processing 117
                      tRNA modification 84
                        2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine-tRNA biosynthesis 0
                        archaeosine-tRNA biosynthetic process 0
                        charged-tRNA amino acid modification + 1
                        cyclic threonylcarbamoyladenosine biosynthetic process 0
                        mitochondrial tRNA modification + 4
                        tRNA acetylation 1
                        tRNA adenosine deamination to inosine 0
                        tRNA demethylation 1
                        tRNA dihydrouridine synthesis 4
                        tRNA methylation + 36
                        tRNA methylthiolation 2
                        tRNA pseudouridine synthesis + 5
                        tRNA seleno-modification 0
                        tRNA thio-modification + 5
                        tRNA threonylcarbamoyladenosine modification + 3
                        tRNA wobble base modification + 22
                        tRNA-guanine transglycosylation 3
                        wybutosine biosynthetic process 5
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.