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| Differntial gene expression between RNA A-to-I edited versus non-edited samples |
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| The effects of the RNA editing to the stability of the RNA structures |
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Gene summary for TRMT13 |
 Gene summary |
| Gene information | Gene symbol | TRMT13 | Gene ID | 54482 |
| Gene name | tRNA methyltransferase 13 homolog | |
| Synonyms | CCDC76 | |
| Cytomap | 1p21.2 | |
| Type of gene | protein-coding | |
| Description | tRNA:m(4)X modification enzyme TRM13 homologcoiled-coil domain containing 76coiled-coil domain-containing protein 76tRNA [Gm4] methyltransferasetRNA guanosine-2'-O-methyltransferase TRM13 homolog | |
| Modification date | 20200313 | |
| UniProtAcc | Q9NUP7, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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RNA A-to-I events for TRMT13 |
| RNA A-to-I editing events in the ROSMAP, MSBB, and Mayo data sets based on Ensembl gene isoform structure. * This pie chart shows the number of RNA A-to-I editing events in different types of transcripts (# event, percentage). |
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| RNA editing frequencies across three data sets. |
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| The number of RNA A-to-I editing events in different types of transcripts (# event, percentage). |
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| RNA A-to-I editing events in AD. |
| ADediting_249(100139989, +), ADediting_250(100140019, +), ADediting_251(100140078, +), ADediting_252(100140106, +), ADediting_253(100145648, +), ADediting_254(100145653, +), ADediting_255(100145685, +), ADediting_256(100145701, +), ADediting_257(100145709, +), ADediting_258(100145737, +), ADediting_259(100145750, +), ADediting_260(100145764, +), ADediting_261(100145786, +), ADediting_262(100145817, +), ADediting_263(100145825, +), ADediting_264(100145828, +), ADediting_265(100145858, +), ADediting_266(100146551, +), ADediting_267(100146556, +), ADediting_268(100146605, +), ADediting_269(100146606, +), ADediting_270(100146610, +), ADediting_271(100146623, +), ADediting_272(100146645, +), ADediting_1513538(100139068, +), ADediting_1513539(100140001, +), ADediting_1513540(100140014, +), ADediting_1513541(100145702, +), ADediting_1513542(100145756, +), ADediting_1513543(100145760, +), ADediting_1513544(100145767, +), ADediting_1513545(100145797, +), ADediting_1513546(100146633, +), ADediting_1513547(100146735, +), |
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RNA editing positional annotations for TRMT13 using Annovar |
| Protein coding RNA editing(s). |
| ADeditome ID | Position | Variant type | ENST | NTchange | AAchange | SIFT_score | Polyphen2_HVAR_score | PROVEAN_pred |
| Gene structure information of RNA editing(s). |
| ADeditome ID | Position | Variant type |
| ADediting_249 | chr1_100139989_+ | intronic |
| ADediting_250 | chr1_100140019_+ | intronic |
| ADediting_251 | chr1_100140078_+ | intronic |
| ADediting_252 | chr1_100140106_+ | intronic |
| ADediting_253 | chr1_100145648_+ | intronic |
| ADediting_254 | chr1_100145653_+ | intronic |
| ADediting_255 | chr1_100145685_+ | intronic |
| ADediting_256 | chr1_100145701_+ | intronic |
| ADediting_257 | chr1_100145709_+ | intronic |
| ADediting_258 | chr1_100145737_+ | intronic |
| ADediting_259 | chr1_100145750_+ | intronic |
| ADediting_260 | chr1_100145764_+ | intronic |
| ADediting_261 | chr1_100145786_+ | intronic |
| ADediting_262 | chr1_100145817_+ | intronic |
| ADediting_263 | chr1_100145825_+ | intronic |
| ADediting_264 | chr1_100145828_+ | intronic |
| ADediting_265 | chr1_100145858_+ | intronic |
| ADediting_266 | chr1_100146551_+ | intronic |
| ADediting_267 | chr1_100146556_+ | intronic |
| ADediting_268 | chr1_100146605_+ | intronic |
| ADediting_269 | chr1_100146606_+ | intronic |
| ADediting_270 | chr1_100146610_+ | intronic |
| ADediting_271 | chr1_100146623_+ | intronic |
| ADediting_272 | chr1_100146645_+ | intronic |
| ADediting_1513538 | chr1_100139068_+ | intronic |
| ADediting_1513539 | chr1_100140001_+ | intronic |
| ADediting_1513540 | chr1_100140014_+ | intronic |
| ADediting_1513541 | chr1_100145702_+ | intronic |
| ADediting_1513542 | chr1_100145756_+ | intronic |
| ADediting_1513543 | chr1_100145760_+ | intronic |
| ADediting_1513544 | chr1_100145767_+ | intronic |
| ADediting_1513545 | chr1_100145797_+ | intronic |
| ADediting_1513546 | chr1_100146633_+ | intronic |
| ADediting_1513547 | chr1_100146735_+ | intronic |
| Repat-regional RNA editing(s). |
| ADeditome ID | Position | Repeat family | Repeat sub family | Repeat name |
| ADediting_253 | chr1_100145648_+ | SINE | Alu | Name=AluJr |
| ADediting_254 | chr1_100145653_+ | SINE | Alu | Name=AluJr |
| ADediting_255 | chr1_100145685_+ | SINE | Alu | Name=AluJr |
| ADediting_256 | chr1_100145701_+ | SINE | Alu | Name=AluJr |
| ADediting_257 | chr1_100145709_+ | SINE | Alu | Name=AluJr |
| ADediting_258 | chr1_100145737_+ | SINE | Alu | Name=AluJr |
| ADediting_259 | chr1_100145750_+ | SINE | Alu | Name=AluJr |
| ADediting_260 | chr1_100145764_+ | SINE | Alu | Name=AluJr |
| ADediting_261 | chr1_100145786_+ | SINE | Alu | Name=AluJr |
| ADediting_262 | chr1_100145817_+ | SINE | Alu | Name=AluJr |
| ADediting_263 | chr1_100145825_+ | SINE | Alu | Name=AluJr |
| ADediting_264 | chr1_100145828_+ | SINE | Alu | Name=AluJr |
| ADediting_265 | chr1_100145858_+ | SINE | Alu | Name=AluJr |
| ADediting_266 | chr1_100146551_+ | SINE | Alu | Name=AluSc8 |
| ADediting_267 | chr1_100146556_+ | SINE | Alu | Name=AluSc8 |
| ADediting_268 | chr1_100146605_+ | SINE | Alu | Name=AluSc8 |
| ADediting_269 | chr1_100146606_+ | SINE | Alu | Name=AluSc8 |
| ADediting_270 | chr1_100146610_+ | SINE | Alu | Name=AluSc8 |
| ADediting_271 | chr1_100146623_+ | SINE | Alu | Name=AluSc8 |
| ADediting_272 | chr1_100146645_+ | SINE | Alu | Name=AluSc8 |
| ADediting_1513538 | chr1_100139068_+ | SINE | Alu | Name=FLAM_C |
| ADediting_1513541 | chr1_100145702_+ | SINE | Alu | Name=AluJr |
| ADediting_1513542 | chr1_100145756_+ | SINE | Alu | Name=AluJr |
| ADediting_1513543 | chr1_100145760_+ | SINE | Alu | Name=AluJr |
| ADediting_1513544 | chr1_100145767_+ | SINE | Alu | Name=AluJr |
| ADediting_1513545 | chr1_100145797_+ | SINE | Alu | Name=AluJr |
| ADediting_1513546 | chr1_100146633_+ | SINE | Alu | Name=AluSc8 |
| ADediting_1513547 | chr1_100146735_+ | SINE | Alu | Name=AluSc8 |
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RNA A-to-I editing events in the alternative splicing sites for TRMT13 |
| RNA A-to-I editing(s) in the alternative splicing sites. |
| AStype | ADeditomID | Editing position | AS position | AS direction | Exonic location | Wildtype sequence | Wildtype splicing strength | RNA edited sequence | RNA edited splicing strength |
| Differential pencent of spliced in (PSI) between RNA A-to-I edited and non-edited samples |
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Differntial gene expression between RNA A-to-I edited versus non-edited samples for TRMT13 |
| Distribution of the averaged gene expression in AD and control with or without RNA A-to-I editing event. * The grey color means N/A. |
| Distribution of the averaged gene isoform expression in AD and control with or without RNA A-to-I editing event. |
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| - Differentially expressed gene between RNA A-to-I edited samples versus non-edited samples. * Click on the image to enlarge it in a new window. |
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| - Differentially expressed transcript between RNA A-to-I edited samples versus non-edited samples. * Click on the image to enlarge it in a new window. |
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| ADeditome ID | Chr | Positoing | Skipped exon | ENSG | ENSTs |
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Protein coding region RNA A-to-I editings for TRMT13 |
| - Lollipop plot for RNA A-to-I editings across protein structure. * Click on the image to enlarge it in a new window. |
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The effects of the RNA editing to the miRNA binding sites for TRMT13 |
| RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in lncRNA gained miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in lncRNA lost miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in miRNAs gained binding to lncRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in miRNAs lost binding to lncRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| ADediting_107020 | chr1_37500952_- | ENSG00000122435.10 | ENST00000370139.1 | TRMT13-201 | hsa-miR-5581-3p | chr1 | 100140671 | 100140677 | 7mer-m8 | 100140657 | 100140678 | 150 | -15.51 |
| ADediting_1097295 | chr3_85385762_+ | ENSG00000122435.10 | ENST00000370141.7 | TRMT13-202 | hsa-miR-5688 | chr1 | 100150325 | 100150331 | 7mer-m8 | 100150311 | 100150332 | 152 | -13.56 |
| ADediting_1596844 | chr1_162342605_+ | ENSG00000122435.10 | ENST00000370141.7 | TRMT13-202 | hsa-miR-556-3p | chr1 | 100148954 | 100148960 | 7mer-m8 | 100148941 | 100148961 | 147 | -9.98 |
| Differentially expressed gene-miRNA network |
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The effects of the RNA editing to the stability of the RNA structures for TRMT13 |
| - RNA A-to-I editing in mRNA. * Click on the image to enlarge it in a new window. |
| ENST | ENST type | RNA structure without RNA A-to-I editing. | RNA structure with RNA A-to-I editing. |
| RNA A-to-I editing in miRNA. |
| ADeditom_ID | ENST | mir_ID | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
| RNA A-to-I editing in mRNA. |
| ADeditom_ID | ENST | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
| RNA A-to-I editing in lncRNA. |
| ADeditom_ID | ENST | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
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Relation with ADAR for TRMT13 |
| Correlation between ADAR gene expression and RNA editing frequency |
| Tissue | ADeditomID | position | ADAR1 (p-val) | ADAR1 (coeff.) | ADAR2 (p-val) | ADAR2 (coeff.) | ADAR3 (p-val) | ADAR3 (coeff.) |
| CER | ADediting_1513539 | chr1_100140001_+ | 0.000106118192766194 | 0.311195181761946 | 0.0052762500066012 | 0.226698433404605 | 0.802254919444236 | -0.0206178184542189 |
| CER | ADediting_1513540 | chr1_100140014_+ | 3.94328077081775e-06 | 0.366623726093468 | 0.000312236343009103 | 0.290401503189734 | 0.557409489657307 | 0.0482792649945491 |
| CER | ADediting_1513543 | chr1_100145760_+ | 2.59400283495362e-05 | 0.336215974212766 | 0.0669312858045114 | 0.150000503430987 | 0.670953699659275 | -0.0349699239345272 |
| CER | ADediting_250 | chr1_100140019_+ | 8.22867717838693e-05 | 0.315878158483321 | 0.000923450422617372 | 0.267777291306954 | 0.8464396713001 | -0.0159449089449847 |
| CER | ADediting_254 | chr1_100145653_+ | 2.79139257177054e-07 | 0.4047327744988 | 0.00119081908090687 | 0.262180611566203 | 0.330711431203698 | -0.0799607998499902 |
| CER | ADediting_257 | chr1_100145709_+ | 6.25945745809317e-08 | 0.4243167942824 | 0.0174775546626861 | 0.193818425302647 | 0.648796141583431 | -0.0374866501722683 |
| CER | ADediting_258 | chr1_100145737_+ | 5.38506540276981e-09 | 0.45398218708629 | 0.00474591733319516 | 0.229397795072742 | 0.296473513034663 | -0.0858048099218034 |
| TCX | ADediting_258 | chr1_100145737_+ | 1.09614231188531e-06 | 0.385646933039615 | 0.0143336352648907 | 0.199596567771068 | 0.655549518896746 | 0.0367160037793973 |
| CER | ADediting_259 | chr1_100145750_+ | 1.12735930759609e-09 | 0.471512984075549 | 0.00103535560785668 | 0.265274537232901 | 0.226322668090077 | -0.0993733542776916 |
| TCX | ADediting_259 | chr1_100145750_+ | 0.00981110978964228 | 0.21024996690503 | 2.65402052356041e-05 | 0.335826655919408 | 0.168674553291988 | -0.112973659286195 |
| CER | ADediting_260 | chr1_100145764_+ | 1.54998680261309e-17 | 0.623598852346731 | 2.03602145208337e-07 | 0.40897135514187 | 0.0424249518033643 | 0.165931521311221 |
| TCX | ADediting_260 | chr1_100145764_+ | 3.61790436513336e-07 | 0.401204498169901 | 0.0342292611840306 | 0.173023079078761 | 0.000265794366134368 | 0.293605441428969 |
| CER | ADediting_261 | chr1_100145786_+ | 9.62816093567085e-13 | 0.540280750497228 | 1.60089063320204e-06 | 0.380142825227406 | 0.878180211308602 | 0.0126200503738533 |
| TCX | ADediting_261 | chr1_100145786_+ | 0.000235587626391198 | 0.295981347350334 | 6.78675380047669e-05 | 0.3193743797041 | 0.84181315000435 | 0.0164315705987036 |
| CER | ADediting_263 | chr1_100145825_+ | 4.44029616584319e-18 | 0.631673701853548 | 4.81988715564266e-12 | 0.525903557261923 | 0.217488115281133 | 0.10128133328415 |
| CER | ADediting_264 | chr1_100145828_+ | 2.41266623852675e-17 | 0.620683487401477 | 1.05676161029595e-11 | 0.518642703068825 | 0.124946736752754 | 0.125832254542516 |
| TCX | ADediting_264 | chr1_100145828_+ | 7.01726610958805e-05 | 0.318771304219528 | 0.00342120448167779 | 0.237554378756946 | 0.362693475527651 | 0.0748429608714445 |
| CER | ADediting_267 | chr1_100146556_+ | 1.03280033883606e-10 | 0.496530895673628 | 2.27035995152478e-08 | 0.436927365765141 | 0.449625489757928 | 0.0621908374449793 |
| CER | ADediting_268 | chr1_100146605_+ | 1.15294135578788e-06 | 0.384918558801071 | 9.36583197042577e-06 | 0.353048375585711 | 0.265125416425381 | -0.0915616755918924 |
| CER | ADediting_269 | chr1_100146606_+ | 7.62740214032305e-14 | 0.561614633184893 | 8.63203063403182e-10 | 0.474409647979124 | 0.834551337220485 | 0.0171965918175771 |
| TCX | ADediting_269 | chr1_100146606_+ | 8.89384211627981e-05 | 0.314455146977879 | 0.0208614481003553 | 0.188532246902244 | 0.983589977741702 | 0.00169356613325931 |
| CER | ADediting_272 | chr1_100146645_+ | 6.15777593491661e-08 | 0.424524586273035 | 0.0118363851887871 | 0.205037932872212 | 0.293825331604394 | -0.08627489864957 |
| Correlation between ADAR gene expression and this gene's expression |
| Tissue | ADAR1 (p-val) | ADAR1 (coeff.) | ADAR2 (p-val) | ADAR2 (coeff.) | ADAR3 (p-val) | ADAR3 (coeff.) |
| DLPFC | 2.20303990276172e-12 | 0.384856196876129 | 1.78816452994072e-15 | 0.431282418064072 | 0.0518796496682046 | 0.110527198688675 |
| AC | 9.72560870367422e-37 | 0.69043773891705 | 1.11173935198129e-22 | 0.567155905298984 | 9.02299985525717e-24 | 0.578928398514321 |
| PCC | 3.85780330135507e-08 | 0.384864291728861 | 2.41977644193369e-06 | 0.33351962595282 | 2.82902083072256e-09 | 0.413235155026569 |
| CER | 1.62742689786121e-29 | 0.760217062416653 | 7.62860625339593e-10 | 0.475741293160136 | 0.470669426321836 | 0.0593457825542283 |
| TCX | 5.08338243029021e-08 | 0.426946906856336 | 0.399981531588253 | -0.069217343875242 | 2.11895219351418e-22 | 0.688498455123828 |
| FP | 2.81228606021293e-22 | 0.644520977881063 | 1.7151007439769e-25 | 0.679890947502853 | 8.23627488117034e-08 | 0.388710403272417 |
| IFG | 0.0184327007922676 | 0.467569779933099 | 0.131205015828835 | 0.310251194823569 | 8.1052223709193e-07 | 0.812455845681848 |
| PG | 7.2668121709094e-41 | 0.789496160862746 | 1.14603428135526e-22 | 0.63822671723635 | 0.143036742333234 | 0.107801418656855 |
| STG | 0.000159657963968327 | 0.400558598611551 | 7.85745364902315e-05 | 0.417265295317033 | 0.0113914739874141 | 0.274873603891178 |
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Relation with AD stages for TRMT13 |
| Correlation between AD stages and RNA editing frequency |
| Tissue | ADeditomID | position | P-val | Coeff. |
| Correlation between AD stages and this gene's expression |
| Tissue | P-val | Coeff. |
| TCX | 6.77971745813141e-08 | 0.495237339056653 |
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RelatedDrugs for TRMT13 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for TRMT13 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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