|
||||||
|
 | |
| |
| Differntial gene expression between RNA A-to-I edited versus non-edited samples |
| |
| |
| The effects of the RNA editing to the stability of the RNA structures |
| |
| |
| |
|
Gene summary for YRDC |
 Gene summary |
| Gene information | Gene symbol | YRDC | Gene ID | 79693 |
| Gene name | yrdC N6-threonylcarbamoyltransferase domain containing | |
| Synonyms | DRIP3|IRIP|SUA5 | |
| Cytomap | 1p34.3 | |
| Type of gene | protein-coding | |
| Description | yrdC domain-containing protein, mitochondrialdopamine receptor interacting protein 3hIRIPischemia/reperfusion inducible proteinischemia/reperfusion-inducible protein homologyrdC N(6)-threonylcarbamoyltransferase domain containingyrdC domain containi | |
| Modification date | 20200313 | |
| UniProtAcc | Q86U90, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| YRDC | GO:0051051 | negative regulation of transport | 2675563 |
Top |
RNA A-to-I events for YRDC |
| 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). |
 |
| RNA editing frequencies across three data sets. |
 |
| The number of RNA A-to-I editing events in different types of transcripts (# event, percentage). |
 |
| RNA A-to-I editing events in AD. |
| ADediting_107324(37805020, -), ADediting_107325(37805021, -), ADediting_107326(37805022, -), ADediting_107327(37805059, -), ADediting_107328(37805076, -), ADediting_107329(37805134, -), ADediting_107330(37805197, -), ADediting_107331(37805198, -), ADediting_107332(37805246, -), ADediting_107333(37806279, -), ADediting_107334(37806359, -), ADediting_107335(37806361, -), ADediting_107336(37806365, -), ADediting_107337(37806370, -), ADediting_107338(37806371, -), ADediting_107339(37806398, -), ADediting_107340(37806415, -), ADediting_107341(37806483, -), ADediting_1519815(37805121, -), ADediting_1519816(37806297, -), |
Top |
RNA editing positional annotations for YRDC 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_107324 | chr1_37805020_- | intronic |
| ADediting_107325 | chr1_37805021_- | intronic |
| ADediting_107326 | chr1_37805022_- | intronic |
| ADediting_107327 | chr1_37805059_- | intronic |
| ADediting_107328 | chr1_37805076_- | intronic |
| ADediting_107329 | chr1_37805134_- | intronic |
| ADediting_107330 | chr1_37805197_- | intronic |
| ADediting_107331 | chr1_37805198_- | intronic |
| ADediting_107332 | chr1_37805246_- | intronic |
| ADediting_107333 | chr1_37806279_- | intronic |
| ADediting_107334 | chr1_37806359_- | intronic |
| ADediting_107335 | chr1_37806361_- | intronic |
| ADediting_107336 | chr1_37806365_- | intronic |
| ADediting_107337 | chr1_37806370_- | intronic |
| ADediting_107338 | chr1_37806371_- | intronic |
| ADediting_107339 | chr1_37806398_- | intronic |
| ADediting_107340 | chr1_37806415_- | intronic |
| ADediting_107341 | chr1_37806483_- | intronic |
| ADediting_1519815 | chr1_37805121_- | intronic |
| ADediting_1519816 | chr1_37806297_- | intronic |
| Repat-regional RNA editing(s). |
| ADeditome ID | Position | Repeat family | Repeat sub family | Repeat name |
| ADediting_107324 | chr1_37805020_- | SINE | Alu | Name=AluSz |
| ADediting_107325 | chr1_37805021_- | SINE | Alu | Name=AluSz |
| ADediting_107326 | chr1_37805022_- | SINE | Alu | Name=AluSz |
| ADediting_107327 | chr1_37805059_- | SINE | Alu | Name=AluSz |
| ADediting_107328 | chr1_37805076_- | SINE | Alu | Name=AluSz |
| ADediting_107329 | chr1_37805134_- | SINE | Alu | Name=AluSz |
| ADediting_107330 | chr1_37805197_- | SINE | Alu | Name=AluSz |
| ADediting_107331 | chr1_37805198_- | SINE | Alu | Name=AluSz |
| ADediting_107332 | chr1_37805246_- | SINE | Alu | Name=AluSz |
| ADediting_107333 | chr1_37806279_- | SINE | Alu | Name=AluSz6 |
| ADediting_107334 | chr1_37806359_- | SINE | Alu | Name=AluSz6 |
| ADediting_107335 | chr1_37806361_- | SINE | Alu | Name=AluSz6 |
| ADediting_107336 | chr1_37806365_- | SINE | Alu | Name=AluSz6 |
| ADediting_107337 | chr1_37806370_- | SINE | Alu | Name=AluSz6 |
| ADediting_107338 | chr1_37806371_- | SINE | Alu | Name=AluSz6 |
| ADediting_107339 | chr1_37806398_- | SINE | Alu | Name=AluSz6 |
| ADediting_107340 | chr1_37806415_- | SINE | Alu | Name=AluSz6 |
| ADediting_107341 | chr1_37806483_- | SINE | Alu | Name=AluSz6 |
| ADediting_1519815 | chr1_37805121_- | SINE | Alu | Name=AluSz |
| ADediting_1519816 | chr1_37806297_- | SINE | Alu | Name=AluSz6 |
Top |
RNA A-to-I editing events in the alternative splicing sites for YRDC |
| 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 |
Top |
Differntial gene expression between RNA A-to-I edited versus non-edited samples for YRDC |
| 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. |
| - 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. |
| - 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. |
| ADeditome ID | Chr | Positoing | Skipped exon | ENSG | ENSTs |
Top |
Protein coding region RNA A-to-I editings for YRDC |
| - Lollipop plot for RNA A-to-I editings across protein structure. * Click on the image to enlarge it in a new window. |
Top |
The effects of the RNA editing to the miRNA binding sites for YRDC |
| 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 |
| ADediting_1391023 | chr8_140732605_- | ENSG00000196449.4 | ENST00000373044.3 | YRDC-201 | hsa-miR-151a-3p | chr1 | 37803183 | 37803190 | 8mer-1a | 37803183 | 37803202 | 162 | -22.64 |
| 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_843620 | chr2_207754818_+ | ENSG00000196449.4 | ENST00000373044.3 | YRDC-201 | hsa-miR-4775 | chr1 | 37803378 | 37803385 | 8mer-1a | 37803378 | 37803400 | 152 | -12.04 |
| Differentially expressed gene-miRNA network |
Top |
The effects of the RNA editing to the stability of the RNA structures for YRDC |
| - 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 |
Top |
Relation with ADAR for YRDC |
| 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.) |
| DLPFC | ADediting_107324 | chr1_37805020_- | 0.0661954883172813 | 0.104476476393093 | 0.771374853679996 | 0.0165694680763296 | 2.44040492521008e-11 | 0.367364906767151 |
| DLPFC | ADediting_107327 | chr1_37805059_- | 0.188619728854984 | 0.0748660383475857 | 0.892509753730091 | -0.00770583645005264 | 2.54949348577355e-13 | 0.399702354620831 |
| CER | ADediting_107327 | chr1_37805059_- | 2.03307522724504e-06 | 0.376617526773915 | 1.97623037838867e-05 | 0.340806170724817 | 0.202650420701858 | 0.104614118300417 |
| CER | ADediting_107328 | chr1_37805076_- | 0.000104747721659961 | 0.311436410385076 | 0.000103797437595657 | 0.311605415127432 | 0.662686734554818 | -0.0359050052776932 |
| CER | ADediting_107333 | chr1_37806279_- | 0.012349459806207 | 0.203842883197372 | 4.29665394267307e-05 | 0.327502578129292 | 0.667723557463796 | -0.0353347487965868 |
| 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 | 2.59990555652928e-68 | 0.793185196950325 | 5.73171468322266e-61 | 0.765636006890744 | 0.203870095021934 | 0.0723630603025169 |
| AC | 3.70768751644155e-76 | 0.864792387629365 | 2.32381159464821e-52 | 0.779801656222511 | 1.2499031834038e-14 | 0.462109865513106 |
| PCC | 1.16633757986766e-26 | 0.674087370320613 | 1.69510830482835e-31 | 0.71745887350578 | 0.228674094127042 | 0.0875097992573012 |
| CER | 1.367862449482e-27 | 0.742979317275171 | 4.24133913094285e-22 | 0.68491669630166 | 0.143335200155805 | 0.120064598720288 |
| TCX | 7.59155588613393e-40 | 0.832822453076901 | 1.92040936899448e-22 | 0.689002095611598 | 0.353000931231183 | 0.0763629217036251 |
| FP | 2.46933828875118e-12 | 0.493864105285582 | 2.1970250440906e-25 | 0.678782810243108 | 0.764280608657943 | 0.0226323567437833 |
| IFG | 0.000407088782277768 | 0.652553760871422 | 0.00211141662904672 | 0.585383241906122 | 0.728406992771691 | -0.0730984299456804 |
| PG | 6.7012781287716e-33 | 0.735223564585981 | 8.11253640776415e-23 | 0.639951477101054 | 0.215782442213289 | -0.0911869422052012 |
| STG | 8.89272319598817e-16 | 0.739960811679325 | 2.2622361962276e-13 | 0.694877544676672 | 0.371965147850545 | -0.0986525779434473 |
Top |
Relation with AD stages for YRDC |
| 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. |
| IFG | 0.0283624040781513 | -0.438422809265047 |
Top |
RelatedDrugs for YRDC |
| 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 |
Top |
RelatedDiseases for YRDC |
| 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)
|