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Center for Computational Systems Medicine
Soverview

Gene summary

Soverview

RNA A-to-I events

Soverview

Differntial gene expression between RNA A-to-I edited versus non-edited samples

Soverview

Protein coding region RNA A-to-I editings

Soverview

The effects of the RNA editing to the miRNA binding sites

Soverview

The effects of the RNA editing to the stability of the RNA structures

Soverview

Relation with ADAR

Soverview

Relation with AD stages

Soverview

Related drugs with this gene

Soverview

Related diseases with this gene


Gene summary for VCPKMT

check button Gene summary
Gene informationGene symbol

VCPKMT

Gene ID

79609

Gene namevalosin containing protein lysine methyltransferase
SynonymsC14orf138|METTL21D|VCP-KMT
Cytomap

14q21.3

Type of geneprotein-coding
Descriptionprotein-lysine methyltransferase METTL21DVCP lysine methyltransferasemethyltransferase like 21Dmethyltransferase-like protein 21Dvalosin containing protein lysine (K) methyltransferase
Modification date20200313
UniProtAcc

Q9H867,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
VCPKMT

GO:0018023

peptidyl-lysine trimethylation

22948820


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RNA A-to-I events for VCPKMT

check buttonRNA 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).
all structure

check button RNA editing frequencies across three data sets.
boxplot

check buttonThe number of RNA A-to-I editing events in different types of transcripts (# event, percentage).
boxplot

check button RNA A-to-I editing events in AD.
ADediting_432313(50110011, -), ADediting_432314(50110053, -), ADediting_432315(50110079, -), ADediting_432316(50110131, -), ADediting_432317(50110184, -), ADediting_432318(50110185, -), ADediting_432319(50111695, -), ADediting_432320(50111791, -), ADediting_432321(50111843, -), ADediting_432322(50111853, -), ADediting_432323(50112283, -), ADediting_432324(50112289, -), ADediting_432325(50112294, -), ADediting_432326(50112301, -), ADediting_432327(50112302, -), ADediting_432328(50112303, -), ADediting_432329(50112316, -), ADediting_432330(50112854, -), ADediting_432331(50112884, -), ADediting_432332(50112899, -), ADediting_432333(50112912, -), ADediting_432334(50112920, -), ADediting_432335(50112925, -), ADediting_432336(50112926, -), ADediting_432337(50112961, -), ADediting_432338(50112967, -), ADediting_432339(50112970, -), ADediting_432340(50112981, -), ADediting_432341(50113028, -), ADediting_432342(50113053, -), ADediting_432343(50113058, -), ADediting_432344(50113059, -), ADediting_432345(50113067, -), ADediting_432346(50113081, -), ADediting_432347(50113096, -), ADediting_432348(50113847, -), ADediting_432349(50113872, -), ADediting_432350(50113902, -), ADediting_432351(50114579, -), ADediting_432352(50114591, -), ADediting_432353(50114618, -), ADediting_432354(50114728, -), ADediting_432355(50114738, -), ADediting_432356(50114740, -), ADediting_432357(50114741, -), ADediting_432358(50114762, -), ADediting_432359(50114766, -), ADediting_432360(50114781, -), ADediting_432361(50114787, -), ADediting_432362(50114798, -), ADediting_432363(50114850, -), ADediting_432364(50115249, -), ADediting_432365(50115274, -), ADediting_432366(50115290, -), ADediting_432367(50115317, -), ADediting_432368(50115384, -), ADediting_432369(50115389, -), ADediting_1536850(50109989, -), ADediting_1536851(50110027, -), ADediting_1536852(50110082, -), ADediting_1536853(50110088, -), ADediting_1536854(50110164, -), ADediting_1536855(50110203, -), ADediting_1536856(50111621, -), ADediting_1536857(50111686, -), ADediting_1536858(50112341, -), ADediting_1536859(50112885, -), ADediting_1536860(50112957, -), ADediting_1536861(50114715, -), ADediting_1536862(50114812, -), ADediting_1536863(50114828, -), ADediting_1536864(50115264, -), ADediting_1619131(50114763, -), ADediting_1619132(50114817, -),

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RNA editing positional annotations for VCPKMT using Annovar

check button Protein coding RNA editing(s).
ADeditome IDPositionVariant typeENSTNTchangeAAchangeSIFT_scorePolyphen2_HVAR_scorePROVEAN_pred

check button Gene structure information of RNA editing(s).
ADeditome IDPositionVariant type
ADediting_432313chr14_50110011_-intronic
ADediting_432314chr14_50110053_-intronic
ADediting_432315chr14_50110079_-intronic
ADediting_432316chr14_50110131_-intronic
ADediting_432317chr14_50110184_-intronic
ADediting_432318chr14_50110185_-intronic
ADediting_432319chr14_50111695_-intronic
ADediting_432320chr14_50111791_-intronic
ADediting_432321chr14_50111843_-intronic
ADediting_432322chr14_50111853_-intronic
ADediting_432323chr14_50112283_-intronic
ADediting_432324chr14_50112289_-intronic
ADediting_432325chr14_50112294_-intronic
ADediting_432326chr14_50112301_-intronic
ADediting_432327chr14_50112302_-intronic
ADediting_432328chr14_50112303_-intronic
ADediting_432329chr14_50112316_-intronic
ADediting_432330chr14_50112854_-intronic
ADediting_432331chr14_50112884_-intronic
ADediting_432332chr14_50112899_-intronic
ADediting_432333chr14_50112912_-intronic
ADediting_432334chr14_50112920_-intronic
ADediting_432335chr14_50112925_-intronic
ADediting_432336chr14_50112926_-intronic
ADediting_432337chr14_50112961_-intronic
ADediting_432338chr14_50112967_-intronic
ADediting_432339chr14_50112970_-intronic
ADediting_432340chr14_50112981_-intronic
ADediting_432341chr14_50113028_-intronic
ADediting_432342chr14_50113053_-intronic
ADediting_432343chr14_50113058_-intronic
ADediting_432344chr14_50113059_-intronic
ADediting_432345chr14_50113067_-intronic
ADediting_432346chr14_50113081_-intronic
ADediting_432347chr14_50113096_-intronic
ADediting_432348chr14_50113847_-intronic
ADediting_432349chr14_50113872_-intronic
ADediting_432350chr14_50113902_-intronic
ADediting_432351chr14_50114579_-intronic
ADediting_432352chr14_50114591_-intronic
ADediting_432353chr14_50114618_-intronic
ADediting_432354chr14_50114728_-intronic
ADediting_432355chr14_50114738_-intronic
ADediting_432356chr14_50114740_-intronic
ADediting_432357chr14_50114741_-intronic
ADediting_432358chr14_50114762_-intronic
ADediting_432359chr14_50114766_-intronic
ADediting_432360chr14_50114781_-intronic
ADediting_432361chr14_50114787_-intronic
ADediting_432362chr14_50114798_-intronic
ADediting_432363chr14_50114850_-intronic
ADediting_432364chr14_50115249_-intronic
ADediting_432365chr14_50115274_-intronic
ADediting_432366chr14_50115290_-intronic
ADediting_432367chr14_50115317_-intronic
ADediting_432368chr14_50115384_-intronic
ADediting_432369chr14_50115389_-intronic
ADediting_1536850chr14_50109989_-intronic
ADediting_1536851chr14_50110027_-intronic
ADediting_1536852chr14_50110082_-intronic
ADediting_1536853chr14_50110088_-intronic
ADediting_1536854chr14_50110164_-intronic
ADediting_1536855chr14_50110203_-intronic
ADediting_1536856chr14_50111621_-intronic
ADediting_1536857chr14_50111686_-intronic
ADediting_1536858chr14_50112341_-intronic
ADediting_1536859chr14_50112885_-intronic
ADediting_1536860chr14_50112957_-intronic
ADediting_1536861chr14_50114715_-intronic
ADediting_1536862chr14_50114812_-intronic
ADediting_1536863chr14_50114828_-intronic
ADediting_1536864chr14_50115264_-intronic
ADediting_1619131chr14_50114763_-intronic
ADediting_1619132chr14_50114817_-intronic

check button Repat-regional RNA editing(s).
ADeditome IDPositionRepeat familyRepeat sub familyRepeat name
ADediting_432313chr14_50110011_-SINEAluName=AluSz
ADediting_432314chr14_50110053_-SINEAluName=AluSz
ADediting_432315chr14_50110079_-SINEAluName=AluSz
ADediting_432316chr14_50110131_-SINEAluName=AluSz
ADediting_432317chr14_50110184_-SINEAluName=AluSz
ADediting_432318chr14_50110185_-SINEAluName=AluSz
ADediting_432319chr14_50111695_-SINEAluName=AluJb
ADediting_432320chr14_50111791_-SINEAluName=AluJb
ADediting_432321chr14_50111843_-SINEAluName=AluJb
ADediting_432322chr14_50111853_-SINEAluName=AluJb
ADediting_432323chr14_50112283_-SINEAluName=AluJb
ADediting_432324chr14_50112289_-SINEAluName=AluJb
ADediting_432325chr14_50112294_-SINEAluName=AluJb
ADediting_432326chr14_50112301_-SINEAluName=AluJb
ADediting_432327chr14_50112302_-SINEAluName=AluJb
ADediting_432328chr14_50112303_-SINEAluName=AluJb
ADediting_432329chr14_50112316_-SINEAluName=AluJb
ADediting_432330chr14_50112854_-SINEAluName=AluSg
ADediting_432331chr14_50112884_-SINEAluName=AluSg
ADediting_432332chr14_50112899_-SINEAluName=AluSg
ADediting_432333chr14_50112912_-SINEAluName=AluSg
ADediting_432334chr14_50112920_-SINEAluName=AluSg
ADediting_432335chr14_50112925_-SINEAluName=AluSg
ADediting_432336chr14_50112926_-SINEAluName=AluSg
ADediting_432337chr14_50112961_-SINEAluName=AluSg
ADediting_432338chr14_50112967_-SINEAluName=AluSg
ADediting_432339chr14_50112970_-SINEAluName=AluSg
ADediting_432340chr14_50112981_-SINEAluName=AluSg
ADediting_432341chr14_50113028_-SINEAluName=AluSg
ADediting_432342chr14_50113053_-SINEAluName=AluSg
ADediting_432343chr14_50113058_-SINEAluName=AluSg
ADediting_432344chr14_50113059_-SINEAluName=AluSg
ADediting_432345chr14_50113067_-SINEAluName=AluSg
ADediting_432346chr14_50113081_-SINEAluName=AluSg
ADediting_432347chr14_50113096_-LINEL1Name=L1ME3
ADediting_432348chr14_50113847_-SINEAluName=AluJb
ADediting_432349chr14_50113872_-SINEAluName=AluJb
ADediting_432350chr14_50113902_-SINEAluName=AluJb
ADediting_432351chr14_50114579_-SINEAluName=AluJr4
ADediting_432352chr14_50114591_-SINEAluName=AluJr4
ADediting_432353chr14_50114618_-SINEAluName=AluJr4
ADediting_432354chr14_50114728_-SINEAluName=AluJr4
ADediting_432355chr14_50114738_-SINEAluName=AluJr4
ADediting_432356chr14_50114740_-SINEAluName=AluJr4
ADediting_432357chr14_50114741_-SINEAluName=AluJr4
ADediting_432358chr14_50114762_-SINEAluName=AluJr4
ADediting_432359chr14_50114766_-SINEAluName=AluJr4
ADediting_432360chr14_50114781_-SINEAluName=AluJr4
ADediting_432361chr14_50114787_-SINEAluName=AluJr4
ADediting_432362chr14_50114798_-SINEAluName=AluJr4
ADediting_432363chr14_50114850_-SINEAluName=AluJr4
ADediting_432364chr14_50115249_-SINEAluName=AluSp
ADediting_432365chr14_50115274_-SINEAluName=AluSp
ADediting_432366chr14_50115290_-SINEAluName=AluSp
ADediting_432367chr14_50115317_-SINEAluName=AluSp
ADediting_432368chr14_50115384_-SINEAluName=AluSp
ADediting_432369chr14_50115389_-SINEAluName=AluSp
ADediting_1536850chr14_50109989_-SINEAluName=AluSz
ADediting_1536851chr14_50110027_-SINEAluName=AluSz
ADediting_1536852chr14_50110082_-SINEAluName=AluSz
ADediting_1536853chr14_50110088_-SINEAluName=AluSz
ADediting_1536854chr14_50110164_-SINEAluName=AluSz
ADediting_1536855chr14_50110203_-SINEAluName=AluSz
ADediting_1536856chr14_50111621_-SINEAluName=AluJb
ADediting_1536857chr14_50111686_-SINEAluName=AluJb
ADediting_1536858chr14_50112341_-SINEAluName=AluJb
ADediting_1536859chr14_50112885_-SINEAluName=AluSg
ADediting_1536860chr14_50112957_-SINEAluName=AluSg
ADediting_1536861chr14_50114715_-SINEAluName=AluJr4
ADediting_1536862chr14_50114812_-SINEAluName=AluJr4
ADediting_1536863chr14_50114828_-SINEAluName=AluJr4
ADediting_1536864chr14_50115264_-SINEAluName=AluSp
ADediting_1619131chr14_50114763_-SINEAluName=AluJr4
ADediting_1619132chr14_50114817_-SINEAluName=AluJr4

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RNA A-to-I editing events in the alternative splicing sites for VCPKMT

check button RNA A-to-I editing(s) in the alternative splicing sites.
AStypeADeditomIDEditing positionAS positionAS directionExonic locationWildtype sequenceWildtype splicing strengthRNA edited sequenceRNA edited splicing strength

check button 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 VCPKMT

check button 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.

check button Distribution of the averaged gene isoform expression in AD and control with or without RNA A-to-I editing event.
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check button - 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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check button - 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 IDChrPositoingSkipped exonENSGENSTs

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Protein coding region RNA A-to-I editings for VCPKMT

check button- 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 VCPKMT


check button RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in lncRNA gained miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in lncRNA lost miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to lncRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs lost binding to lncRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_1097295chr3_85385762_+ENSG00000100483.14ENST00000395860.7VCPKMT-202hsa-miR-5688chr1450109271501092777mer-m85010927050109291140-11.1
ADediting_1535951chr14_100874558_+ENSG00000100483.14ENST00000395860.7VCPKMT-202hsa-miR-337-3pchr1450109352501093598mer-1a5010935250109374150-12.38

check button RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_107020chr1_37500952_-ENSG00000100483.14ENST00000395860.7VCPKMT-202hsa-miR-5581-3pchr1450108982501089887mer-m85010898150109002147-16.22
ADediting_1337757chr7_5495852_-ENSG00000100483.14ENST00000395860.7VCPKMT-202hsa-miR-589-3pchr1450108804501088107mer-m85010880350108827145-10.67
ADediting_1643790chr3_121049689_+ENSG00000100483.14ENST00000395860.7VCPKMT-202hsa-miR-5682chr1450108679501086857mer-m85010867850108699149-17.98
ADediting_527135chr16_24203190_+ENSG00000100483.14ENST00000395859.2VCPKMT-201hsa-miR-1273h-3pchr1450109537501095437mer-m85010953750109557143-18.63
ADediting_527135chr16_24203190_+ENSG00000100483.14ENST00000395860.7VCPKMT-202hsa-miR-1273h-3pchr1450109536501095438mer-1a5010953650109557143-18.91
ADediting_98288chr1_32086990_+ENSG00000100483.14ENST00000395860.7VCPKMT-202hsa-miR-5585-3pchr1450109428501094347mer-1a5010942850109451142-17.38
ADediting_98289chr1_32086992_+ENSG00000100483.14ENST00000395860.7VCPKMT-202hsa-miR-5585-3pchr1450109428501094347mer-1a5010942850109451142-17.38

check button Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for VCPKMT

check button - RNA A-to-I editing in mRNA.
* Click on the image to enlarge it in a new window.
ENSTENST typeRNA structure without RNA A-to-I editing.RNA structure with RNA A-to-I editing.

check button RNA A-to-I editing in miRNA.
ADeditom_IDENSTmir_IDEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

check button RNA A-to-I editing in mRNA.
ADeditom_IDENSTEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

check button RNA A-to-I editing in lncRNA.
ADeditom_IDENSTEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

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Relation with ADAR for VCPKMT

check button Correlation between ADAR gene expression and RNA editing frequency
TissueADeditomIDpositionADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)
CERADediting_432322chr14_50111853_-0.002855684505422840.2419444448372610.0001208007827368840.3087788809008010.185115218212499-0.108788209941658
CERADediting_432324chr14_50112289_-0.0003097395281957630.2905621316486896.86025423446675e-050.3191800285462140.73557997021079-0.027801337322577
CERADediting_432326chr14_50112301_-0.0004844605801064150.2814649958563699.35196521021045e-060.3530721673829160.993094763618557-0.000712601278391475
DLPFCADediting_432343chr14_50113058_-0.006133712090866480.1553342144677020.5679002253683940.03256188973834557.77603688162933e-090.320502784038836
CERADediting_432343chr14_50113058_-4.70823684991331e-050.3258944397878652.87971511732134e-050.3344332368398580.7718721013422590.0238687385168735
DLPFCADediting_432344chr14_50113059_-0.0004656159227632990.1976096728080730.1657136460286580.07892167641140433.12450355658266e-100.347587714075672
CERADediting_432344chr14_50113059_-6.37880396860553e-050.3204903076317446.18633005534828e-050.3210402249373390.957711258348268-0.00436605151152075

check button Correlation between ADAR gene expression and this gene's expression
TissueADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)
DLPFC4.4606925828998e-630.7739605537176011.41449439515594e-610.7680708949382360.4917270805464110.0391943661087736
AC1.55596137702672e-610.8181392324775774.57853355080468e-690.8440578458691570.001812134494349090.196348845468055
PCC3.99121503722754e-390.7724920799254372.34583053643252e-560.8571544672699110.6547835537720610.0325580966519506
CER9.25529522419307e-190.6414782921476956.08158341607575e-180.6296640604128580.96987366918725-0.0031096470743901
TCX4.21866000932751e-260.7286240150059241.41996000031453e-310.7771810509020160.0922966476941824-0.137945536540654
FP2.18705315973442e-100.4529073328937016.39222148385268e-200.6152599831881150.147829978032179-0.108919527563707
IFG0.0007136026807384710.631322252806020.0009136834759288670.6214555690952320.560110942386714-0.122360431154893
PG1.46766599913968e-380.7752473291952991.60471151585435e-370.7684644863759240.100519436459146-0.120795205872345
STG2.29513797060233e-120.6731943445421522.11070498522803e-150.7334826782648490.112698037403212-0.174350689924345

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Relation with AD stages for VCPKMT

check button Correlation between AD stages and RNA editing frequency
TissueADeditomIDpositionP-valCoeff.

check button Correlation between AD stages and this gene's expression
TissueP-valCoeff.

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RelatedDrugs for VCPKMT

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for VCPKMT

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource