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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 COG3

check button Gene summary
Gene informationGene symbol

COG3

Gene ID

83548

Gene namecomponent of oligomeric golgi complex 3
SynonymsSEC34
Cytomap

13q14.13

Type of geneprotein-coding
Descriptionconserved oligomeric Golgi complex subunit 3COG complex subunit 3p94tethering factor SEC34vesicle-docking protein SEC34 homolog
Modification date20200313
UniProtAcc

Q96JB2,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
COG3

GO:0006888

ER to Golgi vesicle-mediated transport

11929878

COG3

GO:0006891

intra-Golgi vesicle-mediated transport

11929878


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RNA A-to-I events for COG3

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_400011(45467337, +), ADediting_400012(45473116, +), ADediting_400013(45494194, +), ADediting_400014(45494202, +), ADediting_400015(45494231, +), ADediting_400016(45494246, +), ADediting_400017(45494925, +), ADediting_400018(45495026, +), ADediting_400019(45495029, +), ADediting_400020(45495106, +), ADediting_400021(45495515, +), ADediting_400022(45495517, +), ADediting_400023(45496791, +), ADediting_400024(45496847, +), ADediting_400025(45496880, +), ADediting_400026(45496947, +), ADediting_400027(45497568, +), ADediting_400028(45505129, +), ADediting_400029(45505137, +), ADediting_400030(45507503, +), ADediting_400031(45507581, +), ADediting_400032(45507586, +), ADediting_400033(45507645, +), ADediting_400034(45507884, +), ADediting_400035(45507922, +), ADediting_400036(45507938, +), ADediting_400037(45507975, +), ADediting_400038(45507984, +), ADediting_400039(45509120, +), ADediting_400040(45509133, +), ADediting_400041(45509157, +), ADediting_400042(45509205, +), ADediting_400043(45509242, +), ADediting_400044(45509299, +), ADediting_400045(45516236, +), ADediting_400046(45518316, +), ADediting_400047(45519792, +), ADediting_400048(45520021, +), ADediting_400049(45520050, +), ADediting_400050(45520102, +), ADediting_400051(45520106, +), ADediting_400052(45520110, +), ADediting_400053(45520142, +), ADediting_400054(45520166, +), ADediting_400055(45520168, +), ADediting_400056(45520199, +), ADediting_400057(45520209, +), ADediting_400058(45520217, +), ADediting_400059(45520237, +), ADediting_400060(45520238, +), ADediting_400061(45520243, +), ADediting_400062(45520258, +), ADediting_400063(45521063, +), ADediting_400064(45521907, +), ADediting_1616938(45466124, +), ADediting_1616939(45495447, +), ADediting_1616940(45495501, +), ADediting_1616941(45497529, +), ADediting_1616942(45497582, +), ADediting_1616943(45497598, +), ADediting_1616944(45497679, +), ADediting_1616945(45497751, +), ADediting_1616946(45518304, +), ADediting_1616947(45521932, +), ADediting_1616948(45521942, +), ADediting_1616949(45521944, +), ADediting_1616950(45521975, +), ADediting_1616951(45521988, +),

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RNA editing positional annotations for COG3 using Annovar

check button Protein coding RNA editing(s).
ADeditome IDPositionVariant typeENSTNTchangeAAchangeSIFT_scorePolyphen2_HVAR_scorePROVEAN_pred
ADediting_400045chr13_45516236_+nonsynonymous SNVENST00000349995.10c.A1903Gp.I635V1.00.0060.4

check button Gene structure information of RNA editing(s).
ADeditome IDPositionVariant type
ADediting_400011chr13_45467337_+intronic
ADediting_400012chr13_45473116_+intronic
ADediting_400013chr13_45494194_+intronic
ADediting_400014chr13_45494202_+intronic
ADediting_400015chr13_45494231_+intronic
ADediting_400016chr13_45494246_+intronic
ADediting_400017chr13_45494925_+intronic
ADediting_400018chr13_45495026_+intronic
ADediting_400019chr13_45495029_+intronic
ADediting_400020chr13_45495106_+intronic
ADediting_400021chr13_45495515_+intronic
ADediting_400022chr13_45495517_+intronic
ADediting_400023chr13_45496791_+intronic
ADediting_400024chr13_45496847_+intronic
ADediting_400025chr13_45496880_+intronic
ADediting_400026chr13_45496947_+intronic
ADediting_400027chr13_45497568_+intronic
ADediting_400028chr13_45505129_+intronic
ADediting_400029chr13_45505137_+intronic
ADediting_400030chr13_45507503_+intronic
ADediting_400031chr13_45507581_+intronic
ADediting_400032chr13_45507586_+intronic
ADediting_400033chr13_45507645_+intronic
ADediting_400034chr13_45507884_+intronic
ADediting_400035chr13_45507922_+intronic
ADediting_400036chr13_45507938_+intronic
ADediting_400037chr13_45507975_+intronic
ADediting_400038chr13_45507984_+intronic
ADediting_400039chr13_45509120_+intronic
ADediting_400040chr13_45509133_+intronic
ADediting_400041chr13_45509157_+intronic
ADediting_400042chr13_45509205_+intronic
ADediting_400043chr13_45509242_+intronic
ADediting_400044chr13_45509299_+intronic
ADediting_400045chr13_45516236_+exonic
ADediting_400046chr13_45518316_+intronic
ADediting_400047chr13_45519792_+intronic
ADediting_400048chr13_45520021_+intronic
ADediting_400049chr13_45520050_+intronic
ADediting_400050chr13_45520102_+intronic
ADediting_400051chr13_45520106_+intronic
ADediting_400052chr13_45520110_+intronic
ADediting_400053chr13_45520142_+intronic
ADediting_400054chr13_45520166_+intronic
ADediting_400055chr13_45520168_+intronic
ADediting_400056chr13_45520199_+intronic
ADediting_400057chr13_45520209_+intronic
ADediting_400058chr13_45520217_+intronic
ADediting_400059chr13_45520237_+intronic
ADediting_400060chr13_45520238_+intronic
ADediting_400061chr13_45520243_+intronic
ADediting_400062chr13_45520258_+intronic
ADediting_400063chr13_45521063_+intronic
ADediting_400064chr13_45521907_+intronic
ADediting_1616938chr13_45466124_+intronic
ADediting_1616939chr13_45495447_+intronic
ADediting_1616940chr13_45495501_+intronic
ADediting_1616941chr13_45497529_+intronic
ADediting_1616942chr13_45497582_+intronic
ADediting_1616943chr13_45497598_+intronic
ADediting_1616944chr13_45497679_+intronic
ADediting_1616945chr13_45497751_+intronic
ADediting_1616946chr13_45518304_+intronic
ADediting_1616947chr13_45521932_+intronic
ADediting_1616948chr13_45521942_+intronic
ADediting_1616949chr13_45521944_+intronic
ADediting_1616950chr13_45521975_+intronic
ADediting_1616951chr13_45521988_+intronic

check button Repat-regional RNA editing(s).
ADeditome IDPositionRepeat familyRepeat sub familyRepeat name
ADediting_400011chr13_45467337_+SINEAluName=AluSz6
ADediting_400012chr13_45473116_+SINEAluName=AluY
ADediting_400013chr13_45494194_+SINEAluName=AluSq2
ADediting_400014chr13_45494202_+SINEAluName=AluSq2
ADediting_400015chr13_45494231_+SINEAluName=AluSq2
ADediting_400016chr13_45494246_+SINEAluName=AluSq2
ADediting_400017chr13_45494925_+SINEAluName=AluSc
ADediting_400018chr13_45495026_+SINEAluName=AluSc
ADediting_400019chr13_45495029_+SINEAluName=AluSc
ADediting_400020chr13_45495106_+SINEAluName=AluSc
ADediting_400021chr13_45495515_+SINEAluName=AluJb
ADediting_400022chr13_45495517_+SINEAluName=AluJb
ADediting_400023chr13_45496791_+SINEAluName=AluY
ADediting_400024chr13_45496847_+SINEAluName=AluY
ADediting_400025chr13_45496880_+SINEAluName=AluY
ADediting_400026chr13_45496947_+SINEAluName=AluY
ADediting_400027chr13_45497568_+SINEAluName=AluJb
ADediting_400028chr13_45505129_+SINEAluName=AluSx
ADediting_400029chr13_45505137_+SINEAluName=AluSx
ADediting_400030chr13_45507503_+SINEAluName=AluSz6
ADediting_400031chr13_45507581_+SINEAluName=AluSz6
ADediting_400032chr13_45507586_+SINEAluName=AluSz6
ADediting_400033chr13_45507645_+SINEAluName=AluSz6
ADediting_400034chr13_45507884_+SINEAluName=AluSc8
ADediting_400035chr13_45507922_+SINEAluName=AluSc8
ADediting_400036chr13_45507938_+SINEAluName=AluSc8
ADediting_400037chr13_45507975_+SINEAluName=AluSc8
ADediting_400038chr13_45507984_+SINEAluName=AluSc8
ADediting_400039chr13_45509120_+SINEAluName=AluSx4
ADediting_400040chr13_45509133_+SINEAluName=AluSx4
ADediting_400041chr13_45509157_+SINEAluName=AluSx4
ADediting_400042chr13_45509205_+SINEAluName=AluSx4
ADediting_400043chr13_45509242_+SINEAluName=AluSx4
ADediting_400044chr13_45509299_+SINEAluName=AluSx4
ADediting_400047chr13_45519792_+DNATcMar-TiggerName=MER6B
ADediting_400048chr13_45520021_+SINEAluName=AluJb
ADediting_400049chr13_45520050_+SINEAluName=AluJb
ADediting_400050chr13_45520102_+SINEAluName=AluJb
ADediting_400051chr13_45520106_+SINEAluName=AluJb
ADediting_400052chr13_45520110_+SINEAluName=AluJb
ADediting_400053chr13_45520142_+SINEAluName=AluJb
ADediting_400054chr13_45520166_+SINEAluName=AluJb
ADediting_400055chr13_45520168_+SINEAluName=AluJb
ADediting_400056chr13_45520199_+SINEAluName=AluJb
ADediting_400057chr13_45520209_+SINEAluName=AluJb
ADediting_400058chr13_45520217_+SINEAluName=AluJb
ADediting_400059chr13_45520237_+SINEAluName=AluJb
ADediting_400060chr13_45520238_+SINEAluName=AluJb
ADediting_400061chr13_45520243_+SINEAluName=AluJb
ADediting_400062chr13_45520258_+SINEAluName=AluJb
ADediting_400063chr13_45521063_+SINEAluName=FLAM_A
ADediting_400064chr13_45521907_+SINEAluName=AluSz
ADediting_1616938chr13_45466124_+SINEAluName=AluSx1
ADediting_1616939chr13_45495447_+SINEAluName=AluJb
ADediting_1616940chr13_45495501_+SINEAluName=AluJb
ADediting_1616941chr13_45497529_+SINEAluName=AluJb
ADediting_1616942chr13_45497582_+SINEAluName=AluJb
ADediting_1616943chr13_45497598_+SINEAluName=AluJb
ADediting_1616944chr13_45497679_+SINEAluName=AluJb
ADediting_1616945chr13_45497751_+SINEAluName=AluJb
ADediting_1616947chr13_45521932_+SINEAluName=AluSz
ADediting_1616948chr13_45521942_+SINEAluName=AluSz
ADediting_1616949chr13_45521944_+SINEAluName=AluSz
ADediting_1616950chr13_45521975_+SINEAluName=AluSz
ADediting_1616951chr13_45521988_+SINEAluName=AluSz

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RNA A-to-I editing events in the alternative splicing sites for COG3

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 COG3

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.
boxplot
boxplot
boxplot

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.

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 COG3

check button- Lollipop plot for RNA A-to-I editings across protein structure.
* Click on the image to enlarge it in a new window.
all structure


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The effects of the RNA editing to the miRNA binding sites for COG3


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_1535951chr14_100874558_+ENSG00000136152.15ENST00000349995.10COG3-201hsa-miR-337-3pchr1345534893455348997mer-m84553488145534900153-14.14
ADediting_1631458chr19_40282624_-ENSG00000136152.15ENST00000349995.10COG3-201hsa-miR-641chr1345535633455356397mer-m84553561945535640151-12.82

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_1337758chr7_5495892_-ENSG00000136152.15ENST00000617493.1COG3-206hsa-miR-589-5pchr1345493924454939307mer-m84549391145493931150-14.28
ADediting_1596844chr1_162342605_+ENSG00000136152.15ENST00000349995.10COG3-201hsa-miR-556-3pchr1345536442455364487mer-m84553642645536449152-14.02
ADediting_843620chr2_207754818_+ENSG00000136152.15ENST00000617493.1COG3-206hsa-miR-4775chr1345493695454937017mer-m84549368145493702140-8.91

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 COG3

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.
ENST00000349995.10protein_codingSoverviewSoverview

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
ADediting_400045ENST00000349995.10chr13_45516236_+2001-1303.60-1303.60-1303.60

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

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Relation with ADAR for COG3

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.)
DLPFCADediting_400036chr13_45507938_+0.921285120227184-0.005635037248723380.0111672313916238-0.1439460788234829.665723715922e-240.528889548378269
DLPFCADediting_400039chr13_45509120_+0.819521565084193-0.01301064987161940.0370524771828676-0.1184917211167381.32407477053841e-120.388428951479538
DLPFCADediting_400040chr13_45509133_+0.926724812941709-0.005244485524106410.0299277042877711-0.123334219629086.36287223787634e-180.463585732026371

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.)
DLPFC5.18760461774327e-440.6835022988604315.34738072114084e-390.6525887366142349.69239371590019e-090.318545632205039
AC4.79195565784526e-760.8644908465041431.70605743502815e-550.7938488968697767.80793028763607e-160.480319366244112
PCC1.54692310652631e-310.7177844145886441.02023488572778e-270.684250385052644.44932660273203e-050.290916750172572
CER1.99068557557755e-230.7003285591692389.86384692345737e-090.4469222208465340.804035808205098-0.0204282981434915
TCX2.92174904246575e-300.7665295798148627.672736406594e-080.4217221563334751.32081594776153e-060.382949961497611
FP6.25061133074733e-230.6521031912785411.32621635559843e-300.7274748701078040.03773691364427420.15587526223287
IFG1.27096646415409e-060.8042397689858957.13275464180982e-050.7095348728301350.002987143584013710.569120745241118
PG5.72810163456151e-430.8016004842325471.43080490653333e-320.7326440661292240.626374018116653-0.0359272718260487
STG9.02694988026691e-170.7562260896235721.50472414925942e-150.7360415857356310.2259208986806360.133531863974477

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Relation with AD stages for COG3

check button Correlation between AD stages and RNA editing frequency
TissueADeditomIDpositionP-valCoeff.
TCXADediting_400045chr13_45516236_+4.70151079664097e-080.500414332066747

check button Correlation between AD stages and this gene's expression
TissueP-valCoeff.
TCX0.0001119453673012350.366426915376408

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RelatedDrugs for COG3

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 COG3

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
COG3C0006142Malignant neoplasm of breast1UNIPROT