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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 tumor samples versus normal 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 cancer stages

Soverview

Relation with survival state

Soverview

Related drugs with this gene

Soverview

Related diseases with this gene

Editing gene: COL28A1 (CAeditome ID:340267)

Gene summary for COL28A1

check button Gene summary
Gene informationGene symbol

COL28A1

Gene ID

340267

Gene namecollagen type XXVIII alpha 1 chain
SynonymsCOL28
Cytomap

7p21.3

Type of geneprotein-coding
Descriptioncollagen alpha-1(XXVIII) chaincollagen, type XXVIII, alpha 1
Modification date20210518
UniProtAcc

Q2UY09

Context

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

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RNA A-to-I events for COL28A1

check buttonRNA A-to-I editing events across TCGA 33 cancers data sets based on Ensembl gene isoform structure.
all structure

check button RNA editing frequencies across 33 cancers of gene: ENSG00000215018.8
boxplot

check button RNA A-to-I editing events in Cancer.
CAediting_528065(7356738, -), CAediting_528066(7357079, -), CAediting_528067(7357102, -), CAediting_528068(7357115, -), CAediting_528069(7357117, -), CAediting_528070(7357118, -), CAediting_528071(7357122, -), CAediting_528072(7357124, -), CAediting_528073(7357126, -), CAediting_528074(7357135, -), CAediting_528075(7357138, -), CAediting_528076(7357155, -), CAediting_528077(7357161, -), CAediting_528078(7357165, -), CAediting_528079(7357178, -), CAediting_528080(7357182, -), CAediting_528081(7357187, -), CAediting_528082(7357188, -), CAediting_528083(7357214, -), CAediting_528084(7357217, -), CAediting_528085(7357218, -), CAediting_528086(7357219, -), CAediting_528087(7357220, -), CAediting_528088(7357223, -), CAediting_528089(7357225, -), CAediting_528090(7357226, -), CAediting_528091(7357229, -), CAediting_528092(7357232, -), CAediting_528093(7357245, -), CAediting_528094(7357246, -), CAediting_528095(7357266, -), CAediting_528096(7357268, -), CAediting_528097(7357277, -), CAediting_528098(7357282, -), CAediting_528099(7357306, -), CAediting_528100(7357314, -), CAediting_528101(7357317, -), CAediting_528102(7357322, -), CAediting_528103(7357323, -), CAediting_528104(7357402, -), CAediting_528105(7357404, -), CAediting_528106(7357409, -), CAediting_528107(7357416, -), CAediting_528108(7357417, -), CAediting_528109(7357458, -), CAediting_528110(7357479, -), CAediting_528111(7357485, -), CAediting_528112(7357486, -), CAediting_528113(7357487, -), CAediting_528114(7357493, -), CAediting_528115(7357496, -), CAediting_528116(7357502, -), CAediting_528117(7357510, -), CAediting_528118(7357511, -), CAediting_528119(7357515, -), CAediting_528120(7357524, -), CAediting_528121(7357535, -), CAediting_528122(7357537, -), CAediting_528123(7357559, -), CAediting_528124(7357572, -), CAediting_528125(7357576, -), CAediting_528126(7357577, -), CAediting_528127(7357596, -), CAediting_528128(7357607, -), CAediting_528129(7357612, -), CAediting_528130(7357621, -), CAediting_528131(7357626, -), CAediting_528132(7357633, -), CAediting_528133(7357653, -),

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RNA editing positional annotations for COL28A1 using Annovar

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

check button Gene structure information of RNA editing(s).
CAeditome IDPositionVariant type
CAediting_528065chr7_7356738_-UTR3
CAediting_528066chr7_7357079_-UTR3
CAediting_528067chr7_7357102_-intronic
CAediting_528068chr7_7357115_-intronic
CAediting_528069chr7_7357117_-intronic
CAediting_528070chr7_7357118_-intronic
CAediting_528071chr7_7357122_-intronic
CAediting_528072chr7_7357124_-intronic
CAediting_528073chr7_7357126_-intronic
CAediting_528074chr7_7357135_-intronic
CAediting_528075chr7_7357138_-intronic
CAediting_528076chr7_7357155_-intronic
CAediting_528077chr7_7357161_-intronic
CAediting_528078chr7_7357165_-intronic
CAediting_528079chr7_7357178_-intronic
CAediting_528080chr7_7357182_-intronic
CAediting_528081chr7_7357187_-intronic
CAediting_528082chr7_7357188_-intronic
CAediting_528083chr7_7357214_-intronic
CAediting_528084chr7_7357217_-intronic
CAediting_528085chr7_7357218_-intronic
CAediting_528086chr7_7357219_-intronic
CAediting_528087chr7_7357220_-intronic
CAediting_528088chr7_7357223_-intronic
CAediting_528089chr7_7357225_-intronic
CAediting_528090chr7_7357226_-intronic
CAediting_528091chr7_7357229_-intronic
CAediting_528092chr7_7357232_-intronic
CAediting_528093chr7_7357245_-intronic
CAediting_528094chr7_7357246_-intronic
CAediting_528095chr7_7357266_-intronic
CAediting_528096chr7_7357268_-intronic
CAediting_528097chr7_7357277_-intronic
CAediting_528098chr7_7357282_-intronic
CAediting_528099chr7_7357306_-intronic
CAediting_528100chr7_7357314_-intronic
CAediting_528101chr7_7357317_-intronic
CAediting_528102chr7_7357322_-intronic
CAediting_528103chr7_7357323_-intronic
CAediting_528104chr7_7357402_-intronic
CAediting_528105chr7_7357404_-intronic
CAediting_528106chr7_7357409_-intronic
CAediting_528107chr7_7357416_-intronic
CAediting_528108chr7_7357417_-intronic
CAediting_528109chr7_7357458_-intronic
CAediting_528110chr7_7357479_-intronic
CAediting_528111chr7_7357485_-intronic
CAediting_528112chr7_7357486_-intronic
CAediting_528113chr7_7357487_-intronic
CAediting_528114chr7_7357493_-intronic
CAediting_528115chr7_7357496_-intronic
CAediting_528116chr7_7357502_-intronic
CAediting_528117chr7_7357510_-intronic
CAediting_528118chr7_7357511_-intronic
CAediting_528119chr7_7357515_-intronic
CAediting_528120chr7_7357524_-intronic
CAediting_528121chr7_7357535_-intronic
CAediting_528122chr7_7357537_-intronic
CAediting_528123chr7_7357559_-intronic
CAediting_528124chr7_7357572_-intronic
CAediting_528125chr7_7357576_-intronic
CAediting_528126chr7_7357577_-intronic
CAediting_528127chr7_7357596_-intronic
CAediting_528128chr7_7357607_-intronic
CAediting_528129chr7_7357612_-intronic
CAediting_528130chr7_7357621_-intronic
CAediting_528131chr7_7357626_-intronic
CAediting_528132chr7_7357633_-UTR3
CAediting_528133chr7_7357653_-UTR3

check button Repat-regional RNA editing(s).
CAeditome IDPositionRepeat familyRepeat sub familyRepeat name
CAediting_528065chr7_7356738_-LINEL1L1PA4
CAediting_528066chr7_7357079_-SINEAluAluSx
CAediting_528067chr7_7357102_-SINEAluAluSx
CAediting_528068chr7_7357115_-SINEAluAluSx
CAediting_528069chr7_7357117_-SINEAluAluSx
CAediting_528070chr7_7357118_-SINEAluAluSx
CAediting_528071chr7_7357122_-SINEAluAluSx
CAediting_528072chr7_7357124_-SINEAluAluSx
CAediting_528073chr7_7357126_-SINEAluAluSx
CAediting_528074chr7_7357135_-SINEAluAluSx
CAediting_528075chr7_7357138_-SINEAluAluSx
CAediting_528076chr7_7357155_-SINEAluAluSx
CAediting_528077chr7_7357161_-SINEAluAluSx
CAediting_528078chr7_7357165_-SINEAluAluSx
CAediting_528079chr7_7357178_-SINEAluAluSx
CAediting_528080chr7_7357182_-SINEAluAluSx
CAediting_528081chr7_7357187_-SINEAluAluSx
CAediting_528082chr7_7357188_-SINEAluAluSx
CAediting_528083chr7_7357214_-SINEAluAluSx
CAediting_528084chr7_7357217_-SINEAluAluSx
CAediting_528085chr7_7357218_-SINEAluAluSx
CAediting_528086chr7_7357219_-SINEAluAluSx
CAediting_528087chr7_7357220_-SINEAluAluSx
CAediting_528088chr7_7357223_-SINEAluAluSx
CAediting_528089chr7_7357225_-SINEAluAluSx
CAediting_528090chr7_7357226_-SINEAluAluSx
CAediting_528091chr7_7357229_-SINEAluAluSx
CAediting_528092chr7_7357232_-SINEAluAluSx
CAediting_528093chr7_7357245_-SINEAluAluSx
CAediting_528094chr7_7357246_-SINEAluAluSx
CAediting_528095chr7_7357266_-SINEAluAluSx
CAediting_528096chr7_7357268_-SINEAluAluSx
CAediting_528097chr7_7357277_-SINEAluAluSx
CAediting_528098chr7_7357282_-SINEAluAluSx
CAediting_528099chr7_7357306_-SINEAluAluSx
CAediting_528100chr7_7357314_-SINEAluAluSx
CAediting_528101chr7_7357317_-SINEAluAluSx
CAediting_528102chr7_7357322_-SINEAluAluSx
CAediting_528103chr7_7357323_-SINEAluAluSx
CAediting_528104chr7_7357402_-SINEAluAluSg
CAediting_528105chr7_7357404_-SINEAluAluSg
CAediting_528106chr7_7357409_-SINEAluAluSg
CAediting_528107chr7_7357416_-SINEAluAluSg
CAediting_528108chr7_7357417_-SINEAluAluSg
CAediting_528109chr7_7357458_-SINEAluAluSg
CAediting_528110chr7_7357479_-SINEAluAluSg
CAediting_528111chr7_7357485_-SINEAluAluSg
CAediting_528112chr7_7357486_-SINEAluAluSg
CAediting_528113chr7_7357487_-SINEAluAluSg
CAediting_528114chr7_7357493_-SINEAluAluSg
CAediting_528115chr7_7357496_-SINEAluAluSg
CAediting_528116chr7_7357502_-SINEAluAluSg
CAediting_528117chr7_7357510_-SINEAluAluSg
CAediting_528118chr7_7357511_-SINEAluAluSg
CAediting_528119chr7_7357515_-SINEAluAluSg
CAediting_528120chr7_7357524_-SINEAluAluSg
CAediting_528121chr7_7357535_-SINEAluAluSg
CAediting_528122chr7_7357537_-SINEAluAluSg
CAediting_528123chr7_7357559_-SINEAluAluSg
CAediting_528124chr7_7357572_-SINEAluAluSg
CAediting_528125chr7_7357576_-SINEAluAluSg
CAediting_528126chr7_7357577_-SINEAluAluSg
CAediting_528127chr7_7357596_-SINEAluAluSg
CAediting_528128chr7_7357607_-SINEAluAluSg
CAediting_528129chr7_7357612_-SINEAluAluSg
CAediting_528130chr7_7357621_-SINEAluAluSg
CAediting_528131chr7_7357626_-SINEAluAluSg
CAediting_528132chr7_7357633_-SINEAluAluSg
CAediting_528133chr7_7357653_-SINEAluAluSg

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RNA A-to-I editing events in the alternative splicing sites for COL28A1

check button RNA A-to-I editing(s) in the alternative splicing sites.
AStypeCAeditomIDEditing positionAS positionAS directionExonic locationWildtype sequenceWildtype splicing strengthRNA edited sequenceRNA edited splicing strength
IRCAediting_528067chr7_7357102_-7357093:73571153SS0+7iATTGCCCCACTGCACTCCAGCCT2.53ATTGCCCCACTGCGCTCCAGCCT2.69
IRCAediting_528068chr7_7357115_-7357093:73571153SS0+20iATTGCCCCACTGCACTCCAGCCT2.53GTTGCCCCACTGCACTCCAGCCT1.9
IRCAediting_528131chr7_7357626_-7357625:73576335SS0+5iAGGCTGGAG-12.94AGGCTGGGG-6.07
IRCAediting_528132chr7_7357633_-7357625:73576335SS3+0iAGGCTGGAG-12.94GGGCTGGAG-15.85

check button Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000215018.8.COL28A1.
boxplot

check button Correlation between RNA A-to-I editing and PSI for ENSG00000215018.8.COL28A1.
boxplot

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for COL28A1

check button Differential gene expressions between RNA A-to-I edited and non-edited tumor samples.
* The grey color means N/A.
boxplot

check button Correlation between RNA A-to-I editing and gene expression.
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.

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Protein coding region RNA A-to-I editings for COL28A1

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 COL28A1

**If you are searching a miRNA gene with RNA editing events in its seed regions, please see the search pages of miRNA targets to discover the effects of this RNA editing event to miRNA regulations. For more information, please check the files in the Download page.

check button RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_528066chr7_7357079_-ENSG00000215018.8ENST00000430711hsa-miR-6838-3p735707573570817mer-m873570747357092160.00-19.68

check button RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_528133chr7_7357653_-ENSG00000215018.8ENST00000430711hsa-miR-3120-5p735765173576588mer-1a73576517357671142-10.39
CAediting_528133chr7_7357653_-ENSG00000215018.8ENST00000430711hsa-miR-4743-3p735765073576567mer-m873576497357669145-11.21
CAediting_528133chr7_7357653_-ENSG00000215018.8ENST00000430711hsa-miR-4778-5p735764973576557mer-m873576487357671155-17.97
CAediting_528133chr7_7357653_-ENSG00000215018.8ENST00000430711hsa-miR-6888-3p735765073576578mer-1a73576507357670142-8.83
CAediting_528066chr7_7357079_-ENSG00000215018.8ENST00000430711hsa-miR-431-5p735707673570816mer73570757357093147-17.55

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

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

check button RNA A-to-I editing in miRNAs gained binding to lncRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs lost binding to lncRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_688081chr9_63819627_+ENSG00000215018.8ENST00000430711hsa-miR-4477b735822973582357mer-m873582287358249152-12.91
CAediting_688081chr9_63819627_+ENSG00000215018.8ENST00000430711hsa-miR-4477b735858873585947mer-m873585877358608163-16.54
CAediting_688081chr9_63819627_+ENSG00000215018.8ENST00000399429hsa-miR-4477b735822973582357mer-m873582287358249152-12.91
CAediting_688081chr9_63819627_+ENSG00000215018.8ENST00000399429hsa-miR-4477b735858873585947mer-m873585877358608163-16.54
CAediting_524911chr7_5495852_-ENSG00000215018.8ENST00000430711hsa-miR-589-3p735764073576467mer-m873576397357663153-15.63
CAediting_1229413chr17_67471544_+ENSG00000215018.8ENST00000430711hsa-miR-548aa735656173565677mer-m873565607356582155-14.19
CAediting_1368054chr19_46709310_-ENSG00000215018.8ENST00000430711hsa-miR-320e735636273563687mer-m873563617356378152-21.43
CAediting_86358chr1_109598906_+ENSG00000215018.8ENST00000430711hsa-miR-197-5p735669573567006mer73566947356715146-31.73
CAediting_228905chr2_188297554_+ENSG00000215018.8ENST00000430711hsa-miR-561-3p735626773562748mer-1a73562677356287150-8.34
CAediting_86358chr1_109598906_+ENSG00000215018.8ENST00000453441hsa-miR-197-5p735669573567006mer73566947356715146-31.73
CAediting_117844chr1_162342605_+ENSG00000215018.8ENST00000444268hsa-miR-556-3p750601575060228mer-1a75060157506037151-13.08

check button RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_524911chr7_5495852_-ENSG00000215018.8ENST00000430711hsa-miR-589-3p735771073577167mer-1a73577107357732148-29.02
CAediting_1368054chr19_46709310_-ENSG00000215018.8ENST00000430711hsa-miR-320e735655573565617mer-m873565547356571141-11.28
CAediting_1229413chr17_67471544_+ENSG00000215018.8ENST00000430711hsa-miR-548aa735659773566037mer-m873565967356623152-12.04

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 COL28A1

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.
ENST00000430711.4nonsense_mediated_decaySoverviewSoverview
ENST00000453441.1protein_codingSoverviewSoverview

check button RNA A-to-I editing in RNA structures for Minimum free energy (MFE).
CAeditom_IDENSTEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI
CAediting_528065ENST00000430711.4chr7_7356738_--640.70-641.00-639.30
CAediting_528066ENST00000430711.4chr7_7357079_--640.70-641.00-639.30
CAediting_528132ENST00000430711.4chr7_7357633_--640.60-641.00-639.30
CAediting_528133ENST00000430711.4chr7_7357653_--640.30-641.00-639.30
CAediting_528065ENST00000453441.1chr7_7356738_--180.80-181.10-180.80

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Relation with ADAR for COL28A1

check button Correlation between ADAR gene expression and RNA editing frequency
CancerCAeditomIDpositionADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)
GBMCAediting_528069chr7_7357117_-0.000363912691339870.384348140379349....
LGGCAediting_528070chr7_7357118_-0.003959029615020670.216771453608982....
LUADCAediting_528070chr7_7357118_-0.01604008516962860.299945885190786....
GBMCAediting_528070chr7_7357118_-0.0001829417027372790.380498735771824....
LGGCAediting_528079chr7_7357178_-2.98177116963933e-050.395423615238142....
GBMCAediting_528079chr7_7357178_-0.004337046998474970.339352257450187....
LGGCAediting_528081chr7_7357187_-0.0006435757620602920.398050575930411....
LGGCAediting_528083chr7_7357214_-0.0004204435657195190.389722478860548....
GBMCAediting_528083chr7_7357214_-0.00471168378530420.348963054677167....
GBMCAediting_528094chr7_7357246_-0.04122996376113240.286899536529748....
LGGCAediting_528103chr7_7357323_-0.02883226093262990.297633364083671....
LGGCAediting_528107chr7_7357416_-0.00145078626432330.368432029823346....
GBMCAediting_528107chr7_7357416_-0.01754035193156760.30568554243395....
GBMCAediting_528114chr7_7357493_-0.03163484409622730.271084316237181....
GBMCAediting_528115chr7_7357496_-..0.02854242287949160.29815006181944..
GBMCAediting_528122chr7_7357537_-0.0201646485252930.324509307651419....
LGGCAediting_528125chr7_7357576_-0.002853567755669770.321606437312426....
GBMCAediting_528125chr7_7357576_-0.01841048290583570.273436321361154....
LGGCAediting_528128chr7_7357607_-0.01485776811422380.25056724542012....
GBMCAediting_528128chr7_7357607_-0.005482289924221440.338181059569439....

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Relation with cancer stages for COL28A1

check button Correlation between Cancer stages and RNA editing frequency
CancerStage_typeCAeditomIDpositionP-valCoeff.

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Relation with survival for COL28A1

check button Correlation between RNA editing and survival
CancerCAeditomIDpositionKMpvalueCoxpvalueCoxHR
LGGCAediting_528070chr7_7357118_-0.03793967048759660.04853840.134466
GBMCAediting_528094chr7_7357246_-0.005883134999306480.011430954.1662
GBMCAediting_528122chr7_7357537_-0.03853691209524150.021926855.2988

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RelatedDrugs for COL28A1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.8 2021-01-03)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for COL28A1

check button Diseases associated with this gene.
(DisGeNet 7.0)
GeneDisease IDDisease name# pubmedsSource
COL28A1C0236733Amphetamine-Related Disorders1CTD_human
COL28A1C0236804Amphetamine Addiction1CTD_human
COL28A1C0236807Amphetamine Abuse1CTD_human