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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: LINC00624 (CAeditome ID:100289211)

Gene summary for LINC00624

check button Gene summary
Gene informationGene symbol

LINC00624

Gene ID

100289211

Gene namelong intergenic non-protein coding RNA 624
Synonyms-
Cytomap

1q21.1-q21.2

Type of genencRNA
Description-
Modification date20210518
UniProtAcc

.

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 LINC00624

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: ENSG00000278811.3
boxplot

check button RNA A-to-I editing events in Cancer.
CAediting_93205(147299839, -), CAediting_93206(147300305, -), CAediting_93207(147382688, -), CAediting_93208(147382727, -), CAediting_93209(147382733, -), CAediting_93210(147382734, -), CAediting_93211(147382752, -), CAediting_93212(147382778, -), CAediting_93213(147382781, -), CAediting_93214(147382800, -), CAediting_93215(147382802, -), CAediting_93216(147383545, -), CAediting_93217(147383546, -), CAediting_93218(147383553, -), CAediting_93219(147383580, -), CAediting_93220(147383587, -), CAediting_93221(147383590, -), CAediting_93222(147383598, -), CAediting_93223(147383605, -), CAediting_93224(147383618, -), CAediting_93225(147383619, -), CAediting_93226(147490360, -), CAediting_93227(147504034, -), CAediting_93228(147504049, -),

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RNA editing positional annotations for LINC00624 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_93205chr1_147299839_-ncRNA_intronic
CAediting_93206chr1_147300305_-ncRNA_intronic
CAediting_93207chr1_147382688_-ncRNA_exonic
CAediting_93208chr1_147382727_-ncRNA_exonic
CAediting_93209chr1_147382733_-ncRNA_exonic
CAediting_93210chr1_147382734_-ncRNA_exonic
CAediting_93211chr1_147382752_-ncRNA_exonic
CAediting_93212chr1_147382778_-ncRNA_exonic
CAediting_93213chr1_147382781_-ncRNA_exonic
CAediting_93214chr1_147382800_-ncRNA_exonic
CAediting_93215chr1_147382802_-ncRNA_exonic
CAediting_93216chr1_147383545_-ncRNA_exonic
CAediting_93217chr1_147383546_-ncRNA_exonic
CAediting_93218chr1_147383553_-ncRNA_exonic
CAediting_93219chr1_147383580_-ncRNA_exonic
CAediting_93220chr1_147383587_-ncRNA_exonic
CAediting_93221chr1_147383590_-ncRNA_exonic
CAediting_93222chr1_147383598_-ncRNA_exonic
CAediting_93223chr1_147383605_-ncRNA_exonic
CAediting_93224chr1_147383618_-ncRNA_exonic
CAediting_93225chr1_147383619_-ncRNA_exonic
CAediting_93226chr1_147490360_-ncRNA_intronic
CAediting_93227chr1_147504034_-ncRNA_intronic
CAediting_93228chr1_147504049_-ncRNA_intronic

check button Repat-regional RNA editing(s).
CAeditome IDPositionRepeat familyRepeat sub familyRepeat name
CAediting_93205chr1_147299839_-SINEAluAluSx1
CAediting_93206chr1_147300305_-SINEAluAluJo
CAediting_93226chr1_147490360_-SINEAluAluSg
CAediting_93227chr1_147504034_-SINEAluAluY
CAediting_93228chr1_147504049_-SINEAluAluY

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RNA A-to-I editing events in the alternative splicing sites for LINC00624

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

check button Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000278811.3.LINC00624.

check button Correlation between RNA A-to-I editing and PSI for ENSG00000278811.3.LINC00624.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for LINC00624

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.
TGCT.CAediting_93209.ENSG00000278811.LINC00624.png
Soverview

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Protein coding region RNA A-to-I editings for LINC00624

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 LINC00624

**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

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

check button RNA A-to-I editing in lncRNA gained miRNA binding sites.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_93207chr1_147382688_-ENSG00000278811.3ENST00000621316.1hsa-miR-548au-3p1473826861473826927mer-m8147382685147382705155-16.28
CAediting_93207chr1_147382688_-ENSG00000278811.3ENST00000621316.1hsa-miR-9351473826881473826947mer-m8147382687147382710142-9.33
CAediting_93208chr1_147382727_-ENSG00000278811.3ENST00000621316.1hsa-miR-132-5p1473827261473827327mer-m8147382725147382746154-19.76
CAediting_93209chr1_147382733_-ENSG00000278811.3ENST00000621316.1hsa-miR-42511473827331473827397mer-m8147382732147382748140-17.6
CAediting_93209chr1_147382733_-ENSG00000278811.3ENST00000621316.1hsa-miR-43241473827321473827387mer-m8147382731147382752145-13.22
CAediting_93209chr1_147382733_-ENSG00000278811.3ENST00000621316.1hsa-miR-6761-5p1473827331473827386mer147382732147382751140-19.86
CAediting_93211chr1_147382752_-ENSG00000278811.3ENST00000621316.1hsa-miR-451b1473827501473827567mer-m8147382749147382770155-13.42
CAediting_93214chr1_147382800_-ENSG00000278811.3ENST00000621316.1hsa-miR-6867-3p1473827961473828027mer-m8147382795147382817145-14.43
CAediting_93216chr1_147383545_-ENSG00000278811.3ENST00000621316.1hsa-miR-6773-3p1473835451473835517mer-m8147383544147383566149-16.38
CAediting_93218chr1_147383553_-ENSG00000278811.3ENST00000621316.1hsa-miR-136-5p1473835531473835597mer-m8147383552147383576156-18.41
CAediting_93219chr1_147383580_-ENSG00000278811.3ENST00000621316.1hsa-miR-6845-3p1473835751473835817mer-m8147383574147383594140-12.57
CAediting_93220chr1_147383587_-ENSG00000278811.3ENST00000621316.1hsa-miR-2114-3p1473835831473835897mer-m8147383582147383605151-18.3
CAediting_93220chr1_147383587_-ENSG00000278811.3ENST00000621316.1hsa-miR-6819-3p1473835841473835907mer-m8147383583147383603140-11.21
CAediting_93220chr1_147383587_-ENSG00000278811.3ENST00000621316.1hsa-miR-6823-3p1473835831473835897mer-m8147383582147383602150-17.01
CAediting_93220chr1_147383587_-ENSG00000278811.3ENST00000621316.1hsa-miR-6877-3p1473835841473835907mer-m8147383583147383603140-12.03
CAediting_93222chr1_147383598_-ENSG00000278811.3ENST00000621316.1hsa-miR-6768-5p1473835951473836017mer-m8147383594147383616142-15.28
CAediting_93223chr1_147383605_-ENSG00000278811.3ENST00000621316.1hsa-miR-51881473836021473836098mer-1a147383602147383624155-14.21

check button RNA A-to-I editing in lncRNA lost miRNA binding sites.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_93207chr1_147382688_-ENSG00000278811.3ENST00000621316.1hsa-miR-1229-5p1473826831473826908mer-1a147382683147382706140-14.87
CAediting_93218chr1_147383553_-ENSG00000278811.3ENST00000621316.1hsa-miR-23a-3p1473835481473835547mer-m8147383547147383566147-13.83
CAediting_93218chr1_147383553_-ENSG00000278811.3ENST00000621316.1hsa-miR-23b-3p1473835481473835547mer-m8147383547147383567148-13.83
CAediting_93222chr1_147383598_-ENSG00000278811.3ENST00000621316.1hsa-miR-331-5p1473835981473836047mer-m8147383597147383619143-12.02
CAediting_93208chr1_147382727_-ENSG00000278811.3ENST00000621316.1hsa-miR-4474-3p1473827271473827337mer-m8147382726147382744151-21.02
CAediting_93223chr1_147383605_-ENSG00000278811.3ENST00000621316.1hsa-miR-4520-2-3p1473836041473836107mer-m8147383603147383624142-12.21
CAediting_93223chr1_147383605_-ENSG00000278811.3ENST00000621316.1hsa-miR-5681b1473836001473836067mer-m8147383599147383619144-13.85

check button RNA A-to-I editing in miRNAs gained binding to lncRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_748296chr10_51299626_+ENSG00000278811.3ENST00000621316.1hsa-miR-605-3p1475178531475178597mer-m8147517852147517873140-16.84
CAediting_846604chr11_93733708_-ENSG00000278811.3ENST00000621316.1hsa-miR-1304-3p1475174791475174868mer-1a147517479147517500150-18.31
CAediting_748296chr10_51299626_+ENSG00000278811.3ENST00000619867.3hsa-miR-605-3p1475178531475178597mer-m8147517852147517873140-16.84
CAediting_846604chr11_93733708_-ENSG00000278811.3ENST00000619867.3hsa-miR-1304-3p1475174791475174868mer-1a147517479147517500150-18.31
CAediting_1351755chr19_40282625_-ENSG00000278811.3ENST00000621316.1hsa-miR-6411473838341473838407mer-m8147383833147383854159-21.11
CAediting_1399425chr20_1392958_-ENSG00000278811.3ENST00000621316.1hsa-miR-6869-5p1473826831473826908mer-1a147382683147382704148-16.3
CAediting_228905chr2_188297554_+ENSG00000278811.3ENST00000621316.1hsa-miR-561-3p1475175831475175897mer-m8147517582147517601146-17.28
CAediting_442554chr5_154685830_+ENSG00000278811.3ENST00000621316.1hsa-miR-13031473842061473842127mer-m8147384205147384228141-12.98
CAediting_573001chr7_92204086_-ENSG00000278811.3ENST00000621316.1hsa-miR-1285-5p1475176111475176177mer-m8147517610147517630146-26.86
CAediting_228905chr2_188297554_+ENSG00000278811.3ENST00000619867.3hsa-miR-561-3p1475175831475175897mer-m8147517582147517601146-17.28
CAediting_442554chr5_154685830_+ENSG00000278811.3ENST00000619867.3hsa-miR-13031472604771472604837mer-m8147260476147260495156-18.46
CAediting_573001chr7_92204086_-ENSG00000278811.3ENST00000619867.3hsa-miR-1285-5p1475176111475176177mer-m8147517610147517630146-26.86
CAediting_1524209chrX_134546392_-ENSG00000278811.3ENST00000621316.1hsa-miR-503-5p1475178561475178616mer147517855147517875152-26.57
CAediting_1524209chrX_134546392_-ENSG00000278811.3ENST00000619867.3hsa-miR-503-5p1475178561475178616mer147517855147517875152-26.57

check button RNA A-to-I editing in miRNAs lost binding to lncRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_1306324chr19_13836464_-ENSG00000278811.3ENST00000621316.1hsa-miR-27a-3p1475155341475155407mer-m8147515533147515553146-13.92
CAediting_1306323chr19_13836462_-ENSG00000278811.3ENST00000621316.1hsa-miR-27a-3p1475155341475155407mer-m8147515533147515553146-13.92
CAediting_688080chr9_63819626_+ENSG00000278811.3ENST00000621316.1hsa-miR-4477b1473840701473840767mer-m8147384069147384092151-15.34
CAediting_1524209chrX_134546392_-ENSG00000278811.3ENST00000621316.1hsa-miR-503-5p1475177981475178036mer147517794147517816147-18.23
CAediting_1524209chrX_134546392_-ENSG00000278811.3ENST00000621316.1hsa-miR-503-5p1475177951475178006mer147517794147517816147-18.23
CAediting_1229414chr17_67471546_+ENSG00000278811.3ENST00000621316.1hsa-miR-548aa1473841521473841587mer-m8147384151147384175149-8.69
CAediting_1229413chr17_67471544_+ENSG00000278811.3ENST00000621316.1hsa-miR-548aa1473841521473841587mer-m8147384151147384175149-8.69
CAediting_1229415chr17_67471547_+ENSG00000278811.3ENST00000621316.1hsa-miR-548aa1473841521473841587mer-m8147384151147384175149-8.69
CAediting_748296chr10_51299626_+ENSG00000278811.3ENST00000621316.1hsa-miR-605-3p1475177331475177397mer-m8147517732147517751147-16.31
CAediting_748296chr10_51299626_+ENSG00000278811.3ENST00000621316.1hsa-miR-605-3p1475156151475156217mer-m8147515614147515635144-15.24
CAediting_980496chr14_31014685_-ENSG00000278811.3ENST00000621316.1hsa-miR-624-3p1473825551473825606mer147382554147382572146-16.81
CAediting_980496chr14_31014685_-ENSG00000278811.3ENST00000621316.1hsa-miR-624-3p1473823391473823457mer-m8147382338147382358143-9.85
CAediting_1306324chr19_13836464_-ENSG00000278811.3ENST00000619867.3hsa-miR-27a-3p1472597551472597617mer-m8147259754147259774140-10.86
CAediting_1306323chr19_13836462_-ENSG00000278811.3ENST00000619867.3hsa-miR-27a-3p1472597551472597617mer-m8147259754147259774140-10.86
CAediting_1306324chr19_13836464_-ENSG00000278811.3ENST00000619867.3hsa-miR-27a-3p1475155341475155407mer-m8147515533147515553146-13.92
CAediting_1306323chr19_13836462_-ENSG00000278811.3ENST00000619867.3hsa-miR-27a-3p1475155341475155407mer-m8147515533147515553146-13.92
CAediting_1524209chrX_134546392_-ENSG00000278811.3ENST00000619867.3hsa-miR-503-5p1475177981475178036mer147517794147517816147-18.23
CAediting_1524209chrX_134546392_-ENSG00000278811.3ENST00000619867.3hsa-miR-503-5p1475177951475178006mer147517794147517816147-18.23
CAediting_748296chr10_51299626_+ENSG00000278811.3ENST00000619867.3hsa-miR-605-3p1475177331475177397mer-m8147517732147517751147-16.31
CAediting_748296chr10_51299626_+ENSG00000278811.3ENST00000619867.3hsa-miR-605-3p1475156151475156217mer-m8147515614147515635144-15.24

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

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

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 LINC00624

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.
ENST00000621316.1antisenseSoverviewSoverview

check button RNA A-to-I editing in RNA structures for Minimum free energy (MFE).
CAeditom_IDENSTEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI
CAediting_93207ENST00000621316.1chr1_147382688_--948.17-948.17-957.87
CAediting_93208ENST00000621316.1chr1_147382727_--948.17-948.17-957.87
CAediting_93209ENST00000621316.1chr1_147382733_--947.87-948.17-957.87
CAediting_93210ENST00000621316.1chr1_147382734_--947.87-948.17-957.87
CAediting_93211ENST00000621316.1chr1_147382752_--948.17-948.17-957.87
CAediting_93212ENST00000621316.1chr1_147382778_--947.77-948.17-957.87
CAediting_93213ENST00000621316.1chr1_147382781_--951.27-948.17-957.87
CAediting_93214ENST00000621316.1chr1_147382800_--947.17-948.17-957.87
CAediting_93215ENST00000621316.1chr1_147382802_--947.87-948.17-957.87
CAediting_93216ENST00000621316.1chr1_147383545_--948.07-948.17-957.87
CAediting_93217ENST00000621316.1chr1_147383546_--951.47-948.17-957.87
CAediting_93218ENST00000621316.1chr1_147383553_--945.17-948.17-957.87
CAediting_93219ENST00000621316.1chr1_147383580_--947.87-948.17-957.87
CAediting_93220ENST00000621316.1chr1_147383587_--947.87-948.17-957.87
CAediting_93221ENST00000621316.1chr1_147383590_--947.27-948.17-957.87
CAediting_93222ENST00000621316.1chr1_147383598_--954.37-948.17-957.87
CAediting_93223ENST00000621316.1chr1_147383605_--951.57-948.17-957.87
CAediting_93224ENST00000621316.1chr1_147383618_--948.17-948.17-957.87
CAediting_93225ENST00000621316.1chr1_147383619_--948.27-948.17-957.87

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Relation with ADAR for LINC00624

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.)

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Relation with cancer stages for LINC00624

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

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Relation with survival for LINC00624

check button Correlation between RNA editing and survival
CancerCAeditomIDpositionKMpvalueCoxpvalueCoxHR

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RelatedDrugs for LINC00624

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 LINC00624

check button Diseases associated with this gene.
(DisGeNet 7.0)
GeneDisease IDDisease name# pubmedsSource