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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: LINC01237 (CAeditome ID:101927289)

Gene summary for LINC01237

check button Gene summary
Gene informationGene symbol

LINC01237

Gene ID

101927289

Gene namelong intergenic non-protein coding RNA 1237
Synonyms-
Cytomap

2q37.3

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 LINC01237

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: ENSG00000233806.6

check button RNA A-to-I editing events in Cancer.
CAediting_253839(241883507, +), CAediting_253840(241883591, +), CAediting_253841(241884906, +), CAediting_253842(241885020, +), CAediting_253843(241885026, +), CAediting_253844(241890233, +), CAediting_253845(241934128, +), CAediting_253846(241934177, +), CAediting_253847(241971577, +), CAediting_253848(241971608, +), CAediting_253849(241971626, +), CAediting_253850(241971627, +), CAediting_253851(241978836, +), CAediting_253852(241978858, +), CAediting_253853(241978867, +), CAediting_253854(241978868, +), CAediting_253855(241979562, +), CAediting_253856(241980581, +), CAediting_253857(241980608, +), CAediting_253858(241980609, +), CAediting_253859(241980613, +), CAediting_253860(241980617, +), CAediting_253861(241980625, +), CAediting_253862(241980630, +), CAediting_253863(241980633, +), CAediting_253864(241980634, +), CAediting_253865(241980635, +), CAediting_253866(241980639, +), CAediting_253867(241980646, +), CAediting_253868(241980648, +), CAediting_253869(241980654, +), CAediting_253870(241980655, +), CAediting_253871(241980666, +), CAediting_253872(241980682, +), CAediting_253873(241980687, +), CAediting_253874(241980710, +), CAediting_253875(241981608, +), CAediting_253876(241981639, +), CAediting_253877(241981670, +), CAediting_253878(241981671, +), CAediting_253879(241981672, +), CAediting_253880(241981677, +), CAediting_253881(241981679, +), CAediting_253882(241981680, +), CAediting_253883(241981681, +), CAediting_253884(241981684, +), CAediting_253885(241981685, +), CAediting_253886(241981687, +), CAediting_253887(241981691, +), CAediting_253888(241981697, +), CAediting_253889(241981698, +), CAediting_253890(241981699, +), CAediting_253891(241981701, +), CAediting_253892(241981703, +), CAediting_253893(241981708, +), CAediting_253894(241981728, +), CAediting_253895(241981732, +), CAediting_253896(241981741, +), CAediting_253897(241992364, +), CAediting_253898(241995841, +), CAediting_253899(242012981, +), CAediting_253900(242013011, +),

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RNA editing positional annotations for LINC01237 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_253839chr2_241883507_+ncRNA_intronic
CAediting_253840chr2_241883591_+ncRNA_intronic
CAediting_253841chr2_241884906_+ncRNA_intronic
CAediting_253842chr2_241885020_+ncRNA_intronic
CAediting_253843chr2_241885026_+ncRNA_intronic
CAediting_253844chr2_241890233_+ncRNA_intronic
CAediting_253845chr2_241934128_+ncRNA_exonic
CAediting_253846chr2_241934177_+ncRNA_exonic
CAediting_253847chr2_241971577_+ncRNA_intronic
CAediting_253848chr2_241971608_+ncRNA_intronic
CAediting_253849chr2_241971626_+ncRNA_intronic
CAediting_253850chr2_241971627_+ncRNA_intronic
CAediting_253851chr2_241978836_+ncRNA_intronic
CAediting_253852chr2_241978858_+ncRNA_intronic
CAediting_253853chr2_241978867_+ncRNA_intronic
CAediting_253854chr2_241978868_+ncRNA_intronic
CAediting_253855chr2_241979562_+ncRNA_intronic
CAediting_253856chr2_241980581_+ncRNA_intronic
CAediting_253857chr2_241980608_+ncRNA_intronic
CAediting_253858chr2_241980609_+ncRNA_intronic
CAediting_253859chr2_241980613_+ncRNA_intronic
CAediting_253860chr2_241980617_+ncRNA_intronic
CAediting_253861chr2_241980625_+ncRNA_intronic
CAediting_253862chr2_241980630_+ncRNA_intronic
CAediting_253863chr2_241980633_+ncRNA_intronic
CAediting_253864chr2_241980634_+ncRNA_intronic
CAediting_253865chr2_241980635_+ncRNA_intronic
CAediting_253866chr2_241980639_+ncRNA_intronic
CAediting_253867chr2_241980646_+ncRNA_intronic
CAediting_253868chr2_241980648_+ncRNA_intronic
CAediting_253869chr2_241980654_+ncRNA_intronic
CAediting_253870chr2_241980655_+ncRNA_intronic
CAediting_253871chr2_241980666_+ncRNA_intronic
CAediting_253872chr2_241980682_+ncRNA_intronic
CAediting_253873chr2_241980687_+ncRNA_intronic
CAediting_253874chr2_241980710_+ncRNA_intronic
CAediting_253875chr2_241981608_+ncRNA_intronic
CAediting_253876chr2_241981639_+ncRNA_intronic
CAediting_253877chr2_241981670_+ncRNA_intronic
CAediting_253878chr2_241981671_+ncRNA_intronic
CAediting_253879chr2_241981672_+ncRNA_intronic
CAediting_253880chr2_241981677_+ncRNA_intronic
CAediting_253881chr2_241981679_+ncRNA_intronic
CAediting_253882chr2_241981680_+ncRNA_intronic
CAediting_253883chr2_241981681_+ncRNA_intronic
CAediting_253884chr2_241981684_+ncRNA_intronic
CAediting_253885chr2_241981685_+ncRNA_intronic
CAediting_253886chr2_241981687_+ncRNA_intronic
CAediting_253887chr2_241981691_+ncRNA_intronic
CAediting_253888chr2_241981697_+ncRNA_intronic
CAediting_253889chr2_241981698_+ncRNA_intronic
CAediting_253890chr2_241981699_+ncRNA_intronic
CAediting_253891chr2_241981701_+ncRNA_intronic
CAediting_253892chr2_241981703_+ncRNA_intronic
CAediting_253893chr2_241981708_+ncRNA_intronic
CAediting_253894chr2_241981728_+ncRNA_intronic
CAediting_253895chr2_241981732_+ncRNA_intronic
CAediting_253896chr2_241981741_+ncRNA_intronic
CAediting_253897chr2_241992364_+ncRNA_intronic
CAediting_253898chr2_241995841_+ncRNA_intronic
CAediting_253899chr2_242012981_+ncRNA_intronic
CAediting_253900chr2_242013011_+ncRNA_intronic

check button Repat-regional RNA editing(s).
CAeditome IDPositionRepeat familyRepeat sub familyRepeat name
CAediting_253839chr2_241883507_+SINEAluAluY
CAediting_253840chr2_241883591_+SINEAluAluY
CAediting_253841chr2_241884906_+SINEAluAluJo
CAediting_253842chr2_241885020_+SINEAluAluJo
CAediting_253843chr2_241885026_+SINEAluAluJo
CAediting_253844chr2_241890233_+SINEAluAluSx
CAediting_253845chr2_241934128_+SINEAluAluSc
CAediting_253846chr2_241934177_+SINEAluAluSc
CAediting_253847chr2_241971577_+LTRERVL-MaLRMLT1A0
CAediting_253848chr2_241971608_+LTRERVL-MaLRMLT1A0
CAediting_253849chr2_241971626_+LTRERVL-MaLRMLT1A0
CAediting_253850chr2_241971627_+LTRERVL-MaLRMLT1A0
CAediting_253851chr2_241978836_+LTRERVL-MaLRMLT1A
CAediting_253852chr2_241978858_+LTRERVL-MaLRMLT1A
CAediting_253853chr2_241978867_+LTRERVL-MaLRMLT1A
CAediting_253854chr2_241978868_+LTRERVL-MaLRMLT1A
CAediting_253855chr2_241979562_+SINEAluAluSz
CAediting_253874chr2_241980710_+LTRERVL-MaLRMLT1B
CAediting_253897chr2_241992364_+SINEAluAluJb
CAediting_253898chr2_241995841_+SINEAluAluSz

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RNA A-to-I editing events in the alternative splicing sites for LINC01237

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 ENSG00000233806.6.LINC01237.

check button Correlation between RNA A-to-I editing and PSI for ENSG00000233806.6.LINC01237.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for LINC01237

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 LINC01237

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 LINC01237

**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_253846chr2_241934177_+ENSG00000233806.6ENST00000429947.1hsa-miR-4691-3p2419341752419341817mer-m8241934155241934182150-26.36
CAediting_253846chr2_241934177_+ENSG00000233806.6ENST00000430555.4hsa-miR-4691-3p2419341752419341817mer-m8241934155241934182150-26.36
CAediting_253846chr2_241934177_+ENSG00000233806.6ENST00000439601.1hsa-miR-4691-3p2419341752419341817mer-m8241934155241934182150-26.36
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000429947.1hsa-miR-17-3p2419341222419341287mer-m8241934109241934129153-16.35
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000429947.1hsa-miR-485-5p2419341262419341327mer-m8241934112241934133156-19.67
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000429947.1hsa-miR-6042419341252419341306mer241934112241934131140-22.94
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000429947.1hsa-miR-6884-5p2419341262419341327mer-m8241934111241934133150-22.61
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000430555.4hsa-miR-17-3p2419341222419341287mer-m8241934109241934129153-16.35
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000430555.4hsa-miR-485-5p2419341262419341327mer-m8241934112241934133156-19.67
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000430555.4hsa-miR-6042419341252419341306mer241934112241934131140-22.94
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000430555.4hsa-miR-6884-5p2419341262419341327mer-m8241934111241934133150-22.61
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000439601.1hsa-miR-17-3p2419341222419341287mer-m8241934109241934129153-16.35
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000439601.1hsa-miR-485-5p2419341262419341327mer-m8241934112241934133156-19.67
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000439601.1hsa-miR-6042419341252419341306mer241934112241934131140-22.94
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000439601.1hsa-miR-6884-5p2419341262419341327mer-m8241934111241934133150-22.61

check button RNA A-to-I editing in lncRNA lost miRNA binding sites.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000429947.1hsa-miR-60862419341262419341327mer-m8241934113241934133145-17.86
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000430555.4hsa-miR-60862419341262419341327mer-m8241934113241934133145-17.86
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000430555.4hsa-miR-6516-5p2419341222419341287mer-m8241934107241934129147-16.72
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000439601.1hsa-miR-60862419341262419341327mer-m8241934113241934133145-17.86
CAediting_253845chr2_241934128_+ENSG00000233806.6ENST00000439601.1hsa-miR-6516-5p2419341222419341287mer-m8241934107241934129147-16.72

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_+ENSG00000233806.6ENST00000429947.1hsa-miR-605-3p2418819682418819747mer-m8241881954241881975156-21.82
CAediting_688080chr9_63819626_+ENSG00000233806.6ENST00000430555.4hsa-miR-4477b2419660712419660777mer-m8241966055241966078148-12.12
CAediting_688080chr9_63819626_+ENSG00000233806.6ENST00000457686.4hsa-miR-4477b2419660712419660777mer-m8241966055241966078148-12.12
CAediting_688080chr9_63819626_+ENSG00000233806.6ENST00000439601.1hsa-miR-4477b2419660712419660777mer-m8241966055241966078148-12.12
CAediting_580943chr7_100356700_+ENSG00000233806.6ENST00000429947.1hsa-miR-6840-3p2419341372419341437mer-m8241934123241934144140-25.13
CAediting_1229413chr17_67471544_+ENSG00000233806.6ENST00000430555.4hsa-miR-548aa2419662222419662298mer-1a241966205241966229156-16.13
CAediting_396018chr5_1062918_-ENSG00000233806.6ENST00000430555.4hsa-miR-46352419660722419660787mer-m8241966059241966079140-12.65
CAediting_580943chr7_100356700_+ENSG00000233806.6ENST00000430555.4hsa-miR-6840-3p2419341372419341437mer-m8241934123241934144140-25.13
CAediting_1229413chr17_67471544_+ENSG00000233806.6ENST00000457686.4hsa-miR-548aa2419662222419662298mer-1a241966205241966229156-16.13
CAediting_396018chr5_1062918_-ENSG00000233806.6ENST00000457686.4hsa-miR-46352419660722419660787mer-m8241966059241966079140-12.65
CAediting_1229415chr17_67471547_+ENSG00000233806.6ENST00000439601.1hsa-miR-548aa2419340142419340218mer-1a241933996241934021148-9.02
CAediting_396018chr5_1062918_-ENSG00000233806.6ENST00000439601.1hsa-miR-46352419660722419660787mer-m8241966059241966079140-12.65
CAediting_580943chr7_100356700_+ENSG00000233806.6ENST00000439601.1hsa-miR-6840-3p2419341372419341437mer-m8241934123241934144140-25.13

check button RNA A-to-I editing in miRNAs lost binding to lncRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_1229413chr17_67471544_+ENSG00000233806.6ENST00000430555.4hsa-miR-548aa2419663062419663127mer-m8241966289241966313155-11.77
CAediting_1229413chr17_67471544_+ENSG00000233806.6ENST00000457686.4hsa-miR-548aa2419663062419663127mer-m8241966289241966313155-11.77

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 LINC01237

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.
ENST00000429947.1lincRNASoverviewSoverview
ENST00000430555.4lincRNASoverviewSoverview
ENST00000439601.1antisenseSoverviewSoverview

check button RNA A-to-I editing in RNA structures for Minimum free energy (MFE).
CAeditom_IDENSTEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI
CAediting_253845ENST00000429947.1chr2_241934128_+-190.30-190.30-190.00
CAediting_253846ENST00000429947.1chr2_241934177_+-190.00-190.30-190.00
CAediting_253845ENST00000430555.4chr2_241934128_+-309.60-309.40-308.50
CAediting_253846ENST00000430555.4chr2_241934177_+-308.30-309.40-308.50
CAediting_253845ENST00000439601.1chr2_241934128_+-176.60-173.70-176.20
CAediting_253846ENST00000439601.1chr2_241934177_+-173.40-173.70-176.20

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Relation with ADAR for LINC01237

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.)
BRCACAediting_253858chr2_241980609_+0.001841476496873510.238603298261713....
BRCACAediting_253874chr2_241980710_+0.0166112722325640.267110351714471....
BRCACAediting_253875chr2_241981608_+0.04431972514803870.171481837791684....
BRCACAediting_253878chr2_241981671_+0.0005554479736475580.366765495353793....
BRCACAediting_253882chr2_241981680_+....0.02365657548291530.242457841973721
BRCACAediting_253892chr2_241981703_+0.01094027941306080.249787542745518....

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Relation with cancer stages for LINC01237

check button Correlation between Cancer stages and RNA editing frequency
CancerStage_typeCAeditomIDpositionP-valCoeff.
BRCApathologic_stageCAediting_253882chr2_241981680_+0.0110719831915261-0.274301526034588

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Relation with survival for LINC01237

check button Correlation between RNA editing and survival
CancerCAeditomIDpositionKMpvalueCoxpvalueCoxHR

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RelatedDrugs for LINC01237

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 LINC01237

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