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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: HM13-IT1 (CAeditome ID:106480432)

Gene summary for HM13-IT1

check button Gene summary
Gene informationGene symbol

HM13-IT1

Gene ID

106480432

Gene nameHM13 intronic transcript 1
Synonyms-
Cytomap

20q11.21

Type of genencRNA
DescriptionHM13 intronic transcript 1 (non-protein coding)
Modification date20190324
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 HM13-IT1

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: ENSG00000235313.1

check button RNA A-to-I editing events in Cancer.
CAediting_1411827(31563389, +), CAediting_1411828(31563394, +), CAediting_1411829(31563404, +), CAediting_1411830(31563423, +), CAediting_1411831(31563424, +), CAediting_1411832(31563427, +), CAediting_1411833(31563428, +), CAediting_1411834(31563441, +), CAediting_1411835(31563449, +), CAediting_1411836(31563450, +), CAediting_1411837(31563453, +), CAediting_1411838(31563463, +), CAediting_1411839(31563465, +), CAediting_1411840(31563473, +), CAediting_1411841(31563481, +), CAediting_1411842(31563485, +), CAediting_1411843(31563498, +), CAediting_1411844(31563504, +), CAediting_1411845(31563507, +), CAediting_1411846(31563513, +), CAediting_1411847(31563518, +), CAediting_1411848(31563521, +), CAediting_1411849(31563524, +), CAediting_1411850(31563533, +), CAediting_1411851(31563544, +), CAediting_1411852(31563545, +), CAediting_1411853(31563546, +), CAediting_1411854(31563558, +), CAediting_1411855(31563571, +), CAediting_1411856(31563576, +), CAediting_1411857(31563585, +), CAediting_1411858(31563586, +), CAediting_1411859(31563598, +), CAediting_1411860(31563600, +), CAediting_1411861(31563601, +), CAediting_1411862(31563607, +), CAediting_1411863(31563815, +), CAediting_1411864(31563821, +), CAediting_1411865(31563822, +), CAediting_1411866(31563843, +), CAediting_1411867(31563844, +), CAediting_1411868(31563862, +), CAediting_1411869(31563876, +), CAediting_1411870(31563887, +), CAediting_1411871(31563891, +), CAediting_1411872(31563897, +), CAediting_1411873(31563900, +), CAediting_1411874(31563901, +), CAediting_1411875(31563912, +), CAediting_1411876(31563915, +), CAediting_1411877(31563916, +), CAediting_1411878(31563917, +), CAediting_1411879(31563918, +), CAediting_1411880(31563921, +), CAediting_1411881(31563924, +), CAediting_1411882(31563926, +), CAediting_1411883(31563929, +), CAediting_1411884(31563955, +), CAediting_1411885(31563956, +), CAediting_1411886(31563961, +), CAediting_1411887(31563965, +), CAediting_1411888(31563972, +), CAediting_1411889(31563978, +), CAediting_1411890(31563982, +), CAediting_1411891(31563988, +), CAediting_1411892(31564001, +), CAediting_1411893(31564020, +), CAediting_1411894(31564032, +), CAediting_1411895(31564064, +), CAediting_1411896(31564076, +),

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RNA editing positional annotations for HM13-IT1 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_1411827chr20_31563389_+ncRNA_exonic
CAediting_1411828chr20_31563394_+ncRNA_exonic
CAediting_1411829chr20_31563404_+ncRNA_exonic
CAediting_1411830chr20_31563423_+ncRNA_intronic
CAediting_1411831chr20_31563424_+ncRNA_intronic
CAediting_1411832chr20_31563427_+ncRNA_intronic
CAediting_1411833chr20_31563428_+ncRNA_intronic
CAediting_1411834chr20_31563441_+ncRNA_intronic
CAediting_1411835chr20_31563449_+ncRNA_intronic
CAediting_1411836chr20_31563450_+ncRNA_intronic
CAediting_1411837chr20_31563453_+ncRNA_intronic
CAediting_1411838chr20_31563463_+ncRNA_intronic
CAediting_1411839chr20_31563465_+ncRNA_intronic
CAediting_1411840chr20_31563473_+ncRNA_intronic
CAediting_1411841chr20_31563481_+ncRNA_intronic
CAediting_1411842chr20_31563485_+ncRNA_intronic
CAediting_1411843chr20_31563498_+ncRNA_intronic
CAediting_1411844chr20_31563504_+ncRNA_intronic
CAediting_1411845chr20_31563507_+ncRNA_intronic
CAediting_1411846chr20_31563513_+ncRNA_intronic
CAediting_1411847chr20_31563518_+ncRNA_intronic
CAediting_1411848chr20_31563521_+ncRNA_intronic
CAediting_1411849chr20_31563524_+ncRNA_intronic
CAediting_1411850chr20_31563533_+ncRNA_intronic
CAediting_1411851chr20_31563544_+ncRNA_intronic
CAediting_1411852chr20_31563545_+ncRNA_intronic
CAediting_1411853chr20_31563546_+ncRNA_intronic
CAediting_1411854chr20_31563558_+ncRNA_intronic
CAediting_1411855chr20_31563571_+ncRNA_intronic
CAediting_1411856chr20_31563576_+ncRNA_intronic
CAediting_1411857chr20_31563585_+ncRNA_intronic
CAediting_1411858chr20_31563586_+ncRNA_intronic
CAediting_1411859chr20_31563598_+ncRNA_intronic
CAediting_1411860chr20_31563600_+ncRNA_intronic
CAediting_1411861chr20_31563601_+ncRNA_intronic
CAediting_1411862chr20_31563607_+ncRNA_intronic
CAediting_1411863chr20_31563815_+ncRNA_intronic
CAediting_1411864chr20_31563821_+ncRNA_intronic
CAediting_1411865chr20_31563822_+ncRNA_intronic
CAediting_1411866chr20_31563843_+ncRNA_intronic
CAediting_1411867chr20_31563844_+ncRNA_intronic
CAediting_1411868chr20_31563862_+ncRNA_intronic
CAediting_1411869chr20_31563876_+ncRNA_intronic
CAediting_1411870chr20_31563887_+ncRNA_intronic
CAediting_1411871chr20_31563891_+ncRNA_intronic
CAediting_1411872chr20_31563897_+ncRNA_intronic
CAediting_1411873chr20_31563900_+ncRNA_intronic
CAediting_1411874chr20_31563901_+ncRNA_intronic
CAediting_1411875chr20_31563912_+ncRNA_intronic
CAediting_1411876chr20_31563915_+ncRNA_intronic
CAediting_1411877chr20_31563916_+ncRNA_intronic
CAediting_1411878chr20_31563917_+ncRNA_intronic
CAediting_1411879chr20_31563918_+ncRNA_intronic
CAediting_1411880chr20_31563921_+ncRNA_intronic
CAediting_1411881chr20_31563924_+ncRNA_intronic
CAediting_1411882chr20_31563926_+ncRNA_intronic
CAediting_1411883chr20_31563929_+ncRNA_intronic
CAediting_1411884chr20_31563955_+ncRNA_intronic
CAediting_1411885chr20_31563956_+ncRNA_intronic
CAediting_1411886chr20_31563961_+ncRNA_intronic
CAediting_1411887chr20_31563965_+ncRNA_intronic
CAediting_1411888chr20_31563972_+ncRNA_splicing
CAediting_1411889chr20_31563978_+ncRNA_exonic
CAediting_1411890chr20_31563982_+ncRNA_exonic
CAediting_1411891chr20_31563988_+ncRNA_exonic
CAediting_1411892chr20_31564001_+ncRNA_exonic
CAediting_1411893chr20_31564020_+ncRNA_exonic
CAediting_1411894chr20_31564032_+ncRNA_exonic
CAediting_1411895chr20_31564064_+ncRNA_exonic
CAediting_1411896chr20_31564076_+ncRNA_exonic

check button Repat-regional RNA editing(s).
CAeditome IDPositionRepeat familyRepeat sub familyRepeat name
CAediting_1411827chr20_31563389_+SINEAluAluSz
CAediting_1411828chr20_31563394_+SINEAluAluSz
CAediting_1411829chr20_31563404_+SINEAluAluSz
CAediting_1411830chr20_31563423_+SINEAluAluSz
CAediting_1411831chr20_31563424_+SINEAluAluSz
CAediting_1411832chr20_31563427_+SINEAluAluSz
CAediting_1411833chr20_31563428_+SINEAluAluSz
CAediting_1411834chr20_31563441_+SINEAluAluSz
CAediting_1411835chr20_31563449_+SINEAluAluSz
CAediting_1411836chr20_31563450_+SINEAluAluSz
CAediting_1411837chr20_31563453_+SINEAluAluSz
CAediting_1411838chr20_31563463_+SINEAluAluSz
CAediting_1411839chr20_31563465_+SINEAluAluSz
CAediting_1411840chr20_31563473_+SINEAluAluSz
CAediting_1411841chr20_31563481_+SINEAluAluSz
CAediting_1411842chr20_31563485_+SINEAluAluSz
CAediting_1411843chr20_31563498_+SINEAluAluSz
CAediting_1411844chr20_31563504_+SINEAluAluSz
CAediting_1411845chr20_31563507_+SINEAluAluSz
CAediting_1411846chr20_31563513_+SINEAluAluSz
CAediting_1411847chr20_31563518_+SINEAluAluSz
CAediting_1411848chr20_31563521_+SINEAluAluSz
CAediting_1411849chr20_31563524_+SINEAluAluSz
CAediting_1411850chr20_31563533_+SINEAluAluSz
CAediting_1411851chr20_31563544_+SINEAluAluSz
CAediting_1411852chr20_31563545_+SINEAluAluSz
CAediting_1411853chr20_31563546_+SINEAluAluSz
CAediting_1411854chr20_31563558_+SINEAluAluSz
CAediting_1411855chr20_31563571_+SINEAluAluSz
CAediting_1411856chr20_31563576_+SINEAluAluSz
CAediting_1411857chr20_31563585_+SINEAluAluSz
CAediting_1411858chr20_31563586_+SINEAluAluSz
CAediting_1411859chr20_31563598_+SINEAluAluSz
CAediting_1411860chr20_31563600_+SINEAluAluSz
CAediting_1411861chr20_31563601_+SINEAluAluSz
CAediting_1411862chr20_31563607_+SINEAluAluSz
CAediting_1411863chr20_31563815_+SINEAluAluSp
CAediting_1411864chr20_31563821_+SINEAluAluSp
CAediting_1411865chr20_31563822_+SINEAluAluSp
CAediting_1411866chr20_31563843_+SINEAluAluSp
CAediting_1411867chr20_31563844_+SINEAluAluSp
CAediting_1411868chr20_31563862_+SINEAluAluSp
CAediting_1411869chr20_31563876_+SINEAluAluSp
CAediting_1411870chr20_31563887_+SINEAluAluSp
CAediting_1411871chr20_31563891_+SINEAluAluSp
CAediting_1411872chr20_31563897_+SINEAluAluSp
CAediting_1411873chr20_31563900_+SINEAluAluSp
CAediting_1411874chr20_31563901_+SINEAluAluSp
CAediting_1411875chr20_31563912_+SINEAluAluSp
CAediting_1411876chr20_31563915_+SINEAluAluSp
CAediting_1411877chr20_31563916_+SINEAluAluSp
CAediting_1411878chr20_31563917_+SINEAluAluSp
CAediting_1411879chr20_31563918_+SINEAluAluSp
CAediting_1411880chr20_31563921_+SINEAluAluSp
CAediting_1411881chr20_31563924_+SINEAluAluSp
CAediting_1411882chr20_31563926_+SINEAluAluSp
CAediting_1411883chr20_31563929_+SINEAluAluSp
CAediting_1411884chr20_31563955_+SINEAluAluSp
CAediting_1411885chr20_31563956_+SINEAluAluSp
CAediting_1411886chr20_31563961_+SINEAluAluSp
CAediting_1411887chr20_31563965_+SINEAluAluSp
CAediting_1411888chr20_31563972_+SINEAluAluSp
CAediting_1411889chr20_31563978_+SINEAluAluSp
CAediting_1411890chr20_31563982_+SINEAluAluSp
CAediting_1411891chr20_31563988_+SINEAluAluSp
CAediting_1411892chr20_31564001_+SINEAluAluSp
CAediting_1411893chr20_31564020_+SINEAluAluSp
CAediting_1411894chr20_31564032_+SINEAluAluSp
CAediting_1411895chr20_31564064_+SINEAluAluSp
CAediting_1411896chr20_31564076_+SINEAluAluSp

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RNA A-to-I editing events in the alternative splicing sites for HM13-IT1

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 ENSG00000235313.1.HM13-IT1.

check button Correlation between RNA A-to-I editing and PSI for ENSG00000235313.1.HM13-IT1.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for HM13-IT1

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

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

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 HM13-IT1

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 HM13-IT1

**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_1411828chr20_31563394_+ENSG00000235313.1ENST00000421894.1hsa-miR-453731563392315633998mer-1a3156337831563399150-24.35
CAediting_1411827chr20_31563389_+ENSG00000235313.1ENST00000421894.1hsa-miR-4786-5p31563387315633948mer-1a3156337131563394151-22.12
CAediting_1411829chr20_31563404_+ENSG00000235313.1ENST00000421894.1hsa-miR-1225-3p31563402315634087mer-m83156338831563409148-17.48
CAediting_1411829chr20_31563404_+ENSG00000235313.1ENST00000421894.1hsa-miR-432331563401315634077mer-m83156339131563408140-14.9
CAediting_1411829chr20_31563404_+ENSG00000235313.1ENST00000421894.1hsa-miR-5699-5p31563400315634067mer-m83156338531563407147-16.54
CAediting_1411889chr20_31563978_+ENSG00000235313.1ENST00000421894.1hsa-miR-191331563977315639837mer-m83156340831563984144-22.28
CAediting_1411891chr20_31563988_+ENSG00000235313.1ENST00000421894.1hsa-miR-443131563985315639917mer-m83156341631563992140-17.94
CAediting_1411892chr20_31564001_+ENSG00000235313.1ENST00000421894.1hsa-miR-6778-3p31564000315640067mer-m83156398731564007142-18.27
CAediting_1411893chr20_31564020_+ENSG00000235313.1ENST00000421894.1hsa-miR-324-3p31564014315640207mer-m83156399931564021149-24.54
CAediting_1411893chr20_31564020_+ENSG00000235313.1ENST00000421894.1hsa-miR-607531564018315640258mer-1a3156400431564025150-25.04
CAediting_1411894chr20_31564032_+ENSG00000235313.1ENST00000421894.1hsa-miR-463431564028315640358mer-1a3156401531564035150-24.65
CAediting_1411895chr20_31564064_+ENSG00000235313.1ENST00000421894.1hsa-miR-4755-5p31564060315640667mer-m83156404331564067153-22.85
CAediting_1411895chr20_31564064_+ENSG00000235313.1ENST00000421894.1hsa-miR-5006-3p31564060315640667mer-m83156404431564067142-18.1
CAediting_1411895chr20_31564064_+ENSG00000235313.1ENST00000421894.1hsa-miR-5088-3p31564058315640658mer-1a3156404731564065151-22.02
CAediting_1411895chr20_31564064_+ENSG00000235313.1ENST00000421894.1hsa-miR-642b-5p31564061315640677mer-m83156404631564068141-16.83

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
CAediting_980496chr14_31014685_-ENSG00000235313.1ENST00000421894.1hsa-miR-624-3p31563290315632967mer-m83156327731563297144-16.34
CAediting_228905chr2_188297554_+ENSG00000235313.1ENST00000421894.1hsa-miR-561-3p31564064315640707mer-m83156405231564071143-15.58
CAediting_442554chr5_154685830_+ENSG00000235313.1ENST00000421894.1hsa-miR-130331563314315633207mer-m83156329931563321152-21.58

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

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 HM13-IT1

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 RNA structures for Minimum free energy (MFE).
CAeditom_IDENSTEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

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Relation with ADAR for HM13-IT1

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.)
STADCAediting_1411828chr20_31563394_+0.01984881467222890.221839375478923....
STADCAediting_1411832chr20_31563427_+0.02358587575220990.257823731070321....

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Relation with cancer stages for HM13-IT1

check button Correlation between Cancer stages and RNA editing frequency
CancerStage_typeCAeditomIDpositionP-valCoeff.
ESCApathologic_stageCAediting_1411828chr20_31563394_+0.00426063360441640.363903351526052
STADpathologic_stageCAediting_1411832chr20_31563427_+0.0002522478191413090.410705775661817

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Relation with survival for HM13-IT1

check button Correlation between RNA editing and survival
CancerCAeditomIDpositionKMpvalueCoxpvalueCoxHR

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RelatedDrugs for HM13-IT1

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 HM13-IT1

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