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Editing gene: MALAT1 (CAeditome ID:378938)

Gene summary for MALAT1

Gene summary

Gene information	Gene symbol	MALAT1
	Gene ID	378938
	Gene name	metastasis associated lung adenocarcinoma transcript 1
	Synonyms	HCN\|LINC00047\|NCRNA00047\|NEAT2\|PRO2853
	Cytomap	11q13.1
	Type of gene	ncRNA
	Description	hepcarcinlong intergenic non-protein coding RNA 47metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)nuclear enriched abundant transcript 2nuclear paraspeckle assembly transcript 2 (non-protein coding)
	Modification date	20210531
	UniProtAcc	.
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene

GO ID

GO term

PubMed ID

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RNA A-to-I events for MALAT1

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

RNA editing frequencies across 33 cancers of gene: ENSG00000251562.6

RNA A-to-I editing events in Cancer.

CAediting_824691(65506159, +), CAediting_824692(65506391, +),

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RNA editing positional annotations for MALAT1 using Annovar

Protein coding RNA editing(s).

CAeditome ID

Position

Variant type

ENST

NTchange

AAchange

SIFT_score

Polyphen2_HVAR_score

PROVEAN_pred

Gene structure information of RNA editing(s).

CAeditome ID	Position	Variant type
CAediting_824691	chr11_65506159_+	ncRNA_exonic
CAediting_824692	chr11_65506391_+	ncRNA_exonic

Repat-regional RNA editing(s).

CAeditome ID

Position

Repeat family

Repeat sub family

Repeat name

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RNA A-to-I editing events in the alternative splicing sites for MALAT1

RNA A-to-I editing(s) in the alternative splicing sites.

AStype

CAeditomID

Editing position

AS position

AS direction

Exonic location

Wildtype sequence

Wildtype splicing strength

RNA edited sequence

RNA edited splicing strength

Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000251562.6.MALAT1.

Correlation between RNA A-to-I editing and PSI for ENSG00000251562.6.MALAT1.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for MALAT1

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

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

- 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.

BRCA.CAediting_824691.ENSG00000251562.MALAT1.png
Soverview

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Protein coding region RNA A-to-I editings for MALAT1

- 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 MALAT1

**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.

RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in lncRNA gained miRNA binding sites.

CAeditom_ID	Position	ENSG	ENST	miRNA	Targetscan start	Targetscan end	Targetscan score	Miranda start	Miranda end	Miranda score	Miranda energy
CAediting_824691	chr11_65506159_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-12113	65506154	65506160	7mer-1a	65506139	65506160	142	-19.38
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-15a-3p	65506389	65506395	7mer-m8	65506375	65506396	142	-18.2
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-1972	65506390	65506396	7mer-m8	65506376	65506397	140	-15.8
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-885-5p	65506386	65506392	7mer-m8	65506373	65506393	141	-10.3
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000610851.1	hsa-miR-15a-3p	65506389	65506395	7mer-m8	65505008	65506396	148	-27.61
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000610851.1	hsa-miR-1972	65506390	65506396	7mer-m8	65505010	65506397	140	-16.26
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000610851.1	hsa-miR-885-5p	65506386	65506392	7mer-m8	65505007	65506393	141	-16.5
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000616691.1	hsa-miR-15a-3p	65506389	65506395	7mer-m8	65505651	65506396	150	-20.53
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000616691.1	hsa-miR-1972	65506390	65506396	7mer-m8	65505653	65506397	140	-19.26
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000616691.1	hsa-miR-885-5p	65506386	65506392	7mer-m8	65505650	65506393	141	-12.01
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000617489.1	hsa-miR-15a-3p	65506389	65506395	7mer-m8	65505651	65506396	150	-20.53
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000617489.1	hsa-miR-1972	65506390	65506396	7mer-m8	65505653	65506397	140	-19.26
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000617489.1	hsa-miR-885-5p	65506386	65506392	7mer-m8	65505650	65506393	141	-12.01
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000618227.1	hsa-miR-15a-3p	65506389	65506395	7mer-m8	65505651	65506396	150	-20.53
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000618227.1	hsa-miR-1972	65506390	65506396	7mer-m8	65505653	65506397	140	-19.26
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000618227.1	hsa-miR-885-5p	65506386	65506392	7mer-m8	65505650	65506393	141	-12.01

RNA A-to-I editing in lncRNA lost miRNA binding sites.

CAeditom_ID	Position	ENSG	ENST	miRNA	Targetscan start	Targetscan end	Targetscan score	Miranda start	Miranda end	Miranda score	Miranda energy
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000610851.1	hsa-miR-556-3p	65505019	65506391	7mer-m8	65505003	65506392	155	-11.22
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-556-3p	65506385	65506391	7mer-m8	65506371	65506392	140	-7.14
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000616691.1	hsa-miR-556-3p	65505662	65506391	7mer-m8	65505647	65506392	149	-7.9
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000618227.1	hsa-miR-556-3p	65505662	65506391	7mer-m8	65505647	65506392	149	-7.9
CAediting_824692	chr11_65506391_+	ENSG00000251562.6	ENST00000617489.1	hsa-miR-556-3p	65505662	65506391	7mer-m8	65505647	65506392	149	-7.9

RNA A-to-I editing in miRNAs gained binding to lncRNA.

CAeditom_ID	Position	ENSG	ENST	miRNA	Targetscan start	Targetscan end	Targetscan score	Miranda start	Miranda end	Miranda score	Miranda energy
CAediting_748296	chr10_51299626_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-605-3p	65497795	65497801	7mer-m8	65497782	65497802	145	-21.26
CAediting_1229414	chr17_67471546_+	ENSG00000251562.6	ENST00000618132.1	hsa-miR-548aa	65504798	65504805	8mer-1a	65504781	65504805	140	-8.15
CAediting_1229414	chr17_67471546_+	ENSG00000251562.6	ENST00000610851.1	hsa-miR-548aa	65504798	65504805	8mer-1a	65504781	65504805	140	-8.15
CAediting_1229413	chr17_67471544_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-548aa	65506138	65506144	7mer-m8	65506122	65506145	145	-15.49
CAediting_1229414	chr17_67471546_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-548aa	65498012	65498018	7mer-m8	65497996	65498019	149	-11.3
CAediting_1229414	chr17_67471546_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-548aa	65501531	65501538	8mer-1a	65501510	65501538	144	-11.96
CAediting_1229414	chr17_67471546_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-548aa	65504798	65504805	8mer-1a	65504781	65504805	140	-8.15
CAediting_1351755	chr19_40282625_-	ENSG00000251562.6	ENST00000534336.1	hsa-miR-641	65502576	65502582	7mer-m8	65502556	65502583	151	-16.87
CAediting_117844	chr1_162342605_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-556-3p	65500782	65500788	7mer-m8	65500770	65500789	147	-14.62
CAediting_117844	chr1_162342605_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-556-3p	65503860	65503866	7mer-m8	65503846	65503867	155	-13.07
CAediting_228905	chr2_188297554_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-561-3p	65497999	65498005	7mer-m8	65497985	65498006	147	-13.32
CAediting_396018	chr5_1062918_-	ENSG00000251562.6	ENST00000534336.1	hsa-miR-4635	65498704	65498711	8mer-1a	65498690	65498711	145	-18.06
CAediting_442554	chr5_154685830_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-1303	65505998	65506004	7mer-m8	65505984	65506005	156	-19.52
CAediting_414656	chr5_72878640_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-4804-3p	65502893	65502899	7mer-m8	65502880	65502900	140	-10.67
CAediting_414656	chr5_72878640_+	ENSG00000251562.6	ENST00000508832.2	hsa-miR-4804-3p	65502893	65502899	7mer-m8	65502880	65502900	140	-10.67
CAediting_414656	chr5_72878640_+	ENSG00000251562.6	ENST00000618925.1	hsa-miR-4804-3p	65502893	65502899	7mer-m8	65502880	65502900	140	-10.67

RNA A-to-I editing in miRNAs lost binding to lncRNA.

CAeditom_ID	Position	ENSG	ENST	miRNA	Targetscan start	Targetscan end	Targetscan score	Miranda start	Miranda end	Miranda score	Miranda energy
CAediting_442554	chr5_154685830_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-1303	65503714	65503720	7mer-m8	65503701	65503721	154	-20.84
CAediting_1160181	chr17_7017644_-	ENSG00000251562.6	ENST00000534336.1	hsa-miR-195-3p	65499876	65499882	7mer-m8	65499860	65499883	146	-8.49
CAediting_393	chr1_1167164_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-200b-3p	65501220	65501226	7mer-m8	65501206	65501227	140	-9.15
CAediting_393	chr1_1167164_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-200b-3p	65503212	65503218	7mer-m8	65503197	65503219	147	-13.72
CAediting_1054808	chr15_66496985_-	ENSG00000251562.6	ENST00000534336.1	hsa-miR-4512	65503868	65503874	7mer-m8	65503851	65503875	153	-20.81
CAediting_396018	chr5_1062918_-	ENSG00000251562.6	ENST00000534336.1	hsa-miR-4635	65504706	65504713	8mer-1a	65504693	65504713	144	-10.77
CAediting_1524209	chrX_134546392_-	ENSG00000251562.6	ENST00000534336.1	hsa-miR-503-5p	65497934	65497940	7mer-1a	65497917	65497940	140	-23.62
CAediting_1524209	chrX_134546392_-	ENSG00000251562.6	ENST00000534336.1	hsa-miR-503-5p	65498493	65498498	6mer	65498478	65498499	143	-22.13
CAediting_117844	chr1_162342605_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-556-3p	65506385	65506391	7mer-m8	65506371	65506392	140	-7.14
CAediting_228905	chr2_188297554_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-561-3p	65502616	65502622	7mer-m8	65502602	65502623	151	-11.77
CAediting_228905	chr2_188297554_+	ENSG00000251562.6	ENST00000534336.1	hsa-miR-561-3p	65503729	65503735	7mer-m8	65503711	65503736	147	-15.59
CAediting_524911	chr7_5495852_-	ENSG00000251562.6	ENST00000534336.1	hsa-miR-589-3p	65504366	65504372	7mer-m8	65504350	65504373	144	-13.65
CAediting_524911	chr7_5495852_-	ENSG00000251562.6	ENST00000534336.1	hsa-miR-589-3p	65504393	65504400	8mer-1a	65504376	65504400	145	-13.36
CAediting_393	chr1_1167164_+	ENSG00000251562.6	ENST00000508832.2	hsa-miR-200b-3p	65503212	65503218	7mer-m8	65503197	65503219	147	-13.72

RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for MALAT1

- RNA A-to-I editing in mRNA.
* Click on the image to enlarge it in a new window.

ENST

ENST type

RNA structure without RNA A-to-I editing.

RNA structure with RNA A-to-I editing.

RNA A-to-I editing in RNA structures for Minimum free energy (MFE).

CAeditom_ID

ENST

Editing_Position

MFE_withoneAI

MFE_withoutAI

MFE_withmultipleAI

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Relation with ADAR for MALAT1

Correlation between ADAR gene expression and RNA editing frequency

Cancer	CAeditomID	position	ADAR1 (p-val)	ADAR1 (coeff.)	ADAR2 (p-val)	ADAR2 (coeff.)	ADAR3 (p-val)	ADAR3 (coeff.)
BLCA	CAediting_824691	chr11_65506159_+	0.00142377932843773	0.197585473328019	.	.	.	.
LGG	CAediting_824691	chr11_65506159_+	0.0370851152141551	0.119244033051494	.	.	.	.
PRAD	CAediting_824691	chr11_65506159_+	.	.	.	.	0.0365228262802605	0.184320961385017
HNSC	CAediting_824691	chr11_65506159_+	0.0170909515230932	0.152556369408214	.	.	.	.
PAAD	CAediting_824691	chr11_65506159_+	.	.	.	.	0.0126980358838748	0.23692807989845
TGCT	CAediting_824691	chr11_65506159_+	0.0217476050030056	0.279984499516179	.	.	.	.

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Relation with cancer stages for MALAT1

Correlation between Cancer stages and RNA editing frequency

Cancer	Stage_type	CAeditomID	position	P-val	Coeff.
CESC	clinical_stage	CAediting_824691	chr11_65506159_+	0.0218380756150068	0.163738312589516
ESCA	clinical_stage	CAediting_824691	chr11_65506159_+	0.0485530361157497	0.322154588277935
KIRC	pathologic_stage	CAediting_824691	chr11_65506159_+	0.0242080904072424	-0.157778125115886
THCA	pathologic_stage	CAediting_824691	chr11_65506159_+	0.0378329898282607	0.123300285478691

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Relation with survival for MALAT1

Correlation between RNA editing and survival

Cancer

CAeditomID

position

KMpvalue

Coxpvalue

CoxHR

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RelatedDrugs for MALAT1

Approved drugs targeting this gene.
(DrugBank Version 5.1.8 2021-01-03)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for MALAT1

Diseases associated with this gene.
(DisGeNet 7.0)

Gene	Disease ID	Disease name	# pubmeds	Source
MALAT1	C0006142	Malignant neoplasm of breast	2	CTD_human
MALAT1	C0027627	Neoplasm Metastasis	2	CTD_human
MALAT1	C0678222	Breast Carcinoma	2	CTD_human
MALAT1	C1257931	Mammary Neoplasms, Human	2	CTD_human
MALAT1	C1458155	Mammary Neoplasms	2	CTD_human
MALAT1	C4704874	Mammary Carcinoma, Human	2	CTD_human
MALAT1	C0019193	Hepatitis, Toxic	1	CTD_human
MALAT1	C0023467	Leukemia, Myelocytic, Acute	1	CTD_human
MALAT1	C0023893	Liver Cirrhosis, Experimental	1	CTD_human
MALAT1	C0023903	Liver neoplasms	1	CTD_human
MALAT1	C0026998	Acute Myeloid Leukemia, M1	1	CTD_human
MALAT1	C0027626	Neoplasm Invasiveness	1	CTD_human
MALAT1	C0032460	Polycystic Ovary Syndrome	1	CTD_human
MALAT1	C0236663	Alcohol withdrawal syndrome	1	PSYGENET
MALAT1	C0279626	Squamous cell carcinoma of esophagus	1	CTD_human
MALAT1	C0345904	Malignant neoplasm of liver	1	CTD_human
MALAT1	C0860207	Drug-Induced Liver Disease	1	CTD_human
MALAT1	C1136382	Sclerocystic Ovaries	1	CTD_human
MALAT1	C1262760	Hepatitis, Drug-Induced	1	CTD_human
MALAT1	C1879321	Acute Myeloid Leukemia (AML-M2)	1	CTD_human
MALAT1	C3658290	Drug-Induced Acute Liver Injury	1	CTD_human
MALAT1	C4277682	Chemical and Drug Induced Liver Injury	1	CTD_human
MALAT1	C4279912	Chemically-Induced Liver Toxicity	1	CTD_human

	Gene summary
	RNA A-to-I events
	Differntial gene expression between RNA A-to-I edited tumor samples versus normal samples
	Protein coding region RNA A-to-I editings
	The effects of the RNA editing to the miRNA binding sites
	The effects of the RNA editing to the stability of the RNA structures
	Relation with ADAR
	Relation with cancer stages
	Relation with survival state
	Related drugs with this gene
	Related diseases with this gene