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lncRNA: ENSG00000266490

Summary for CTD-2349P21.9

Gene summary

Gene information	Ensembl ID	ENSG00000266490
	Gene symbol	CTD-2349P21.9
	Gene name
	HGNC
	Entrez ID
	Gene type	lincRNA
	Synonyms
	UniProtAcc

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Structure and expression level for CTD-2349P21.9

Differentially expressed gene analysis between cancer and normal samples.

Ensembl ID	Base mean	log2FC(AD/control)	lfcSE	Stat	P-value	Adjc.p-value	DEG direction	Cancer type
ENSG00000266490	3.296555e+01	1.576744e+00	3.564278e-01	4.423742e+00	9.700000e-06	5.270000e-05	UP	CHOL
ENSG00000266490	3.731534e+01	1.033782e+00	1.220435e-01	8.470609e+00	2.440000e-17	1.260000e-16	UP	KIRC
ENSG00000266490	4.742478e+01	1.138623e+00	1.917809e-01	5.937105e+00	2.900000e-09	1.890000e-08	UP	KIRP
ENSG00000266490	4.703796e+01	1.012118e+00	1.326034e-01	7.632672e+00	2.300000e-14	1.540000e-13	UP	LUAD
ENSG00000266490	2.546268e+01	1.286133e+00	1.796484e-01	7.159165e+00	8.120000e-13	5.990000e-12	UP	COAD

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000266490	5.983933e-01	1.414849e-05	CHOL	8.560348e-05

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lncRNA-Protein interaction for CTD-2349P21.9

lncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID

LncRNA ENST ID

LncRNA Name

Protein Ensembl ID

Protein Name

CatRAPID Score

Lncpro Score

UniPortID

Gene Subtype

Public source

lncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000266490	ENST00000580085	CTD-2349P21.9	ENSG00000118058	KMT2A	86.39	91.3411	Q03164	TF,Epi	NA

lncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000266490	ENST00000580085	CTD-2349P21.9	ENSG00000167978	SRRM2	21.65	91.5966	Q9UQ35	RBP	NA

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lncRNA-DNA interaction for CTD-2349P21.9

lncRNA targets the enhancer region and positively regulates the gene expression.

lncRNA targets the promoter region and positively regulates the gene expression.

lncRNA targets the promoter region and negatively regulates the gene expression.

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lncRNA-RNA interaction for CTD-2349P21.9

lncRNA targets the 3'UTR region and negatively regulates the mRNA.

Only predicted by lncTar

RNH1

Exist in public source

lncRNA targets the skipped exon region.

-lncRNA and exonskipping events are positively correlated.

lncRNA and exonskipping events positive correlated

LncRNA Ensembl ID	LncRNA ENST ID	Exon ID	Skipped Exon	dG	ndG	Gene name with skipped exon	TransID with skipped exon	ORF mutation
ENSG00000266490	ENST00000580085	exon_skip_386274	chr3:108049618-108049651	-3.75	-0.2679	CD47	ENST00000361309	In-frame
ENSG00000266490	ENST00000580085	exon_skip_1234	chr1:11658532-11658628	-13.27	-0.3686	FBXO44	ENST00000251547,ENST00000376770	In-frame
ENSG00000266490	ENST00000580085	exon_skip_470077	chr7:102397619-102397698	-6.86	-0.2144	PRKRIP1	ENST00000397912,ENST00000496391	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_51046	chr10:73439871-73439901	-6.19	-0.2814	PPP3CB	ENST00000360663	In-frame

-lncRNA and exonskipping events are negatively correlated.

lncRNA and exonskipping events negative correlated

LncRNA Ensembl ID	LncRNA ENST ID	Exon ID	Skipped Exon	dG	ndG	Gene name with skipped exon	TransID with skipped exon	LOF
ENSG00000266490	ENST00000580085	exon_skip_66482	chr11:126274926-126275021	-14.55	-0.1617	FOXRED1	ENST00000263578	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_111863	chr14:23565815-23565892	-9.92	-0.2111	AP1G2	ENST00000308724,ENST00000397120	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_114365	chr14:74290026-74290118	-10.10	-0.1403	ABCD4	ENST00000356924	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_377198	chr3:123130479-123130616	-11.47	-0.1170	PDIA5	ENST00000316218	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_382458	chr3:38131595-38131638	-6.23	-0.2832	ACAA1	ENST00000333167	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_499567	chr9:128325142-128325239	-9.81	-0.1557	COQ4	ENST00000300452	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_11029	chr1:154989559-154989707	-16.59	-0.1136	FLAD1	ENST00000292180	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_95407	chr12:95040475-95040597	-14.43	-0.1233	NR2C1	ENST00000333003	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_99811	chr13:37002272-37002309	-6.52	-0.5433	EXOSC8	ENST00000389704	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_139933	chr16:90035632-90035687	-9.32	-0.3883	GAS8	ENST00000268699	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_370518	chr22:50247691-50247776	-10.99	-0.1773	HDAC10	ENST00000216271	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_374497	chr3:49999439-49999513	-7.12	-0.1295	RBM6	ENST00000266022	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_374551	chr3:50100531-50100605	-6.61	-0.1574	RBM5	ENST00000347869	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_436035	chr5:79656957-79657001	-7.06	-0.2615	TENT2	ENST00000296783,ENST00000428308,ENST00000453514	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_38175	chr1:234398381-234398553	-8.00	-0.2000	TARBP1	ENST00000040877	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_53559	chr10:101793912-101793998	-8.53	-0.1053	OGA	ENST00000361464	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_92074	chr12:50142052-50142110	-4.61	-0.2305	CERS5	ENST00000317551	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_290158	chr17:42953723-42953778	-6.59	-0.1402	AARSD1	ENST00000427569	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_324294	chr2:27774423-27774530	-11.52	-0.1200	MRPL33	ENST00000296102	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_438188	chr5:141638954-141639021	-9.11	-0.1402	RELL2	ENST00000297164,ENST00000444782	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_444499	chr5:138164086-138164133	-4.07	-0.1272	BRD8	ENST00000254900	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_462160	chr6:127316449-127316502	-6.11	-0.1971	ECHDC1	ENST00000531967	Frame-shift
ENSG00000266490	ENST00000580085	exon_skip_476008	chr7:65970281-65970366	-8.50	-0.1197	GUSB	ENST00000304895	Frame-shift

lncRNA targets by miRNA.

LncRNA Ensembl ID	miRNA ID	LncRNA ENST ID	Binding site in lncRNA	Score	Energy	Align Len	Public source
ENSG00000266490	hsa-mir-22	ENST00000580085	chr17:30792464-30792546	163.00	-73.34	84	NA
ENSG00000266490	hsa-mir-22	ENST00000580085	chr17:30792611-30792695	159.00	-70.18	84	NA
ENSG00000266490	hsa-mir-22	ENST00000580085	chr17:30792386-30792464	149.00	-71.13	72	NA

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Variants for CTD-2349P21.9

RNA A-to-I editing events in lncRNA.

LncRNAediting ID

LncRNA Ensembl ID

Chromosome

Editing Position

Strand

Gene Type

Gene Name

Transcript ID

Transcript Type

Transcript Name

Edited-associated DElncRNAs in cancer.

LncRNA Ensembl ID

LncRNA Index

Cancer Type

Chr_Postion_Strand

AVE1

AVE2

log2FC

W-value

P-value

Adjc.p-value

Change

Correlation between RNA A-to-I editing events's frequecy and lncRNA expression.

LncRNA Ensembl ID

LncRNA Index

Correlation

P-value

Adjc.p-value

Cis-expression quantitative trait loci(cis-eQTL) of lncRNA.

LncRNA Ensembl ID

LncRNA Name

SNP info

Number of Positive corelated Cancer

Positive corelated Cancer

Number of Negative corelated Cancer

Negative corelated Cancer

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lncRNAs regulate the target genes through functioning as enhancers

lncRNA regulates differentially expressed genes by function as enhancer.

LncRNA Ensembl ID

PC Gene ID

PC Gene Name

Positive correlated cancers

Cancer with PC gene up-regulation

Cancer with PC gene down-regulation

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lncRNAs regulate the target genes through recruiting transcript factors

LncRNA-TF complex positively regulates the gene expression by target promoter region (#cancer types with positive correlation >= 5).

lncRNA ID

TF ID

TF Name

PCgene ID

PCgene Name

Number of Cancer

Canaer Types

LncRNA-TF complex negatively regulates the gene expression by target promoter region (#cancer types with negative correlation >= 5).

lncRNA ID

TF ID

TF Name

PCgene ID

PCgene Name

Number of Cancer

Canaer Types

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lncRNAs regulate the alternative splicing event through interacting with splicing factor

LncRNA-RBP complex positively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

LncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

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lncRNAs regulate mRNA through targeting the 3'-UTR region

lncRNA regulates differential expressed mRNA by directly targeting 3' UTR region.

LncRNA Ensembl ID

LncRNA ENST ID

PC Gene Name

PC Gene ID

PC ENST ID

nDG

Cancer with PC gene up-regulation

Cancer with PC gene Down-regulation

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lncRNAs regulate mRNA by competing with miRNA

lncRNA regulates mRNA by competing the miRNA binding site with mRNA.

LncRNA Ensembl ID	lncRNA-miRNA-mRNA	Cancer Types
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,RXRB	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,RING1	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,PHC1	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,HEXIM2	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,VEZF1	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,PAXBP1	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,SBK1	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,RBMX	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,JADE1	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,C14orf93	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,MKS1	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,PCIF1	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,DET1	CESC,CHOL,LGG,SARC,KIRP
ENSG00000266490	CTD-2349P21.9,hsa-mir-22,NSMCE4A	CESC,CHOL,LGG,SARC,KIRP

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lncRNA coding potential

ORFfinder result for the gencode.v22.lncRNA.transcript.fa.

lncRNA Ensembl ID	lncRNA ENST ID	length(AA)	start at transcript	end at transcript
ENSG00000266490.1	ENST00000580085.1	44	103	237

	lncRNA summary
	lncRNA structure and expression level
	lncRNA-Protein interaction
	lncRNA-DNA interaction
	lncRNA-RNA interaction
	Variants in lncRNA
	lncRNAs regulate the target genes through functioning as enhancers
	lncRNAs regulate the target genes through recruiting transcript factors
	lncRNAs regulate the alternative splicing events through interacting with splicing factor
	lncRNAs regulate mRNA through targeting the 3'-UTR region
	lncRNAs regulate mRNA by competing with miRNA
	lncRNA coding potential