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lncRNA: ENSG00000272836

Summary for RP3-402G11.27

Gene summary

Gene information	Ensembl ID	ENSG00000272836
	Gene symbol	RP3-402G11.27
	Gene name
	HGNC
	Entrez ID
	Gene type	antisense
	Synonyms
	UniProtAcc

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Structure and expression level for RP3-402G11.27

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
ENSG00000272836	3.158775e+01	1.338125e+00	1.312976e-01	1.019154e+01	2.160000e-24	1.660000e-23	UP	KIRC

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000272836	6.115927e-01	8.071728e-06	CHOL	6.721112e-05

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lncRNA-Protein interaction for RP3-402G11.27

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
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000128908	INO80	68.39	93.3814	Q9ULG1	Epi	NA
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000149311	ATM	65.34	90.7804	Q13315	Epi	NA
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000147130	ZMYM3	44.0	90.3382	Q14202	Epi	NA
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000104885	DOT1L	43.28	93.4144	Q8TEK3	TF,Epi	NA
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000120616	EPC1	25.46	92.6834	Q9H2F5	Epi	NA
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000196498	NCOR2	46.3	91.5061	Q9Y618	Epi	NA
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000173120	KDM2A	38.64	91.3389	Q9Y2K7	TF,Epi	NA
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000115524	SF3B1	38.24	94.6908	O75533	Epi	NA

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
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000170581	STAT2	46.87	91.2121	P52630	TF	NA
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000104885	DOT1L	43.28	93.7529	Q8TEK3	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
ENSG00000272836	ENST00000610050	RP3-402G11.27	ENSG00000129566	TEP1	51.28	93.2817	Q99973	RBP	NA

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lncRNA-DNA interaction for RP3-402G11.27

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 RP3-402G11.27

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

Only predicted by lncTar

CNIH1,SEC23B,SMIM12,PNPO,LDHA,HSPA8,CHP1,NTMT1,HSPA4,SSR3,CCT7,PRDX1,ATP5F1B,PLEKHB2,TUBA1C,DPP3,GPN1,GDI2,ATP5PB,PSMD1,ORMDL2

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
ENSG00000272836	ENST00000610050	exon_skip_1234	chr1:11658532-11658628	-18.38	-0.2042	FBXO44	ENST00000251547,ENST00000376770	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
ENSG00000272836	ENST00000610050	exon_skip_62623	chr11:69079833-69079883	-14.11	-0.4409	TPCN2	ENST00000294309	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_66482	chr11:126274926-126275021	-11.77	-0.1435	FOXRED1	ENST00000263578	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_110959	chr14:20372732-20372857	-14.54	-0.1671	TEP1	ENST00000262715	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_111863	chr14:23565815-23565892	-15.31	-0.2686	AP1G2	ENST00000308724,ENST00000397120	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_114376	chr14:74293153-74293248	-15.55	-0.1690	ABCD4	ENST00000356924	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_302168	chr19:10680345-10680443	-13.35	-0.1517	ILF3	ENST00000590261	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_370518	chr22:50247691-50247776	-16.29	-0.3017	HDAC10	ENST00000216271	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_382458	chr3:38131595-38131638	-8.90	-0.5933	ACAA1	ENST00000333167	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_290158	chr17:42953723-42953778	-9.42	-0.1777	AARSD1	ENST00000427569	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_431827	chr4:109696409-109696486	-6.48	-0.2400	CASP6	ENST00000265164	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_462144	chr6:125298713-125298816	-17.60	-0.2286	HDDC2	ENST00000398153	Frame-shift
ENSG00000272836	ENST00000610050	exon_skip_470226	chr7:103307595-103307708	-14.39	-0.1893	PMPCB	ENST00000249269	Frame-shift

lncRNA targets by miRNA.

LncRNA Ensembl ID	miRNA ID	LncRNA ENST ID	Binding site in lncRNA	Score	Energy	Align Len	Public source
ENSG00000272836	hsa-mir-22	ENST00000610050	chr22:50205590-50205670	154.00	-81.67	79	NA
ENSG00000272836	hsa-mir-22	ENST00000610050	chr22:50205776-50205856	151.00	-88.10	80	NA

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Variants for RP3-402G11.27

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
ENSG00000272836	RP3-402G11.27,hsa-mir-22,WDR33	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,MUS81	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,CRMP1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,PHF2	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,COIL	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,YTHDC1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,PRR14	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,C2orf68	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,TSNARE1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,ZNF7	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,ZC3H4	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,NAA16	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,PHC1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,CRAMP1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,PAXBP1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,TNRC18	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,PAGR1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,TIA1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,DPF2	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,EDRF1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,SBK1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,RBMX	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,FBXO46	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,MKRN1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,RBM14	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,PCIF1	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,DGCR8	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,CTDSPL2	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,PARP6	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,CLK3	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,ILF3	PCPG,CHOL,LGG,SARC,KIRP
ENSG00000272836	RP3-402G11.27,hsa-mir-22,EDC3	PCPG,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
ENSG00000272836.1	ENST00000610050.1	198	101	697

	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