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lncRNA: ENSG00000260966

Summary for RP11-690D19.3

Gene summary

Gene information	Ensembl ID	ENSG00000260966
	Gene symbol	RP11-690D19.3
	Gene name
	HGNC
	Entrez ID
	Gene type	sense_overlapping
	Synonyms
	UniProtAcc

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Structure and expression level for RP11-690D19.3

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
ENSG00000260966	3.182760e+02	-2.585356e+00	3.242867e-01	-7.972439e+00	1.560000e-15	7.120000e-14	DOWN	GBM
ENSG00000260966	7.148808e+02	1.714276e+00	3.378471e-01	5.074117e+00	3.890000e-07	1.530000e-05	UP	PCPG

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID

Correlation

P-value

Cancer Type

Adjc.p-value

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lncRNA-Protein interaction for RP11-690D19.3

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
ENSG00000260966	ENST00000561652	RP11-690D19.3	ENSG00000185658	BRWD1	66.85	96.1783	Q9NSI6	Epi	NA
ENSG00000260966	ENST00000561652	RP11-690D19.3	ENSG00000059758	CDK17	38.08	95.5556	Q00537	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
ENSG00000260966	ENST00000561652	RP11-690D19.3	ENSG00000175395	ZNF25	19.79	92.2472	P17030	TF	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

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lncRNA-DNA interaction for RP11-690D19.3

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

Only predicted by TDF

KBTBD6,CLASP2,MIGA1,LMBRD2,CDS2,ZC3H13,ATP2B1,LANCL1,PREPL,MBD5,TTBK2,PIKFYVE,KLHL42,NAPB,DNAJC27,CDK17,PDZD8,ARPP19,MBLAC2,AASDHPPT,MTMR9,N4BP2L1,KIF3A,ZNF91,SLC30A9,CHIC1,TRIM23,SCAMP1,BRWD1,GNAQ,TTC3,SIK3,NR1D2,PLA2G12A,ACADSB,DNAJB14,USP12,IKZF5,SPRYD7,SUGT1,MOSMO,NKIRAS1,ATAD1,PPM1A,SCAPER,RUFY2,ZNF25,VPS36

Exist in public source

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

Only predicted by TDF

USP12,NAA30,LANCL1,NKIRAS1,VPS36,PLA2G12A,GNAQ,ATP2B1,SIK3,AKAP11

Exist in public source

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

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lncRNA-RNA interaction for RP11-690D19.3

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

Only predicted by lncTar

ARPC2,CLIC1,CAPG,TSPO,TYMP,PSMB10

Exist in public source

lncRNA targets the skipped exon region.

-lncRNA and exonskipping events are positively correlated.

LncRNA Ensembl ID

LncRNA ENST ID

Exon ID

Skipped Exon

ndG

Gene name with skipped exon

TransID with skipped exon

ORF mutation

-lncRNA and exonskipping events are negatively correlated.

LncRNA Ensembl ID

LncRNA ENST ID

Exon ID

Skipped Exon

ndG

Gene name with skipped exon

TransID with skipped exon

LOF

lncRNA targets by miRNA.

LncRNA Ensembl ID

miRNA ID

LncRNA ENST ID

Binding site in lncRNA

Score

Energy

Align Len

Public source

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Variants for RP11-690D19.3

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
ENSG00000260966	ENSG00000059758	CDK17	BRCA,GBM,LGG,PCPG,THYM		GBM
ENSG00000260966	ENSG00000070961	ATP2B1	BRCA,GBM,LGG,PCPG,THYM	PCPG	GBM
ENSG00000260966	ENSG00000087448	KLHL42	BRCA,GBM,LAML,PCPG,THYM		GBM
ENSG00000260966	ENSG00000100614	PPM1A	BRCA,GBM,LAML,LGG,PCPG,THYM		GBM
ENSG00000260966	ENSG00000101290	CDS2	BRCA,GBM,LGG,PCPG,THYM	PCPG	GBM
ENSG00000260966	ENSG00000104643	MTMR9	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000113595	TRIM23	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000115137	DNAJC27	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000115365	LANCL1	BRCA,GBM,LAML,LGG,PCPG,THYM		GBM
ENSG00000260966	ENSG00000123200	ZC3H13	BRCA,GBM,LAML,PCPG,THYM		GBM
ENSG00000260966	ENSG00000128881	TTBK2	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000131437	KIF3A	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000136100	VPS36	BRCA,GBM,LAML,PCPG,THYM		GBM
ENSG00000260966	ENSG00000138078	PREPL	BRCA,GBM,LAML,LGG,PCPG,THYM	PCPG	GBM
ENSG00000260966	ENSG00000138138	ATAD1	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000139597	N4BP2L1	BRCA,GBM,LGG,PCPG,THYM	PCPG	GBM
ENSG00000260966	ENSG00000140386	SCAPER	BRCA,GBM,LAML,LGG,PCPG,THYM	PCPG	GBM
ENSG00000260966	ENSG00000152484	USP12	BRCA,GBM,LAML,LGG,PCPG,THYM	PCPG	GBM
ENSG00000260966	ENSG00000156052	GNAQ	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000160584	SIK3	BRCA,GBM,LGG,PCPG,THYM		GBM
ENSG00000260966	ENSG00000163539	CLASP2	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000164031	DNAJB14	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000164187	LMBRD2	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000165572	KBTBD6	BRCA,GBM,LAML,LGG,PCPG,THYM	PCPG	GBM
ENSG00000260966	ENSG00000165650	PDZD8	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000176055	MBLAC2	BRCA,GBM,LAML,LGG,PCPG,THYM		GBM
ENSG00000260966	ENSG00000180488	MIGA1	BRCA,GBM,LAML,LGG,PCPG,THYM		GBM
ENSG00000260966	ENSG00000182670	TTC3	BRCA,GBM,LAML,PCPG,THYM		GBM
ENSG00000260966	ENSG00000185658	BRWD1	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000185716	MOSMO	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000196177	ACADSB	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000197885	NKIRAS1	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000204116	CHIC1	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000204130	RUFY2	BRCA,GBM,LAML,LGG,THYM		GBM
ENSG00000260966	ENSG00000123178	SPRYD7	GBM,LAML,LGG,PCPG,THYM		GBM
ENSG00000260966	ENSG00000128989	ARPP19	GBM,LAML,LGG,PCPG,THYM		GBM

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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	dG	nDG	Cancer with PC gene up-regulation	Cancer with PC gene Down-regulation
ENSG00000260966	ENST00000561652	TYMP	ENSG00000025708	ENST00000395680	-0.6140	4280	GBM	-
ENSG00000260966	ENST00000561652	TYMP	ENSG00000025708	ENST00000395681	-0.6140	4280	GBM	-
ENSG00000260966	ENST00000561652	TYMP	ENSG00000025708	ENST00000252029	-0.6140	4280	GBM	-
ENSG00000260966	ENST00000561652	TYMP	ENSG00000025708	ENST00000613148	-0.6140	4283	GBM	-
ENSG00000260966	ENST00000561652	TYMP	ENSG00000025708	ENST00000395678	-0.6140	4284	GBM	-
ENSG00000260966	ENST00000561652	CAPG	ENSG00000042493	ENST00000263867	-0.1316	4263	GBM	-
ENSG00000260966	ENST00000561652	CAPG	ENSG00000042493	ENST00000453973	-0.1569	4263	GBM	-
ENSG00000260966	ENST00000561652	CAPG	ENSG00000042493	ENST00000409921	-0.1788	4263	GBM	-
ENSG00000260966	ENST00000561652	CAPG	ENSG00000042493	ENST00000409670	-0.5129	4256	GBM	-
ENSG00000260966	ENST00000561652	TSPO	ENSG00000100300	ENST00000329563	-0.1206	3874	GBM	-
ENSG00000260966	ENST00000561652	CLIC1	ENSG00000213719	ENST00000375784	-0.1117	1194	GBM	-
ENSG00000260966	ENST00000561652	CLIC1	ENSG00000213719	ENST00000375779	-0.1117	1194	GBM	-
ENSG00000260966	ENST00000561652	CLIC1	ENSG00000213719	ENST00000375780	-0.1117	1194	GBM	-
ENSG00000260966	ENST00000561652	CLIC1	ENSG00000213719	ENST00000395892	-0.1117	1194	GBM	-
ENSG00000260966	ENST00000561652	CLIC1	ENSG00000213719	ENST00000616760	-0.1117	1196	GBM	-

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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

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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
ENSG00000260966.1	ENST00000561652.1	94	660	376

	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