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lncRNA: ENSG00000277978

Summary for RP11-403P17.6

Gene summary

Gene information	Ensembl ID	ENSG00000277978
	Gene symbol	RP11-403P17.6
	Gene name
	HGNC
	Entrez ID
	Gene type	antisense
	Synonyms
	UniProtAcc

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Structure and expression level for RP11-403P17.6

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
ENSG00000277978	4.128801e+01	1.836279e+00	3.656866e-01	5.021457e+00	5.130000e-07	3.560000e-06	UP	CHOL
ENSG00000277978	6.241387e+01	1.608844e+00	2.310646e-01	6.962745e+00	3.340000e-12	2.460000e-11	UP	KICH
ENSG00000277978	4.736017e+01	1.257743e+00	2.348182e-01	5.356242e+00	8.500000e-08	9.720000e-07	UP	BLCA
ENSG00000277978	6.640424e+01	1.893496e+00	5.123171e-01	3.695946e+00	2.190700e-04	2.325895e-03	UP	CESC
ENSG00000277978	3.089283e+01	1.165337e+00	1.601179e-01	7.277989e+00	3.390000e-13	2.580000e-12	UP	COAD
ENSG00000277978	4.519247e+01	1.132049e+00	1.764602e-01	6.415324e+00	1.410000e-10	1.950000e-09	UP	STAD
ENSG00000277978	2.531425e+01	1.144792e+00	2.621755e-01	4.366512e+00	1.260000e-05	1.212830e-04	UP	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000277978	5.461488e-01	1.041164e-04	CHOL	3.091446e-04

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lncRNA-Protein interaction for RP11-403P17.6

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

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 RP11-403P17.6

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 RP11-403P17.6

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

Only predicted by lncTar

IDH3A,COPB2,CLTC,ATP2A2,WIPF2,SNX2,SEC23B,PRKAR2A,LZIC,THTPA,RAB5C,EIF3L,NBR1,HBP1,HSPA8,SPTLC1,CSNK1A1,M6PR,LARS2,NIPA2,KTN1,ILK,PFKM,BECN1,RDX,SLC35A5,COPS4,ERLIN2,CTNNA1,KBTBD4,RNF40,APP,CCT7,MAIP1,MRPS28,ARL2BP,GBA,TSR1,EVC,MID2,NCOA4,KIAA0100,BTD,PLEKHB2,ITFG1,EIF4G1,RAB7A,IARS1,DOLK,TMLHE,PRMT5,AIMP2,DDB1,TMBIM6,RTCB,AZI2,PSMD1,RECQL,OS9,IPO5,MPDZ,MCFD2,CAP1,PSME3,NDUFS1,AP2B1,NOMO2

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
ENSG00000277978	ENST00000612427	exon_skip_1234	chr1:11658532-11658628	-12.11	-0.1288	FBXO44	ENST00000251547,ENST00000376770	In-frame
ENSG00000277978	ENST00000612427	exon_skip_435005	chr5:65655635-65655653	-4.90	-0.2882	TRAPPC13	ENST00000399438	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
ENSG00000277978	ENST00000612427	exon_skip_52671	chr10:97461495-97461622	-12.95	-0.2312	MMS19	ENST00000370782,ENST00000438925	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_133217	chr16:8635038-8635079	-7.89	-0.2721	METTL22	ENST00000381920	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_287874	chr17:29085603-29085648	-4.60	-0.3833	MYO18A	ENST00000527372	In-frame
ENSG00000277978	ENST00000612427	exon_skip_309204	chr19:49181348-49181461	-13.88	-0.2012	TRPM4	ENST00000252826	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_340759	chr2:85552415-85552567	-12.22	-0.1260	GGCX	ENST00000233838	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_353131	chr20:58669290-58669453	-18.58	-0.2382	STX16	ENST00000371141	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_379903	chr3:184180644-184180650	-1.87	-0.9350	AP2M1	ENST00000292807	In-frame
ENSG00000277978	ENST00000612427	exon_skip_382458	chr3:38131595-38131638	-6.09	-0.4350	ACAA1	ENST00000333167	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_9446	chr1:147270931-147271005	-12.34	-0.3335	CHD1L	ENST00000369258	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_11029	chr1:154989559-154989707	-16.19	-0.1236	FLAD1	ENST00000292180	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_66482	chr11:126274926-126275021	-8.79	-0.1256	FOXRED1	ENST00000263578	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_127618	chr15:58890280-58890461	-11.43	-0.1155	SLTM	ENST00000380516	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_290158	chr17:42953723-42953778	-4.95	-0.2605	AARSD1	ENST00000427569	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_302168	chr19:10680345-10680443	-10.44	-0.1147	ILF3	ENST00000590261	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_358821	chr20:63943652-63943669	-5.57	-2.7850	UCKL1	ENST00000354216	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_365497	chr22:38067703-38067770	-9.76	-0.1842	PICK1	ENST00000356976,ENST00000404072	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_370518	chr22:50247691-50247776	-10.49	-0.2559	HDAC10	ENST00000216271	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_438188	chr5:141638954-141639021	-10.33	-0.1722	RELL2	ENST00000297164,ENST00000444782	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_444499	chr5:138164086-138164133	-5.44	-0.1648	BRD8	ENST00000254900	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_470226	chr7:103307595-103307708	-8.41	-0.1051	PMPCB	ENST00000249269	Frame-shift
ENSG00000277978	ENST00000612427	exon_skip_499791	chr9:128627924-128627942	-3.10	-0.6200	SPTAN1	ENST00000372731	In-frame

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 RP11-403P17.6

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	dG	nDG	Cancer with PC gene up-regulation	Cancer with PC gene Down-regulation
ENSG00000277978	ENST00000612427	TMBIM6	ENSG00000139644	ENST00000552635	-0.1310	32	-	CHOL
ENSG00000277978	ENST00000612427	TMBIM6	ENSG00000139644	ENST00000552370	-0.3050	25	-	CHOL
ENSG00000277978	ENST00000612427	EIF3L	ENSG00000100129	ENST00000381683	-0.6600	358	-	CESC
ENSG00000277978	ENST00000612427	NDUFS1	ENSG00000023228	ENST00000457011	-0.1433	1	-	CHOL
ENSG00000277978	ENST00000612427	MPDZ	ENSG00000107186	ENST00000319217	-0.1776	1	-	CHOL,BLCA,STAD
ENSG00000277978	ENST00000612427	MPDZ	ENSG00000107186	ENST00000541718	-0.1776	1	-	CHOL,BLCA,STAD
ENSG00000277978	ENST00000612427	MPDZ	ENSG00000107186	ENST00000381022	-0.1776	1	-	CHOL,BLCA,STAD
ENSG00000277978	ENST00000612427	MPDZ	ENSG00000107186	ENST00000438511	-0.1776	1	-	CHOL,BLCA,STAD
ENSG00000277978	ENST00000612427	MPDZ	ENSG00000107186	ENST00000545857	-0.1776	1	-	CHOL,BLCA,STAD
ENSG00000277978	ENST00000612427	MPDZ	ENSG00000107186	ENST00000538841	-0.1776	1	-	CHOL,BLCA,STAD
ENSG00000277978	ENST00000612427	MPDZ	ENSG00000107186	ENST00000536827	-0.1776	1	-	CHOL,BLCA,STAD
ENSG00000277978	ENST00000612427	MPDZ	ENSG00000107186	ENST00000447879	-0.1776	1	-	CHOL,BLCA,STAD
ENSG00000277978	ENST00000612427	MPDZ	ENSG00000107186	ENST00000546205	-0.3742	35	-	CHOL,BLCA,STAD
ENSG00000277978	ENST00000612427	RDX	ENSG00000137710	ENST00000534683	-0.3265	110	-	CHOL,READ
ENSG00000277978	ENST00000612427	MRPS28	ENSG00000147586	ENST00000521434	-0.2188	262	-	CHOL
ENSG00000277978	ENST00000612427	MAIP1	ENSG00000162972	ENST00000295079	-0.1550	1	-	CHOL
ENSG00000277978	ENST00000612427	MAIP1	ENSG00000162972	ENST00000392290	-0.1550	1	-	CHOL
ENSG00000277978	ENST00000612427	MAIP1	ENSG00000162972	ENST00000435773	-0.1589	151	-	CHOL
ENSG00000277978	ENST00000612427	BTD	ENSG00000169814	ENST00000449107	-0.2272	86	-	CHOL,CESC,COAD,STAD
ENSG00000277978	ENST00000612427	BTD	ENSG00000169814	ENST00000303498	-0.1269	1	-	CHOL,CESC,COAD,STAD
ENSG00000277978	ENST00000612427	BTD	ENSG00000169814	ENST00000437172	-0.1269	1	-	CHOL,CESC,COAD,STAD
ENSG00000277978	ENST00000612427	BTD	ENSG00000169814	ENST00000383778	-0.1269	1	-	CHOL,CESC,COAD,STAD
ENSG00000277978	ENST00000612427	NCOA4	ENSG00000266412	ENST00000585056	-0.1033	1	-	CHOL,COAD,READ
ENSG00000277978	ENST00000612427	NCOA4	ENSG00000266412	ENST00000583565	-0.1094	1	-	CHOL,COAD,READ
ENSG00000277978	ENST00000612427	NCOA4	ENSG00000266412	ENST00000580070	-0.1033	1	-	CHOL,COAD,READ
ENSG00000277978	ENST00000612427	NCOA4	ENSG00000266412	ENST00000578454	-0.1200	1	-	CHOL,COAD,READ
ENSG00000277978	ENST00000612427	NCOA4	ENSG00000266412	ENST00000579039	-0.1033	1	-	CHOL,COAD,READ
ENSG00000277978	ENST00000612427	EVC	ENSG00000072840	ENST00000509451	-0.1009	53	-	KICH,BLCA,READ
ENSG00000277978	ENST00000612427	MID2	ENSG00000080561	ENST00000262843	-0.1564	321	-	BLCA,STAD
ENSG00000277978	ENST00000612427	MID2	ENSG00000080561	ENST00000443968	-0.1564	321	-	BLCA,STAD
ENSG00000277978	ENST00000612427	ILK	ENSG00000166333	ENST00000532063	-0.1261	1	-	BLCA,CESC,COAD,STAD,READ
ENSG00000277978	ENST00000612427	ILK	ENSG00000166333	ENST00000299421	-0.1261	1	-	BLCA,CESC,COAD,STAD,READ
ENSG00000277978	ENST00000612427	ILK	ENSG00000166333	ENST00000537806	-0.1261	1	-	BLCA,CESC,COAD,STAD,READ
ENSG00000277978	ENST00000612427	ILK	ENSG00000166333	ENST00000420936	-0.1261	1	-	BLCA,CESC,COAD,STAD,READ
ENSG00000277978	ENST00000612427	ILK	ENSG00000166333	ENST00000528995	-0.1261	1	-	BLCA,CESC,COAD,STAD,READ
ENSG00000277978	ENST00000612427	ILK	ENSG00000166333	ENST00000396751	-0.1261	1	-	BLCA,CESC,COAD,STAD,READ
ENSG00000277978	ENST00000612427	ILK	ENSG00000166333	ENST00000526318	-0.1261	1	-	BLCA,CESC,COAD,STAD,READ

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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
ENSG00000277978.1	ENST00000612427.1	310	162	1094

	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