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lncRNA: ENSG00000260418

Summary for RP3-406A7.7

Gene summary

Gene information	Ensembl ID	ENSG00000260418
	Gene symbol	RP3-406A7.7
	Gene name
	HGNC
	Entrez ID
	Gene type	lincRNA
	Synonyms
	UniProtAcc

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Structure and expression level for RP3-406A7.7

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
ENSG00000260418	3.858946e+01	-3.610019e+00	5.023250e-01	-7.186621e+00	6.640000e-13	1.970000e-11	DOWN	GBM
ENSG00000260418	1.505590e+02	1.196946e+00	3.220421e-01	3.716737e+00	2.018120e-04	9.604540e-04	UP	BLCA
ENSG00000260418	1.814476e+02	3.327036e+00	6.944123e-01	4.791154e+00	1.660000e-06	3.870000e-05	UP	CESC
ENSG00000260418	3.261078e+02	1.437365e+00	2.140001e-01	6.716656e+00	1.860000e-11	1.650000e-10	UP	KIRP
ENSG00000260418	8.502251e+01	1.469826e+00	1.989810e-01	7.386765e+00	1.500000e-13	1.380000e-12	UP	UCEC
ENSG00000260418	8.909040e+01	1.012541e+00	2.204907e-01	4.592215e+00	4.390000e-06	2.520000e-05	UP	STAD

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000260418	-5.459605e-01	3.137944e-08	KICH	1.414532e-07

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lncRNA-Protein interaction for RP3-406A7.7

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
ENSG00000260418	ENST00000564248	RP3-406A7.7	ENSG00000154832	CXXC1	32.27	90.5378	Q9P0U4	TF,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
ENSG00000260418	ENST00000564248	RP3-406A7.7	ENSG00000130254	SAFB2	55.03	91.1248	Q14151	TF,RBP	NA
ENSG00000260418	ENST00000564248	RP3-406A7.7	ENSG00000099326	MZF1	50.18	90.2662	P28698	TF	NA
ENSG00000260418	ENST00000564248	RP3-406A7.7	ENSG00000154832	CXXC1	32.27	90.69	Q9P0U4	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
ENSG00000260418	ENST00000564248	RP3-406A7.7	ENSG00000111641	NOP2	59.7	90.4103	P46087	RBP	NA
ENSG00000260418	ENST00000564248	RP3-406A7.7	ENSG00000130254	SAFB2	55.03	90.2975	Q14151	TF,RBP	NA
ENSG00000260418	ENST00000564248	RP3-406A7.7	ENSG00000004534	RBM6	53.56	92.4161	P78332	RBP	NA

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lncRNA-DNA interaction for RP3-406A7.7

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 RP3-406A7.7

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

Only predicted by lncTar

SMAD1,CELF2,SON,AGFG1,DHX8,REST,HBP1,ZEB1,ASCC1,BBX,NAF1,BRF2,ELF1,ZNF28,PHF20,FOXN3,NOP9,G3BP1,EEA1,XRN1,SART3,SF3A1,RFX5,CPSF2,NCOA2,ATF1,ADAT1,GLYR1,MTF1,DDX3X,RBM7,CREB1

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
ENSG00000260418	ENST00000564248	exon_skip_384879	chr3:52554723-52554879	-29.91	-0.2021	PBRM1	ENST00000296302	In-frame
ENSG00000260418	ENST00000564248	exon_skip_461111	chr6:90544551-90544632	-11.64	-0.2007	MAP3K7	ENST00000369329	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
ENSG00000260418	ENST00000564248	exon_skip_5818	chr1:45568484-45568684	-21.19	-0.1171	AKR1A1	ENST00000351829,ENST00000372070	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_309204	chr19:49181348-49181461	-16.86	-0.1669	TRPM4	ENST00000252826	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_334405	chr2:227352513-227352573	-9.73	-0.2263	MFF	ENST00000353339	In-frame
ENSG00000260418	ENST00000564248	exon_skip_361434	chr21:25997359-25997416	-11.98	-0.2260	APP	ENST00000346798	In-frame
ENSG00000260418	ENST00000564248	exon_skip_368285	chr22:29329711-29329720	-2.79	-1.3950	AP1B1	ENST00000357586,ENST00000405198	In-frame
ENSG00000260418	ENST00000564248	exon_skip_380242	chr3:186784961-186785101	-16.04	-0.1215	EIF4A2	ENST00000323963	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_382458	chr3:38131595-38131638	-6.34	-0.1626	ACAA1	ENST00000333167	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_514511	chrX:41555599-41555635	-6.43	-0.2923	CASK	ENST00000378163	In-frame
ENSG00000260418	ENST00000564248	exon_skip_53559	chr10:101793912-101793998	-11.25	-0.1679	OGA	ENST00000361464	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_66482	chr11:126274926-126275021	-17.80	-0.2046	FOXRED1	ENST00000263578	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_95500	chr12:96003837-96003920	-9.45	-0.1817	LTA4H	ENST00000228740	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_111863	chr14:23565815-23565892	-12.26	-0.1635	AP1G2	ENST00000308724,ENST00000397120	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_319223	chr19:43526200-43526349	-17.42	-0.1235	ETHE1	ENST00000292147	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_339830	chr2:69423581-69423717	-14.60	-0.2281	NFU1	ENST00000410022	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_370525	chr22:50250426-50250523	-17.01	-0.2126	HDAC10	ENST00000216271	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_371367	chr3:9697710-9697866	-19.77	-0.1634	MTMR14	ENST00000296003	In-frame
ENSG00000260418	ENST00000564248	exon_skip_374375	chr3:49675182-49675309	-20.56	-0.2077	APEH	ENST00000296456	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_377198	chr3:123130479-123130616	-16.95	-0.1436	PDIA5	ENST00000316218	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_436035	chr5:79656957-79657001	-6.18	-0.3433	TENT2	ENST00000296783,ENST00000428308,ENST00000453514	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_442657	chr5:74730259-74730398	-18.53	-0.1570	GFM2	ENST00000296805,ENST00000509430	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_445390	chr5:150403120-150403312	-22.01	-0.1318	CD74	ENST00000009530	In-frame
ENSG00000260418	ENST00000564248	exon_skip_470226	chr7:103307595-103307708	-8.35	-0.1113	PMPCB	ENST00000249269	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_326741	chr2:73946718-73946906	-16.05	-0.1084	DGUOK	ENST00000264093	Frame-shift
ENSG00000260418	ENST00000564248	exon_skip_389267	chr3:146528613-146528831	-27.70	-0.1325	PLSCR1	ENST00000342435	Frame-shift

lncRNA targets by miRNA.

LncRNA Ensembl ID	miRNA ID	LncRNA ENST ID	Binding site in lncRNA	Score	Energy	Align Len	Public source
ENSG00000260418	hsa-mir-22	ENST00000564248	chr6:136335830-136335912	186.00	-78.10	85	NA
ENSG00000260418	hsa-mir-22	ENST00000564248	chr6:136335917-136336004	151.00	-84.12	81	NA

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Variants for RP3-406A7.7

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

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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

	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