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lncRNA: ENSG00000269946

Summary for RP11-2B6.3

Gene summary

Gene information	Ensembl ID	ENSG00000269946
	Gene symbol	RP11-2B6.3
	Gene name
	HGNC
	Entrez ID
	Gene type	lincRNA
	Synonyms
	UniProtAcc

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Structure and expression level for RP11-2B6.3

AS events and RNA A-to-I editing events of lncRNA in TCGA based on Genvode V22 structure.

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
ENSG00000269946	1.715812e+01	1.928697e+00	4.874002e-01	3.957112e+00	7.590000e-05	3.889810e-04	UP	GBM
ENSG00000269946	4.293926e+01	1.313216e+00	1.311035e-01	1.001664e+01	1.290000e-23	2.440000e-22	UP	THCA
ENSG00000269946	1.618847e+01	1.114460e+00	1.363459e-01	8.173773e+00	2.990000e-16	1.440000e-15	UP	KIRC
ENSG00000269946	1.880946e+01	1.248879e+00	2.442447e-01	5.113230e+00	3.170000e-07	1.300000e-06	UP	KICH
ENSG00000269946	1.646033e+01	1.072339e+00	2.222749e-01	4.824381e+00	1.400000e-06	5.970000e-06	UP	KIRP
ENSG00000269946	8.323379e+00	1.247692e+00	3.992766e-01	3.124882e+00	1.778765e-03	9.169100e-03	UP	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000269946	5.874939e-01	2.207927e-05	CHOL	1.085887e-04
ENSG00000269946	3.664750e-01	4.121638e-04	KICH	6.186294e-04

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lncRNA-Protein interaction for RP11-2B6.3

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

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 RP11-2B6.3

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

Only predicted by TDF

DDX11,PHF1,RBM6,SLIRP,GLI4,DDX49,RBM39,CENPT,TTC14,NOL3,MYPOP,HSF4,THOC6,RBM42,RBM5,IRF3,CIRBP,SUGP1,DDX56,IMP3,TIGD5,MZF1,LSM4,DMTF1,REXO4,TIGD1,CPSF1,RBM10,DDX51,TRA2A,MBD3,PCBP4,THAP3,CWC15,DHX34,HINFP,XPA,FIZ1,NR2C1,PPIE,USF2,ZMAT1,ZNF83,RALY,USF1,CXXC1,NR1H2,SNRPA,SAFB2,THOC1,ZNF18

Exist in public source

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 RP11-2B6.3

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

Only predicted by lncTar

SMAD1,ZFP91,SON,AGFG1,GTF2I,STAU1,REST,CEBPZ,CSDE1,HBP1,ZXDA,LARP4,TEAD1,ADNP,NAF1,ASH1L,BRF2,FOXN3,IREB2,SP2,EEA1,AGO1,SF3A1,BPTF,CPSF2,ATF1,NCOA2,DDX3X,DDX46,MTF1,GLYR1,KLF11,SYNJ1,RBM12,AQR,RBM18,ATMIN,NCOA1

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 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
ENSG00000269946	ENST00000602703	exon_skip_3490	chr1:28742402-28743986	-25.28	-0.1296	YTHDF2	ENST00000373812,ENST00000542507	In-frame
ENSG00000269946	ENST00000602703	exon_skip_380242	chr3:186784961-186785101	-13.42	-0.1091	EIF4A2	ENST00000323963	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_7523	chr1:78660553-78660654	-9.19	-0.1178	IFI44	ENST00000370747	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_29583	chr1:114780109-114780215	-10.73	-0.1882	SIKE1	ENST00000060969	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_41813	chr10:68337857-68337996	-15.67	-0.1178	HNRNPH3	ENST00000265866	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_53559	chr10:101793912-101793998	-10.61	-0.1798	OGA	ENST00000361464	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_66482	chr11:126274926-126275021	-14.50	-0.1790	FOXRED1	ENST00000263578	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_127623	chr15:58899468-58899937	-23.31	-0.1055	SLTM	ENST00000380516	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_300663	chr19:1425877-1425960	-9.16	-0.2349	DAZAP1	ENST00000233078	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_302168	chr19:10680345-10680443	-9.96	-0.1132	ILF3	ENST00000590261	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_370518	chr22:50247691-50247776	-14.47	-0.1904	HDAC10	ENST00000216271	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_374497	chr3:49999439-49999513	-10.41	-0.4338	RBM6	ENST00000266022	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_377198	chr3:123130479-123130616	-15.83	-0.1740	PDIA5	ENST00000316218	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_382458	chr3:38131595-38131638	-12.70	-0.3432	ACAA1	ENST00000333167	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_442657	chr5:74730259-74730398	-14.18	-0.1377	GFM2	ENST00000296805,ENST00000509430	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_462144	chr6:125298713-125298816	-13.03	-0.1498	HDDC2	ENST00000398153	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_470226	chr7:103307595-103307708	-11.33	-0.1122	PMPCB	ENST00000249269	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_476549	chr7:76013741-76013887	-19.64	-0.2112	STYXL1	ENST00000248600,ENST00000359697,ENST00000431581	Frame-shift
ENSG00000269946	ENST00000602703	exon_skip_481699	chr8:19824802-19824972	-14.26	-0.1927	INTS10	ENST00000397977	Frame-shift

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 RP11-2B6.3

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

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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
ENSG00000269946.1	ENST00000602703.1	101	781	1086

	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