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Center for Computational Systems Medicine
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lncRNA summary

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lncRNA structure and expression level

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lncRNA-Protein interaction

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lncRNA-DNA interaction

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lncRNA-RNA interaction

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Variants in lncRNA

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lncRNAs regulate the target genes through functioning as enhancers

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lncRNAs regulate the target genes through recruiting transcript factors

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lncRNAs regulate the alternative splicing events through interacting with splicing factor

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lncRNAs regulate mRNA through targeting the 3'-UTR region

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lncRNAs regulate mRNA by competing with miRNA

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lncRNA coding potential

lncRNA: ENSG00000269946

Summary for RP11-2B6.3

check button Gene summary

Gene informationEnsembl ID

ENSG00000269946

Gene symbol

RP11-2B6.3

Gene name
HGNC
Entrez ID
Gene typelincRNA
Synonyms
UniProtAcc

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Structure and expression level for RP11-2B6.3

check buttonAS events and RNA A-to-I editing events of lncRNA in TCGA based on Genvode V22 structure.
UCSC result

check buttonDifferentially expressed gene analysis between cancer and normal samples.
DEG result
Ensembl IDBase meanlog2FC(AD/control)lfcSEStatP-valueAdjc.p-valueDEG direction Cancer type
ENSG000002699461.715812e+011.928697e+004.874002e-013.957112e+007.590000e-053.889810e-04UPGBM
ENSG000002699464.293926e+011.313216e+001.311035e-011.001664e+011.290000e-232.440000e-22UPTHCA
ENSG000002699461.618847e+011.114460e+001.363459e-018.173773e+002.990000e-161.440000e-15UPKIRC
ENSG000002699461.880946e+011.248879e+002.442447e-015.113230e+003.170000e-071.300000e-06UPKICH
ENSG000002699461.646033e+011.072339e+002.222749e-014.824381e+001.400000e-065.970000e-06UPKIRP
ENSG000002699468.323379e+001.247692e+003.992766e-013.124882e+001.778765e-039.169100e-03UPREAD

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000002699465.874939e-012.207927e-05CHOL1.085887e-04
ENSG000002699463.664750e-014.121638e-04KICH6.186294e-04

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lncRNA-Protein interaction for RP11-2B6.3

lncrna_protein
check buttonlncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source

check buttonlncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source

check buttonlncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source

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lncRNA-DNA interaction for RP11-2B6.3

lncrna_DNA
check buttonlncRNA 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
NA

check buttonlncRNA targets the promoter region and positively regulates the gene expression.

check buttonlncRNA targets the promoter region and negatively regulates the gene expression.

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lncRNA-RNA interaction for RP11-2B6.3

lncrna_RNA
check buttonlncRNA 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
NA

check buttonlncRNA targets the skipped exon region.
-lncRNA and exonskipping events are positively correlated.
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonORF mutation

-lncRNA and exonskipping events are negatively correlated.
lncRNA and exonskipping events negative correlated
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonLOF
ENSG00000269946ENST00000602703exon_skip_3490chr1:28742402-28743986-25.28-0.1296YTHDF2ENST00000373812,ENST00000542507In-frame
ENSG00000269946ENST00000602703exon_skip_380242chr3:186784961-186785101-13.42-0.1091EIF4A2ENST00000323963Frame-shift
ENSG00000269946ENST00000602703exon_skip_7523chr1:78660553-78660654-9.19-0.1178IFI44ENST00000370747Frame-shift
ENSG00000269946ENST00000602703exon_skip_29583chr1:114780109-114780215-10.73-0.1882SIKE1ENST00000060969Frame-shift
ENSG00000269946ENST00000602703exon_skip_41813chr10:68337857-68337996-15.67-0.1178HNRNPH3ENST00000265866Frame-shift
ENSG00000269946ENST00000602703exon_skip_53559chr10:101793912-101793998-10.61-0.1798OGAENST00000361464Frame-shift
ENSG00000269946ENST00000602703exon_skip_66482chr11:126274926-126275021-14.50-0.1790FOXRED1ENST00000263578Frame-shift
ENSG00000269946ENST00000602703exon_skip_127623chr15:58899468-58899937-23.31-0.1055SLTMENST00000380516Frame-shift
ENSG00000269946ENST00000602703exon_skip_300663chr19:1425877-1425960-9.16-0.2349DAZAP1ENST00000233078Frame-shift
ENSG00000269946ENST00000602703exon_skip_302168chr19:10680345-10680443-9.96-0.1132ILF3ENST00000590261Frame-shift
ENSG00000269946ENST00000602703exon_skip_370518chr22:50247691-50247776-14.47-0.1904HDAC10ENST00000216271Frame-shift
ENSG00000269946ENST00000602703exon_skip_374497chr3:49999439-49999513-10.41-0.4338RBM6ENST00000266022Frame-shift
ENSG00000269946ENST00000602703exon_skip_377198chr3:123130479-123130616-15.83-0.1740PDIA5ENST00000316218Frame-shift
ENSG00000269946ENST00000602703exon_skip_382458chr3:38131595-38131638-12.70-0.3432ACAA1ENST00000333167Frame-shift
ENSG00000269946ENST00000602703exon_skip_442657chr5:74730259-74730398-14.18-0.1377GFM2ENST00000296805,ENST00000509430Frame-shift
ENSG00000269946ENST00000602703exon_skip_462144chr6:125298713-125298816-13.03-0.1498HDDC2ENST00000398153Frame-shift
ENSG00000269946ENST00000602703exon_skip_470226chr7:103307595-103307708-11.33-0.1122PMPCBENST00000249269Frame-shift
ENSG00000269946ENST00000602703exon_skip_476549chr7:76013741-76013887-19.64-0.2112STYXL1ENST00000248600,ENST00000359697,ENST00000431581Frame-shift
ENSG00000269946ENST00000602703exon_skip_481699chr8:19824802-19824972-14.26-0.1927INTS10ENST00000397977Frame-shift

check buttonlncRNA targets by miRNA.
LncRNA Ensembl IDmiRNA IDLncRNA ENST IDBinding site in lncRNAScoreEnergyAlign LenPublic source

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Variants for RP11-2B6.3

check buttonRNA A-to-I editing events in lncRNA.
LncRNAediting IDLncRNA Ensembl IDChromosomeEditing PositionStrandGene TypeGene NameTranscript IDTranscript TypeTranscript Name

check buttonEdited-associated DElncRNAs in cancer.
LncRNA Ensembl IDLncRNA IndexCancer TypeChr_Postion_StrandAVE1AVE2log2FCW-valueP-valueAdjc.p-valueChange

check buttonCorrelation between RNA A-to-I editing events's frequecy and lncRNA expression.
LncRNA Ensembl IDLncRNA IndexCorrelationP-valueAdjc.p-value

check buttonCis-expression quantitative trait loci(cis-eQTL) of lncRNA.
LncRNA Ensembl IDLncRNA NameSNP infoNumber of Positive corelated CancerPositive corelated CancerNumber of Negative corelated CancerNegative corelated Cancer

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lncRNAs regulate the target genes through functioning as enhancers

lncrna_enhancer
check buttonlncRNA regulates differentially expressed genes by function as enhancer.
LncRNA Ensembl IDPC Gene IDPC Gene NamePositive correlated cancersCancer with PC gene up-regulationCancer with PC gene down-regulation

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lncRNAs regulate the target genes through recruiting transcript factors

lncrna_TF
check buttonLncRNA-TF complex positively regulates the gene expression by target promoter region (#cancer types with positive correlation >= 5).
lncRNA IDTF IDTF NamePCgene IDPCgene NameNumber of CancerCanaer Types

check buttonLncRNA-TF complex negatively regulates the gene expression by target promoter region (#cancer types with negative correlation >= 5).
lncRNA IDTF IDTF NamePCgene IDPCgene NameNumber of CancerCanaer Types

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lncRNAs regulate the alternative splicing event through interacting with splicing factor

lncrna_AS
check buttonLncRNA-RBP complex positively regulates the exon skippping events by target skipped eoxon region.
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type

check buttonLncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type

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lncRNAs regulate mRNA through targeting the 3'-UTR region

lncrna_mRNA
check buttonlncRNA regulates differential expressed mRNA by directly targeting 3' UTR region.
LncRNA Ensembl IDLncRNA ENST IDPC Gene NamePC Gene IDPC ENST IDdGnDGCancer with PC gene up-regulationCancer with PC gene Down-regulation

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lncRNAs regulate mRNA by competing with miRNA

lncrna_miRNA
check buttonlncRNA regulates mRNA by competing the miRNA binding site with mRNA.
LncRNA Ensembl IDlncRNA-miRNA-mRNACancer Types

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lncRNA coding potential

check buttonORFfinder result for the gencode.v22.lncRNA.transcript.fa.
lncRNA Ensembl IDlncRNA ENST IDlength(AA)start at transcriptend at transcript
ENSG00000269946.1ENST00000602703.11017811086