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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: ENSG00000272405

Summary for RP11-284F21.10

check button Gene summary

Gene informationEnsembl ID

ENSG00000272405

Gene symbol

RP11-284F21.10

Gene name
HGNC
Entrez ID
Gene typeantisense
Synonyms
UniProtAcc

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Structure and expression level for RP11-284F21.10

check buttonDifferentially expressed gene analysis between cancer and normal samples.
DEG result
Ensembl IDBase meanlog2FC(AD/control)lfcSEStatP-valueAdjc.p-valueDEG direction Cancer type
ENSG000002724052.348559e+021.432957e+003.736917e-013.834597e+001.257700e-046.070110e-04UPGBM
ENSG000002724051.065531e+035.429094e+005.350078e-011.014769e+013.390000e-243.050000e-22UPCHOL
ENSG000002724054.489916e+022.559112e+001.514513e-011.689725e+014.710000e-641.870000e-62UPKIRC
ENSG000002724056.999031e+023.779040e+008.709176e-014.339147e+001.430000e-052.417240e-04UPCESC
ENSG000002724053.887761e+023.207412e+002.924256e-011.096830e+015.430000e-282.440000e-26UPHNSC
ENSG000002724051.451137e+034.759020e+002.399292e-011.983510e+011.480000e-874.650000e-84UPKIRP
ENSG000002724051.908686e+022.378778e+003.550028e-016.700730e+002.070000e-111.520000e-10UPUCEC
ENSG000002724056.411291e+023.786762e+003.163739e-011.196926e+015.150000e-336.340000e-32UPLUSC
ENSG000002724055.170065e+021.937682e+001.926545e-011.005781e+018.490000e-246.570000e-23UPBRCA
ENSG000002724055.661396e+024.437493e+002.723731e-011.629197e+011.130000e-599.650000e-58UPLUAD
ENSG000002724051.106021e+031.136143e+001.480684e-017.673096e+001.680000e-141.450000e-13UPCOAD
ENSG000002724055.674782e+023.768711e+002.977050e-011.265921e+019.950000e-378.350000e-35UPLIHC
ENSG000002724051.096454e+031.452190e+002.643646e-015.493134e+003.950000e-083.460000e-07UPSTAD
ENSG000002724051.217432e+031.258883e+003.377138e-013.727662e+001.932640e-041.343675e-03UPREAD

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000002724055.826370e-012.678431e-05CHOL1.244509e-04
ENSG000002724053.681812e-015.903057e-21KIRC5.366415e-20
ENSG000002724054.898256e-015.007042e-19KIRP6.118606e-17
ENSG000002724053.512759e-011.847433e-18LUAD5.735074e-17

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lncRNA-Protein interaction for RP11-284F21.10

lncrna_protein
check buttonlncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).
Epi result
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source
ENSG00000272405ENST00000605886RP11-284F21.10ENSG00000077152UBE2T50.7590.5533Q9NPD8EpiNA

check buttonlncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).
TF result
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source
ENSG00000272405ENST00000605886RP11-284F21.10ENSG00000143157POGK45.4193.8243Q9P215TFNA

check buttonlncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).
RBP result
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source
ENSG00000272405ENST00000605886RP11-284F21.10ENSG00000136937NCBP157.595.3439Q09161RBPNA
ENSG00000272405ENST00000605886RP11-284F21.10ENSG00000140694PARN50.993.8325O95453RBPNA
ENSG00000272405ENST00000605886RP11-284F21.10ENSG00000152332UHMK18.3592.7992Q8TAS1RBPNA

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lncRNA-DNA interaction for RP11-284F21.10

lncrna_DNA
check buttonlncRNA targets the enhancer region and positively regulates the gene expression.
Only predicted by TDF
GPX2,TBRG4,PMM2,NOB1,CEP20,ARHGEF2,EEF2KMT,EPRS1,SMG7,CCT3,PYGO2,C1orf56,TWNK,RTKN,RRNAD1,INTS3,MSTO1,MAFG,UBQLN4,SLC39A1,DARS2,NPRL3,UNKL,ADPRHL1,SPATA5L1,MTX1,EFTUD2,MFSD10,VARS1,DAP3,PYCR2,FAM136A,NDUFS2,PIGM,CHTOP,TFAP4,MRPL10,GOLGA1,UBE2T,TRIM16,QSOX2,RPAP1,IFT140,NOLC1,CTDNEP1,HDGF,IMP4,MRPL24,INTS7,MRM1,ADSS2,UBE2Q1,TFB2M,TMCO1,RCCD1,FAM189B,MARS2,RNPS1,CLK2,NCBP1,MFSD9,C1orf131,MYO19,GPATCH4,MGRN1,RRP12,LAD1,C1orf43,MORC2,PGAP2,ISG20L2,EXD3,MRRF,FLII,NQO1,DOK4,HSPD1,KLHL12,TNFRSF10B,IQGAP3,ALDOA,ELMO3,UBAP2L,C8orf33,ANKS3,CERS2,ETFA,JPT2,TKT,KNOP1,SCAMP3,TMEM186,PARN,TOR4A,SF3B4,ZDHHC9,ARL8A,TPM3,UCK2,UCHL5,MTIF2,RNPEP,COASY,MVP,PLCB3,PLOD3,ANKEF1,ABCC3,CAD,SMARCD1,GOLPH3L,PLS1,AATF,AXIN1,TRAP1,F11R,ATXN2L,NAA35,ABCB6,CSNK2A2,SRXN1,BROX,HARS2,CRTC2,TTLL12,SLC22A18,NOL8
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 RP11-284F21.10

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.
Only predicted by lncTar
CGRRF1
Exist in public source
NA

check buttonlncRNA targets the skipped exon region.
-lncRNA and exonskipping events are positively correlated.
lncRNA and exonskipping events positive correlated
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonORF mutation
ENSG00000272405ENST00000605886exon_skip_44998chr10:110132304-110132400-12.33-0.1486ADD3ENST00000356080In-frame
ENSG00000272405ENST00000605886exon_skip_131398chr15:101286213-101286293-15.23-0.1928SNRPA1ENST00000254193Frame-shift
ENSG00000272405ENST00000605886exon_skip_423795chr4:55888887-55888932-10.60-0.3533EXOC1ENST00000346134,ENST00000381295In-frame
ENSG00000272405ENST00000605886exon_skip_325891chr2:62987930-62988038-14.42-0.2289EHBP1ENST00000263991In-frame

-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
ENSG00000272405ENST00000605886exon_skip_21610chr1:9737497-9737554-12.73-0.2767CLSTN1ENST00000377298In-frame
ENSG00000272405ENST00000605886exon_skip_33516chr1:156938417-156938513-17.80-0.2781ARHGEF11ENST00000361409In-frame
ENSG00000272405ENST00000605886exon_skip_376144chr3:100311832-100311877-9.59-0.3552TBC1D23ENST00000394144In-frame

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

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Variants for RP11-284F21.10

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
ENSG00000272405ENSG00000052749RRP12ACC,CHOL,COAD,KIRP,PAAD,STADCHOL,COAD
ENSG00000272405ENSG00000066117SMARCD1ACC,CHOL,COAD,KIRP,LGGCHOL
ENSG00000272405ENSG00000107815TWNKACC,CHOL,ESCA,KIRP,LGG,STADSTAD
ENSG00000272405ENSG00000108846ABCC3ACC,CHOL,ESCA,HNSC,KIRC,KIRP,LIHC,LUSC,PAAD,UCSKIRC,KIRP
ENSG00000272405ENSG00000144381HSPD1ACC,CHOL,LUAD,MESO,STADLUAD,STAD
ENSG00000272405ENSG00000153531ADPRHL1BLCA,CHOL,ESCA,LUAD,PAADLUAD
ENSG00000272405ENSG00000110628SLC22A18BRCA,ESCA,KIRP,LIHC,PAAD,UCSBRCA
ENSG00000272405ENSG00000143457GOLPH3LBRCA,CHOL,ESCA,MESO,PAADCHOL
ENSG00000272405ENSG00000035141FAM136ACHOL,ESCA,KIRC,KIRP,LUSC,PAADLUSC
ENSG00000272405ENSG00000077152UBE2TCHOL,ESCA,KIRP,PAAD,STADCHOL,KIRP,STAD
ENSG00000272405ENSG00000084774CADCHOL,COAD,KIRC,KIRP,LGGCHOL,COAD
ENSG00000272405ENSG00000103126AXIN1CHOL,ESCA,GBM,KIRC,KIRP,LGG,LIHC,MESO,PAADKIRP
ENSG00000272405ENSG00000103550KNOP1CHOL,KIRP,LIHC,MESO,PAADCHOL
ENSG00000272405ENSG00000109736MFSD10CHOL,KIRC,KIRP,PAAD,UCSCHOL,KIRP
ENSG00000272405ENSG00000114993RTKNCHOL,COAD,ESCA,MESO,PAAD,READCOAD,READ
ENSG00000272405ENSG00000116521SCAMP3CHOL,KIRC,LIHC,LUSC,PAADCHOL,LIHC
ENSG00000272405ENSG00000116584ARHGEF2CHOL,COAD,ESCA,MESO,PAAD,READCHOL
ENSG00000272405ENSG00000117593DARS2CHOL,ESCA,HNSC,LUAD,LUSC,PAAD,STADLUAD,LUSC,STAD
ENSG00000272405ENSG00000120889TNFRSF10BCHOL,COAD,KIRC,KIRP,PAAD,READ,STAD,UCSCOAD,KIRC,KIRP,READ,STAD
ENSG00000272405ENSG00000125459MSTO1CHOL,COAD,GBM,MESO,PAADCHOL
ENSG00000272405ENSG00000126602TRAP1CHOL,ESCA,KIRC,KIRP,LGG,LUAD,MESO,PAAD,STADLUAD
ENSG00000272405ENSG00000143179UCK2CHOL,KIRP,LGG,LIHC,LUAD,LUSC,PAAD,STADCHOL,LIHC,LUAD,LUSC
ENSG00000272405ENSG00000143314MRPL24CHOL,ESCA,LIHC,LUSC,PAADLUSC
ENSG00000272405ENSG00000143569UBAP2LCHOL,COAD,GBM,LGG,MESO,PAAD,READCHOL
ENSG00000272405ENSG00000143570SLC39A1CHOL,ESCA,KIRC,KIRP,PAADCHOL
ENSG00000272405ENSG00000149782PLCB3CHOL,GBM,LGG,PAAD,STADCHOL
ENSG00000272405ENSG00000149925ALDOACHOL,KIRC,KIRP,LIHC,PAADCHOL,KIRC,KIRP,LIHC
ENSG00000272405ENSG00000159166LAD1CHOL,COAD,PAAD,READ,STAD,UCSCHOL
ENSG00000272405ENSG00000160767FAM189BCHOL,HNSC,KIRC,KIRP,PAADCHOL
ENSG00000272405ENSG00000160818GPATCH4CHOL,COAD,ESCA,LIHC,PAAD,READCHOL
ENSG00000272405ENSG00000163348PYGO2CHOL,ESCA,GBM,HNSC,PAADCHOL
ENSG00000272405ENSG00000163468CCT3CHOL,ESCA,KIRP,LIHC,MESO,PAAD,STADLIHC
ENSG00000272405ENSG00000166965RCCD1CHOL,GBM,LGG,LUAD,PAADLUAD
ENSG00000272405ENSG00000168096ANKS3CHOL,GBM,KIRC,LGG,LIHCCHOL,LIHC
ENSG00000272405ENSG00000182307C8orf33CHOL,KIRP,LIHC,STAD,UCSLIHC
ENSG00000272405ENSG00000183856IQGAP3CHOL,ESCA,GBM,KIRC,KIRP,PAAD,STADCHOL,GBM,KIRC,KIRP,STAD
ENSG00000272405ENSG00000187535IFT140CHOL,GBM,KIRC,KIRP,MESOCHOL
ENSG00000272405ENSG00000198113TOR4ACHOL,ESCA,KIRP,PAAD,STAD,UCSCHOL,KIRP
ENSG00000272405ENSG00000206053JPT2CHOL,KIRC,KIRP,LIHC,MESOCHOL
ENSG00000272405ENSG00000278259MYO19CHOL,GBM,LGG,PAAD,STAD,UCSCHOL
ENSG00000272405ENSG00000013364MVPESCA,KIRC,KIRP,LIHC,PAADKIRP
ENSG00000272405ENSG00000135953MFSD9ESCA,HNSC,LUAD,MESO,PAAD,STADLUAD
ENSG00000272405ENSG00000165661QSOX2ESCA,HNSC,KIRP,LGG,STADHNSC,STAD
ENSG00000272405ENSG00000181019NQO1ESCA,KIRP,LIHC,LUAD,LUSC,PAADKIRP,LIHC,LUAD,LUSC
ENSG00000272405ENSG00000059145UNKLHNSC,KIRP,LIHC,LUSC,MESOLIHC
ENSG00000272405ENSG00000115657ABCB6HNSC,KIRC,KIRP,LGG,LIHC,LUAD,LUSCKIRC,KIRP,LUAD,LUSC
ENSG00000272405ENSG00000163931TKTHNSC,KIRP,LIHC,LUAD,LUSCKIRP,LIHC
ENSG00000272405ENSG00000271303SRXN1HNSC,KIRP,LIHC,LUAD,LUSCLIHC,LUAD,LUSC
ENSG00000272405ENSG00000221926TRIM16KIRP,LGG,LIHC,LUAD,LUSC,UCECKIRP,LIHC,LUSC

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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
ENSG00000272405ENST00000605886CGRRF1ENSG00000100532ENST00000554791-0.10082182-CESC,READ

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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
ENSG00000272405.1ENST00000605886.115028892437