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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: ENSG00000230177

Summary for RP5-1112D6.4

check button Gene summary

Gene informationEnsembl ID

ENSG00000230177

Gene symbol

RP5-1112D6.4

Gene name
HGNC
Entrez ID
Gene typeantisense
Synonyms
UniProtAcc

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Structure and expression level for RP5-1112D6.4

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
ENSG000002301773.158386e+022.819691e+001.693205e-011.665298e+012.880000e-621.070000e-60UPKIRC
ENSG000002301778.969181e+011.351154e+002.291315e-015.896851e+003.710000e-095.680000e-08UPBLCA
ENSG000002301772.270462e+022.101317e+002.062079e-011.019028e+012.190000e-248.390000e-23UPKIRP
ENSG000002301776.547166e+011.055965e+001.230914e-018.578706e+009.590000e-188.290000e-17UPLUAD
ENSG000002301776.517896e+011.064429e+001.317223e-018.080858e+006.430000e-167.930000e-15UPLIHC

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000002301775.789744e-013.092194e-05CHOL1.383263e-04
ENSG00000230177-3.713667e-013.397088e-04KICH5.225291e-04
ENSG000002301773.694294e-014.260009e-21KIRC4.078732e-20
ENSG000002301773.363702e-014.891700e-12LIHC2.449007e-11

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lncRNA-Protein interaction for RP5-1112D6.4

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
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000183495EP40037.5993.513Q96L91EpiNA
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000120071KANSL127.6190.0048Q7Z3B3EpiNA
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000168137SETD559.6891.4691Q9C0A6EpiNA
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000146247PHIP58.1792.8835Q8WWQ0EpiNA
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000185658BRWD150.3990.5441Q9NSI6EpiNA
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000171634BPTF42.4393.4953Q12830TF,EpiNA
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000197323TRIM3332.6790.7458Q9UPN9EpiNA

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
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000171634BPTF42.4393.9873Q12830TF,EpiNA
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000170448NFXL129.8990.0433Q6ZNB6TFNA

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
ENSG00000230177ENST00000444259RP5-1112D6.4ENSG00000129351ILF326.5190.2745Q12906RBPNA

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lncRNA-DNA interaction for RP5-1112D6.4

lncrna_DNA
check buttonlncRNA targets the enhancer region and positively regulates the gene expression.

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 RP5-1112D6.4

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.
Only predicted by lncTar
SMAD1,GNA11,SEC23B,FBXL14,CTNNB1,PSMD2,EIF3L,ATP6V0D1,M6PR,MYOF,MYH9,MYL6,RNF123,CAPN1,UQCRC1,MFSD1,LRP10,PKM,CYB5R3,DAZAP2,EIF4G1,CRB3,GRHPR,TMED1,ZFPL1,DDB1,UBC,PRMT5,ABHD5,ATP6V0C,CLTC,ALAS1
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
ENSG00000230177ENST00000444259exon_skip_1234chr1:11658532-11658628-10.00-0.1562FBXO44ENST00000251547,ENST00000376770In-frame
ENSG00000230177ENST00000444259exon_skip_470077chr7:102397619-102397698-9.88-0.1372PRKRIP1ENST00000397912,ENST00000496391Frame-shift

-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
ENSG00000230177ENST00000444259exon_skip_111863chr14:23565815-23565892-10.80-0.1929AP1G2ENST00000308724,ENST00000397120Frame-shift
ENSG00000230177ENST00000444259exon_skip_309204chr19:49181348-49181461-13.14-0.2796TRPM4ENST00000252826Frame-shift
ENSG00000230177ENST00000444259exon_skip_353131chr20:58669290-58669453-18.57-0.1214STX16ENST00000371141Frame-shift
ENSG00000230177ENST00000444259exon_skip_382458chr3:38131595-38131638-6.18-0.3433ACAA1ENST00000333167Frame-shift
ENSG00000230177ENST00000444259exon_skip_436035chr5:79656957-79657001-6.72-0.1976TENT2ENST00000296783,ENST00000428308,ENST00000453514Frame-shift
ENSG00000230177ENST00000444259exon_skip_16568chr1:201989382-201989531-12.63-0.1640RNPEPENST00000295640Frame-shift
ENSG00000230177ENST00000444259exon_skip_41813chr10:68337857-68337996-13.99-0.1147HNRNPH3ENST00000265866Frame-shift
ENSG00000230177ENST00000444259exon_skip_53559chr10:101793912-101793998-9.67-0.1307OGAENST00000361464Frame-shift
ENSG00000230177ENST00000444259exon_skip_92074chr12:50142052-50142110-5.86-0.1274CERS5ENST00000317551Frame-shift
ENSG00000230177ENST00000444259exon_skip_290158chr17:42953723-42953778-9.55-0.2653AARSD1ENST00000427569Frame-shift
ENSG00000230177ENST00000444259exon_skip_377198chr3:123130479-123130616-14.25-0.1370PDIA5ENST00000316218Frame-shift
ENSG00000230177ENST00000444259exon_skip_387016chr3:121788283-121788432-8.82-0.1038IQCB1ENST00000310864Frame-shift
ENSG00000230177ENST00000444259exon_skip_445390chr5:150403120-150403312-16.35-0.1202CD74ENST00000009530In-frame
ENSG00000230177ENST00000444259exon_skip_462160chr6:127316449-127316502-5.06-0.1581ECHDC1ENST00000531967Frame-shift
ENSG00000230177ENST00000444259exon_skip_114365chr14:74290026-74290118-12.31-0.2052ABCD4ENST00000356924Frame-shift
ENSG00000230177ENST00000444259exon_skip_446758chr5:178212972-178213103-12.86-0.1837PHYKPLENST00000308158Frame-shift
ENSG00000230177ENST00000444259exon_skip_324294chr2:27774423-27774530-11.96-0.1161MRPL33ENST00000296102Frame-shift

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

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Variants for RP5-1112D6.4

check buttonRNA A-to-I editing events in lncRNA.
LncRNAediting IDLncRNA Ensembl IDChromosomeEditing PositionStrandGene TypeGene NameTranscript IDTranscript TypeTranscript Name
LncEditing_171978ENSG00000230177.1chr6111278447+antisenseRP5-1112D6.4ENST00000444259.1antisenseRP5-1112D6.4-001
LncEditing_171979ENSG00000230177.1chr6111278449+antisenseRP5-1112D6.4ENST00000444259.1antisenseRP5-1112D6.4-001
LncEditing_171982ENSG00000230177.1chr6111278524+antisenseRP5-1112D6.4ENST00000444259.1antisenseRP5-1112D6.4-001
LncEditing_171990ENSG00000230177.1chr6111278682+antisenseRP5-1112D6.4ENST00000444259.1antisenseRP5-1112D6.4-001

check buttonEdited-associated DElncRNAs in cancer.
Differentially expressed gene
LncRNA Ensembl IDLncRNA IndexCancer TypeChr_Postion_StrandAVE1AVE2log2FCW-valueP-valueAdjc.p-valueChange
ENSG00000230177LncEditing_171979UCECchr6_111278449_+1.101833e+011.270893e+01-4.855851e+004.333874e+001.465083e-051.805969e-05DOWN
ENSG00000230177LncEditing_171979DLBCchr6_111278449_+5.982828e+002.882537e+009.492276e-014.126044e+003.690560e-053.222143e-04UP
ENSG00000230177LncEditing_171979GBMchr6_111278449_+2.279961e+001.134806e+009.934791e-015.752750e+008.780324e-092.440991e-08UP
ENSG00000230177LncEditing_171979BLCAchr6_111278449_+5.759450e+002.508896e+008.341129e-011.204701e+012.011223e-334.558773e-32UP
ENSG00000230177LncEditing_171982BLCAchr6_111278524_+7.137606e+003.204119e+008.654167e-017.456483e+008.886276e-141.965095e-13UP
ENSG00000230177LncEditing_171979ACCchr6_111278449_+3.730818e+001.838281e+009.793031e-013.536586e+004.053345e-048.575673e-04UP
ENSG00000230177LncEditing_171979LUSCchr6_111278449_+4.239665e+001.975251e+009.075112e-011.151905e+011.057658e-307.591633e-30UP
ENSG00000230177LncEditing_171979SKCMchr6_111278449_+3.294541e+001.581664e+009.446133e-018.998556e+002.287054e-194.229484e-19UP
ENSG00000230177LncEditing_171978LAMLchr6_111278447_+1.303479e+019.899084e+002.518891e+004.049880e+005.124390e-058.517661e-05UP
ENSG00000230177LncEditing_171979LAMLchr6_111278449_+1.176607e+017.898413e+001.739138e+006.165279e+007.035896e-103.330968e-09UP
ENSG00000230177LncEditing_171982LAMLchr6_111278524_+1.173015e+019.525243e+003.328967e+003.855841e+001.153322e-041.798425e-04UP
ENSG00000230177LncEditing_171990LAMLchr6_111278682_+1.211548e+019.640115e+003.032788e+003.495227e+004.736585e-046.557940e-04UP
ENSG00000230177LncEditing_171979PCPGchr6_111278449_+4.477823e+002.190158e+009.692151e-019.170858e+004.692680e-201.900535e-18UP
ENSG00000230177LncEditing_171982PCPGchr6_111278524_+4.386890e+002.788234e+001.529411e+004.907711e+009.214558e-072.092652e-06UP
ENSG00000230177LncEditing_171979KIRPchr6_111278449_+9.408199e+008.066759e+004.505936e+006.149134e+007.790717e-101.642269e-09UP
ENSG00000230177LncEditing_171979THCAchr6_111278449_+2.826895e+001.662635e+001.305914e+001.024074e+011.302298e-247.367632e-24UP
ENSG00000230177LncEditing_171979CHOLchr6_111278449_+5.710085e+002.920606e+001.033865e+003.072715e+002.121207e-035.982839e-03UP
ENSG00000230177LncEditing_171982CHOLchr6_111278524_+5.986944e+003.040752e+001.023131e+002.701619e+006.900278e-031.278581e-02UP
ENSG00000230177LncEditing_171990CHOLchr6_111278682_+7.077648e+003.272688e+008.986389e-012.768519e+005.631175e-031.130722e-02UP
ENSG00000230177LncEditing_171978THYMchr6_111278447_+6.938930e+004.375669e+001.503285e+003.117859e+001.821699e-032.431923e-03UP
ENSG00000230177LncEditing_171979THYMchr6_111278449_+5.381106e+003.275627e+001.396391e+006.134334e+008.551684e-106.917930e-09UP
ENSG00000230177LncEditing_171982THYMchr6_111278524_+5.321098e+004.221325e+002.993759e+004.457575e+008.289198e-061.818925e-05UP
ENSG00000230177LncEditing_171978TGCTchr6_111278447_+1.123978e+017.534929e+001.733258e+003.918592e+008.906788e-051.247560e-04UP
ENSG00000230177LncEditing_171982TGCTchr6_111278524_+1.025659e+015.552997e+001.129673e+006.264082e+003.750272e-101.257263e-09UP
ENSG00000230177LncEditing_171990TGCTchr6_111278682_+1.189592e+016.936230e+001.284945e+005.363553e+008.160063e-081.685589e-07UP
ENSG00000230177LncEditing_171979READchr6_111278449_+4.519287e+002.041663e+008.723334e-016.037181e+001.568301e-097.707081e-09UP
ENSG00000230177LncEditing_171979LUADchr6_111278449_+4.742740e+002.260387e+009.353216e-011.113460e+018.512827e-296.826026e-28UP
ENSG00000230177LncEditing_171979STADchr6_111278449_+3.377588e+001.632431e+009.533150e-011.183111e+012.695685e-326.772317e-31UP
ENSG00000230177LncEditing_171982STADchr6_111278524_+3.674908e+002.205986e+001.358171e+006.525426e+006.780844e-111.143718e-10UP
ENSG00000230177LncEditing_171990STADchr6_111278682_+4.697088e+002.281545e+009.599181e-016.160141e+007.268024e-101.136224e-09UP
ENSG00000230177LncEditing_171979CESCchr6_111278449_+3.837790e+002.136112e+001.183027e+008.555996e+001.168552e-177.011313e-17UP
ENSG00000230177LncEditing_171979PRADchr6_111278449_+3.715818e+002.264965e+001.400186e+001.055366e+014.885568e-262.673491e-25UP
ENSG00000230177LncEditing_171982PRADchr6_111278524_+4.063579e+002.433104e+001.351437e+007.689594e+001.476023e-143.760042e-14UP
ENSG00000230177LncEditing_171979PAADchr6_111278449_+3.660089e+001.843867e+001.010975e+006.439640e+001.197569e-106.096717e-10UP
ENSG00000230177LncEditing_171979ESCAchr6_111278449_+3.358631e+001.824096e+001.135471e+005.958161e+002.550914e-096.253469e-09UP
ENSG00000230177LncEditing_171982ESCAchr6_111278524_+3.671845e+002.652554e+002.131637e+004.383995e+001.165227e-051.617427e-05UP
ENSG00000230177LncEditing_171990ESCAchr6_111278682_+4.254630e+002.736003e+001.569948e+004.261746e+002.028358e-052.742864e-05UP

check buttonCorrelation between RNA A-to-I editing events's frequecy and lncRNA expression.
LncRNA Ensembl IDLncRNA IndexCorrelationP-valueAdjc.p-value
ENSG00000230177LncEditing_171978-5.630181e-012.231702e-036.492225e-03
ENSG00000230177LncEditing_171990-5.744341e-011.312269e-041.574722e-03
ENSG00000230177LncEditing_171982-4.162006e-013.616795e-031.222227e-02
ENSG00000230177LncEditing_171982-4.589609e-014.869502e-031.015343e-02
ENSG00000230177LncEditing_171982-3.721640e-013.038885e-048.446664e-04
ENSG00000230177LncEditing_171990-6.073071e-011.572953e-051.261938e-04
ENSG00000230177LncEditing_171979-3.812507e-011.474266e-052.383396e-03
ENSG00000230177LncEditing_171982-3.747210e-016.200776e-031.526587e-02
ENSG00000230177LncEditing_171990-4.414077e-012.398230e-023.304379e-02
ENSG00000230177LncEditing_171982-4.372256e-012.418185e-044.322506e-04
ENSG00000230177LncEditing_171979-3.665607e-012.870963e-071.102856e-05

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
ENSG00000230177ENST00000444259GRHPRENSG00000137106ENST00000318158-0.12091-LIHC
ENSG00000230177ENST00000444259GRHPRENSG00000137106ENST00000494290-0.18881-LIHC

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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
ENSG00000230177.1ENST00000444259.15522154