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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: ENSG00000259865

Summary for RP11-488L18.10

check button Gene summary

Gene informationEnsembl ID

ENSG00000259865

Gene symbol

RP11-488L18.10

Gene name
HGNC
Entrez ID
Gene typelincRNA
Synonyms
UniProtAcc

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Structure and expression level for RP11-488L18.10

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
ENSG000002598653.538359e+021.590738e+002.456728e-016.475025e+009.480000e-111.250000e-09UPCHOL
ENSG000002598653.998790e+021.362584e+001.150354e-011.184491e+012.290000e-322.610000e-31UPKIRC
ENSG000002598654.574260e+021.016927e+002.214416e-014.592305e+004.380000e-063.330000e-05UPBLCA
ENSG000002598653.942750e+021.508119e+001.876962e-018.034895e+009.370000e-161.430000e-14UPKIRP
ENSG000002598651.973079e+021.287106e+001.543851e-018.336984e+007.620000e-171.040000e-15UPLIHC
ENSG000002598654.425383e+021.145074e+001.707655e-016.705531e+002.010000e-113.210000e-10UPSTAD

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000002598657.270697e-011.549344e-08CHOL2.171663e-06
ENSG00000259865-3.193814e-012.282566e-03KICH2.957795e-03
ENSG000002598653.235070e-012.802603e-16KIRC1.393559e-15
ENSG000002598653.418775e-012.079251e-12LIHC1.153985e-11

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lncRNA-Protein interaction for RP11-488L18.10

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
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000272333KMT2B61.5390.0969Q9UMN6TF,EpiNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000084093REST79.9394.4088Q13127TF,EpiNA

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
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000123636BAZ2B145.3395.0535Q9UIF8TF,EpiNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000144747TMF1125.6591.6381P82094TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000118058KMT2A114.4896.6488Q03164TF,EpiNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000067066SP100104.8292.2169P23497TF,EpiNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000116731PRDM298.1893.6824Q13029TF,EpiNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000105127AKAP898.0992.1065O43823TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000187605TET392.6392.7868O43151TF,EpiNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000099326MZF192.3592.0222P28698TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000125482TTF189.7390.4323Q15361TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000070476ZXDC81.7490.1283Q2QGD7TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000084093REST79.9394.3398Q13127TF,EpiNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000167232ZNF9177.9493.4239Q05481TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000106948AKNA75.3794.0215Q7Z591TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000196670ZFP6267.6790.9711Q8NB50TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000126804ZBTB163.9192.0865Q9Y2K1TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000272333KMT2B61.5392.7317Q9UMN6TF,EpiNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000125812GZF159.4991.9979Q9H116TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000198040ZNF8458.4690.6471P51523TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000146587RBAK57.7490.4102Q9NYW8TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000256223ZNF108.0990.2763P21506TFNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000175691ZNF776.590.6831Q15935TFNA

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
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000004534RBM6108.0590.939P78332RBPNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000162775RBM1583.7990.1261Q96T37RBPNA
ENSG00000259865ENST00000566446RP11-488L18.10ENSG00000167978SRRM231.3790.4418Q9UQ35RBPNA

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lncRNA-DNA interaction for RP11-488L18.10

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 RP11-488L18.10

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.
Only predicted by lncTar
RNH1
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
ENSG00000259865ENST00000566446exon_skip_1234chr1:11658532-11658628-17.62-0.2049FBXO44ENST00000251547,ENST00000376770In-frame
ENSG00000259865ENST00000566446exon_skip_470077chr7:102397619-102397698-8.80-0.1760PRKRIP1ENST00000397912,ENST00000496391Frame-shift
ENSG00000259865ENST00000566446exon_skip_44998chr10:110132304-110132400-8.58-0.1059ADD3ENST00000356080In-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
ENSG00000259865ENST00000566446exon_skip_52671chr10:97461495-97461622-12.78-0.1006MMS19ENST00000370782,ENST00000438925Frame-shift
ENSG00000259865ENST00000566446exon_skip_438188chr5:141638954-141639021-7.79-0.1298RELL2ENST00000297164,ENST00000444782Frame-shift
ENSG00000259865ENST00000566446exon_skip_5818chr1:45568484-45568684-14.01-0.1069AKR1A1ENST00000351829,ENST00000372070Frame-shift
ENSG00000259865ENST00000566446exon_skip_41813chr10:68337857-68337996-12.42-0.1044HNRNPH3ENST00000265866Frame-shift
ENSG00000259865ENST00000566446exon_skip_95407chr12:95040475-95040597-11.23-0.1291NR2C1ENST00000333003Frame-shift
ENSG00000259865ENST00000566446exon_skip_110968chr14:20381552-20381686-12.11-0.1236TEP1ENST00000262715Frame-shift
ENSG00000259865ENST00000566446exon_skip_133217chr16:8635038-8635079-5.61-0.2805METTL22ENST00000381920Frame-shift
ENSG00000259865ENST00000566446exon_skip_309204chr19:49181348-49181461-13.25-0.1352TRPM4ENST00000252826Frame-shift
ENSG00000259865ENST00000566446exon_skip_353131chr20:58669290-58669453-15.82-0.1521STX16ENST00000371141Frame-shift
ENSG00000259865ENST00000566446exon_skip_370518chr22:50247691-50247776-8.16-0.1484HDAC10ENST00000216271Frame-shift
ENSG00000259865ENST00000566446exon_skip_374551chr3:50100531-50100605-8.01-0.1635RBM5ENST00000347869Frame-shift
ENSG00000259865ENST00000566446exon_skip_374552chr3:50104247-50104308-6.28-0.1256RBM5ENST00000347869Frame-shift
ENSG00000259865ENST00000566446exon_skip_380242chr3:186784961-186785101-11.60-0.1785EIF4A2ENST00000323963Frame-shift
ENSG00000259865ENST00000566446exon_skip_382458chr3:38131595-38131638-6.59-0.3295ACAA1ENST00000333167Frame-shift
ENSG00000259865ENST00000566446exon_skip_436035chr5:79656957-79657001-9.87-0.2531TENT2ENST00000296783,ENST00000428308,ENST00000453514Frame-shift
ENSG00000259865ENST00000566446exon_skip_446758chr5:178212972-178213103-11.32-0.1797PHYKPLENST00000308158Frame-shift
ENSG00000259865ENST00000566446exon_skip_2106chr1:17648553-17648675-10.94-0.1042ARHGEF10LENST00000361221Frame-shift
ENSG00000259865ENST00000566446exon_skip_9446chr1:147270931-147271005-6.85-0.1489CHD1LENST00000369258Frame-shift
ENSG00000259865ENST00000566446exon_skip_23423chr1:26294204-26294331-8.78-0.1688UBXN11ENST00000374221,ENST00000374222Frame-shift
ENSG00000259865ENST00000566446exon_skip_41841chr10:68756272-68756483-17.87-0.1324CCAR1ENST00000265872Frame-shift
ENSG00000259865ENST00000566446exon_skip_53559chr10:101793912-101793998-11.03-0.1902OGAENST00000361464Frame-shift
ENSG00000259865ENST00000566446exon_skip_66482chr11:126274926-126275021-9.83-0.1068FOXRED1ENST00000263578Frame-shift
ENSG00000259865ENST00000566446exon_skip_74009chr11:64773429-64773505-12.28-0.2456SF1ENST00000377390Frame-shift
ENSG00000259865ENST00000566446exon_skip_87733chr12:120571190-120571291-7.57-0.1066RNF10ENST00000325954Frame-shift
ENSG00000259865ENST00000566446exon_skip_92074chr12:50142052-50142110-6.22-0.1244CERS5ENST00000317551Frame-shift
ENSG00000259865ENST00000566446exon_skip_111863chr14:23565815-23565892-9.10-0.1857AP1G2ENST00000308724,ENST00000397120Frame-shift
ENSG00000259865ENST00000566446exon_skip_114365chr14:74290026-74290118-10.64-0.1237ABCD4ENST00000356924Frame-shift
ENSG00000259865ENST00000566446exon_skip_289852chr17:42103607-42103798-20.07-0.1287DHX58ENST00000251642Frame-shift
ENSG00000259865ENST00000566446exon_skip_290158chr17:42953723-42953778-7.86-0.1709AARSD1ENST00000427569Frame-shift
ENSG00000259865ENST00000566446exon_skip_292904chr17:69251746-69251866-10.41-0.1335ABCA5ENST00000392676,ENST00000588877In-frame
ENSG00000259865ENST00000566446exon_skip_325393chr2:47021861-47021979-11.86-0.1119TTC7AENST00000319190Frame-shift
ENSG00000259865ENST00000566446exon_skip_327748chr2:95410863-95411026-13.49-0.1336FAHD2AENST00000233379,ENST00000447036Frame-shift
ENSG00000259865ENST00000566446exon_skip_364260chr22:29291561-29291599-9.20-0.8364EWSR1ENST00000397938Frame-shift
ENSG00000259865ENST00000566446exon_skip_365497chr22:38067703-38067770-8.85-0.1883PICK1ENST00000356976,ENST00000404072Frame-shift
ENSG00000259865ENST00000566446exon_skip_371367chr3:9697710-9697866-12.92-0.2153MTMR14ENST00000296003In-frame
ENSG00000259865ENST00000566446exon_skip_374497chr3:49999439-49999513-7.27-0.1398RBM6ENST00000266022Frame-shift
ENSG00000259865ENST00000566446exon_skip_377198chr3:123130479-123130616-9.30-0.1388PDIA5ENST00000316218Frame-shift
ENSG00000259865ENST00000566446exon_skip_440477chr5:181233412-181233435-5.86-0.4508TRIM41ENST00000315073Frame-shift
ENSG00000259865ENST00000566446exon_skip_442657chr5:74730259-74730398-12.29-0.1078GFM2ENST00000296805,ENST00000509430Frame-shift
ENSG00000259865ENST00000566446exon_skip_444499chr5:138164086-138164133-4.77-0.2271BRD8ENST00000254900Frame-shift
ENSG00000259865ENST00000566446exon_skip_470226chr7:103307595-103307708-11.31-0.1285PMPCBENST00000249269Frame-shift
ENSG00000259865ENST00000566446exon_skip_11029chr1:154989559-154989707-15.29-0.1470FLAD1ENST00000292180Frame-shift
ENSG00000259865ENST00000566446exon_skip_59071chr11:47234756-47234934-13.43-0.1041DDB2ENST00000256996Frame-shift
ENSG00000259865ENST00000566446exon_skip_43507chr10:84499874-84499959-8.12-0.1624CCSER2ENST00000224756Frame-shift
ENSG00000259865ENST00000566446exon_skip_52891chr10:98429790-98429889-13.87-0.2522HPS1ENST00000325103,ENST00000361490In-frame
ENSG00000259865ENST00000566446exon_skip_48296chr10:26755654-26755741-9.29-0.1548ABI1ENST00000376142In-frame

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

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Variants for RP11-488L18.10

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

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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-RBP complex positive regulation
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type
ENSG00000259865ENSG00000004534RBM6exon_skip_470077ENSG00000128563:chr7:102397619-102397698PRKRIP1ENST00000397912,ENST00000496391Frame-shiftSKCM,READ,THYM,PCPG,THCA

check buttonLncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.
LncRNA-RBP complex negative regulation
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type
ENSG00000259865ENSG00000004534RBM6exon_skip_41813ENSG00000096746:chr10:68337857-68337996HNRNPH3ENST00000265866Frame-shiftSTAD,UVM,SKCM,THYM,PCPG,PAAD,THCA
ENSG00000259865ENSG00000004534RBM6exon_skip_95407ENSG00000120798:chr12:95040475-95040597NR2C1ENST00000333003Frame-shiftUVM,SKCM,THYM,PCPG,PAAD
ENSG00000259865ENSG00000004534RBM6exon_skip_370518ENSG00000100429:chr22:50247691-50247776HDAC10ENST00000216271Frame-shiftSTAD,UVM,SKCM,READ,THYM,PAAD,THCA
ENSG00000259865ENSG00000004534RBM6exon_skip_382458ENSG00000060971:chr3:38131595-38131638ACAA1ENST00000333167Frame-shiftSTAD,UVM,SKCM,READ,MESO,THYM,PCPG,PAAD,THCA
ENSG00000259865ENSG00000004534RBM6exon_skip_53559ENSG00000198408:chr10:101793912-101793998OGAENST00000361464Frame-shiftUVM,SKCM,THYM,PCPG,PAAD,THCA
ENSG00000259865ENSG00000004534RBM6exon_skip_290158ENSG00000266967:chr17:42953723-42953778AARSD1ENST00000427569Frame-shiftSKCM,READ,PRAD,PAAD,TGCT
ENSG00000259865ENSG00000004534RBM6exon_skip_377198ENSG00000065485:chr3:123130479-123130616PDIA5ENST00000316218Frame-shiftUVM,SKCM,READ,PCPG,PAAD,TGCT
ENSG00000259865ENSG00000004534RBM6exon_skip_442657ENSG00000164347:chr5:74730259-74730398GFM2ENST00000296805,ENST00000509430Frame-shiftUVM,SKCM,THYM,PCPG,PAAD,THCA
ENSG00000259865ENSG00000004534RBM6exon_skip_470226ENSG00000105819:chr7:103307595-103307708PMPCBENST00000249269Frame-shiftUVM,SKCM,LIHC,THYM,PCPG,PAAD,TGCT,THCA

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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
ENSG00000259865.1ENST00000566446.1420134280