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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: ENSG00000255224

Summary for CTD-3065J16.9

check button Gene summary

Gene informationEnsembl ID

ENSG00000255224

Gene symbol

CTD-3065J16.9

Gene name
HGNC
Entrez ID
Gene typeantisense
Synonyms
UniProtAcc

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Structure and expression level for CTD-3065J16.9

check buttonDifferentially expressed gene analysis between cancer and normal samples.
DEG result
Ensembl IDBase meanlog2FC(AD/control)lfcSEStatP-valueAdjc.p-valueDEG direction Cancer type
ENSG000002552249.068314e+011.358959e+002.084687e-016.518766e+007.090000e-111.530000e-09UPBLCA
ENSG000002552249.371213e+011.775305e+001.644490e-011.079548e+013.620000e-279.940000e-26UPUCEC
ENSG000002552249.839614e+011.869640e+001.325477e-011.410542e+013.520000e-457.100000e-44UPLUSC
ENSG000002552241.183989e+021.443679e+001.142928e-011.263141e+011.420000e-361.870000e-35UPBRCA
ENSG000002552245.805796e+011.297085e+001.301310e-019.967529e+002.110000e-232.740000e-22UPLUAD
ENSG000002552248.761926e+012.078669e+001.815618e-011.144882e+012.380000e-301.220000e-28UPLIHC
ENSG000002552246.396291e+011.146881e+002.871653e-013.993800e+006.500000e-055.161750e-04UPREAD

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000002552243.815035e-012.631656e-15LIHC3.651423e-14
ENSG000002552243.470013e-014.727122e-18UCEC1.145179e-16

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lncRNA-Protein interaction for CTD-3065J16.9

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
ENSG00000255224ENST00000524499CTD-3065J16.9ENSG00000149929HIRIP314.5390.1694Q9BW71EpiNA

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 CTD-3065J16.9

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 CTD-3065J16.9

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.
Only predicted by lncTar
RBMS2,CNOT1,ASB8,FNIP1,QKI,CEBPZ,FEZ2,PPP4R1,VPS4B,OXSR1,TRAPPC11,KLHL28,NT5C2,ZMYND11,VWA5A,HIPK1,SECISBP2L,SEPTIN10,UBR1,PCDHGC3,PPP1R12A,MBNL1,TAOK3,NPEPPS,SMAD4,KIAA1109,PTPN11,HPS3,ITGB1,ARHGAP21,HECTD1,NEDD1,FCHO2,MAT2B,PBX1,SLAIN2,PBRM1,ANKFY1,PKN2,ERBIN,ABLIM1,SEC24B,ATRN,RABL3,CREBRF,SEC24A,SON,SH3GLB1,NBR1,MACF1,ATP11B,CTNNB1,RIC1,NUMB,PDPK1,KTN1,C5orf24,MFSD6,ACBD5,SNX29,PHF3,APAF1,ZEB2,USP33,BBX,CPEB4,ILK,CEP120,RNF111,PTPN21,PCNX1,SGMS1,CDC42SE2,UBE2D3,SNRK,KIDINS220,CYLD,IQGAP1,CDC27,DYNC1I2,GIGYF2,SMARCA2,SLMAP,CLIP1,STAT3,ARNT,RAD50,FBXO11,APPBP2,FBXW11,DDX6,PIAS1,CLASP2,SEC23A,IQGAP2,ATF2,CCNI,MKLN1,ARHGAP5,AFF4,DDX3X,ITSN2,ASXL2,MFSD14A,USP47,SMAD1,HIPK2,PIKFYVE,MIER3,ROCK2,MYOF,MTMR9,PDLIM5,TIPARP,KIF13B,PCM1,ASH1L,DYNC1LI2,VEZT,KBTBD4,RAB18,UEVLD,YAP1,ZNF106,HNMT,RASA1,DENND4A,ARL1,FOXN3,CERT1,WDR7,TMEM131,SSH1,MARCHF7,OSBPL8,SWAP70,SMG6,KDM6A,CHURC1,AFTPH,MED13L,SEPTIN2,KIAA0232,KLHL5,COG6,EPS15,LYSMD3,ACTR2,DOCK9,CCNG1,SYNJ1,VAMP7,PIGN,RBM7,AKAP10,GPATCH8,CNOT8,PLSCR4,TRIP12,PDCD6IP,GALC,GTF2A1,APH1B,PRKAA1,SEMA3C,ANTXR2,RHOT1,KIF2A,GTF2I,MED1,PPIG,PLS1,EIF3L,REST,SNX4,HBP1,MORC3,SMAD5,SEC62,NEK7,EIF4G2,CSNK1A1,STX7,SOS2,CD46,FAM160B1,CSNK1G3,CAB39,ATP8A1,POLK,PRKAR1A,ACADM,PPP3CB,MIS18BP1,SEC31A,ERAP1,ELF1,BACH1,IL6ST,YME1L1,OSBPL1A,BLOC1S6,RB1,AFF1,GCC2,LPP,CAST,USP8,PICALM,DENND5A,FAM114A2,FAM13B,ITFG1,FEM1B,FNDC3B,WWC2,ATF1,SPG11,VAPA,MPRIP,CTDSP2,NEMF,FAM172A,AHNAK,DHX36,LATS1,FYCO1,DOCK1,MCFD2,IBTK,SPOPL,SCAF11,RAB6A
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
ENSG00000255224ENST00000524499exon_skip_462673chr6:138926400-138926481-10.64-0.1612REPS1ENST00000450536In-frame
ENSG00000255224ENST00000524499exon_skip_430601chr4:82842139-82842481-35.95-0.1123SEC31AENST00000355196,ENST00000395310,ENST00000448323In-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
ENSG00000255224ENST00000524499exon_skip_5818chr1:45568484-45568684-24.65-0.1318AKR1A1ENST00000351829,ENST00000372070Frame-shift
ENSG00000255224ENST00000524499exon_skip_445390chr5:150403120-150403312-25.57-0.1445CD74ENST00000009530In-frame
ENSG00000255224ENST00000524499exon_skip_300022chr18:79919183-79919400-32.27-0.1876PQLC1ENST00000397778Frame-shift
ENSG00000255224ENST00000524499exon_skip_303345chr19:17227839-17228005-22.43-0.1420OCEL1ENST00000215061Frame-shift
ENSG00000255224ENST00000524499exon_skip_307385chr19:40783777-40783840-17.45-0.3009RAB4BENST00000357052,ENST00000594800In-frame

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

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Variants for CTD-3065J16.9

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
ENSG00000255224ENST00000524499FYCO1ENSG00000163820ENST00000438446-0.1150738-BLCA,UCEC,LUSC,READ
ENSG00000255224ENST00000524499SEC23AENSG00000100934ENST00000557280-0.155039-BLCA,UCEC
ENSG00000255224ENST00000524499SEC23AENSG00000100934ENST00000553970-0.155039-BLCA,UCEC
ENSG00000255224ENST00000524499CLIP1ENSG00000130779ENST00000540539-0.1231788-BLCA
ENSG00000255224ENST00000524499CLIP1ENSG00000130779ENST00000540338-0.5016669-BLCA
ENSG00000255224ENST00000524499PDLIM5ENSG00000163110ENST00000512274-0.1568207-BLCA,UCEC,LIHC
ENSG00000255224ENST00000524499PDLIM5ENSG00000163110ENST00000509357-0.1228613-BLCA,UCEC,LIHC
ENSG00000255224ENST00000524499PDLIM5ENSG00000163110ENST00000506632-0.1156808-BLCA,UCEC,LIHC
ENSG00000255224ENST00000524499SEPTIN10ENSG00000186522ENST00000437928-0.1179334-BLCA,UCEC
ENSG00000255224ENST00000524499SEPTIN10ENSG00000186522ENST00000425498-0.143818-BLCA,UCEC
ENSG00000255224ENST00000524499PCDHGC3ENSG00000240184ENST00000611950-0.3280302-BLCA,UCEC,LUSC,LUAD
ENSG00000255224ENST00000524499PCDHGC3ENSG00000240184ENST00000617222-0.4086616-BLCA,UCEC,LUSC,LUAD
ENSG00000255224ENST00000524499DENND4AENSG00000174485ENST00000431932-0.1207387-UCEC
ENSG00000255224ENST00000524499CHURC1ENSG00000258289ENST00000548752-0.13061-BLCA,UCEC,READ
ENSG00000255224ENST00000524499CHURC1ENSG00000258289ENST00000547625-0.4889966-BLCA,UCEC,READ
ENSG00000255224ENST00000524499PPP1R12AENSG00000058272ENST00000550903-0.13031-BLCA,UCEC,READ
ENSG00000255224ENST00000524499PPP1R12AENSG00000058272ENST00000550299-0.1830807-BLCA,UCEC,READ
ENSG00000255224ENST00000524499PPP1R12AENSG00000058272ENST00000546369-0.15001152-BLCA,UCEC,READ
ENSG00000255224ENST00000524499IL6STENSG00000134352ENST00000502326-0.2109230-BLCA,UCEC,LUSC,LIHC,READ
ENSG00000255224ENST00000524499PTPN21ENSG00000070778ENST00000553531-0.1181637-BLCA,UCEC,LUSC,BRCA,LUAD,READ
ENSG00000255224ENST00000524499SMARCA2ENSG00000080503ENST00000382186-0.4700552-UCEC
ENSG00000255224ENST00000524499VAPAENSG00000101558ENST00000340541-0.1109410-READ
ENSG00000255224ENST00000524499VWA5AENSG00000110002ENST00000392744-0.2172570-LUSC,READ
ENSG00000255224ENST00000524499ACADMENSG00000117054ENST00000530953-0.1127719-LIHC,READ
ENSG00000255224ENST00000524499ACADMENSG00000117054ENST00000420607-0.1708390-LIHC,READ
ENSG00000255224ENST00000524499ACADMENSG00000117054ENST00000528016-0.1224441-LIHC,READ
ENSG00000255224ENST00000524499VPS4BENSG00000119541ENST00000591519-0.3645724-READ
ENSG00000255224ENST00000524499ATP8A1ENSG00000124406ENST00000515872-0.1016754-LUSC,READ
ENSG00000255224ENST00000524499ATP8A1ENSG00000124406ENST00000504024-0.11051-LUSC,READ
ENSG00000255224ENST00000524499SECISBP2LENSG00000138593ENST00000561428-0.2479164-LUSC,LUAD,READ
ENSG00000255224ENST00000524499OSBPL1AENSG00000141447ENST00000357041-0.3848150-BLCA,UCEC,READ
ENSG00000255224ENST00000524499OSBPL1AENSG00000141447ENST00000578013-0.4643679-BLCA,UCEC,READ
ENSG00000255224ENST00000524499OSBPL1AENSG00000141447ENST00000578055-0.15801079-BLCA,UCEC,READ
ENSG00000255224ENST00000524499IQGAP2ENSG00000145703ENST00000396234-0.1513106-LUSC,READ
ENSG00000255224ENST00000524499IQGAP2ENSG00000145703ENST00000502745-0.114199-LUSC,READ
ENSG00000255224ENST00000524499NEK7ENSG00000151414ENST00000367383-0.1563980-UCEC,LUSC,READ
ENSG00000255224ENST00000524499MIER3ENSG00000155545ENST00000451637-0.125660-READ
ENSG00000255224ENST00000524499CDC42SE2ENSG00000158985ENST00000502582-0.1109496-READ
ENSG00000255224ENST00000524499MORC3ENSG00000159256ENST00000549948-0.10151-UCEC
ENSG00000255224ENST00000524499MORC3ENSG00000159256ENST00000552581-0.14641-UCEC
ENSG00000255224ENST00000524499ANTXR2ENSG00000163297ENST00000404191-0.2947837-BLCA,UCEC,LUSC,BRCA,LIHC,READ
ENSG00000255224ENST00000524499ANTXR2ENSG00000163297ENST00000346652-0.3720679-BLCA,UCEC,LUSC,BRCA,LIHC,READ
ENSG00000255224ENST00000524499FEM1BENSG00000169018ENST00000566008-0.14491089-UCEC
ENSG00000255224ENST00000524499FEZ2ENSG00000171055ENST00000414288-0.1373241-UCEC,READ
ENSG00000255224ENST00000524499KIF13BENSG00000197892ENST00000523130-2.9550819-LUSC,READ
ENSG00000255224ENST00000524499MED13LENSG00000123066ENST00000552340-0.1093870-UCEC
ENSG00000255224ENST00000524499FAM13BENSG00000031003ENST00000425075-0.118589-BLCA,LUSC,READ
ENSG00000255224ENST00000524499FAM13BENSG00000031003ENST00000420893-0.1766983-BLCA,LUSC,READ
ENSG00000255224ENST00000524499KLHL5ENSG00000109790ENST00000515612-0.1492100-BLCA,READ
ENSG00000255224ENST00000524499YAP1ENSG00000137693ENST00000531439-0.5977786-UCEC,BRCA
ENSG00000255224ENST00000524499ILKENSG00000166333ENST00000532063-0.134779-BLCA,UCEC,LUSC,READ
ENSG00000255224ENST00000524499ILKENSG00000166333ENST00000299421-0.151083-BLCA,UCEC,LUSC,READ
ENSG00000255224ENST00000524499ILKENSG00000166333ENST00000537806-0.1392118-BLCA,UCEC,LUSC,READ
ENSG00000255224ENST00000524499ILKENSG00000166333ENST00000420936-0.1384120-BLCA,UCEC,LUSC,READ
ENSG00000255224ENST00000524499ILKENSG00000166333ENST00000528995-0.151087-BLCA,UCEC,LUSC,READ
ENSG00000255224ENST00000524499ILKENSG00000166333ENST00000396751-0.151083-BLCA,UCEC,LUSC,READ
ENSG00000255224ENST00000524499ILKENSG00000166333ENST00000526318-0.151082-BLCA,UCEC,LUSC,READ
ENSG00000255224ENST00000524499ROCK2ENSG00000134318ENST00000401753-0.1052808-BLCA,UCEC
ENSG00000255224ENST00000524499LPPENSG00000145012ENST00000415906-0.127066-BLCA,UCEC,READ
ENSG00000255224ENST00000524499SOS2ENSG00000100485ENST00000543680-0.3140232-READ
ENSG00000255224ENST00000524499SOS2ENSG00000100485ENST00000556452-0.159529-READ
ENSG00000255224ENST00000524499PCNX1ENSG00000100731ENST00000439984-0.1760143-BRCA
ENSG00000255224ENST00000524499PCNX1ENSG00000100731ENST00000554691-0.1760108-BRCA
ENSG00000255224ENST00000524499PCNX1ENSG00000100731ENST00000555780-0.3372100-BRCA
ENSG00000255224ENST00000524499MTMR9ENSG00000104643ENST00000526292-0.1155605-READ
ENSG00000255224ENST00000524499PPP3CBENSG00000107758ENST00000430762-0.5083479-BLCA,READ
ENSG00000255224ENST00000524499PLSCR4ENSG00000114698ENST00000446574-0.1293792-BLCA,UCEC,LUSC,BRCA,LUAD,LIHC,READ
ENSG00000255224ENST00000524499PLSCR4ENSG00000114698ENST00000493382-0.1819699-BLCA,UCEC,LUSC,BRCA,LUAD,LIHC,READ
ENSG00000255224ENST00000524499AHNAKENSG00000124942ENST00000530124-0.1215240-BLCA,UCEC,LUSC,BRCA,LUAD,READ
ENSG00000255224ENST00000524499AHNAKENSG00000124942ENST00000257247-0.1215244-BLCA,UCEC,LUSC,BRCA,LUAD,READ
ENSG00000255224ENST00000524499SEC24BENSG00000138802ENST00000504968-0.1886191-LIHC
ENSG00000255224ENST00000524499SEC24BENSG00000138802ENST00000399100-0.8600608-LIHC
ENSG00000255224ENST00000524499HNMTENSG00000150540ENST00000410115-0.1292985-UCEC,LUSC
ENSG00000255224ENST00000524499HNMTENSG00000150540ENST00000329366-0.1581164-UCEC,LUSC
ENSG00000255224ENST00000524499FCHO2ENSG00000157107ENST00000287761-0.1507826-LUSC,READ
ENSG00000255224ENST00000524499SLMAPENSG00000163681ENST00000416658-0.11371-BLCA,UCEC,READ
ENSG00000255224ENST00000524499SLMAPENSG00000163681ENST00000495364-0.2050860-BLCA,UCEC,READ
ENSG00000255224ENST00000524499SLMAPENSG00000163681ENST00000494088-0.12552-BLCA,UCEC,READ
ENSG00000255224ENST00000524499SNRKENSG00000163788ENST00000437827-0.1377808-BLCA,UCEC,LUSC,LUAD,READ
ENSG00000255224ENST00000524499CREBRFENSG00000164463ENST00000520420-0.14711-BLCA,UCEC,LUSC,READ
ENSG00000255224ENST00000524499CEP120ENSG00000168944ENST00000515110-0.49301037-UCEC
ENSG00000255224ENST00000524499AFF1ENSG00000172493ENST00000544085-0.6750396-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
ENSG00000255224.1ENST00000524499.12641049255