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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: ENSG00000267317

Summary for CTB-25B13.12

check button Gene summary

Gene informationEnsembl ID

ENSG00000267317

Gene symbol

CTB-25B13.12

Gene name
HGNC
Entrez ID
Gene typeantisense
Synonyms
UniProtAcc

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Structure and expression level for CTB-25B13.12

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
ENSG000002673172.424166e+021.108747e+003.460562e-013.203951e+001.355556e-034.932389e-03UPGBM
ENSG000002673175.830233e+021.683491e+001.628072e-011.034040e+014.630000e-251.190000e-23UPKICH
ENSG000002673174.683606e+021.003022e+001.281477e-017.827078e+004.990000e-156.950000e-14UPKIRP

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000002673173.894152e-018.192265e-03CHOL9.870623e-03
ENSG000002673175.977881e-016.206963e-10KICH5.437840e-09
ENSG00000267317-3.057331e-013.629456e-14UCEC2.873320e-13

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lncRNA-Protein interaction for CTB-25B13.12

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
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000204371EHMT258.6292.9643Q96KQ7EpiNA
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000167670CHAF1A47.8894.5688Q13111EpiNA
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000001497LAS1L38.590.8388Q9Y4W2EpiNA
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000130726TRIM2829.9990.7137Q13263EpiNA
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000130382MLLT118.390.3563Q03111EpiNA
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000105619TFPT11.2891.7637P0C1Z6EpiNA
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000071655MBD311.0790.3396O95983TF,EpiNA
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000127616SMARCA456.4295.7087P51532EpiNA
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000149929HIRIP312.5693.9791Q9BW71EpiNA

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
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000167967E4F149.6592.5023Q66K89TFNA
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000180035ZNF4812.2292.2709Q96MX3TFNA

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
ENSG00000267317ENST00000591252CTB-25B13.12ENSG00000125970RALY6.0990.6278Q9UKM9RBPNA

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lncRNA-DNA interaction for CTB-25B13.12

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 CTB-25B13.12

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.
Only predicted by lncTar
SPICE1,NEK4,MYO6,ATM,MAP4K3,RDX,QSER1,PPP1R12A,GNL3L,KIAA1109,STRN3,RASAL2,FCHO2,MAT2B,PBRM1,ANKRD28,PSMC1,VPS13B,MAN1A2,L2HGDH,PRRC2C,SNX19,CSPP1,ENOPH1,ACBD5,PHF3,ARFIP1,CEP120,PAK2,STRN,CCDC32,GOLIM4,COPA,PHF20,KIDINS220,CYLD,CDC27,GTF2H3,BTBD10,FBXO11,DDX59,ETFDH,SEC23A,MKLN1,ITSN2,RB1CC1,TIMM23B,SMAD1,CLPX,GPD2,HSPA9,UBE4B,TP53BP2,TAB2,POC1B,GTF3C3,INPP5F,UVRAG,OSBPL8,NCOA4,DDX5,CAMK2G,MTRR,ACTR2,VAMP7,GPATCH8,PPA1,ALMS1,ABL2,FASTKD2,TUT7,SEC23B,ATP8B1,MED1,NUP58,CNST,CD46,CLASP1,NIN,CUL2,NAA50,GON4L,CAB39,HUWE1,PRKAR1A,SLC25A40,TEP1,ERAP1,YME1L1,KMT2E,TLK1,RABEP1,FAM13B,MED23,UGDH,EPM2AIP1,ITCH,SUCO,ATF1,ARHGAP32,LATS1,RPRD1A,SPOPL,NOMO2,LRP6,TMEM87B,PHF6,DHTKD1,SINHCAF,ARHGEF3,VPS4B,UHRF1BP1L,NAF1,PIBF1,FRS2,USF3,UCHL5,FAM104A,SCP2,FOXJ3,MBNL1,LARP1,RCHY1,RNF214,BZW1,HECTD1,DCTN4,TUT4,SLAIN2,PKN2,MSH3,PDXDC1,PUM1,CHORDC1,C1orf43,FOXN2,ZFAND5,CTNNB1,BCL2L13,FUBP1,ANAPC1,TP53BP1,COMMD10,PPIP5K2,USP32,G3BP1,MORF4L1,FERMT2,PIAS1,RIOK2,AFF4,FBXO22,DDX3X,IPO5,ASXL2,NIPBL,POLR2B,ESF1,FRYL,RHOBTB3,UTRN,CEP350,PIKFYVE,BLZF1,SLC35A5,SLC10A7,DENND4A,DNAJC13,MED13,RAP1B,GALK2,USP46,INVS,KIAA0232,TRIM23,PSMD5,MICU1,GTF2A1,PRKAA1,SOS1,SMAD5,SLC12A6,CSNK1A1,PPP3CB,ELF1,RPE,VRK2,TAF2,GCC2,CHD6,PLAA,TRIM33,MED21,HEATR5A,FEM1B,TNFRSF10A,THOC2,DOCK1,NEMF,PSMD1,NCOR1,FNBP1L,TAF5L,SCAF11,DSTYK,CAMSAP2,MAPK8,PBLD,PCF11,RBBP4,USP15,NCBP3,EIF4G3,STX17,SECISBP2L,UBR1,PHACTR1,IL1R1,MED14,PNPT1,PRDM2,IARS1,UBE4A,VPS26A,DCUN1D1,MAP3K2,MTMR4,EDNRB,PDHX,ZC3H11A,MACF1,RIC1,NUMB,CCAR1,KTN1,C5orf24,SLC25A16,ILK,SDHD,PTPN4,FARP2,UBE2D3,SNRK,YIPF5,SEPTIN11,CLIP1,NSUN3,ARNT,FAM219B,RAB2B,NCOA2,RC3H2,ERRFI1,BCL2L2,CCSER2,MAPK1,RNF169,PRKAR2A,ELL2,NAA16,USP9X,ROCK2,ATF3,C1orf109,UEVLD,HSPA14,CPEB2,WNK1,TMLHE,KLHL5,EPS15,RUFY3,OSBPL9,PPARA,GFM2,GALC,SNX2,KIF2A,PLS1,SOS2,POLK,IDS,DCAF17,ETFRF1,IL6ST,AFF1,ABCE1,PICALM,CDC37L1,FAM114A2,SNX18,ABCD3,ECD,SPG11,SMC6,FAM172A,IBTK,FER,BAZ1A,TANK,RAB6A,LRRC8B,GSK3B,CEP170,OXSR1,NT5C2,ZMYND11,HIPK1,PIK3CB,TACC1,SNX6,ANKRD46,CEP104,INTS6,HBS1L,TRIM37,ZMYM5,PTPN11,WDR36,SCYL2,PLEKHB2,AMN1,ANKFY1,PDE8A,DNAJC11,NR2C2,CLTC,ATRN,AP1AR,FOS,PARG,SDHC,ATP2A2,SON,LZIC,BIRC2,M6PR,APAF1,ASCC1,SNX5,TAF1,PCNX1,UBR4,DDI2,ITGAV,SMARCA2,GABBR1,SLMAP,GUCY1B1,SESTD1,CMTR2,CIPC,SDCBP,RFX5,GTDC1,ARHGAP5,NKIRAS1,MPDZ,THAP6,PPP1CB,COPB2,SEC14L1,ARSB,PDLIM5,DYNC1LI2,KBTBD4,RASA1,MED13L,SEPTIN2,COG6,SIK3,ABHD5,IGF2R,TAF1B,DOCK9,NCOA3,SYNJ1,ZFP36,TBC1D23,PIGN,TNPO1,HNMT,PGM3,NEK7,SPTLC1,RO60,CSNK1G3,HEATR5B,BIRC6,ACADM,SEC31A,POGLUT1,ARL2BP,TMEM184C,BCOR,BDP1,MIA3,MCFD2,NDUFS1,YTHDC2
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
ENSG00000267317ENST00000591252exon_skip_81515chr12:42351884-42352049-15.27-0.1053PPHLN1ENST00000395568In-frame

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

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Variants for CTB-25B13.12

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
ENSG00000267317ENST00000591252WNK1ENSG00000060237ENST00000574564-0.1748771-KIRP
ENSG00000267317ENST00000591252GUCY1B1ENSG00000061918ENST00000503520-0.1049549-GBM,KICH
ENSG00000267317ENST00000591252SMARCA2ENSG00000080503ENST00000382186-0.7883353-GBM,KIRP
ENSG00000267317ENST00000591252L2HGDHENSG00000087299ENST00000261699-0.4606777-KIRP
ENSG00000267317ENST00000591252L2HGDHENSG00000087299ENST00000555423-0.1725685-KIRP
ENSG00000267317ENST00000591252MAPK8ENSG00000107643ENST00000374174-0.1821731-GBM
ENSG00000267317ENST00000591252PPP3CBENSG00000107758ENST00000430762-0.3590479-GBM
ENSG00000267317ENST00000591252CUL2ENSG00000108094ENST00000421317-0.6654481-GBM
ENSG00000267317ENST00000591252TRIM37ENSG00000108395ENST00000580973-0.1207425-GBM
ENSG00000267317ENST00000591252TRIM37ENSG00000108395ENST00000580122-0.1353435-GBM
ENSG00000267317ENST00000591252TRIM37ENSG00000108395ENST00000584889-0.1776709-GBM
ENSG00000267317ENST00000591252USP46ENSG00000109189ENST00000508499-0.2709603-GBM,KIRP
ENSG00000267317ENST00000591252USP46ENSG00000109189ENST00000512656-0.1688762-GBM,KIRP
ENSG00000267317ENST00000591252ARSBENSG00000113273ENST00000565165-0.3183556-KICH
ENSG00000267317ENST00000591252IL1R1ENSG00000115594ENST00000409288-0.1388778-KICH
ENSG00000267317ENST00000591252IL1R1ENSG00000115594ENST00000410023-0.16771-KICH
ENSG00000267317ENST00000591252IL1R1ENSG00000115594ENST00000422532-0.1350687-KICH
ENSG00000267317ENST00000591252PLEKHB2ENSG00000115762ENST00000404460-0.1339481-GBM
ENSG00000267317ENST00000591252PBLDENSG00000108187ENST00000468798-0.480111-KICH,KIRP
ENSG00000267317ENST00000591252ERRFI1ENSG00000116285ENST00000474874-0.1687586-KICH,KIRP
ENSG00000267317ENST00000591252ACADMENSG00000117054ENST00000420607-0.8357441-KICH,KIRP
ENSG00000267317ENST00000591252ACADMENSG00000117054ENST00000528016-0.1125478-KICH,KIRP
ENSG00000267317ENST00000591252GTDC1ENSG00000121964ENST00000429978-0.1624461-GBM
ENSG00000267317ENST00000591252ZFP36ENSG00000128016ENST00000594045-0.1108261-KICH,KIRP
ENSG00000267317ENST00000591252TACC1ENSG00000147526ENST00000518415-0.12771-GBM,KIRP
ENSG00000267317ENST00000591252TACC1ENSG00000147526ENST00000521866-0.12771-GBM,KIRP
ENSG00000267317ENST00000591252HNMTENSG00000150540ENST00000280096-0.39771-KICH
ENSG00000267317ENST00000591252HNMTENSG00000150540ENST00000475675-0.39771-KICH
ENSG00000267317ENST00000591252DOCK1ENSG00000150760ENST00000623213-0.3542301-KICH
ENSG00000267317ENST00000591252UTRNENSG00000152818ENST00000367526-0.5100567-KICH,KIRP
ENSG00000267317ENST00000591252SEPTIN2ENSG00000168385ENST00000401990-0.1098535-KICH
ENSG00000267317ENST00000591252SEPTIN2ENSG00000168385ENST00000457335-0.1102466-KICH
ENSG00000267317ENST00000591252LRRC8BENSG00000197147ENST00000330947-0.40541-GBM
ENSG00000267317ENST00000591252LRRC8BENSG00000197147ENST00000439853-0.40541-GBM
ENSG00000267317ENST00000591252PTPN4ENSG00000088179ENST00000431283-0.6233805-GBM,KIRP
ENSG00000267317ENST00000591252PTPN4ENSG00000088179ENST00000441089-0.378929-GBM,KIRP
ENSG00000267317ENST00000591252PHACTR1ENSG00000112137ENST00000379348-0.1424626-GBM,KICH,KIRP
ENSG00000267317ENST00000591252PHACTR1ENSG00000112137ENST00000434977-0.21951-GBM,KICH,KIRP
ENSG00000267317ENST00000591252PHACTR1ENSG00000112137ENST00000379329-0.1128409-GBM,KICH,KIRP
ENSG00000267317ENST00000591252CAMK2GENSG00000148660ENST00000433289-0.1256448-GBM
ENSG00000267317ENST00000591252CAMK2GENSG00000148660ENST00000305762-0.1256448-GBM
ENSG00000267317ENST00000591252CAMK2GENSG00000148660ENST00000372765-0.1256448-GBM
ENSG00000267317ENST00000591252CAMK2GENSG00000148660ENST00000441192-0.1271569-GBM
ENSG00000267317ENST00000591252AMN1ENSG00000151743ENST00000536761-0.2871272-GBM
ENSG00000267317ENST00000591252DHTKD1ENSG00000181192ENST00000263035-0.10211-KICH
ENSG00000267317ENST00000591252DHTKD1ENSG00000181192ENST00000448829-0.1314577-KICH
ENSG00000267317ENST00000591252NKIRAS1ENSG00000197885ENST00000416026-0.3427567-GBM
ENSG00000267317ENST00000591252AMN1ENSG00000151743ENST00000542781-0.1400484-GBM
ENSG00000267317ENST00000591252ANKRD46ENSG00000186106ENST00000519316-0.2449332-GBM,KIRP
ENSG00000267317ENST00000591252GABBR1ENSG00000204681ENST00000489385-0.1734262-GBM
ENSG00000267317ENST00000591252PLS1ENSG00000120756ENST00000497002-0.3444335-KICH
ENSG00000267317ENST00000591252SNX18ENSG00000178996ENST00000326277-0.283671-KIRP
ENSG00000267317ENST00000591252CIPCENSG00000198894ENST00000555437-0.1928752-GBM,KIRP
ENSG00000267317ENST00000591252CIPCENSG00000198894ENST00000555611-0.1054325-GBM,KIRP
ENSG00000267317ENST00000591252DNAJC11ENSG00000007923ENST00000451196-0.1003303-KIRP
ENSG00000267317ENST00000591252RUFY3ENSG00000018189ENST00000504805-0.1204615-GBM

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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
ENSG00000267317.2ENST00000591252.213239437