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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: ENSG00000231160

Summary for KLF3-AS1

check button Gene summary

Gene informationEnsembl ID

ENSG00000231160

Gene symbol

KLF3-AS1

Gene nameKLF3 antisense RNA 1
HGNC

25796

Entrez ID
Gene typeprocessed_transcript
Synonyms04p14|KLF3-AS1
UniProtAcc

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Structure and expression level for KLF3-AS1

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.
Ensembl IDBase meanlog2FC(AD/control)lfcSEStatP-valueAdjc.p-valueDEG direction Cancer type

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value

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lncRNA-Protein interaction for KLF3-AS1

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
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000123636BAZ2B138.6195.516Q9UIF8TF,EpiPredict
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000108799EZH178.9293.2209Q92800EpiChIP-seq
ENSG00000231160ENST00000504219KLF3-AS1ENSG00000183495EP40053.1791.7843Q96L91EpiNA
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000120071KANSL150.6691.8735Q7Z3B3EpiNA
ENSG00000231160ENST00000504219KLF3-AS1ENSG00000120071KANSL138.2690.638Q7Z3B3EpiNA
ENSG00000231160ENST00000436901KLF3-AS1ENSG00000115524SF3B133.7694.1179O75533EpiNA
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000168137SETD5100.1790.9909Q9C0A6EpiPredict
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000117625RCOR321.5492.3961Q9P2K3EpiNA
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000108799EZH160.7892.0186Q92800EpiChIP-seq
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000183495EP40054.494.8482Q96L91EpiNA
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000120071KANSL138.5991.8656Q7Z3B3EpiNA
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000168137SETD5120.0492.6478Q9C0A6EpiPredict
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000117625RCOR322.2291.7473Q9P2K3EpiNA

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
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000167232ZNF9159.5891.2731Q05481TFNA
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000126804ZBTB147.2191.1955Q9Y2K1TFPredict
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000197857ZNF4417.5290.0537P15621TFNA
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000123636BAZ2B138.6195.8015Q9UIF8TF,EpiPredict
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000167232ZNF9175.091.1165Q05481TFNA
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000126804ZBTB162.9691.5072Q9Y2K1TFPredict
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000168795ZBTB545.8793.9215O15062TFNA

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
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000106344RBM2891.9692.2451Q9NW13RBPPredict
ENSG00000231160ENST00000436901KLF3-AS1ENSG00000082898XPO145.3792.7649O14980RBPNA
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000133226SRRM141.595.3536Q8IYB3RBPNA
ENSG00000231160ENST00000507091KLF3-AS1ENSG00000167978SRRM229.1596.9627Q9UQ35RBPNA
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000106344RBM2874.4492.6687Q9NW13RBPPredict
ENSG00000231160ENST00000610668KLF3-AS1ENSG00000167978SRRM224.3394.9185Q9UQ35RBPNA

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lncRNA-DNA interaction for KLF3-AS1

lncrna_DNA
check buttonlncRNA targets the enhancer region and positively regulates the gene expression.
Only predicted by TDF
ATM,PBX2,TTC17,RBM39,MFSD8,GPATCH8,LENG8,PGS1,PER2,ZCCHC8,MYSM1,AKAP8,BBOF1,ZXDC,INTS3,N4BP2L2,DMTF1,L3HYPDH,MLLT6,UNKL,CSAD,PIGG,SPIN3,NHLRC3,GPCPD1,RBM28,DCAF8,USP36,SF3B1,KLHDC1,POFUT2,ZBTB5,ZFP14,RNPC3,ANKRD10,MSANTD2,THOC1,TUBGCP6,PAN3,WDR59,ZBED5,ZMYM5,TTC14,S100PBP,CCNT2,CALCOCO1,SLC2A11,ZNF44,POGZ,ZNF91,NFRKB,CHD6,PKD1,RIMKLB,RBM4B,PHC1,ECHDC2,OGT,SCML1,BCLAF3,RBM25,IKZF4,POLG2,TUT4,MLH3,SETD6,EP400,POLI,UBN2,PRPF39,LRIG2,EZH1,MRNIP,KIAA0753,RABL2A,THAP6,ELMOD3,DDX17,SRRM2,GSTM2,SENP7,MTRF1,RAD52,ZNF717,NBPF11,CEP44,CEP290,SDR39U1,MAU2,NAPB,ARGLU1,WSB1,GPALPP1,SETD5,GON4L,FNBP4,YTHDC1,CHD2,ATG14,RNFT1,CCDC93,STK36,TTC32,TIA1,ZMAT1,ZNF83,HEMK1,KANSL1,CCDC191,ADHFE1,STRADA,DIDO1,DPH1,GOLGA8A,SETD4,ALG9,GIGYF1,TRMT13,XPO1,RBM5,ATG2B,NKTR,ZFC3H1,CRAMP1,MBTD1,ZNF84,DDX42,BAZ2B,PARP6,CEP192,TRA2A,MAPKAPK5,REV1,KHDC4,PNISR,MAN2C1,AMT,USPL1,MRPL38,WBP1,RABL2B,RBM33,ZNF10
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 KLF3-AS1

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.

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 Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonLOF

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

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Variants for KLF3-AS1

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

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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
ENSG00000231160.8ENST00000440181.467159362
ENSG00000231160.8ENST00000504219.113592499
ENSG00000231160.8ENST00000620339.312283451
ENSG00000231160.8ENST00000507091.482102350
ENSG00000231160.8ENST00000505240.48274322
ENSG00000231160.8ENST00000610668.3798247
ENSG00000231160.8ENST00000436901.28295343