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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: ENSG00000255135

Summary for EMSY-DT

check button Gene summary

Gene informationEnsembl ID

ENSG00000255135

Gene symbol

EMSY-DT

Gene nameEMSY divergent transcript
HGNC

55507

Entrez ID
Gene typelincRNA
SynonymsEMSY-DT|RP11-111M22.3|11q13.5
UniProtAcc

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Structure and expression level for EMSY-DT

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
ENSG000002551352.825898e+021.003168e+001.771762e-015.661978e+001.500000e-087.960000e-08UPUCEC
ENSG000002551352.382313e+021.377602e+001.325471e-011.039330e+012.660000e-252.270000e-24UPLUSC
ENSG000002551351.381824e+021.116561e+001.603414e-016.963643e+003.320000e-122.660000e-11UPLIHC

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000002551355.534741e-018.028312e-05CHOL2.637426e-04
ENSG000002551353.596457e-011.170026e-13LIHC9.549480e-13

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lncRNA-Protein interaction for EMSY-DT

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
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000071655MBD39.9290.4779O95983TF,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
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000130254SAFB246.1995.1707Q14151TF,RBPNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000166526ZNF315.7390.4744P17036TFNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000071655MBD39.9290.8903O95983TF,EpiNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000185670ZBTB39.290.6805Q9H5J0TFNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000180035ZNF489.1692.0774Q96MX3TFNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000148300REXO47.8790.5075Q9GZR2TFNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000130254SAFB276.0394.4876Q14151TF,RBPNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000071655MBD311.0290.6573O95983TF,EpiNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000180035ZNF4810.4293.673Q96MX3TFNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000176946THAP47.2692.3069Q8WY91TFNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000221944TIGD15.1290.1778Q96MW7TFNA

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
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000130254SAFB276.0394.4105Q14151TF,RBPNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000160917CPSF423.3790.9314O95639RBPNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000148296SURF620.5890.5175O75683RBPNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000135314KHDC116.4891.7569Q4VXA5RBPNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000150316CWC1513.4690.2112Q9P013RBPNA
ENSG00000255135ENST00000530759RP11-111M22.3ENSG00000134597RBMX212.0991.2876Q9Y388RBPNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000130254SAFB246.1995.3564Q14151TF,RBPNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000148296SURF623.5391.8535O75683RBPNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000105705SUGP115.9290.2143Q8IWZ8RBPNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000134597RBMX214.6891.4086Q9Y388RBPNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000205937RNPS19.9492.3084Q15287RBPNA
ENSG00000255135ENST00000572035RP11-111M22.3ENSG00000204356NELFE7.7290.8034P18615RBPNA

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lncRNA-DNA interaction for EMSY-DT

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 EMSY-DT

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.
Only predicted by lncTar
UBR5,CIC,NFAT5,GTF2I,BAZ2A,QKI,REST,HBP1,AEBP2,HELZ2,NAF1,PRDM1,TEP1,ZNF28,PHF20,NOP9,FOXJ3,STAT6,IREB2,SART3,SF3A1,DDX6,DNMT1,NCOA2,AHR,DDX60,DDX3X,MTF1,PUM1,GLYR1
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
ENSG00000255135ENST00000572035exon_skip_319223chr19:43526200-43526349-18.25-0.1313ETHE1ENST00000292147Frame-shift
ENSG00000255135ENST00000572035exon_skip_324294chr2:27774423-27774530-12.83-0.1782MRPL33ENST00000296102Frame-shift
ENSG00000255135ENST00000572035exon_skip_445390chr5:150403120-150403312-21.78-0.1296CD74ENST00000009530In-frame
ENSG00000255135ENST00000572035exon_skip_303345chr19:17227839-17228005-17.28-0.1361OCEL1ENST00000215061Frame-shift
ENSG00000255135ENST00000572035exon_skip_106783chr14:55673171-55673255-5.74-0.1196KTN1ENST00000395314In-frame
ENSG00000255135ENST00000572035exon_skip_436498chr5:96729152-96729209-6.27-0.2850CASTENST00000341926,ENST00000395813In-frame
ENSG00000255135ENST00000572035exon_skip_29583chr1:114780109-114780215-10.56-0.1135SIKE1ENST00000060969Frame-shift

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

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Variants for EMSY-DT

check buttonRNA A-to-I editing events in lncRNA.
LncRNAediting IDLncRNA Ensembl IDChromosomeEditing PositionStrandGene TypeGene NameTranscript IDTranscript TypeTranscript Name
LncEditing_245786ENSG00000255135.3chr1176441484-lincRNARP11-111M22.3ENST00000572035.1lincRNARP11-111M22.3-006

check buttonEdited-associated DElncRNAs in cancer.
Differentially expressed gene
LncRNA Ensembl IDLncRNA IndexCancer TypeChr_Postion_StrandAVE1AVE2log2FCW-valueP-valueAdjc.p-valueChange
ENSG00000255135LncEditing_245786GBMchr11_76441484_-9.936814e+008.094370e+003.379925e+002.428589e+001.515769e-021.619891e-02UP

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
ENSG00000255135.3ENST00000530759.1124311685
ENSG00000255135.3ENST00000572035.151564409