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lncRNA: ENSG00000235313

Summary for HM13-IT1

Gene summary

Gene information	Ensembl ID	ENSG00000235313
	Gene symbol	HM13-IT1
	Gene name	HM13 intronic transcript 1
	HGNC	41424
	Entrez ID
	Gene type	sense_intronic
	Synonyms	20q11.21\|HM13-IT1
	UniProtAcc

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Structure and expression level for HM13-IT1

AS events and RNA A-to-I editing events of lncRNA in TCGA based on Genvode V22 structure.

Differentially expressed gene analysis between cancer and normal samples.

Ensembl ID	Base mean	log2FC(AD/control)	lfcSE	Stat	P-value	Adjc.p-value	DEG direction	Cancer type
ENSG00000235313	2.487231e+01	2.292534e+00	1.579789e-01	1.451165e+01	1.020000e-47	2.250000e-46	UP	KIRC
ENSG00000235313	1.669732e+01	1.420846e+00	1.832245e-01	7.754675e+00	8.860000e-15	7.860000e-14	UP	COAD
ENSG00000235313	1.786726e+01	1.749635e+00	3.309460e-01	5.286770e+00	1.240000e-07	1.960000e-06	UP	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000235313	3.468987e-01	1.238343e-18	KIRC	8.018047e-18

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lncRNA-Protein interaction for HM13-IT1

lncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000149311	ATM	20.84	91.6125	Q13315	Epi	NA
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000146247	PHIP	20.72	92.8112	Q8WWQ0	Epi	NA
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000196367	TRRAP	17.95	90.075	Q9Y4A5	Epi	NA
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000124177	CHD6	16.04	94.6154	Q8TD26	Epi	NA
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000185658	BRWD1	15.65	93.4202	Q9NSI6	Epi	NA
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000131149	GSE1	13.4	91.4509	Q14687	Epi	NA
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000120616	EPC1	12.75	90.3121	Q9H2F5	Epi	NA
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000165288	BRWD3	15.69	93.2852	Q6RI45	Epi	NA

lncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID

LncRNA ENST ID

LncRNA Name

Protein Ensembl ID

Protein Name

CatRAPID Score

Lncpro Score

UniPortID

Gene Subtype

Public source

lncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000129566	TEP1	16.57	91.9647	Q99973	RBP	NA
ENSG00000235313	ENST00000421894	HM13-IT1	ENSG00000114127	XRN1	16.56	91.2536	Q8IZH2	RBP	NA

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lncRNA-DNA interaction for HM13-IT1

lncRNA targets the enhancer region and positively regulates the gene expression.

lncRNA targets the promoter region and positively regulates the gene expression.

lncRNA targets the promoter region and negatively regulates the gene expression.

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lncRNA-RNA interaction for HM13-IT1

lncRNA targets the 3'UTR region and negatively regulates the mRNA.

lncRNA targets the skipped exon region.

-lncRNA and exonskipping events are positively correlated.

LncRNA Ensembl ID

LncRNA ENST ID

Exon ID

Skipped Exon

ndG

Gene name with skipped exon

TransID with skipped exon

ORF mutation

-lncRNA and exonskipping events are negatively correlated.

lncRNA and exonskipping events negative correlated

LncRNA Ensembl ID	LncRNA ENST ID	Exon ID	Skipped Exon	dG	ndG	Gene name with skipped exon	TransID with skipped exon	LOF
ENSG00000235313	ENST00000421894	exon_skip_382458	chr3:38131595-38131638	-10.05	-0.3141	ACAA1	ENST00000333167	Frame-shift

lncRNA targets by miRNA.

LncRNA Ensembl ID

miRNA ID

LncRNA ENST ID

Binding site in lncRNA

Score

Energy

Align Len

Public source

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Variants for HM13-IT1

RNA A-to-I editing events in lncRNA.

LncRNAediting ID	LncRNA Ensembl ID	Chromosome	Editing Position	Strand	Gene Type	Gene Name	Transcript ID	Transcript Type	Transcript Name
LncEditing_365380	ENSG00000235313.1	chr20	31563394	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365383	ENSG00000235313.1	chr20	31563424	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365384	ENSG00000235313.1	chr20	31563427	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365386	ENSG00000235313.1	chr20	31563441	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365388	ENSG00000235313.1	chr20	31563450	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365389	ENSG00000235313.1	chr20	31563453	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365390	ENSG00000235313.1	chr20	31563463	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365397	ENSG00000235313.1	chr20	31563507	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365401	ENSG00000235313.1	chr20	31563524	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365408	ENSG00000235313.1	chr20	31563576	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365410	ENSG00000235313.1	chr20	31563586	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365422	ENSG00000235313.1	chr20	31563887	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365427	ENSG00000235313.1	chr20	31563912	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365436	ENSG00000235313.1	chr20	31563955	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005
LncEditing_365437	ENSG00000235313.1	chr20	31563956	+	sense_intronic	HM13-IT1	ENST00000421894.1	sense_intronic	HM13-IT1-005

Edited-associated DElncRNAs in cancer.

LncRNA Ensembl ID	LncRNA Index	Cancer Type	Chr_Postion_Strand	AVE1	AVE2	log2FC	W-value	P-value	Adjc.p-value	Change
ENSG00000235313	LncEditing_365380	LAML	chr20_31563394_+	1.641582e+01	1.274814e+01	2.741228e+00	4.226166e+00	2.377063e-05	4.181870e-05	UP
ENSG00000235313	LncEditing_365401	LAML	chr20_31563524_+	1.801272e+01	1.329241e+01	2.280953e+00	3.228369e+00	1.244981e-03	1.594971e-03	UP
ENSG00000235313	LncEditing_365422	LAML	chr20_31563887_+	1.709183e+01	1.340155e+01	2.849763e+00	2.067607e+00	3.867696e-02	3.921679e-02	UP
ENSG00000235313	LncEditing_365427	LAML	chr20_31563912_+	1.897887e+01	1.313461e+01	1.883167e+00	3.591053e+00	3.293448e-04	4.653785e-04	UP
ENSG00000235313	LncEditing_365380	OV	chr20_31563394_+	4.494469e+00	2.563688e+00	1.234675e+00	8.593078e+00	8.467018e-18	3.095595e-17	UP
ENSG00000235313	LncEditing_365422	OV	chr20_31563887_+	4.836576e+00	2.623381e+00	1.133069e+00	7.582336e+00	3.393869e-14	8.753613e-14	UP
ENSG00000235313	LncEditing_365427	OV	chr20_31563912_+	4.894562e+00	2.557542e+00	1.067894e+00	8.322577e+00	8.607149e-17	2.811465e-16	UP
ENSG00000235313	LncEditing_365436	OV	chr20_31563955_+	4.274731e+00	2.759833e+00	1.584152e+00	5.297966e+00	1.170995e-07	1.628941e-07	UP
ENSG00000235313	LncEditing_365437	OV	chr20_31563956_+	4.464791e+00	2.685481e+00	1.363490e+00	6.479566e+00	9.198707e-11	1.688266e-10	UP
ENSG00000235313	LncEditing_365380	STAD	chr20_31563394_+	5.243228e+00	2.246624e+00	8.178643e-01	1.219313e+01	3.381825e-34	1.153041e-32	UP
ENSG00000235313	LncEditing_365383	STAD	chr20_31563424_+	6.186590e+00	2.621804e+00	8.073734e-01	9.026940e+00	1.765389e-19	7.285410e-19	UP
ENSG00000235313	LncEditing_365386	STAD	chr20_31563441_+	6.043830e+00	2.737709e+00	8.752783e-01	8.055916e+00	7.888611e-16	2.111494e-15	UP
ENSG00000235313	LncEditing_365408	STAD	chr20_31563576_+	5.463947e+00	2.774162e+00	1.022608e+00	7.938107e+00	2.052899e-15	5.287322e-15	UP
ENSG00000235313	LncEditing_365427	STAD	chr20_31563912_+	5.624024e+00	2.810514e+00	9.992319e-01	7.474457e+00	7.752347e-14	1.687137e-13	UP
ENSG00000235313	LncEditing_365436	STAD	chr20_31563955_+	5.538148e+00	2.837565e+00	1.036538e+00	7.109884e+00	1.161405e-12	2.278264e-12	UP
ENSG00000235313	LncEditing_365437	STAD	chr20_31563956_+	5.397521e+00	2.823623e+00	1.069806e+00	7.043375e+00	1.876385e-12	3.606689e-12	UP
ENSG00000235313	LncEditing_365380	ESCA	chr20_31563394_+	4.759975e+00	2.467031e+00	1.054654e+00	7.187864e+00	6.581263e-13	3.315944e-12	UP
ENSG00000235313	LncEditing_365383	ESCA	chr20_31563424_+	5.788048e+00	2.897992e+00	1.001980e+00	5.922043e+00	3.179673e-09	7.625395e-09	UP
ENSG00000235313	LncEditing_365384	ESCA	chr20_31563427_+	5.348858e+00	2.716684e+00	1.023139e+00	6.726983e+00	1.732174e-11	6.649519e-11	UP
ENSG00000235313	LncEditing_365386	ESCA	chr20_31563441_+	6.193017e+00	3.001652e+00	9.570424e-01	5.442537e+00	5.252717e-08	1.021307e-07	UP
ENSG00000235313	LncEditing_365388	ESCA	chr20_31563450_+	6.528116e+00	2.847324e+00	8.353800e-01	6.859327e+00	6.918574e-12	2.865876e-11	UP
ENSG00000235313	LncEditing_365389	ESCA	chr20_31563453_+	6.158620e+00	2.938257e+00	9.366395e-01	5.794334e+00	6.859275e-09	1.529472e-08	UP
ENSG00000235313	LncEditing_365390	ESCA	chr20_31563463_+	6.186774e+00	2.861062e+00	8.987662e-01	6.622138e+00	3.540415e-11	1.259883e-10	UP
ENSG00000235313	LncEditing_365397	ESCA	chr20_31563507_+	6.838773e+00	3.013980e+00	8.459754e-01	5.511430e+00	3.559309e-08	7.098298e-08	UP
ENSG00000235313	LncEditing_365408	ESCA	chr20_31563576_+	5.189335e+00	3.076203e+00	1.325559e+00	5.119571e+00	3.062319e-07	5.329048e-07	UP
ENSG00000235313	LncEditing_365410	ESCA	chr20_31563586_+	5.683918e+00	3.149377e+00	1.173958e+00	4.604243e+00	4.139682e-06	6.149379e-06	UP
ENSG00000235313	LncEditing_365422	ESCA	chr20_31563887_+	5.708297e+00	3.016574e+00	1.086780e+00	5.605747e+00	2.073584e-08	4.265193e-08	UP
ENSG00000235313	LncEditing_365427	ESCA	chr20_31563912_+	5.346484e+00	2.921336e+00	1.146839e+00	5.873993e+00	4.254204e-09	9.896572e-09	UP
ENSG00000235313	LncEditing_365436	ESCA	chr20_31563955_+	5.437064e+00	3.063745e+00	1.208413e+00	4.606236e+00	4.100223e-06	6.095083e-06	UP
ENSG00000235313	LncEditing_365437	ESCA	chr20_31563956_+	5.067658e+00	3.039822e+00	1.356241e+00	5.174048e+00	2.290756e-07	4.055258e-07	UP

Correlation between RNA A-to-I editing events's frequecy and lncRNA expression.

LncRNA Ensembl ID	LncRNA Index	Correlation	P-value	Adjc.p-value
ENSG00000235313	LncEditing_365422	-4.874693e-01	3.300952e-04	9.550753e-04
ENSG00000235313	LncEditing_365436	-4.761593e-01	2.183322e-03	3.745304e-03
ENSG00000235313	LncEditing_365437	-3.916669e-01	5.385351e-03	7.467227e-03
ENSG00000235313	LncEditing_365383	-3.657219e-01	7.081278e-03	8.991694e-03
ENSG00000235313	LncEditing_365380	-3.781246e-01	1.605768e-03	7.211090e-03
ENSG00000235313	LncEditing_365388	-4.709605e-01	1.749044e-02	2.692972e-02
ENSG00000235313	LncEditing_365436	-4.606884e-01	2.347969e-02	3.253614e-02
ENSG00000235313	LncEditing_365437	-4.715599e-01	8.523213e-03	1.801401e-02
ENSG00000235313	LncEditing_365380	-5.384878e-01	1.953768e-04	2.575421e-03

Cis-expression quantitative trait loci(cis-eQTL) of lncRNA.

LncRNA Ensembl ID

LncRNA Name

SNP info

Number of Positive corelated Cancer

Positive corelated Cancer

Number of Negative corelated Cancer

Negative corelated Cancer

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lncRNAs regulate the target genes through functioning as enhancers

lncRNA regulates differentially expressed genes by function as enhancer.

LncRNA Ensembl ID

PC Gene ID

PC Gene Name

Positive correlated cancers

Cancer with PC gene up-regulation

Cancer with PC gene down-regulation

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lncRNAs regulate the target genes through recruiting transcript factors

LncRNA-TF complex positively regulates the gene expression by target promoter region (#cancer types with positive correlation >= 5).

lncRNA ID

TF ID

TF Name

PCgene ID

PCgene Name

Number of Cancer

Canaer Types

LncRNA-TF complex negatively regulates the gene expression by target promoter region (#cancer types with negative correlation >= 5).

lncRNA ID

TF ID

TF Name

PCgene ID

PCgene Name

Number of Cancer

Canaer Types

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lncRNAs regulate the alternative splicing event through interacting with splicing factor

LncRNA-RBP complex positively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

LncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

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lncRNAs regulate mRNA through targeting the 3'-UTR region

lncRNA regulates differential expressed mRNA by directly targeting 3' UTR region.

LncRNA Ensembl ID

LncRNA ENST ID

PC Gene Name

PC Gene ID

PC ENST ID

nDG

Cancer with PC gene up-regulation

Cancer with PC gene Down-regulation

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lncRNAs regulate mRNA by competing with miRNA

lncRNA regulates mRNA by competing the miRNA binding site with mRNA.

LncRNA Ensembl ID

lncRNA-miRNA-mRNA

Cancer Types

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lncRNA coding potential

ORFfinder result for the gencode.v22.lncRNA.transcript.fa.

lncRNA Ensembl ID	lncRNA ENST ID	length(AA)	start at transcript	end at transcript
ENSG00000235313.1	ENST00000421894.1	80	102	344

	lncRNA summary
	lncRNA structure and expression level
	lncRNA-Protein interaction
	lncRNA-DNA interaction
	lncRNA-RNA interaction
	Variants in lncRNA
	lncRNAs regulate the target genes through functioning as enhancers
	lncRNAs regulate the target genes through recruiting transcript factors
	lncRNAs regulate the alternative splicing events through interacting with splicing factor
	lncRNAs regulate mRNA through targeting the 3'-UTR region
	lncRNAs regulate mRNA by competing with miRNA
	lncRNA coding potential