ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ARNT

Gene summary

Gene information	Gene symbol	ARNT
	Gene ID	405
	Gene name	aryl hydrocarbon receptor nuclear translocator
	Synonyms	HIF-1-beta\|HIF-1beta\|HIF1-beta\|HIF1B\|HIF1BETA\|TANGO\|bHLHe2
	Cytomap	1q21.3
	Type of gene	protein-coding
	Description	aryl hydrocarbon receptor nuclear translocatorclass E basic helix-loop-helix protein 2dioxin receptor, nuclear translocatorhypoxia-inducible factor 1, beta subunit
	Modification date	20180522
	UniProtAcc	P27540
	Context	PubMed: ARNT [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
ARNT	GO:0001666	response to hypoxia	8756616
ARNT	GO:0010575	positive regulation of vascular endothelial growth factor production	8756616
ARNT	GO:0043619	regulation of transcription from RNA polymerase II promoter in response to oxidative stress	8089148
ARNT	GO:0045893	positive regulation of transcription, DNA-templated	8089148
ARNT	GO:0046886	positive regulation of hormone biosynthetic process	1448077

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Exon skipping events across known transcript of Ensembl for ARNT from UCSC genome browser

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Gene isoform structures and expression levels for ARNT

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for ARNT

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_30338	1	150785647:150785814:150786552:150786715:150788734:150788876	150786552:150786715	ENSG00000143437.16	ENST00000515192.1,ENST00000354396.2,ENST00000505755.1,ENST00000358595.5
exon_skip_30339	1	150788734:150788882:150789263:150789366:150789557:150789678	150789263:150789366	ENSG00000143437.16	ENST00000515192.1,ENST00000505755.1,ENST00000358595.5
exon_skip_30340	1	150789869:150789909:150790395:150790506:150795669:150795722	150790395:150790506	ENSG00000143437.16	ENST00000515192.1,ENST00000354396.2,ENST00000505755.1,ENST00000358595.5
exon_skip_30345	1	150790403:150790506:150795669:150795821:150799018:150799093	150795669:150795821	ENSG00000143437.16	ENST00000515192.1,ENST00000354396.2,ENST00000505755.1,ENST00000358595.5
exon_skip_30348	1	150799018:150799093:150801568:150801703:150802379:150802441	150801568:150801703	ENSG00000143437.16	ENST00000515192.1,ENST00000471844.2,ENST00000354396.2,ENST00000505755.1,ENST00000358595.5
exon_skip_30355	1	150804809:150804875:150807013:150807116:150808755:150808969	150807013:150807116	ENSG00000143437.16	ENST00000515192.1,ENST00000471844.2,ENST00000354396.2,ENST00000468970.1,ENST00000505755.1,ENST00000358595.5
exon_skip_30357	1	150808899:150808969:150811916:150812130:150818738:150818783	150811916:150812130	ENSG00000143437.16	ENST00000497108.2,ENST00000505755.1
exon_skip_30360	1	150812083:150812130:150814899:150814944:150818738:150818783	150814899:150814944	ENSG00000143437.16	ENST00000515192.1,ENST00000471844.2,ENST00000505979.1,ENST00000354396.2,ENST00000504358.1,ENST00000358595.5
exon_skip_30363	1	150812083:150812130:150818738:150818783:150825237:150825282	150818738:150818783	ENSG00000143437.16	ENST00000497108.2,ENST00000505755.1
exon_skip_30368	1	150818738:150818783:150825237:150825282:150830824:150830936	150825237:150825282	ENSG00000143437.16	ENST00000515192.1,ENST00000471844.2,ENST00000505979.1,ENST00000354396.2,ENST00000505755.1,ENST00000358595.5
exon_skip_30370	1	150818738:150818783:150825237:150825316:150830824:150830936	150825237:150825316	ENSG00000143437.16	ENST00000497108.2
exon_skip_30371	1	150825237:150825282:150825631:150825754:150830824:150830936	150825631:150825754	ENSG00000143437.16	ENST00000504358.1
exon_skip_30372	1	150830824:150830936:150833722:150833778:150849018:150849044	150833722:150833778	ENSG00000143437.16	ENST00000515192.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ARNT

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_30338	1	150785647:150785814:150786552:150786715:150788734:150788876	150786552:150786715	ENSG00000143437.16	ENST00000358595.5,ENST00000354396.2,ENST00000515192.1,ENST00000505755.1
exon_skip_30339	1	150788734:150788882:150789263:150789366:150789557:150789678	150789263:150789366	ENSG00000143437.16	ENST00000358595.5,ENST00000515192.1,ENST00000505755.1
exon_skip_30340	1	150789869:150789909:150790395:150790506:150795669:150795722	150790395:150790506	ENSG00000143437.16	ENST00000358595.5,ENST00000354396.2,ENST00000515192.1,ENST00000505755.1
exon_skip_30345	1	150790403:150790506:150795669:150795821:150799018:150799093	150795669:150795821	ENSG00000143437.16	ENST00000358595.5,ENST00000354396.2,ENST00000515192.1,ENST00000505755.1
exon_skip_30355	1	150804809:150804875:150807013:150807116:150808755:150808969	150807013:150807116	ENSG00000143437.16	ENST00000358595.5,ENST00000471844.2,ENST00000354396.2,ENST00000515192.1,ENST00000505755.1,ENST00000468970.1
exon_skip_30357	1	150808899:150808969:150811916:150812130:150818738:150818783	150811916:150812130	ENSG00000143437.16	ENST00000505755.1,ENST00000497108.2
exon_skip_30360	1	150812083:150812130:150814899:150814944:150818738:150818783	150814899:150814944	ENSG00000143437.16	ENST00000358595.5,ENST00000471844.2,ENST00000354396.2,ENST00000515192.1,ENST00000505979.1,ENST00000504358.1
exon_skip_30363	1	150812083:150812130:150818738:150818783:150825237:150825282	150818738:150818783	ENSG00000143437.16	ENST00000505755.1,ENST00000497108.2
exon_skip_30368	1	150818738:150818783:150825237:150825282:150830824:150830936	150825237:150825282	ENSG00000143437.16	ENST00000358595.5,ENST00000471844.2,ENST00000354396.2,ENST00000515192.1,ENST00000505755.1,ENST00000505979.1
exon_skip_30370	1	150818738:150818783:150825237:150825316:150830824:150830936	150825237:150825316	ENSG00000143437.16	ENST00000497108.2
exon_skip_30371	1	150825237:150825282:150825631:150825754:150830824:150830936	150825631:150825754	ENSG00000143437.16	ENST00000504358.1
exon_skip_30372	1	150830824:150830936:150833722:150833778:150849018:150849044	150833722:150833778	ENSG00000143437.16	ENST00000515192.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for ARNT

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000358595	150786552	150786715	Frame-shift
ENST00000358595	150789263	150789366	Frame-shift
ENST00000358595	150795669	150795821	Frame-shift
ENST00000358595	150807013	150807116	Frame-shift
ENST00000358595	150790395	150790506	In-frame
ENST00000358595	150801568	150801703	In-frame
ENST00000358595	150814899	150814944	In-frame
ENST00000358595	150825237	150825282	In-frame

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000358595	150786552	150786715	Frame-shift
ENST00000358595	150789263	150789366	Frame-shift
ENST00000358595	150795669	150795821	Frame-shift
ENST00000358595	150807013	150807116	Frame-shift
ENST00000358595	150790395	150790506	In-frame
ENST00000358595	150814899	150814944	In-frame
ENST00000358595	150825237	150825282	In-frame

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Infer the effects of exon skipping event on protein functional features for ARNT

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000358595	4904	789	150825237	150825282	339	383	46	60
ENST00000358595	4904	789	150814899	150814944	429	473	76	90
ENST00000358595	4904	789	150801568	150801703	1234	1368	344	389
ENST00000358595	4904	789	150790395	150790506	1596	1706	465	501

Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000358595	4904	789	150825237	150825282	339	383	46	60
ENST00000358595	4904	789	150814899	150814944	429	473	76	90
ENST00000358595	4904	789	150790395	150790506	1596	1706	465	501

Lost protein functional features of individual exon skipping events in TCGA.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P27540	46	60	2	789	Chain	ID=PRO_0000127118;Note=Aryl hydrocarbon receptor nuclear translocator
P27540	46	60	58	58	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
P27540	76	90	77	91	Alternative sequence	ID=VSP_002092;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1852076;Dbxref=PMID:1852076
P27540	76	90	2	789	Chain	ID=PRO_0000127118;Note=Aryl hydrocarbon receptor nuclear translocator
P27540	76	90	89	142	Domain	Note=bHLH;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00981
P27540	76	90	77	77	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
P27540	76	90	88	128	Region	Note=DNA-binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28396409;Dbxref=PMID:28396409
P27540	344	389	356	358	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2K7S
P27540	344	389	362	367	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3F1P
P27540	344	389	371	376	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3F1P
P27540	344	389	2	789	Chain	ID=PRO_0000127118;Note=Aryl hydrocarbon receptor nuclear translocator
P27540	344	389	349	419	Domain	Note=PAS 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00140
P27540	344	389	380	384	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3F1P
P27540	344	389	388	390	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3F1P
P27540	465	501	2	789	Chain	ID=PRO_0000127118;Note=Aryl hydrocarbon receptor nuclear translocator
P27540	465	501	424	467	Domain	Note=PAC

Lost protein functional features of individual exon skipping events in GTEx.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P27540	46	60	2	789	Chain	ID=PRO_0000127118;Note=Aryl hydrocarbon receptor nuclear translocator
P27540	46	60	58	58	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
P27540	76	90	77	91	Alternative sequence	ID=VSP_002092;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1852076;Dbxref=PMID:1852076
P27540	76	90	2	789	Chain	ID=PRO_0000127118;Note=Aryl hydrocarbon receptor nuclear translocator
P27540	76	90	89	142	Domain	Note=bHLH;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00981
P27540	76	90	77	77	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
P27540	76	90	88	128	Region	Note=DNA-binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28396409;Dbxref=PMID:28396409
P27540	465	501	2	789	Chain	ID=PRO_0000127118;Note=Aryl hydrocarbon receptor nuclear translocator
P27540	465	501	424	467	Domain	Note=PAC

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SNVs in the skipped exons for ARNT

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-DD-A3A1-01	exon_skip_30339	150789264	150789366	150789267	150789267	Frame_Shift_Del	A	-	p.F600fs
LIHC	TCGA-DD-A3A0-01	exon_skip_30339	150789264	150789366	150789283	150789283	Frame_Shift_Del	G	-	p.R595fs
STAD	TCGA-BR-8372-01	exon_skip_30339	150789264	150789366	150789283	150789283	Frame_Shift_Del	G	-	p.R595fs
STAD	TCGA-CG-4442-01	exon_skip_30339	150789264	150789366	150789283	150789283	Frame_Shift_Del	G	-	p.R595fs
LUAD	TCGA-78-7162-01	exon_skip_30339	150789264	150789366	150789322	150789326	Frame_Shift_Del	GTTGG	-	p.T580fs
LUAD	TCGA-78-7162-01	exon_skip_30339	150789264	150789366	150789322	150789326	Frame_Shift_Del	GTTGG	-	p.TQQ580fs
LUAD	TCGA-05-5715-01	exon_skip_30339	150789264	150789366	150789333	150789333	Frame_Shift_Del	G	-	p.P578fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_30345	150795670	150795821	150795807	150795807	Frame_Shift_Del	T	-	p.K419fs
PCPG	TCGA-SP-A6QJ-01		150814900	150814944	150814926	150814930	Frame_Shift_Del	GCTCT	-	p.81_83del
PCPG	TCGA-SP-A6QJ-01		150814900	150814944	150814926	150814930	Frame_Shift_Del	GCTCT	-	p.QS81fs
UCEC	TCGA-A5-A0GN-01	exon_skip_30339	150789264	150789366	150789282	150789283	Frame_Shift_Ins	-	G	p.R595fs
UCEC	TCGA-B5-A0K7-01	exon_skip_30339	150789264	150789366	150789282	150789283	Frame_Shift_Ins	-	G	p.R595fs
UCEC	TCGA-BG-A0M9-01	exon_skip_30339	150789264	150789366	150789282	150789283	Frame_Shift_Ins	-	G	p.R595fs
UCEC	TCGA-A5-A0GW-01	exon_skip_30338	150786553	150786715	150786565	150786565	Nonsense_Mutation	C	A	p.G701*
CESC	TCGA-JX-A3Q0-01	exon_skip_30339	150789264	150789366	150789274	150789274	Nonsense_Mutation	C	A	p.E598*
UCEC	TCGA-AP-A059-01	exon_skip_30355	150807014	150807116	150807021	150807021	Nonsense_Mutation	G	A	p.R266*
BRCA	TCGA-BH-A0AU-01	exon_skip_30355	150807014	150807116	150807078	150807078	Nonsense_Mutation	C	A	p.E247*
READ	TCGA-AG-A002-01	exon_skip_30357	150811917	150812130	150812072	150812072	Nonsense_Mutation	C	A	p.E96X
UCEC	TCGA-AP-A0LE-01	exon_skip_30338	150786553	150786715	150786552	150786552	Splice_Site	C	T	e20+1
UCEC	TCGA-AP-A0LE-01	exon_skip_30338	150786553	150786715	150786552	150786552	Splice_Site	C	T	p.A705_splice

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
HEC151_ENDOMETRIUM	150789264	150789366	150789283	150789283	Frame_Shift_Del	G	-	p.R595fs
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	150789264	150789366	150789283	150789283	Frame_Shift_Del	G	-	p.R595fs
SNUC4_LARGE_INTESTINE	150789264	150789366	150789282	150789283	Frame_Shift_Ins	-	G	p.R595fs
COLO684_ENDOMETRIUM	150786553	150786715	150786607	150786607	Missense_Mutation	C	T	p.A687T
COLO704_OVARY	150786553	150786715	150786607	150786607	Missense_Mutation	C	T	p.A687T
NCIH720_LUNG	150786553	150786715	150786648	150786648	Missense_Mutation	G	T	p.P673Q
SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	150789264	150789366	150789279	150789279	Missense_Mutation	G	A	p.P596L
BICR18_UPPER_AERODIGESTIVE_TRACT	150789264	150789366	150789288	150789288	Missense_Mutation	G	T	p.T593N
BICR18_UPPER_AERODIGESTIVE_TRACT	150789264	150789366	150789301	150789301	Missense_Mutation	T	A	p.T589S
BICR18_UPPER_AERODIGESTIVE_TRACT	150789264	150789366	150789303	150789303	Missense_Mutation	T	C	p.N588S
ABC1_LUNG	150789264	150789366	150789312	150789312	Missense_Mutation	G	A	p.S585F
HEC108_ENDOMETRIUM	150790396	150790506	150790447	150790447	Missense_Mutation	C	T	p.G485D
CW2_LARGE_INTESTINE	150795670	150795821	150795674	150795674	Missense_Mutation	C	T	p.V464M
SNU175_LARGE_INTESTINE	150795670	150795821	150795677	150795677	Missense_Mutation	T	C	p.N463D
SNU349_KIDNEY	150795670	150795821	150795682	150795682	Missense_Mutation	T	G	p.N461T
SNGM_ENDOMETRIUM	150795670	150795821	150795731	150795731	Missense_Mutation	T	C	p.T445A
MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	150795670	150795821	150795818	150795818	Missense_Mutation	C	T	p.V416M
SNU1040_LARGE_INTESTINE	150801569	150801703	150801601	150801601	Missense_Mutation	G	A	p.R379C
NCIH520_LUNG	150801569	150801703	150801643	150801643	Missense_Mutation	A	G	p.S365P
OVCAR4_OVARY	150807014	150807116	150807069	150807069	Missense_Mutation	G	T	p.Q250K
TGBC11TKB_STOMACH	150807014	150807116	150807114	150807114	Missense_Mutation	G	A	p.R235C
HEC151_ENDOMETRIUM	150811917	150812130	150812017	150812017	Missense_Mutation	A	G	p.L129P
SNU1033_LARGE_INTESTINE	150811917	150812130	150812024	150812024	Missense_Mutation	C	G	p.D127H
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	150811917	150812130	150812051	150812051	Missense_Mutation	T	C	p.T118A
SNU1040_LARGE_INTESTINE	150811917	150812130	150812058	150812058	Missense_Mutation	C	T	p.M115I
HEC1B_ENDOMETRIUM	150814900	150814944	150814925	150814925	Missense_Mutation	A	C	p.S83A
CS1_BONE	150795670	150795821	150795707	150795707	Nonsense_Mutation	C	A	p.E453*
SNU61_LARGE_INTESTINE	150786553	150786715	150786714	150786714	Splice_Site	T	A	p.Q651L
HEC59_ENDOMETRIUM	150807014	150807116	150807115	150807115	Splice_Site	C	T	p.G234G
GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	150811917	150812130	150811917	150811917	Splice_Site	C	A	p.Q162H
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	150814900	150814944	150814900	150814900	Splice_Site	C	T	p.R91K

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARNT

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARNT

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARNT

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RelatedDrugs for ARNT

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for ARNT

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
ARNT	C0000786	Spontaneous abortion	1	CTD_human
ARNT	C0009404	Colorectal Neoplasms	1	CTD_human
ARNT	C0014175	Endometriosis	1	CTD_human
ARNT	C0023890	Liver Cirrhosis	1	CTD_human
ARNT	C0025202	melanoma	1	CTD_human
ARNT	C0027659	Neoplasms, Experimental	1	CTD_human
ARNT	C1961102	Precursor Cell Lymphoblastic Leukemia Lymphoma	1	CTD_human
ARNT	C4277682	Chemical and Drug Induced Liver Injury	1	CTD_human

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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