ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for NRG1

Gene summary

Gene information	Gene symbol	NRG1
	Gene ID	3084
	Gene name	neuregulin 1
	Synonyms	ARIA\|GGF\|GGF2\|HGL\|HRG\|HRG1\|HRGA\|MST131\|MSTP131\|NDF\|NRG1-IT2\|SMDF
	Cytomap	8p12
	Type of gene	protein-coding
	Description	pro-neuregulin-1, membrane-bound isoformacetylcholine receptor-inducing activityglial growth factor 2heregulin, alpha (45kD, ERBB2 p185-activator)neu differentiation factorpro-NRG1sensory and motor neuron derived factor
	Modification date	20200320
	UniProtAcc	A0A024QY88, A0A087X0X9, A0A494BZT4, A0A494C043, A0A494C054, A0A494C0K4, A0A494C0L9, A0A494C0Q4, A0A494C0T5, A0A494C114, A0A494C1B5, A0A494C1F5, A0A494C1F8, A0A494C1G2, A0A5F9ZHA5, A5YAK6, A5YAK7, A5YAK8, A6MW54, A6MW55, A6MW56, B0FWZ3, B0FYA7, B0FYA8, B0FYA9, B5BU95, B7Z168, B9EK51, E3SFM9, E3SFN0, E5RHP6, E5RHQ1, E5RIG8, F6RJN6, H0YBA3, H0YCP0, H0YDC2, Q02297, Q6ICV5, Q6PK61, Q7RTV8, Q7RTW3, Q7RTW4, Q7RTW5, Q86WJ0, Q96IB3,
	Context	- 26913607(Neuregulin-1 Attenuates Cognitive Function Impairments in a Transgenic Mouse Model of Alzheimer's Disease)

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

Gene	GO ID	GO term	PubMed ID
NRG1	GO:0003222	ventricular trabecula myocardium morphogenesis	17336907
NRG1	GO:0031334	positive regulation of protein complex assembly	10559227
NRG1	GO:0038127	ERBB signaling pathway	11389077
NRG1	GO:0038129	ERBB3 signaling pathway	27353365
NRG1	GO:0045892	negative regulation of transcription, DNA-templated	15073182
NRG1	GO:0051048	negative regulation of secretion	10559227
NRG1	GO:0060379	cardiac muscle cell myoblast differentiation	17336907
NRG1	GO:0060956	endocardial cell differentiation	17336907

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Gene structures and expression levels for NRG1

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000157168

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
PCC	DOWN	ENST00000519301.6	NRG1-208:protein_coding:NRG1	8.477502e+00	-8.536466e-01	2.872781e-03	4.879906e-02
PG	DOWN	ENST00000521463.5	NRG1-IT1-202:lncRNA:NRG1	3.033353e+00	-8.485831e-01	5.193583e-06	3.107984e-04
PG	DOWN	ENST00000520407.5	NRG1-209:protein_coding:NRG1	5.273310e+00	-9.480072e-01	1.723020e-04	4.086747e-03
PG	DOWN	ENST00000651335.1	NRG1-232:protein_coding:NRG1	1.075246e+00	-8.820702e-01	1.909062e-03	2.307819e-02
TC	DOWN	ENST00000518206.5	NRG1-206:protein_coding:NRG1	6.376188e+00	-9.425220e-01	2.654584e-03	2.080057e-02

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NRG1

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_124211	chr8	32727949:32728078:32742008:32742075:32742675:32742733	32742008:32742075
exon_skip_128998	chr8	32754372:32754474:32756403:32756529:32759306:32759436	32756403:32756529
exon_skip_129763	chr8	32727949:32728078:32742675:32742733:32754372:32754474	32742675:32742733
exon_skip_179313	chr8	32760200:32760406:32763218:32763359:32763748:32763998	32763218:32763359
exon_skip_192362	chr8	32605562:32605683:32614514:32614564:32727949:32728078	32614514:32614564
exon_skip_214879	chr8	32614514:32614564:32616835:32616885:32727949:32728078	32616835:32616885
exon_skip_224719	chr8	32742675:32742733:32749561:32749584:32754372:32754423	32749561:32749584
exon_skip_246595	chr8	32727949:32728078:32742008:32742075:32742675:32743224	32742008:32742075
exon_skip_74866	chr8	32727949:32728078:32742675:32742733:32754372:32754423	32742675:32742733
exon_skip_96436	chr8	32727949:32728078:32742008:32742075:32754372:32754474	32742008:32742075

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for NRG1

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000405005	32742008	32742075	Frame-shift
ENST00000405005	32616835	32616885	In-frame

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000405005	32616835	32616885	In-frame

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000405005	32756403	32756529	Frame-shift
ENST00000405005	32616835	32616885	In-frame

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Infer the effects of exon skipping event on protein functional features for NRG1

p-ENSG00000157168_img4.png
boxplot

Loci of skipped exons in ROSMAP 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
ENST00000405005	2009	640	32616835	32616885	453	502	151	167

Loci of skipped exons in MSBB 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
ENST00000405005	2009	640	32616835	32616885	453	502	151	167

Loci of skipped exons in Mayo 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
ENST00000405005	2009	640	32616835	32616885	453	502	151	167

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

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
Q02297	151	167	1	166	Alternative sequence	ID=VSP_037562;Note=In isoform 10. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:7782315;Dbxref=PMID:14702039,PMID:15489334,PMID:7782315
Q02297	151	167	134	168	Alternative sequence	ID=VSP_003426;Note=In isoform 9 and isoform 11. EIITGMPASTEGAYVSSESPIRISVSTEGANTSSS->A;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:17565985,ECO:0000303\|PubMed:8096067;Dbxref=PMID:17565985,PMID:8096067
Q02297	151	167	167	167	Alternative sequence	ID=VSP_037565;Note=In isoform 10. S->MEIYSPDMSEVAAERSSSPSTQLSADPSLDGLPAAEDMPEPQTEDGRTPGLVGLAVPCCACLEAERLRGCLNSEKICIVPILACLVSLCLCIAGLKWVFVDKIFEYDSPTHLDPGGLGQDPIISLDATAASAVWVSSEAYTSPVSRAQSESEVQVTVQGDKAVVSFEPSAAPTPKNRIFAFSFLPSTAPSFPSPTRNPEVRTPKSATQPQTTETNLQT
Q02297	151	167	20	640	Chain	ID=PRO_0000019463;Note=Pro-neuregulin-1%2C membrane-bound isoform
Q02297	151	167	20	241	Chain	ID=PRO_0000019464;Note=Neuregulin-1
Q02297	151	167	165	177	Compositional bias	Note=Ser/Thr-rich
Q02297	151	167	164	164	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02297	151	167	20	242	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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

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
Q02297	151	167	1	166	Alternative sequence	ID=VSP_037562;Note=In isoform 10. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:7782315;Dbxref=PMID:14702039,PMID:15489334,PMID:7782315
Q02297	151	167	134	168	Alternative sequence	ID=VSP_003426;Note=In isoform 9 and isoform 11. EIITGMPASTEGAYVSSESPIRISVSTEGANTSSS->A;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:17565985,ECO:0000303\|PubMed:8096067;Dbxref=PMID:17565985,PMID:8096067
Q02297	151	167	167	167	Alternative sequence	ID=VSP_037565;Note=In isoform 10. S->MEIYSPDMSEVAAERSSSPSTQLSADPSLDGLPAAEDMPEPQTEDGRTPGLVGLAVPCCACLEAERLRGCLNSEKICIVPILACLVSLCLCIAGLKWVFVDKIFEYDSPTHLDPGGLGQDPIISLDATAASAVWVSSEAYTSPVSRAQSESEVQVTVQGDKAVVSFEPSAAPTPKNRIFAFSFLPSTAPSFPSPTRNPEVRTPKSATQPQTTETNLQT
Q02297	151	167	20	640	Chain	ID=PRO_0000019463;Note=Pro-neuregulin-1%2C membrane-bound isoform
Q02297	151	167	20	241	Chain	ID=PRO_0000019464;Note=Neuregulin-1
Q02297	151	167	165	177	Compositional bias	Note=Ser/Thr-rich
Q02297	151	167	164	164	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02297	151	167	20	242	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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

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
Q02297	151	167	1	166	Alternative sequence	ID=VSP_037562;Note=In isoform 10. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:7782315;Dbxref=PMID:14702039,PMID:15489334,PMID:7782315
Q02297	151	167	134	168	Alternative sequence	ID=VSP_003426;Note=In isoform 9 and isoform 11. EIITGMPASTEGAYVSSESPIRISVSTEGANTSSS->A;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:17565985,ECO:0000303\|PubMed:8096067;Dbxref=PMID:17565985,PMID:8096067
Q02297	151	167	167	167	Alternative sequence	ID=VSP_037565;Note=In isoform 10. S->MEIYSPDMSEVAAERSSSPSTQLSADPSLDGLPAAEDMPEPQTEDGRTPGLVGLAVPCCACLEAERLRGCLNSEKICIVPILACLVSLCLCIAGLKWVFVDKIFEYDSPTHLDPGGLGQDPIISLDATAASAVWVSSEAYTSPVSRAQSESEVQVTVQGDKAVVSFEPSAAPTPKNRIFAFSFLPSTAPSFPSPTRNPEVRTPKSATQPQTTETNLQT
Q02297	151	167	20	640	Chain	ID=PRO_0000019463;Note=Pro-neuregulin-1%2C membrane-bound isoform
Q02297	151	167	20	241	Chain	ID=PRO_0000019464;Note=Neuregulin-1
Q02297	151	167	165	177	Compositional bias	Note=Ser/Thr-rich
Q02297	151	167	164	164	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02297	151	167	20	242	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in NRG1

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for NRG1

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- 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

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AD stage-associated exon skippint events for NRG1

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NRG1

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for NRG1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for NRG1

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

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for NRG1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for NRG1

Gene structures and expression levels for NRG1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NRG1

Open reading frame (ORF) annotation in the exon skipping event for NRG1

Infer the effects of exon skipping event on protein functional features for NRG1

3'-UTR located exon skipping events that lost miRNA binding sites in NRG1

SNVs in the skipped exons for NRG1

AD stage-associated exon skippint events for NRG1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NRG1

Correlation with RNA binding proteins (RBPs) for NRG1

RelatedDrugs for NRG1

RelatedDiseases for NRG1