ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for NRXN1

Gene summary

Gene information	Gene symbol	NRXN1
	Gene ID	9378
	Gene name	neurexin 1
	Synonyms	Hs.22998\|PTHSL2\|SCZD17
	Cytomap	2p16.3
	Type of gene	protein-coding
	Description	neurexin-1neurexin I
	Modification date	20200320
	UniProtAcc	A0A0D9SEJ1, A0A0D9SEM5, A0A0D9SEQ7, A0A0D9SF07, A0A0D9SF36, A0A0D9SFF4, A0A0D9SFY6, A0A0D9SG60, A0A0D9SG96, A0A0R4J2G7, A0A0U1RQP8, A0A0U1RR00, A0A0U1RRK7, A0A1B0GTL0, A0A1B0GU94, A0A1B0GUQ1, A0A1B0GUR2, A0A1B0GVF4, A0A1D5RMU6, A4FVB9, E7EQN4, E7ERL8, F5GYC7, F8WB18, H0Y568, H7BYC7, P58400, Q08AH0, Q49A31, Q9ULB1,
	Context	- 29229705(Proteolytic Processing of Neurexins by Presenilins Sustains Synaptic Vesicle Release)

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

Gene

GO ID

GO term

PubMed ID

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Gene structures and expression levels for NRXN1

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.

ENSG00000179915

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
PG	DOWN	ENST00000406316.6	NRXN1-210:protein_coding:NRXN1	2.562754e+02	-1.289897e+00	3.577364e-04	6.955118e-03
PG	UP	ENST00000635310.1	NRXN1-241:lncRNA:NRXN1	4.704519e+00	4.614613e+00	5.924589e-04	9.959594e-03
PG	UP	ENST00000495871.2	NRXN1-218:protein_coding:NRXN1	2.056082e+00	4.064109e+00	4.028952e-03	3.928562e-02
CB	UP	ENST00000331040.9	NRXN1-201:nonsense_mediated_decay:NRXN1	1.037821e+02	1.324791e+00	1.343328e-06	1.926627e-05
CB	UP	ENST00000412315.5	NRXN1-212:protein_coding:NRXN1	1.487721e+02	1.231596e+00	1.018600e-05	1.070509e-04
CB	DOWN	ENST00000636066.1	NRXN1-244:protein_coding:NRXN1	4.574276e+01	-9.919986e-01	1.596697e-04	1.101961e-03
CB	UP	ENST00000378262.7	NRXN1-203:protein_coding:NRXN1	8.240438e+01	8.977661e-01	2.701687e-04	1.717293e-03
CB	UP	ENST00000405472.7	NRXN1-208:protein_coding:NRXN1	1.210267e+02	1.191269e+00	3.429374e-04	2.097412e-03

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 NRXN1

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_101467	chr2	50053271:50053590:50054955:50055044:50091323:50091494	50054955:50055044
exon_skip_103221	chr2	49920073:49922251:49926288:49926390:49943713:49943791	49926288:49926390
exon_skip_103386	chr2	50623314:50623615:50921869:50921880:50922658:50922687	50921869:50921880
exon_skip_111239	chr2	49943713:49943791:50053271:50053590:50091323:50091494	50053271:50053590
exon_skip_131878	chr2	49922217:49922251:49926288:49926390:49943713:49943791	49926288:49926390
exon_skip_146148	chr2	50620055:50620183:50621205:50621249:50623314:50623370	50621205:50621249
exon_skip_146517	chr2	49943713:49943791:49972671:49972782:49973968:49974118	49972671:49972782
exon_skip_155806	chr2	49943704:49943791:49969687:49970617:49973968:49974107	49969687:49970617
exon_skip_170542	chr2	50912879:50912993:50921869:50921880:50922658:50922687	50921869:50921880
exon_skip_174628	chr2	50091323:50091494:50236789:50236970:50346691:50346832	50236789:50236970
exon_skip_210628	chr2	49943713:49943791:49945113:49945206:49973968:49974115	49945113:49945206
exon_skip_218707	chr2	49943713:49943791:49972671:49972782:49973968:49974107	49972671:49972782
exon_skip_220214	chr2	49943713:49943791:49945113:49945206:49973968:49974107	49945113:49945206
exon_skip_228639	chr2	50925938:50925955:51026371:51026469:51027502:51027703	51026371:51026469
exon_skip_23423	chr2	49922216:49922251:49926288:49926390:49943713:49943791	49926288:49926390
exon_skip_239287	chr2	50465443:50465561:50466461:50466487:50472298:50472471	50466461:50466487
exon_skip_240058	chr2	50497679:50497714:50506495:50506617:50531227:50531430	50506495:50506617
exon_skip_243992	chr2	50921869:50921880:50922658:50922687:50925938:50925952	50922658:50922687
exon_skip_24517	chr2	50925938:50925955:51026371:51026469:51027502:51027567	51026371:51026469
exon_skip_249544	chr2	50506600:50506617:50528625:50528651:50531227:50531428	50528625:50528651
exon_skip_257853	chr2	49921520:49922251:49926288:49926390:49943713:49943791	49926288:49926390
exon_skip_27103	chr2	50531227:50531430:50538253:50538636:50552587:50552610	50538253:50538636
exon_skip_287805	chr2	49943713:49943791:49969687:49970617:49973968:49974107	49969687:49970617
exon_skip_290205	chr2	50922658:50922687:50925938:50925955:51027502:51027567	50925938:50925955
exon_skip_293342	chr2	50620055:50620183:50621226:50621249:50623314:50623370	50621226:50621249
exon_skip_295371	chr2	50506600:50506617:50528625:50528651:50531227:50531430	50528625:50528651
exon_skip_296085	chr2	50053271:50053590:50054955:50055044:50091323:50091488	50054955:50055044
exon_skip_38916	chr2	49943713:49943791:49966590:49966672:49973968:49974166	49966590:49966672
exon_skip_43350	chr2	50922658:50922687:50925938:50925952:51027502:51027567	50925938:50925952
exon_skip_48640	chr2	50916826:50919268:50921869:50921880:50922658:50922687	50921869:50921880
exon_skip_62224	chr2	50619645:50619968:50620055:50620183:50623314:50623370	50620055:50620183

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
exon_skip_295371	Mayo_TC	3.390123e-01	4.582759e-01	-1.192635e-01	2.938799e-06

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Open reading frame (ORF) annotation in the exon skipping event for NRXN1

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
ENST00000342183	50053271	50053590	Frame-shift
ENST00000406316	50053271	50053590	Frame-shift
ENST00000342183	50236789	50236970	Frame-shift
ENST00000406316	50528625	50528651	In-frame
ENST00000406316	50621226	50621249	In-frame
ENST00000406316	50921869	50921880	In-frame
ENST00000406316	50922658	50922687	In-frame
ENST00000406316	50925938	50925955	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
ENST00000342183	50053271	50053590	Frame-shift
ENST00000406316	50053271	50053590	Frame-shift
ENST00000406316	50528625	50528651	In-frame
ENST00000406316	50621226	50621249	In-frame
ENST00000406316	50921869	50921880	In-frame
ENST00000406316	50922658	50922687	In-frame
ENST00000406316	50925938	50925955	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
ENST00000342183	50053271	50053590	Frame-shift
ENST00000406316	50053271	50053590	Frame-shift
ENST00000406316	50528625	50528651	In-frame
ENST00000406316	50538253	50538636	In-frame
ENST00000406316	50621226	50621249	In-frame
ENST00000406316	50921869	50921880	In-frame
ENST00000406316	50922658	50922687	In-frame
ENST00000406316	50925938	50925955	In-frame

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Infer the effects of exon skipping event on protein functional features for NRXN1

p-ENSG00000179915_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
ENST00000406316	9392	1477	50922658	50922687	2293	2321	263	273

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
ENST00000406316	9392	1477	50922658	50922687	2293	2321	263	273

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
ENST00000406316	9392	1477	50922658	50922687	2293	2321	263	273
ENST00000406316	9392	1477	50538253	50538636	3262	3644	586	714

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
Q9ULB1	263	273	1	1335	Alternative sequence	ID=VSP_058200;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11230166;Dbxref=PMID:11230166
Q9ULB1	263	273	31	1477	Chain	ID=PRO_0000019490;Note=Neurexin-1
Q9ULB1	263	273	31	1401	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
Q9ULB1	263	273	1	1335	Alternative sequence	ID=VSP_058200;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11230166;Dbxref=PMID:11230166
Q9ULB1	263	273	31	1477	Chain	ID=PRO_0000019490;Note=Neurexin-1
Q9ULB1	263	273	31	1401	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
Q9ULB1	263	273	1	1335	Alternative sequence	ID=VSP_058200;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11230166;Dbxref=PMID:11230166
Q9ULB1	263	273	31	1477	Chain	ID=PRO_0000019490;Note=Neurexin-1
Q9ULB1	263	273	31	1401	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9ULB1	586	714	1	1335	Alternative sequence	ID=VSP_058200;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11230166;Dbxref=PMID:11230166
Q9ULB1	586	714	31	1477	Chain	ID=PRO_0000019490;Note=Neurexin-1
Q9ULB1	586	714	643	672	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULB1	586	714	680	691	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULB1	586	714	685	700	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULB1	586	714	702	712	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULB1	586	714	480	672	Domain	Note=Laminin G-like 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00122
Q9ULB1	586	714	676	713	Domain	Note=EGF-like 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
Q9ULB1	586	714	31	1401	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 NRXN1

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 NRXN1

- 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 NRXN1

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
ADstage	MSBB	IFG	exon_skip_295371	-5.290473e-01	3.795638e-03	chr2	-	50506600	50506617	50528625	50528651	50531227	50531430
ADstage	MSBB	IFG	exon_skip_103386	-3.753309e-01	4.905141e-02	chr2	-	50623314	50623615	50921869	50921880	50922658	50922687
CDR	MSBB	IFG	exon_skip_295371	-4.992384e-01	6.838703e-03	chr2	-	50506600	50506617	50528625	50528651	50531227	50531430
CDR	MSBB	IFG	exon_skip_239287	-3.986527e-01	3.561466e-02	chr2	-	50465443	50465561	50466461	50466487	50472298	50472471
CDR	MSBB	IFG	exon_skip_103386	-3.744804e-01	4.960801e-02	chr2	-	50623314	50623615	50921869	50921880	50922658	50922687

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NRXN1

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_101467	rs11681792	chr2:49957256	4.448343e-08	9.566614e-06
HCC	exon_skip_101467	rs1895132	chr2:50032596	1.292311e-07	2.531714e-05
HCC	exon_skip_101467	rs12468006	chr2:50141490	1.864072e-07	3.545446e-05
HCC	exon_skip_101467	rs10191989	chr2:50041573	7.237273e-04	4.537347e-02
PCC	exon_skip_293342	rs13000907	chr2:50592953	1.352940e-04	2.187252e-02

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Correlation with RNA binding proteins (RBPs) for NRXN1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
FL	MSI1	exon_skip_249544	-6.025719e-01	5.901228e-21
FL	G3BP2	exon_skip_249544	5.942438e-01	2.739747e-20
FL	ILF2	exon_skip_293342	4.754774e-01	1.456123e-12
HCC	MSI1	exon_skip_295371	-6.514907e-01	2.124914e-33
HCC	SFPQ	exon_skip_295371	-4.533586e-01	7.742595e-15
HCC	HNRNPAB	exon_skip_295371	-4.218350e-01	7.389551e-13
HCC	PTBP1	exon_skip_291134	-4.106329e-01	5.352574e-12
IFG	NOVA1	exon_skip_101467	-4.126210e-01	2.910085e-02
IFG	MSI1	exon_skip_295371	-6.494120e-01	1.845589e-04
IFG	G3BP2	exon_skip_295371	4.447517e-01	1.772262e-02
IFG	ZNF326	exon_skip_146148	-4.113057e-01	2.966973e-02
IFG	NUP42	exon_skip_103386	6.153246e-01	4.921631e-04
IFG	TIA1	exon_skip_291134	-4.065247e-01	3.181376e-02
PCC	MSI1	exon_skip_249544	-6.627515e-01	3.670709e-26
PCC	G3BP2	exon_skip_249544	6.407118e-01	4.828208e-24
PCC	MSI1	exon_skip_290205	-4.084542e-01	5.393208e-09
PG	NOVA1	exon_skip_101467	-4.148982e-01	1.524222e-08
PG	MSI1	exon_skip_295371	-4.583671e-01	6.904282e-12
PG	G3BP2	exon_skip_295371	7.418673e-01	1.460911e-36
PG	HNRNPAB	exon_skip_295371	4.071274e-01	1.821413e-09
PG	ZCRB1	exon_skip_295371	5.175884e-01	3.078795e-15
STG	ZC3H10	exon_skip_101467	4.201921e-01	4.140468e-05
STG	MSI1	exon_skip_249544	-4.904767e-01	8.002283e-07
STG	G3BP2	exon_skip_249544	5.841227e-01	1.217013e-09
STG	ILF2	exon_skip_293342	5.273165e-01	7.862376e-08
TC	MBNL1	exon_skip_296085	-4.380475e-01	2.578843e-08
TC	ENOX1	exon_skip_296085	-4.798048e-01	6.818703e-10
TC	NUP42	exon_skip_296085	-4.259719e-01	6.752982e-08
TC	NOVA1	exon_skip_296085	-4.932081e-01	1.908269e-10
TC	MSI1	exon_skip_295371	-5.980360e-01	7.640398e-15
TC	G3BP2	exon_skip_295371	7.426652e-01	1.264128e-25
TC	ILF2	exon_skip_293342	4.020227e-01	1.769288e-06
TC	MSI1	exon_skip_290205	-4.576717e-01	1.882602e-07

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RelatedDrugs for NRXN1

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
Q9ULB1	approved\|investigational	DB11093	Calcium Citrate	small molecule	Q9ULB1
Q9ULB1	approved	DB11348	Calcium Phosphate	small molecule	Q9ULB1

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RelatedDiseases for NRXN1

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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