ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for NUP98

Gene summary

Gene information	Gene symbol	NUP98
	Gene ID	4928
	Gene name	nucleoporin 98 and 96 precursor
	Synonyms	ADIR2\|NUP196\|NUP96\|Nup98-96
	Cytomap	11p15.4
	Type of gene	protein-coding
	Description	nuclear pore complex protein Nup98-Nup96nuclear pore complex protein Nup98GLFG-repeat containing nucleoporinNUP98/PHF23 fusion 2 proteinNup98-Nup96nucleoporin 96nucleoporin 98kDnucleoporin 98kDa
	Modification date	20200313
	UniProtAcc	A0A024RCC4, A0A1D8GZ55, A0A1D8GZ56, A0A1D8GZ64, A0A3B3ITD8, E9PNN0, H0YCR0, H0YCT1, H0YDA1, H0YDF4, H0YEN4, H7BYP8, H7C3P6, P52948, Q9HDC8,
	Context

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 NUP98

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.

ENSG00000110713

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
CB	UP	ENST00000650171.1	NUP98-221:nonsense_mediated_decay:NUP98	1.477644e+02	1.238288e+00	1.037568e-06	1.545450e-05
TC	UP	ENST00000529379.1	NUP98-216:protein_coding:NUP98	8.975404e-01	1.399324e+00	4.061654e-04	4.893194e-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 NUP98

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_111848	chr11	3679638:3679708:3683200:3683441:3691347:3691489	3683200:3683441
exon_skip_13108	chr11	3702772:3702892:3705200:3705356:3706445:3706535	3705200:3705356
exon_skip_142007	chr11	3735191:3735324:3744509:3744649:3753316:3753408	3744509:3744649
exon_skip_158104	chr11	3753316:3753408:3760388:3760626:3762902:3762933	3760388:3760626
exon_skip_176978	chr11	3695519:3695606:3699082:3699348:3702463:3702651	3699082:3699348
exon_skip_179428	chr11	3753316:3753408:3760539:3760626:3762902:3762933	3760539:3760626
exon_skip_186106	chr11	3676509:3676620:3679554:3679708:3683200:3683441	3679554:3679708
exon_skip_215110	chr11	3768581:3768744:3771748:3771928:3773632:3773739	3771748:3771928
exon_skip_215404	chr11	3753316:3753408:3760488:3760626:3762902:3762933	3760488:3760626
exon_skip_225635	chr11	3683200:3683441:3686064:3686194:3691347:3691489	3686064:3686194
exon_skip_228596	chr11	3691347:3691489:3693232:3693375:3695449:3695558	3693232:3693375
exon_skip_235009	chr11	3699082:3699348:3700610:3700839:3702463:3702651	3700610:3700839
exon_skip_236252	chr11	3771748:3771928:3773632:3773739:3775882:3776021	3773632:3773739
exon_skip_252857	chr11	3695519:3695606:3696685:3696800:3699082:3699348	3696685:3696800
exon_skip_274881	chr11	3725103:3725219:3731391:3731578:3735191:3735324	3731391:3731578
exon_skip_280976	chr11	3723157:3723455:3725103:3725219:3731391:3731578	3725103:3725219
exon_skip_62762	chr11	3683200:3683441:3685973:3686194:3691347:3691489	3685973:3686194
exon_skip_68856	chr11	3706445:3706627:3712564:3712728:3713818:3713995	3712564:3712728
exon_skip_98786	chr11	3700610:3700839:3702463:3702892:3705200:3705356	3702463:3702892

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 NUP98

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
ENST00000359171	3679554	3679708	Frame-shift
ENST00000359171	3700610	3700839	Frame-shift
ENST00000359171	3702463	3702892	Frame-shift
ENST00000359171	3731391	3731578	Frame-shift
ENST00000359171	3760488	3760626	Frame-shift
ENST00000359171	3771748	3771928	Frame-shift
ENST00000359171	3685973	3686194	In-frame
ENST00000359171	3725103	3725219	In-frame
ENST00000359171	3744509	3744649	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
ENST00000359171	3679554	3679708	Frame-shift
ENST00000359171	3700610	3700839	Frame-shift
ENST00000359171	3760488	3760626	Frame-shift
ENST00000359171	3771748	3771928	Frame-shift
ENST00000359171	3685973	3686194	In-frame
ENST00000359171	3744509	3744649	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
ENST00000359171	3679554	3679708	Frame-shift
ENST00000359171	3700610	3700839	Frame-shift
ENST00000359171	3702463	3702892	Frame-shift
ENST00000359171	3705200	3705356	Frame-shift
ENST00000359171	3731391	3731578	Frame-shift
ENST00000359171	3760488	3760626	Frame-shift
ENST00000359171	3771748	3771928	Frame-shift
ENST00000359171	3685973	3686194	In-frame
ENST00000359171	3693232	3693375	In-frame
ENST00000359171	3712564	3712728	In-frame
ENST00000359171	3744509	3744649	In-frame
ENST00000359171	3773632	3773739	In-frame

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Infer the effects of exon skipping event on protein functional features for NUP98

p-ENSG00000110713_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
ENST00000359171	7040	1817	3744509	3744649	1740	1879	439	486
ENST00000359171	7040	1817	3725103	3725219	2203	2318	594	632
ENST00000359171	7040	1817	3685973	3686194	4927	5147	1502	1575

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
ENST00000359171	7040	1817	3744509	3744649	1740	1879	439	486
ENST00000359171	7040	1817	3685973	3686194	4927	5147	1502	1575

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
ENST00000359171	7040	1817	3773632	3773739	917	1023	165	200
ENST00000359171	7040	1817	3744509	3744649	1740	1879	439	486
ENST00000359171	7040	1817	3712564	3712728	3050	3213	876	930
ENST00000359171	7040	1817	3693232	3693375	4640	4782	1406	1453
ENST00000359171	7040	1817	3685973	3686194	4927	5147	1502	1575

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
P52948	439	486	1	880	Chain	ID=PRO_0000019929;Note=Nuclear pore complex protein Nup98
P52948	439	486	7	480	Compositional bias	Note=Gly/Thr-rich
P52948	439	486	214	480	Region	Note=FG repeats 2
P52948	594	632	1	880	Chain	ID=PRO_0000019929;Note=Nuclear pore complex protein Nup98
P52948	594	632	603	603	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
P52948	594	632	603	603	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P52948	594	632	608	608	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:16964243,ECO:0000244\|PubMed:17081983,ECO:0000244\|PubMed:18220336,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,E
P52948	594	632	612	612	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:16964243,ECO:0000244\|PubMed:17081983,ECO:0000244\|PubMed:18220336,ECO:0000244\|PubMed:19690332,ECO:0
P52948	594	632	618	618	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
P52948	594	632	623	623	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:16964243,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,E
P52948	594	632	625	625	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
P52948	1502	1575	938	1817	Alternative sequence	ID=VSP_007943;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:8563754,ECO:0000303\|Ref.2;Dbxref=PMID:15489334,PMID:8563754
P52948	1502	1575	1502	1576	Alternative sequence	ID=VSP_007944;Note=In isoform 2. RHYDLNQLLEPRSITADPLDYRLSWHLWEVLRALNYTHLSAQCEGVLQASYAGQLESEGLWEWAIFVLLHIDNSG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10087256;Dbxref=PMID:10087256
P52948	1502	1575	881	1817	Chain	ID=PRO_0000019930;Note=Nuclear pore complex protein Nup96
P52948	1502	1575	1534	1536	Sequence conflict	Note=ALN->DLK;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
P52948	439	486	1	880	Chain	ID=PRO_0000019929;Note=Nuclear pore complex protein Nup98
P52948	439	486	7	480	Compositional bias	Note=Gly/Thr-rich
P52948	439	486	214	480	Region	Note=FG repeats 2
P52948	1502	1575	938	1817	Alternative sequence	ID=VSP_007943;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:8563754,ECO:0000303\|Ref.2;Dbxref=PMID:15489334,PMID:8563754
P52948	1502	1575	1502	1576	Alternative sequence	ID=VSP_007944;Note=In isoform 2. RHYDLNQLLEPRSITADPLDYRLSWHLWEVLRALNYTHLSAQCEGVLQASYAGQLESEGLWEWAIFVLLHIDNSG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10087256;Dbxref=PMID:10087256
P52948	1502	1575	881	1817	Chain	ID=PRO_0000019930;Note=Nuclear pore complex protein Nup96
P52948	1502	1575	1534	1536	Sequence conflict	Note=ALN->DLK;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
P52948	165	200	168	172	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3MMY
P52948	165	200	181	186	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3MMY
P52948	165	200	1	880	Chain	ID=PRO_0000019929;Note=Nuclear pore complex protein Nup98
P52948	165	200	7	480	Compositional bias	Note=Gly/Thr-rich
P52948	165	200	189	191	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3MMY
P52948	165	200	200	209	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3MMY
P52948	165	200	157	213	Region	Note=GLEBS%3B interaction with RAE1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10209021;Dbxref=PMID:10209021
P52948	165	200	193	197	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3MMY
P52948	439	486	1	880	Chain	ID=PRO_0000019929;Note=Nuclear pore complex protein Nup98
P52948	439	486	7	480	Compositional bias	Note=Gly/Thr-rich
P52948	439	486	214	480	Region	Note=FG repeats 2
P52948	876	930	881	881	Active site	Note=Nucleophile;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12191480,ECO:0000269\|PubMed:18287282;Dbxref=PMID:12191480,PMID:18287282
P52948	876	930	872	879	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2Q5X
P52948	876	930	1	880	Chain	ID=PRO_0000019929;Note=Nuclear pore complex protein Nup98
P52948	876	930	881	1817	Chain	ID=PRO_0000019930;Note=Nuclear pore complex protein Nup96
P52948	876	930	890	894	Compositional bias	Note=Poly-Glu
P52948	876	930	738	880	Domain	Note=Peptidase S59;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00765
P52948	876	930	888	888	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17081983,ECO:0000244\|PubMed:18318008,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:18691976,ECO:0
P52948	876	930	897	897	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24275569;Dbxref=PMID:24275569
P52948	876	930	879	879	Mutagenesis	Note=Moderate reduction in autoprocessing. H->A%2CQ;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12191480;Dbxref=PMID:12191480
P52948	876	930	880	883	Mutagenesis	Note=Loss of processing. Loss of nuclear membrane localization. FSKY->SSKR;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10087256;Dbxref=PMID:10087256
P52948	876	930	881	881	Mutagenesis	Note=Loss of autoprocessing. Loss of nuclear membrane localization. S->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12191480,ECO:0000269\|PubMed:18287282;Dbxref=PMID:12191480,PMID:18287282
P52948	876	930	882	882	Mutagenesis	Note=No effect in autoprocessing. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12191480;Dbxref=PMID:12191480
P52948	876	930	880	881	Site	Note=Cleavage%3B by autolysis;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:10087256,ECO:0000269\|PubMed:12191480,ECO:0000269\|PubMed:18287282;Dbxref=PMID:10087256,PMID:12191480,PMID:18287282
P52948	1406	1453	938	1817	Alternative sequence	ID=VSP_007943;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:8563754,ECO:0000303\|Ref.2;Dbxref=PMID:15489334,PMID:8563754
P52948	1406	1453	881	1817	Chain	ID=PRO_0000019930;Note=Nuclear pore complex protein Nup96
P52948	1502	1575	938	1817	Alternative sequence	ID=VSP_007943;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:8563754,ECO:0000303\|Ref.2;Dbxref=PMID:15489334,PMID:8563754
P52948	1502	1575	1502	1576	Alternative sequence	ID=VSP_007944;Note=In isoform 2. RHYDLNQLLEPRSITADPLDYRLSWHLWEVLRALNYTHLSAQCEGVLQASYAGQLESEGLWEWAIFVLLHIDNSG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10087256;Dbxref=PMID:10087256
P52948	1502	1575	881	1817	Chain	ID=PRO_0000019930;Note=Nuclear pore complex protein Nup96
P52948	1502	1575	1534	1536	Sequence conflict	Note=ALN->DLK;Ontology_term=ECO:0000305;evidence=ECO:0000305

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3'-UTR located exon skipping events that lost miRNA binding sites in NUP98

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 NUP98

- 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 NUP98

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 NUP98

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_215404	rs4910811	chr11:3792774	4.680943e-04	3.217296e-02
PCC	exon_skip_235009	rs10834744	chr11:3660620	2.625702e-05	5.783998e-03

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Correlation with RNA binding proteins (RBPs) for NUP98

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	ZNF638	exon_skip_186106	-4.834385e-01	1.084313e-10
CB	RBM6	exon_skip_186106	-5.137127e-01	4.362832e-12

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RelatedDrugs for NUP98

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 NUP98

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 NUP98

Gene structures and expression levels for NUP98

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NUP98

Open reading frame (ORF) annotation in the exon skipping event for NUP98

Infer the effects of exon skipping event on protein functional features for NUP98

3'-UTR located exon skipping events that lost miRNA binding sites in NUP98

SNVs in the skipped exons for NUP98

AD stage-associated exon skippint events for NUP98

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NUP98

Correlation with RNA binding proteins (RBPs) for NUP98

RelatedDrugs for NUP98

RelatedDiseases for NUP98