ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for NF1

Gene summary

Gene information	Gene symbol	NF1
	Gene ID	4763
	Gene name	neurofibromin 1
	Synonyms	NFNS\|VRNF\|WSS
	Cytomap	17q11.2
	Type of gene	protein-coding
	Description	neurofibrominneurofibromatosis 1neurofibromatosis-related protein NF-1truncated neurofibromin 1
	Modification date	20200322
	UniProtAcc	A0A1J0F939, A0A1J0F943, A0A1J0F944, A0A1J0F955, A0A1W2PPA7, A0A1W2PS74, H0UIC3, H0Y465, J3KRT8, J3KSB5, J3KSX8, J3QLS2, J3QQN8, J3QSG6, K7EID4, K7EJE7, K7ENT2, P21359, Q4W6X4, Q9UMU3,
	Context

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

Gene	GO ID	GO term	PubMed ID
NF1	GO:0043547	positive regulation of GTPase activity	2121371

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Gene structures and expression levels for NF1

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.

ENSG00000196712

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	UP	ENST00000579760.6	C1QTNF1-206:protein_coding:C1QTNF1	4.834196e+01	1.088764e+00	2.067259e-05	8.570703e-04
PG	UP	ENST00000584328.1	NF1-223:retained_intron:NF1	1.731282e+01	8.410799e-01	1.835225e-03	2.243192e-02
PG	UP	ENST00000580474.1	C1QTNF1-208:protein_coding:C1QTNF1	1.542126e+00	1.505404e+00	5.331954e-03	4.779036e-02
CB	DOWN	ENST00000311661.4	C1QTNF1-201:protein_coding:C1QTNF1	4.960283e+01	-1.502668e+00	5.696305e-04	3.217871e-03
CB	DOWN	ENST00000488981.1	NF1-212:lncRNA:NF1	2.811025e+00	-1.552300e+00	1.180100e-02	3.979336e-02
CB	UP	ENST00000479536.2	NF1-209:nonsense_mediated_decay:NF1	2.630401e+00	8.504876e-01	1.234176e-02	4.124610e-02
TC	DOWN	ENST00000488981.1	NF1-212:lncRNA:NF1	2.482838e+00	-1.699638e+00	1.282906e-05	3.150712e-04
TC	UP	ENST00000582295.1	C1QTNF1-210:lncRNA:C1QTNF1	2.767006e+00	9.439654e-01	7.998966e-04	8.312350e-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 NF1

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_113867	chr17	31360487:31360703:31367225:31367278:31374013:31374129	31367225:31367278
exon_skip_147415	chr17	31226435:31226684:31227218:31227291:31227523:31227606	31227218:31227291
exon_skip_151870	chr17	31350183:31350318:31352257:31352414:31356460:31356511	31352257:31352414
exon_skip_152482	chr17	31360487:31360703:31367225:31367278:31374013:31374031	31367225:31367278
exon_skip_162185	chr17	31360487:31360703:31367225:31367278:31374013:31374073	31367225:31367278
exon_skip_168194	chr17	31206240:31206371:31214451:31214585:31219005:31219118	31214451:31214585
exon_skip_175306	chr17	31248984:31249119:31257687:31257726:31258344:31258502	31257687:31257726
exon_skip_1884	chr17	31330329:31330498:31334664:31334730:31334838:31335031	31334664:31334730
exon_skip_21226	chr17	31229835:31229974:31230260:31230382:31230842:31230925	31230260:31230382
exon_skip_22661	chr17	31182508:31182665:31200422:31200595:31201037:31201159	31200422:31200595
exon_skip_244675	chr17	31219005:31219118:31221850:31221929:31223444:31223567	31221850:31221929
exon_skip_25493	chr17	31248984:31249119:31252938:31253000:31257687:31257726	31252938:31253000
exon_skip_259999	chr17	31163195:31163376:31169891:31169997:31181422:31181489	31169891:31169997
exon_skip_264083	chr17	31352257:31352414:31356460:31356582:31356960:31357090	31356460:31356582
exon_skip_268253	chr17	31378891:31379023:31379106:31379357:31381873:31381887	31379106:31379357
exon_skip_272512	chr17	31325820:31326252:31327499:31327839:31330296:31330498	31327499:31327839
exon_skip_274769	chr17	31337819:31337880:31338025:31338139:31338704:31338805	31338025:31338139
exon_skip_274888	chr17	31358969:31359015:31360487:31360703:31374013:31374129	31360487:31360703
exon_skip_280793	chr17	31248989:31249119:31252938:31253000:31258344:31258502	31252938:31253000
exon_skip_284299	chr17	31338025:31338139:31338704:31338805:31340505:31340645	31338704:31338805
exon_skip_284705	chr17	31163186:31163376:31169891:31169997:31181422:31181489	31169891:31169997
exon_skip_4013	chr17	31248989:31249119:31257687:31257726:31258344:31258502	31257687:31257726
exon_skip_45374	chr17	31248984:31249119:31252938:31253000:31258344:31258502	31252938:31253000
exon_skip_59267	chr17	31327499:31327839:31330296:31330498:31334838:31335027	31330296:31330498
exon_skip_6112	chr17	31252938:31253000:31257687:31257726:31258344:31258502	31257687:31257726
exon_skip_62727	chr17	31330329:31330498:31334664:31334730:31334838:31335027	31334664:31334730
exon_skip_64595	chr17	31360550:31360703:31367225:31367278:31374013:31374129	31367225:31367278
exon_skip_67300	chr17	31265229:31265339:31299510:31299606:31325820:31326252	31299510:31299606
exon_skip_84840	chr17	31374013:31374129:31378888:31379023:31381873:31381887	31378888:31379023
exon_skip_85214	chr17	31248989:31249119:31252938:31253000:31257687:31257726	31252938:31253000
exon_skip_86147	chr17	31327499:31327839:31330296:31330498:31334838:31335031	31330296:31330498
exon_skip_90803	chr17	31356960:31357090:31357269:31357369:31358480:31358622	31357269:31357369

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_87992	MSBB_PG	2.565248e-01	4.198182e-01	-1.632934e-01	1.525726e-07
exon_skip_280793	MSBB_PG	4.481690e-01	2.937037e-01	1.544653e-01	7.090992e-06

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Open reading frame (ORF) annotation in the exon skipping event for NF1

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
ENST00000358273	31169891	31169997	Frame-shift
ENST00000358273	31221850	31221929	Frame-shift
ENST00000358273	31327499	31327839	Frame-shift
ENST00000358273	31338025	31338139	Frame-shift
ENST00000358273	31352257	31352414	Frame-shift
ENST00000358273	31214451	31214585	In-frame
ENST00000358273	31230260	31230382	In-frame
ENST00000358273	31252938	31253000	In-frame
ENST00000358273	31338704	31338805	In-frame
ENST00000358273	31356460	31356582	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
ENST00000358273	31169891	31169997	Frame-shift
ENST00000358273	31327499	31327839	Frame-shift
ENST00000358273	31352257	31352414	Frame-shift
ENST00000358273	31214451	31214585	In-frame
ENST00000358273	31230260	31230382	In-frame
ENST00000358273	31252938	31253000	In-frame
ENST00000358273	31356460	31356582	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
ENST00000358273	31169891	31169997	Frame-shift
ENST00000358273	31221850	31221929	Frame-shift
ENST00000358273	31227218	31227291	Frame-shift
ENST00000358273	31327499	31327839	Frame-shift
ENST00000358273	31330296	31330498	Frame-shift
ENST00000358273	31338025	31338139	Frame-shift
ENST00000358273	31357269	31357369	Frame-shift
ENST00000358273	31360487	31360703	Frame-shift
ENST00000358273	31200422	31200595	In-frame
ENST00000358273	31230260	31230382	In-frame
ENST00000358273	31252938	31253000	In-frame
ENST00000358273	31356460	31356582	In-frame

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Infer the effects of exon skipping event on protein functional features for NF1

p-ENSG00000196712_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
ENST00000358273	12442	2839	31214451	31214585	1777	1910	464	509
ENST00000358273	12442	2839	31230260	31230382	3375	3496	997	1037
ENST00000358273	12442	2839	31252938	31253000	4495	4556	1370	1391
ENST00000358273	12442	2839	31338704	31338805	7204	7304	2273	2307
ENST00000358273	12442	2839	31356460	31356582	8000	8121	2539	2579

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
ENST00000358273	12442	2839	31214451	31214585	1777	1910	464	509
ENST00000358273	12442	2839	31230260	31230382	3375	3496	997	1037
ENST00000358273	12442	2839	31252938	31253000	4495	4556	1370	1391
ENST00000358273	12442	2839	31356460	31356582	8000	8121	2539	2579

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
ENST00000358273	12442	2839	31200422	31200595	1273	1445	296	354
ENST00000358273	12442	2839	31230260	31230382	3375	3496	997	1037
ENST00000358273	12442	2839	31252938	31253000	4495	4556	1370	1391
ENST00000358273	12442	2839	31356460	31356582	8000	8121	2539	2579

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
P21359	464	509	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	464	509	2	1305	Chain	ID=PRO_0000010774;Note=Neurofibromin truncated
P21359	464	509	489	489	Natural variant	ID=VAR_032465;Note=In NF1. Y->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15060124;Dbxref=dbSNP:rs137854557,PMID:15060124
P21359	464	509	491	491	Natural variant	ID=VAR_021734;Note=In NF1. Y->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10712197;Dbxref=dbSNP:rs199474757,PMID:10712197
P21359	464	509	508	508	Natural variant	ID=VAR_010991;Note=In NF1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11258625;Dbxref=dbSNP:rs137854558,PMID:11258625
P21359	464	509	496	496	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
P21359	464	509	496	496	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
P21359	997	1037	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	997	1037	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	997	1037	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	997	1037	2	1305	Chain	ID=PRO_0000010774;Note=Neurofibromin truncated
P21359	997	1037	1035	1035	Natural variant	ID=VAR_002657;Note=In NF1. M->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8807336;Dbxref=dbSNP:rs137854553,PMID:8807336
P21359	1370	1391	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	1370	1391	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	1370	1391	1371	1391	Alternative sequence	ID=VSP_001628;Note=In isoform 1 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:1457041,ECO:0000303\|PubMed:1783401,ECO:0000303\|PubMed:1923522,ECO:0000303\|PubMed:21142
P21359	1370	1391	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	1370	1391	1235	1451	Domain	Note=Ras-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00167
P21359	1370	1391	1361	1370	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1NF1
P21359	2273	2307	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	2273	2307	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	2273	2307	1599	2839	Alternative sequence	ID=VSP_001632;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:2121370;Dbxref=PMID:2121370
P21359	2273	2307	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	2539	2579	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	2539	2579	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	2539	2579	1599	2839	Alternative sequence	ID=VSP_001632;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:2121370;Dbxref=PMID:2121370
P21359	2539	2579	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	2539	2579	2543	2543	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:21406692,PMID:23186163,PMID
P21359	2539	2579	2565	2565	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P21359	2539	2579	2555	2571	Motif	Note=Bipartite nuclear localization signal

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
P21359	464	509	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	464	509	2	1305	Chain	ID=PRO_0000010774;Note=Neurofibromin truncated
P21359	464	509	489	489	Natural variant	ID=VAR_032465;Note=In NF1. Y->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15060124;Dbxref=dbSNP:rs137854557,PMID:15060124
P21359	464	509	491	491	Natural variant	ID=VAR_021734;Note=In NF1. Y->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10712197;Dbxref=dbSNP:rs199474757,PMID:10712197
P21359	464	509	508	508	Natural variant	ID=VAR_010991;Note=In NF1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11258625;Dbxref=dbSNP:rs137854558,PMID:11258625
P21359	464	509	496	496	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
P21359	464	509	496	496	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
P21359	997	1037	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	997	1037	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	997	1037	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	997	1037	2	1305	Chain	ID=PRO_0000010774;Note=Neurofibromin truncated
P21359	997	1037	1035	1035	Natural variant	ID=VAR_002657;Note=In NF1. M->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8807336;Dbxref=dbSNP:rs137854553,PMID:8807336
P21359	1370	1391	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	1370	1391	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	1370	1391	1371	1391	Alternative sequence	ID=VSP_001628;Note=In isoform 1 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:1457041,ECO:0000303\|PubMed:1783401,ECO:0000303\|PubMed:1923522,ECO:0000303\|PubMed:21142
P21359	1370	1391	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	1370	1391	1235	1451	Domain	Note=Ras-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00167
P21359	1370	1391	1361	1370	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1NF1
P21359	2539	2579	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	2539	2579	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	2539	2579	1599	2839	Alternative sequence	ID=VSP_001632;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:2121370;Dbxref=PMID:2121370
P21359	2539	2579	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	2539	2579	2543	2543	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:21406692,PMID:23186163,PMID
P21359	2539	2579	2565	2565	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P21359	2539	2579	2555	2571	Motif	Note=Bipartite nuclear localization signal

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
P21359	296	354	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	296	354	2	1305	Chain	ID=PRO_0000010774;Note=Neurofibromin truncated
P21359	296	354	324	324	Natural variant	ID=VAR_032463;Note=In NF1. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15060124;Dbxref=dbSNP:rs199474735,PMID:15060124
P21359	296	354	330	330	Natural variant	ID=VAR_067201;Note=In a cutaneous neurofibroma from a patient with neurofibromatosis%3B somatic mutation. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22108604;Dbxref=dbSNP:rs199474767,PMID:22108604
P21359	296	354	337	337	Natural variant	ID=VAR_032464;Note=In NF1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15060124;Dbxref=dbSNP:rs199474736,PMID:15060124
P21359	296	354	338	338	Natural variant	ID=VAR_010990;Note=In NF1. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9298829;Dbxref=dbSNP:rs199474773,PMID:9298829
P21359	997	1037	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	997	1037	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	997	1037	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	997	1037	2	1305	Chain	ID=PRO_0000010774;Note=Neurofibromin truncated
P21359	997	1037	1035	1035	Natural variant	ID=VAR_002657;Note=In NF1. M->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8807336;Dbxref=dbSNP:rs137854553,PMID:8807336
P21359	1370	1391	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	1370	1391	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	1370	1391	1371	1391	Alternative sequence	ID=VSP_001628;Note=In isoform 1 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:1457041,ECO:0000303\|PubMed:1783401,ECO:0000303\|PubMed:1923522,ECO:0000303\|PubMed:21142
P21359	1370	1391	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	1370	1391	1235	1451	Domain	Note=Ras-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00167
P21359	1370	1391	1361	1370	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1NF1
P21359	2539	2579	552	2839	Alternative sequence	ID=VSP_001630;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1339276;Dbxref=PMID:1339276
P21359	2539	2579	594	2839	Alternative sequence	ID=VSP_043468;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:7570581;Dbxref=PMID:7570581
P21359	2539	2579	1599	2839	Alternative sequence	ID=VSP_001632;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:2121370;Dbxref=PMID:2121370
P21359	2539	2579	2	2839	Chain	ID=PRO_0000010773;Note=Neurofibromin
P21359	2539	2579	2543	2543	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:21406692,PMID:23186163,PMID
P21359	2539	2579	2565	2565	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P21359	2539	2579	2555	2571	Motif	Note=Bipartite nuclear localization signal

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3'-UTR located exon skipping events that lost miRNA binding sites in NF1

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 NF1

- 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 NF1

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 NF1

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 NF1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	PABPC3	exon_skip_45374	5.299145e-01	7.584394e-11
CB	NUP42	exon_skip_113867	6.175686e-01	1.140539e-17
FL	KHDRBS2	exon_skip_45374	-4.575841e-01	1.554934e-11
FL	KHDRBS3	exon_skip_45374	-6.461934e-01	1.489412e-24
FL	NUP42	exon_skip_45374	-4.448936e-01	6.445208e-11
FL	HNRNPL	exon_skip_45374	-4.971087e-01	1.250496e-13
FL	SRSF9	exon_skip_45374	-5.322738e-01	9.834043e-16
FL	SART3	exon_skip_45374	-4.087121e-01	2.728311e-09
HCC	RBM6	exon_skip_45374	5.809020e-01	2.598878e-25
HCC	RBM5	exon_skip_45374	5.542726e-01	9.608425e-23
HCC	IGF2BP2	exon_skip_45374	4.136799e-01	2.229298e-12
HCC	PCBP4	exon_skip_45374	5.871979e-01	5.925906e-26
HCC	KHDRBS3	exon_skip_45374	5.272749e-01	2.298832e-20
HCC	PABPC1	exon_skip_45374	4.670210e-01	9.231624e-16
IFG	IGF2BP2	exon_skip_45374	5.124314e-01	5.303894e-03
IFG	KHDRBS2	exon_skip_45374	-4.435926e-01	1.805688e-02
IFG	KHDRBS3	exon_skip_45374	-5.328588e-01	3.506864e-03
IFG	NUP42	exon_skip_45374	-5.038336e-01	6.266342e-03
IFG	RBM5	exon_skip_113867	-4.350457e-01	2.333573e-02
IFG	SRSF4	exon_skip_113867	-5.396607e-01	3.669958e-03
PCC	RBM6	exon_skip_45374	4.263143e-01	4.661668e-10
PCC	PCBP4	exon_skip_45374	4.360335e-01	1.680804e-10
PCC	PABPC3	exon_skip_45374	4.118015e-01	2.015591e-09
PCC	PABPC1	exon_skip_45374	4.900986e-01	3.079394e-13
PG	KHDRBS2	exon_skip_280793	-5.426983e-01	2.092640e-16
PG	KHDRBS3	exon_skip_280793	-5.809555e-01	4.400818e-19
PG	HNRNPL	exon_skip_280793	-4.587459e-01	1.361119e-11
PG	SART3	exon_skip_280793	-4.245196e-01	5.608188e-10
STG	KHDRBS2	exon_skip_280793	-5.122954e-01	3.358159e-07
STG	KHDRBS3	exon_skip_280793	-5.563234e-01	1.827492e-08
TC	KHDRBS2	exon_skip_280793	-7.163195e-01	5.265049e-23
TC	KHDRBS3	exon_skip_280793	-6.802149e-01	4.501035e-20
TC	HNRNPD	exon_skip_280793	-5.040664e-01	2.924433e-10
TC	NUP42	exon_skip_280793	-5.932316e-01	1.762415e-14
TC	SRSF9	exon_skip_280793	-4.018371e-01	1.033780e-06

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RelatedDrugs for NF1

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 NF1

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 NF1

Gene structures and expression levels for NF1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NF1

Open reading frame (ORF) annotation in the exon skipping event for NF1

Infer the effects of exon skipping event on protein functional features for NF1

3'-UTR located exon skipping events that lost miRNA binding sites in NF1

SNVs in the skipped exons for NF1

AD stage-associated exon skippint events for NF1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NF1

Correlation with RNA binding proteins (RBPs) for NF1

RelatedDrugs for NF1

RelatedDiseases for NF1