ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for NAV3

Gene summary

Gene information	Gene symbol	NAV3
	Gene ID	89795
	Gene name	neuron navigator 3
	Synonyms	POMFIL1\|STEERIN3\|unc53H3
	Cytomap	12q21.2
	Type of gene	protein-coding
	Description	neuron navigator 3pore membrane and/or filament interacting like protein 1unc-53 homolog 3
	Modification date	20180523
	UniProtAcc	Q8IVL0
	Context	PubMed: NAV3 [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

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Exon skipping events across known transcript of Ensembl for NAV3 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 NAV3

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 NAV3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_85584	12	78362298:78362482:78388582:78388651:78392116:78392256	78388582:78388651	ENSG00000067798.9	ENST00000266692.7,ENST00000549464.1,ENST00000536525.2,ENST00000228327.6,ENST00000397909.2
exon_skip_85585	12	78513016:78513725:78515719:78516208:78520946:78520988	78515719:78516208	ENSG00000067798.9	ENST00000536525.2,ENST00000228327.6,ENST00000397909.2
exon_skip_85588	12	78516041:78516208:78520946:78520988:78522485:78522646	78520946:78520988	ENSG00000067798.9	ENST00000536525.2,ENST00000228327.6,ENST00000397909.2
exon_skip_85589	12	78569085:78569207:78570218:78570239:78570920:78571093	78570218:78570239	ENSG00000067798.9	ENST00000266692.7,ENST00000552895.1,ENST00000536525.2,ENST00000228327.6,ENST00000397909.2
exon_skip_85590	12	78570920:78571093:78571399:78571465:78573308:78573462	78571399:78571465	ENSG00000067798.9	ENST00000397909.2
exon_skip_85592	12	78592384:78592456:78593114:78593311:78594252:78594342	78593114:78593311	ENSG00000067798.9	ENST00000266692.7,ENST00000552895.1,ENST00000536525.2,ENST00000228327.6,ENST00000397909.2
exon_skip_85594	12	78593114:78593311:78594252:78594371:78598714:78598918	78594252:78594371	ENSG00000067798.9	ENST00000266692.7,ENST00000552895.1,ENST00000536525.2,ENST00000551162.1,ENST00000541270.1,ENST00000228327.6,ENST00000397909.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for NAV3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_85584	12	78362298:78362482:78388582:78388651:78392116:78392256	78388582:78388651	ENSG00000067798.9	ENST00000549464.1,ENST00000536525.2,ENST00000397909.2,ENST00000228327.6,ENST00000266692.7
exon_skip_85585	12	78513016:78513725:78515719:78516208:78520946:78520988	78515719:78516208	ENSG00000067798.9	ENST00000536525.2,ENST00000397909.2,ENST00000228327.6
exon_skip_85588	12	78516041:78516208:78520946:78520988:78522485:78522646	78520946:78520988	ENSG00000067798.9	ENST00000536525.2,ENST00000397909.2,ENST00000228327.6
exon_skip_85589	12	78569085:78569207:78570218:78570239:78570920:78571093	78570218:78570239	ENSG00000067798.9	ENST00000536525.2,ENST00000397909.2,ENST00000228327.6,ENST00000266692.7,ENST00000552895.1
exon_skip_85590	12	78570920:78571093:78571399:78571465:78573308:78573462	78571399:78571465	ENSG00000067798.9	ENST00000397909.2
exon_skip_85591	12	78582027:78582123:78582388:78582557:78583763:78583970	78582388:78582557	ENSG00000067798.9	ENST00000536525.2,ENST00000397909.2,ENST00000228327.6,ENST00000266692.7,ENST00000552895.1,ENST00000550788.1
exon_skip_85592	12	78592384:78592456:78593114:78593311:78594252:78594342	78593114:78593311	ENSG00000067798.9	ENST00000536525.2,ENST00000397909.2,ENST00000228327.6,ENST00000266692.7,ENST00000552895.1
exon_skip_85594	12	78593114:78593311:78594252:78594371:78598714:78598918	78594252:78594371	ENSG00000067798.9	ENST00000536525.2,ENST00000397909.2,ENST00000228327.6,ENST00000266692.7,ENST00000552895.1,ENST00000551162.1,ENST00000541270.1

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 NAV3

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
ENST00000397909	78593114	78593311	Frame-shift
ENST00000397909	78594252	78594371	Frame-shift
ENST00000397909	78388582	78388651	In-frame
ENST00000397909	78515719	78516208	In-frame
ENST00000397909	78520946	78520988	In-frame
ENST00000397909	78570218	78570239	In-frame
ENST00000397909	78571399	78571465	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
ENST00000397909	78582388	78582557	Frame-shift
ENST00000397909	78593114	78593311	Frame-shift
ENST00000397909	78594252	78594371	Frame-shift
ENST00000397909	78388582	78388651	In-frame
ENST00000397909	78515719	78516208	In-frame
ENST00000397909	78520946	78520988	In-frame
ENST00000397909	78570218	78570239	In-frame
ENST00000397909	78571399	78571465	In-frame

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Infer the effects of exon skipping event on protein functional features for NAV3

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
ENST00000397909	9838	2385	78388582	78388651	845	913	224	246
ENST00000397909	9838	2385	78515719	78516208	3923	4411	1250	1412
ENST00000397909	9838	2385	78520946	78520988	4412	4453	1413	1426
ENST00000397909	9838	2385	78571399	78571465	5471	5536	1766	1787

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
ENST00000397909	9838	2385	78388582	78388651	845	913	224	246
ENST00000397909	9838	2385	78515719	78516208	3923	4411	1250	1412
ENST00000397909	9838	2385	78520946	78520988	4412	4453	1413	1426
ENST00000397909	9838	2385	78571399	78571465	5471	5536	1766	1787

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
Q8IVL0	224	246	1	2385	Chain	ID=PRO_0000286976;Note=Neuron navigator 3
Q8IVL0	1250	1412	1250	1426	Alternative sequence	ID=VSP_025268;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10231032;Dbxref=PMID:10231032
Q8IVL0	1250	1412	1	2385	Chain	ID=PRO_0000286976;Note=Neuron navigator 3
Q8IVL0	1250	1412	1032	1560	Compositional bias	Note=Ser-rich
Q8IVL0	1413	1426	1250	1426	Alternative sequence	ID=VSP_025268;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10231032;Dbxref=PMID:10231032
Q8IVL0	1413	1426	1	2385	Chain	ID=PRO_0000286976;Note=Neuron navigator 3
Q8IVL0	1413	1426	1032	1560	Compositional bias	Note=Ser-rich
Q8IVL0	1766	1787	1767	1788	Alternative sequence	ID=VSP_025269;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10231032,ECO:0000303\|PubMed:12079279;Dbxref=PMID:10231032,PMID:12079279
Q8IVL0	1766	1787	1	2385	Chain	ID=PRO_0000286976;Note=Neuron navigator 3

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
Q8IVL0	224	246	1	2385	Chain	ID=PRO_0000286976;Note=Neuron navigator 3
Q8IVL0	1250	1412	1250	1426	Alternative sequence	ID=VSP_025268;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10231032;Dbxref=PMID:10231032
Q8IVL0	1250	1412	1	2385	Chain	ID=PRO_0000286976;Note=Neuron navigator 3
Q8IVL0	1250	1412	1032	1560	Compositional bias	Note=Ser-rich
Q8IVL0	1413	1426	1250	1426	Alternative sequence	ID=VSP_025268;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10231032;Dbxref=PMID:10231032
Q8IVL0	1413	1426	1	2385	Chain	ID=PRO_0000286976;Note=Neuron navigator 3
Q8IVL0	1413	1426	1032	1560	Compositional bias	Note=Ser-rich
Q8IVL0	1766	1787	1767	1788	Alternative sequence	ID=VSP_025269;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10231032,ECO:0000303\|PubMed:12079279;Dbxref=PMID:10231032,PMID:12079279
Q8IVL0	1766	1787	1	2385	Chain	ID=PRO_0000286976;Note=Neuron navigator 3

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SNVs in the skipped exons for NAV3

- 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
STAD	TCGA-CG-4305-01	exon_skip_85584	78388583	78388651	78388636	78388636	Frame_Shift_Del	A	-	p.Q242fs
LUAD	TCGA-17-Z023-01	exon_skip_85585	78515720	78516208	78516143	78516153	Frame_Shift_Del	AGGCACTCACG	-	p.TGTHE1391fs
LIHC	TCGA-DD-A39Y-01	exon_skip_85588	78520947	78520988	78520975	78520975	Frame_Shift_Del	A	-	p.K1424fs
PRAD	TCGA-J4-8198-01	exon_skip_85592	78593115	78593311	78593154	78593155	Frame_Shift_Ins	-	T	p.F2187fs
PRAD	TCGA-J4-8198-01	exon_skip_85592	78593115	78593311	78593154	78593155	Frame_Shift_Ins	-	T	p.GF2186fs
LUAD	TCGA-78-7154-01	exon_skip_85592	78593115	78593311	78593140	78593140	Nonsense_Mutation	G	T	p.E2182*
UCEC	TCGA-D1-A16Y-01	exon_skip_85592	78593115	78593311	78593140	78593140	Nonsense_Mutation	G	T	p.E2160*
SKCM	TCGA-FS-A1ZQ-06	exon_skip_85592	78593115	78593311	78593243	78593243	Nonsense_Mutation	G	A	p.W2194X
SKCM	TCGA-FS-A1ZQ-06	exon_skip_85592	78593115	78593311	78593243	78593243	Nonsense_Mutation	G	A	p.W2216*
UCEC	TCGA-B5-A11E-01	exon_skip_85594	78594253	78594371	78594320	78594320	Nonsense_Mutation	G	A	p.W2239*
CHOL	TCGA-W6-AA0S-01	exon_skip_85588	78520947	78520988	78520946	78520946	Splice_Site	G	T	.
UCEC	TCGA-AP-A05N-01	exon_skip_85592	78593115	78593311	78593312	78593312	Splice_Site	G	A	p.G2239_splice
UCEC	TCGA-B5-A11G-01	exon_skip_85592	78593115	78593311	78593313	78593313	Splice_Site	T	C	e36+2
SKCM	TCGA-GN-A266-06	exon_skip_85594	78594253	78594371	78594372	78594372	Splice_Site	G	A	.

- 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
SKMEL28_SKIN	78388583	78388651	78388627	78388630	Frame_Shift_Del	CAAC	-	p.AT239fs
HEC6_ENDOMETRIUM	78594253	78594371	78594273	78594274	Frame_Shift_Ins	-	G	p.C2246fs
NCIH1793_LUNG	78388583	78388651	78388600	78388600	Missense_Mutation	C	G	p.A230G
SNU81_LARGE_INTESTINE	78388583	78388651	78388611	78388611	Missense_Mutation	A	G	p.N234D
NCIH1648_LUNG	78388583	78388651	78388648	78388648	Missense_Mutation	C	A	p.T246N
NCIH748_LUNG	78515720	78516208	78515727	78515727	Missense_Mutation	G	T	p.G1253C
UACC812_BREAST	78515720	78516208	78515761	78515761	Missense_Mutation	C	A	p.P1264H
NCIH810_LUNG	78515720	78516208	78515785	78515785	Missense_Mutation	C	A	p.S1272Y
GP5D_LARGE_INTESTINE	78515720	78516208	78515791	78515791	Missense_Mutation	T	C	p.V1274A
ONS76_CENTRAL_NERVOUS_SYSTEM	78515720	78516208	78515809	78515809	Missense_Mutation	C	T	p.T1280I
CAL120_BREAST	78515720	78516208	78515848	78515848	Missense_Mutation	C	G	p.S1293C
NCIH838_LUNG	78515720	78516208	78515880	78515880	Missense_Mutation	C	A	p.L1304I
IGROV1_OVARY	78515720	78516208	78515890	78515890	Missense_Mutation	G	A	p.S1307N
NCIH740_LUNG	78515720	78516208	78515890	78515890	Missense_Mutation	G	T	p.S1307I
MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78515720	78516208	78516003	78516003	Missense_Mutation	G	A	p.V1345M
HCC2998_LARGE_INTESTINE	78515720	78516208	78516006	78516006	Missense_Mutation	T	G	p.W1346G
NCIH1944_LUNG	78515720	78516208	78516008	78516008	Missense_Mutation	G	T	p.W1346C
HCT15_LARGE_INTESTINE	78515720	78516208	78516022	78516022	Missense_Mutation	G	A	p.S1351N
LN340_CENTRAL_NERVOUS_SYSTEM	78515720	78516208	78516068	78516068	Missense_Mutation	G	A	p.M1366I
NCIH2135_LUNG	78515720	78516208	78516099	78516099	Missense_Mutation	G	A	p.D1377N
HCT15_LARGE_INTESTINE	78515720	78516208	78516103	78516103	Missense_Mutation	T	C	p.L1378P
DU145_PROSTATE	78515720	78516208	78516180	78516180	Missense_Mutation	G	T	p.G1404C
DU145_PROSTATE	78515720	78516208	78516180	78516181	Missense_Mutation	GG	TT	p.G1404F
DU145_PROSTATE	78515720	78516208	78516181	78516181	Missense_Mutation	G	T	p.G1404V
L82_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78520947	78520988	78520955	78520955	Missense_Mutation	T	G	p.L1416R
VMRCLCD_LUNG	78571400	78571465	78571454	78571454	Missense_Mutation	G	T	p.K1784N
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78593115	78593311	78593170	78593170	Missense_Mutation	C	T	p.L2192F
HOP92_LUNG	78593115	78593311	78593182	78593182	Missense_Mutation	C	T	p.L2196F
NCIH650_LUNG	78593115	78593311	78593273	78593273	Missense_Mutation	G	T	p.S2226I
SNU324_PANCREAS	78593115	78593311	78593288	78593288	Missense_Mutation	A	G	p.H2231R
RPMI8866_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78594253	78594371	78594312	78594312	Missense_Mutation	G	A	p.D2259N
EBC1_LUNG	78594253	78594371	78594339	78594339	Missense_Mutation	T	C	p.Y2268H
SW1271_LUNG	78515720	78516208	78516059	78516060	Nonsense_Mutation	CC	AT	p.1363_1364YQ>**
SW1271_LUNG	78515720	78516208	78516059	78516059	Nonsense_Mutation	C	A	p.Y1363*
SW1271_LUNG	78515720	78516208	78516060	78516060	Nonsense_Mutation	C	T	p.Q1364*
A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78388583	78388651	78388651	78388651	Splice_Site	G	A	p.R247K
A4FUK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78571400	78571465	78571465	78571465	Splice_Site	G	A	p.R1788Q
SNU761_LIVER	78571400	78571465	78571465	78571465	Splice_Site	G	A	p.R1788Q
MKN45_STOMACH	78571400	78571465	78571465	78571465	Splice_Site	G	A	p.R1788Q
OSC20_UPPER_AERODIGESTIVE_TRACT	78571400	78571465	78571465	78571465	Splice_Site	G	A	p.R1788Q
SISO_CERVIX	78571400	78571465	78571465	78571465	Splice_Site	G	A	p.R1788Q

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NAV3

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 NAV3

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NAV3

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RelatedDrugs for NAV3

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 NAV3

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
NAV3	C0007134	Renal Cell Carcinoma	1	CTD_human
NAV3	C0027412	Opioid-Related Disorders	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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