ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for NBEAL1

Gene summary

Gene information	Gene symbol	NBEAL1
	Gene ID	65065
	Gene name	neurobeachin like 1
	Synonyms	A530083I02Rik\|ALS2CR16\|ALS2CR17
	Cytomap	2q33.2
	Type of gene	protein-coding
	Description	neurobeachin-like protein 1amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17amyotrophic lateral sclerosis 2 chromosomal region candidate gene 16 protein
	Modification date	20180519
	UniProtAcc	Q6ZS30
	Context	PubMed: NBEAL1 [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 NBEAL1 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 NBEAL1

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 NBEAL1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_332612	2	203881087:203881158:203906487:203906579:203914536:203914698	203906487:203906579	ENSG00000144426.14	ENST00000460416.2,ENST00000478884.1,ENST00000449802.1,ENST00000497505.1
exon_skip_332613	2	203906487:203906579:203914536:203914698:203921149:203921231	203914536:203914698	ENSG00000144426.14	ENST00000478884.1,ENST00000449802.1,ENST00000497505.1
exon_skip_332615	2	203914536:203914698:203921149:203921231:203922048:203922176	203921149:203921231	ENSG00000144426.14	ENST00000478884.1,ENST00000449802.1,ENST00000497505.1
exon_skip_332619	2	203977737:203978041:203980707:203980793:203986976:203987066	203980707:203980793	ENSG00000144426.14	ENST00000449802.1
exon_skip_332620	2	203991546:203991649:203992503:203992660:203995040:203995199	203992503:203992660	ENSG00000144426.14	ENST00000449802.1
exon_skip_332622	2	204001321:204001497:204002884:204003038:204003342:204003471	204002884:204003038	ENSG00000144426.14	ENST00000449802.1
exon_skip_332625	2	204016187:204016312:204022421:204022548:204030871:204031020	204022421:204022548	ENSG00000144426.14	ENST00000449802.1
exon_skip_332626	2	204034469:204034574:204036650:204036746:204037451:204037576	204036650:204036746	ENSG00000144426.14	ENST00000449802.1
exon_skip_332627	2	204037451:204037576:204039869:204040010:204045104:204045235	204039869:204040010	ENSG00000144426.14	ENST00000414576.2,ENST00000449802.1
exon_skip_332628	2	204045104:204045235:204048001:204048111:204053194:204053312	204048001:204048111	ENSG00000144426.14	ENST00000414576.2,ENST00000449802.1
exon_skip_332631	2	204055014:204055112:204058517:204058634:204062024:204062114	204058517:204058634	ENSG00000144426.14	ENST00000414576.2,ENST00000449802.1
exon_skip_332634	2	204058517:204058634:204062024:204062114:204064060:204064170	204062024:204062114	ENSG00000144426.14	ENST00000414576.2,ENST00000449802.1
exon_skip_332635	2	204064060:204064170:204066265:204066438:204067409:204067504	204066265:204066438	ENSG00000144426.14	ENST00000414576.2,ENST00000449802.1
exon_skip_332636	2	204073359:204073476:204073883:204074045:204075680:204075829	204073883:204074045	ENSG00000144426.14	ENST00000414576.2,ENST00000434469.1,ENST00000449802.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for NBEAL1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_332612	2	203881087:203881158:203906487:203906579:203914536:203914698	203906487:203906579	ENSG00000144426.14	ENST00000497505.1,ENST00000449802.1,ENST00000478884.1,ENST00000460416.2
exon_skip_332613	2	203906487:203906579:203914536:203914698:203921149:203921231	203914536:203914698	ENSG00000144426.14	ENST00000497505.1,ENST00000449802.1,ENST00000478884.1
exon_skip_332615	2	203914536:203914698:203921149:203921231:203922048:203922176	203921149:203921231	ENSG00000144426.14	ENST00000497505.1,ENST00000449802.1,ENST00000478884.1
exon_skip_332619	2	203977737:203978041:203980707:203980793:203986976:203987066	203980707:203980793	ENSG00000144426.14	ENST00000449802.1
exon_skip_332620	2	203991546:203991649:203992503:203992660:203995040:203995199	203992503:203992660	ENSG00000144426.14	ENST00000449802.1
exon_skip_332622	2	204001321:204001497:204002884:204003038:204003342:204003471	204002884:204003038	ENSG00000144426.14	ENST00000449802.1
exon_skip_332625	2	204016187:204016312:204022421:204022548:204030871:204031020	204022421:204022548	ENSG00000144426.14	ENST00000449802.1
exon_skip_332626	2	204034469:204034574:204036650:204036746:204037451:204037576	204036650:204036746	ENSG00000144426.14	ENST00000449802.1
exon_skip_332627	2	204037451:204037576:204039869:204040010:204045104:204045235	204039869:204040010	ENSG00000144426.14	ENST00000449802.1,ENST00000414576.2
exon_skip_332628	2	204045104:204045235:204048001:204048111:204053194:204053312	204048001:204048111	ENSG00000144426.14	ENST00000449802.1,ENST00000414576.2
exon_skip_332631	2	204055014:204055112:204058517:204058634:204062024:204062114	204058517:204058634	ENSG00000144426.14	ENST00000449802.1,ENST00000414576.2
exon_skip_332634	2	204058517:204058634:204062024:204062114:204064060:204064170	204062024:204062114	ENSG00000144426.14	ENST00000449802.1,ENST00000414576.2
exon_skip_332635	2	204064060:204064170:204066265:204066438:204067409:204067504	204066265:204066438	ENSG00000144426.14	ENST00000449802.1,ENST00000414576.2
exon_skip_332636	2	204073359:204073476:204073883:204074045:204075680:204075829	204073883:204074045	ENSG00000144426.14	ENST00000449802.1,ENST00000414576.2,ENST00000434469.1
exon_skip_332637	2	204078240:204078376:204081975:204082073:204090845:204091101	204081975:204082073	ENSG00000144426.14	ENST00000434469.1

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 NBEAL1

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

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

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Infer the effects of exon skipping event on protein functional features for NBEAL1

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

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

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

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

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SNVs in the skipped exons for NBEAL1

- 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
LIHC	TCGA-G3-A3CJ-01	exon_skip_332613	203914537	203914698	203914665	203914665	Frame_Shift_Del	T	-	p.I91fs
LIHC	TCGA-DD-A3A0-01	exon_skip_332620	203992504	203992660	203992617	203992617	Frame_Shift_Del	A	-	p.Q1092fs
DLBC	TCGA-G8-6914-01	exon_skip_332622	204002885	204003038	204002925	204002926	Frame_Shift_Del	AG	-	p.1506_1507del
CHOL	TCGA-W5-AA2G-01	exon_skip_332625	204022422	204022548	204022462	204022462	Frame_Shift_Del	G	-	p.L1847fs
LIHC	TCGA-DD-A1EG-01	exon_skip_332626	204036651	204036746	204036694	204036694	Frame_Shift_Del	A	-	p.Q2020fs
LIHC	TCGA-DD-A1EG-01	exon_skip_332626	204036651	204036746	204036698	204036698	Frame_Shift_Del	A	-	p.I2021fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_332626	204036651	204036746	204036698	204036698	Frame_Shift_Del	A	-	p.I2021fs
COAD	TCGA-G4-6628-01	exon_skip_332631	204058518	204058634	204058623	204058623	Frame_Shift_Del	T	-	p.S2313fs
ESCA	TCGA-L5-A8NM-01	exon_skip_332631	204058518	204058634	204058623	204058623	Frame_Shift_Del	T	-	p.F2315fs
ESCA	TCGA-L5-A8NM-01	exon_skip_332631	204058518	204058634	204058623	204058623	Frame_Shift_Del	T	-	p.S2313fs
STAD	TCGA-BR-4361-01	exon_skip_332631	204058518	204058634	204058623	204058623	Frame_Shift_Del	T	-	p.S2313fs
LIHC	TCGA-DD-A39Y-01	exon_skip_332634	204062025	204062114	204062056	204062056	Frame_Shift_Del	C	-	p.A2328fs
LIHC	TCGA-DD-A3A0-01	exon_skip_332634	204062025	204062114	204062067	204062067	Frame_Shift_Del	A	-	p.K2332fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_332635	204066266	204066438	204066401	204066401	Frame_Shift_Del	A	-	p.T2429fs
LIHC	TCGA-DD-A3A1-01	exon_skip_332636	204073884	204074045	204073977	204073977	Frame_Shift_Del	A	-	p.N2544fs
SKCM	TCGA-D3-A51G-06	exon_skip_332636	204073884	204074045	204073989	204073989	Frame_Shift_Del	T	-	p.I2547fs
SKCM	TCGA-D3-A51G-06	exon_skip_332636	204073884	204074045	204073989	204073989	Frame_Shift_Del	T	-	p.S2548fs
COAD	TCGA-CM-6171-01	exon_skip_332636	204073884	204074045	204074029	204074029	Frame_Shift_Del	A	-	p.E2561fs
LIHC	TCGA-DD-A1EG-01	exon_skip_332636	204073884	204074045	204074029	204074029	Frame_Shift_Del	A	-	p.E2561fs
BLCA	TCGA-BT-A42E-01	exon_skip_332622	204002885	204003038	204002917	204002917	Nonsense_Mutation	C	G	p.S1504*
PRAD	TCGA-EJ-5530-01	exon_skip_332627	204039870	204040010	204039932	204039932	Nonsense_Mutation	C	G	p.S2100*
BLCA	TCGA-E7-A541-01	exon_skip_332631	204058518	204058634	204058599	204058599	Nonsense_Mutation	C	T	p.Q2306*
BRCA	TCGA-E9-A1R4-01	exon_skip_332631	204058518	204058634	204058611	204058611	Nonsense_Mutation	G	T	p.E2310*
CESC	TCGA-C5-A1MK-01	exon_skip_332636	204073884	204074045	204073911	204073911	Nonsense_Mutation	C	T	p.Q2522*
UCEC	TCGA-B5-A11O-01	exon_skip_332619	203980708	203980793	203980794	203980794	Splice_Site	G	T	p.K835_splice

- 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
LS411N_LARGE_INTESTINE	203906488	203906579	203906523	203906524	Frame_Shift_Del	TT	-	p.F30fs
SNU1076_UPPER_AERODIGESTIVE_TRACT	203992504	203992660	203992568	203992568	Frame_Shift_Del	G	-	p.G1076fs
KM12_LARGE_INTESTINE	204058518	204058634	204058623	204058623	Frame_Shift_Del	T	-	p.F2315fs
NCIH630_LARGE_INTESTINE	204058518	204058634	204058623	204058623	Frame_Shift_Del	T	-	p.F2315fs
SNU1040_LARGE_INTESTINE	204058518	204058634	204058623	204058623	Frame_Shift_Del	T	-	p.F2315fs
CL14_LARGE_INTESTINE	203906488	203906579	203906554	203906554	Missense_Mutation	G	A	p.V40I
SNU175_LARGE_INTESTINE	203914537	203914698	203914568	203914568	Missense_Mutation	C	A	p.L59I
BICR18_UPPER_AERODIGESTIVE_TRACT	203914537	203914698	203914612	203914612	Missense_Mutation	G	C	p.Q73H
HSC2_UPPER_AERODIGESTIVE_TRACT	203992504	203992660	203992530	203992530	Missense_Mutation	C	T	p.S1063F
SKN3_UPPER_AERODIGESTIVE_TRACT	203992504	203992660	203992533	203992533	Missense_Mutation	T	C	p.L1064P
SW684_SOFT_TISSUE	203992504	203992660	203992560	203992560	Missense_Mutation	C	T	p.S1073F
KYSE180_OESOPHAGUS	203992504	203992660	203992579	203992579	Missense_Mutation	A	T	p.K1079N
YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	203992504	203992660	203992579	203992579	Missense_Mutation	A	T	p.K1079N
NCIH650_LUNG	203992504	203992660	203992627	203992627	Missense_Mutation	G	A	p.M1095I
NCIH650_LUNG	203992504	203992660	203992627	203992628	Missense_Mutation	GG	AT	p.1095_1096MG>IW
NCIH650_LUNG	203992504	203992660	203992628	203992628	Missense_Mutation	G	T	p.G1096W
HMVII_SKIN	204002885	204003038	204002888	204002888	Missense_Mutation	G	C	p.L1494F
SCC3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	204002885	204003038	204002977	204002977	Missense_Mutation	T	C	p.L1524P
PACADD188_PANCREAS	204022422	204022548	204022463	204022463	Missense_Mutation	G	A	p.E1848K
KMS12BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	204022422	204022548	204022523	204022523	Missense_Mutation	G	C	p.E1868Q
TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	204022422	204022548	204022546	204022546	Missense_Mutation	T	G	p.N1875K
NCIH2227_LUNG	204036651	204036746	204036661	204036661	Missense_Mutation	A	G	p.N2009S
BT474_BREAST	204036651	204036746	204036664	204036664	Missense_Mutation	G	C	p.R2010T
OE19_OESOPHAGUS	204039870	204040010	204039883	204039883	Missense_Mutation	G	C	p.E2084Q
HEC151_ENDOMETRIUM	204039870	204040010	204039953	204039953	Missense_Mutation	A	G	p.H2107R
GOTO_AUTONOMIC_GANGLIA	204039870	204040010	204039964	204039964	Missense_Mutation	C	T	p.R2111C
LNCAPCLONEFGC_PROSTATE	204039870	204040010	204039965	204039965	Missense_Mutation	G	A	p.R2111H
JSC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	204058518	204058634	204058545	204058545	Missense_Mutation	G	C	p.E2288Q
HCT116_LARGE_INTESTINE	204058518	204058634	204058604	204058604	Missense_Mutation	C	A	p.H2307Q
BICR18_UPPER_AERODIGESTIVE_TRACT	204062025	204062114	204062059	204062059	Missense_Mutation	C	T	p.T2329I
NCIH1755_LUNG	204062025	204062114	204062075	204062075	Missense_Mutation	G	T	p.Q2334H
RCCFG2_KIDNEY	204062025	204062114	204062076	204062076	Missense_Mutation	T	C	p.Y2335H
BICR18_UPPER_AERODIGESTIVE_TRACT	204062025	204062114	204062077	204062077	Missense_Mutation	A	C	p.Y2335S
K562_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	204066266	204066438	204066300	204066300	Missense_Mutation	G	A	p.G2396R
CAL51_BREAST	204066266	204066438	204066300	204066300	Missense_Mutation	G	T	p.G2396W
FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	204066266	204066438	204066330	204066330	Missense_Mutation	G	A	p.V2406I
ESS1_ENDOMETRIUM	204066266	204066438	204066412	204066412	Missense_Mutation	T	G	p.I2433S
HCT15_LARGE_INTESTINE	204066266	204066438	204066421	204066421	Missense_Mutation	A	G	p.H2436R
SW684_SOFT_TISSUE	204073884	204074045	204073908	204073908	Missense_Mutation	A	G	p.I2521V
JEG3_PLACENTA	204073884	204074045	204073954	204073954	Missense_Mutation	G	A	p.S2536N
HSC1_SKIN	203914537	203914698	203914652	203914652	Nonsense_Mutation	C	T	p.Q87*
NCIH1688_LUNG	204039870	204040010	204039932	204039932	Nonsense_Mutation	C	G	p.S2100*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NBEAL1

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 NBEAL1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NBEAL1

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RelatedDrugs for NBEAL1

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 NBEAL1

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 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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Gene summary for NBEAL1

Exon skipping events across known transcript of Ensembl for NBEAL1 from UCSC genome browser

Gene isoform structures and expression levels for NBEAL1

Exon skipping events with PSIs in TCGA for NBEAL1

Exon skipping events with PSIs in GTEx for NBEAL1

Open reading frame (ORF) annotation in the exon skipping event for NBEAL1

Infer the effects of exon skipping event on protein functional features for NBEAL1

SNVs in the skipped exons for NBEAL1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NBEAL1

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NBEAL1

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NBEAL1

RelatedDrugs for NBEAL1

RelatedDiseases for NBEAL1