ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SNX1

Gene summary

Gene information	Gene symbol	SNX1
	Gene ID	6642
	Gene name	sorting nexin 1
	Synonyms	HsT17379\|VPS5
	Cytomap	15q22.31
	Type of gene	protein-coding
	Description	sorting nexin-1sorting nexin 1A
	Modification date	20180527
	UniProtAcc	Q13596
	Context	PubMed: SNX1 [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
SNX1	GO:0072673	lamellipodium morphogenesis	20604901

Top

Exon skipping events across known transcript of Ensembl for SNX1 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.

Top

Gene isoform structures and expression levels for SNX1

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

Top

Exon skipping events with PSIs in TCGA for SNX1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_122670	15	64388229:64388371:64404771:64404883:64418277:64418298	64404771:64404883	ENSG00000028528.10	ENST00000560260.1
exon_skip_122673	15	64404771:64404883:64407787:64407905:64410315:64410365	64407787:64407905	ENSG00000028528.10	ENST00000559061.1,ENST00000559389.1
exon_skip_122678	15	64404771:64404883:64415701:64415745:64418277:64418298	64415701:64415745	ENSG00000028528.10	ENST00000561026.1
exon_skip_122680	15	64404771:64404883:64418277:64418419:64419372:64419451	64418277:64418419	ENSG00000028528.10	ENST00000560260.1
exon_skip_122681	15	64410401:64410443:64410986:64411053:64415701:64415745	64410986:64411053	ENSG00000028528.10	ENST00000353874.4,ENST00000559061.1,ENST00000559844.1,ENST00000261889.5,ENST00000559389.1,ENST00000380285.3,ENST00000560829.1
exon_skip_122686	15	64410990:64411053:64415701:64415745:64418277:64418298	64415701:64415745	ENSG00000028528.10	ENST00000353874.4,ENST00000559061.1,ENST00000559844.1,ENST00000261889.5,ENST00000559389.1,ENST00000380285.3
exon_skip_122687	15	64410986:64411053:64415701:64415745:64419372:64419451	64415701:64415745	ENSG00000028528.10	ENST00000560829.1
exon_skip_122689	15	64415701:64415745:64418277:64418419:64419372:64419451	64418277:64418419	ENSG00000028528.10	ENST00000353874.4,ENST00000559844.1,ENST00000261889.5,ENST00000561026.1,ENST00000380285.3
exon_skip_122690	15	64422426:64422520:64423885:64424091:64426862:64427000	64423885:64424091	ENSG00000028528.10	ENST00000559844.1,ENST00000261889.5,ENST00000560260.1,ENST00000561026.1,ENST00000380285.3,ENST00000560829.1
exon_skip_122695	15	64424027:64424091:64426862:64427006:64428528:64428608	64426862:64427006	ENSG00000028528.10	ENST00000559844.1,ENST00000261889.5,ENST00000561026.1,ENST00000380285.3,ENST00000560829.1
exon_skip_122698	15	64426862:64427006:64428528:64428609:64429059:64429131	64428528:64428609	ENSG00000028528.10	ENST00000559844.1,ENST00000261889.5,ENST00000561026.1,ENST00000380285.3,ENST00000560829.1

PSI values of skipped exons in TCGA.

Top

Exon skipping events with PSIs in GTEx for SNX1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_122670	15	64388229:64388371:64404771:64404883:64418277:64418298	64404771:64404883	ENSG00000028528.10	ENST00000560260.1
exon_skip_122673	15	64404771:64404883:64407787:64407905:64410315:64410365	64407787:64407905	ENSG00000028528.10	ENST00000559061.1,ENST00000559389.1
exon_skip_122678	15	64404771:64404883:64415701:64415745:64418277:64418298	64415701:64415745	ENSG00000028528.10	ENST00000561026.1
exon_skip_122680	15	64404771:64404883:64418277:64418419:64419372:64419451	64418277:64418419	ENSG00000028528.10	ENST00000560260.1
exon_skip_122681	15	64410401:64410443:64410986:64411053:64415701:64415745	64410986:64411053	ENSG00000028528.10	ENST00000560829.1,ENST00000559061.1,ENST00000353874.4,ENST00000380285.3,ENST00000261889.5,ENST00000559844.1,ENST00000559389.1
exon_skip_122686	15	64410990:64411053:64415701:64415745:64418277:64418298	64415701:64415745	ENSG00000028528.10	ENST00000559061.1,ENST00000353874.4,ENST00000380285.3,ENST00000261889.5,ENST00000559844.1,ENST00000559389.1
exon_skip_122687	15	64410986:64411053:64415701:64415745:64419372:64419451	64415701:64415745	ENSG00000028528.10	ENST00000560829.1
exon_skip_122689	15	64415701:64415745:64418277:64418419:64419372:64419451	64418277:64418419	ENSG00000028528.10	ENST00000353874.4,ENST00000380285.3,ENST00000261889.5,ENST00000559844.1,ENST00000561026.1
exon_skip_122690	15	64422426:64422520:64423885:64424091:64426862:64427000	64423885:64424091	ENSG00000028528.10	ENST00000560829.1,ENST00000380285.3,ENST00000261889.5,ENST00000559844.1,ENST00000560260.1,ENST00000561026.1
exon_skip_122695	15	64424027:64424091:64426862:64427006:64428528:64428608	64426862:64427006	ENSG00000028528.10	ENST00000560829.1,ENST00000380285.3,ENST00000261889.5,ENST00000559844.1,ENST00000561026.1
exon_skip_122698	15	64426862:64427006:64428528:64428609:64429059:64429131	64428528:64428609	ENSG00000028528.10	ENST00000560829.1,ENST00000380285.3,ENST00000261889.5,ENST00000559844.1,ENST00000561026.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

Top

Open reading frame (ORF) annotation in the exon skipping event for SNX1

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
ENST00000559844	64410986	64411053	Frame-shift
ENST00000559844	64415701	64415745	Frame-shift
ENST00000559844	64418277	64418419	Frame-shift
ENST00000559844	64423885	64424091	Frame-shift
ENST00000559844	64426862	64427006	In-frame
ENST00000559844	64428528	64428609	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
ENST00000559844	64410986	64411053	Frame-shift
ENST00000559844	64415701	64415745	Frame-shift
ENST00000559844	64418277	64418419	Frame-shift
ENST00000559844	64423885	64424091	Frame-shift
ENST00000559844	64426862	64427006	In-frame
ENST00000559844	64428528	64428609	In-frame

Top

Infer the effects of exon skipping event on protein functional features for SNX1

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
ENST00000559844	1988	522	64426862	64427006	1236	1379	407	455
ENST00000559844	1988	522	64428528	64428609	1380	1460	455	482

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
ENST00000559844	1988	522	64426862	64427006	1236	1379	407	455
ENST00000559844	1988	522	64428528	64428609	1380	1460	455	482

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
Q13596	407	455	1	522	Chain	ID=PRO_0000213835;Note=Sorting nexin-1
Q13596	407	455	302	522	Domain	Note=BAR
Q13596	407	455	388	440	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4FZS
Q13596	407	455	443	483	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4FZS
Q13596	407	455	429	431	Mutagenesis	Note=Loss of endosomal location. KKR->EEE;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15498486;Dbxref=PMID:15498486
Q13596	407	455	442	442	Mutagenesis	Note=No effect on membrane remodeling and membrane binding%3B when associated with A-445. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23085988;Dbxref=PMID:23085988
Q13596	407	455	445	445	Mutagenesis	Note=No effect on membrane remodeling and membrane binding%3B when associated with A-442. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23085988;Dbxref=PMID:23085988
Q13596	455	482	1	522	Chain	ID=PRO_0000213835;Note=Sorting nexin-1
Q13596	455	482	302	522	Domain	Note=BAR
Q13596	455	482	443	483	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4FZS
Q13596	455	482	466	466	Natural variant	ID=VAR_034507;Note=D->N;Dbxref=dbSNP:rs1802376

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
Q13596	407	455	1	522	Chain	ID=PRO_0000213835;Note=Sorting nexin-1
Q13596	407	455	302	522	Domain	Note=BAR
Q13596	407	455	388	440	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4FZS
Q13596	407	455	443	483	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4FZS
Q13596	407	455	429	431	Mutagenesis	Note=Loss of endosomal location. KKR->EEE;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15498486;Dbxref=PMID:15498486
Q13596	407	455	442	442	Mutagenesis	Note=No effect on membrane remodeling and membrane binding%3B when associated with A-445. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23085988;Dbxref=PMID:23085988
Q13596	407	455	445	445	Mutagenesis	Note=No effect on membrane remodeling and membrane binding%3B when associated with A-442. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23085988;Dbxref=PMID:23085988
Q13596	455	482	1	522	Chain	ID=PRO_0000213835;Note=Sorting nexin-1
Q13596	455	482	302	522	Domain	Note=BAR
Q13596	455	482	443	483	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4FZS
Q13596	455	482	466	466	Natural variant	ID=VAR_034507;Note=D->N;Dbxref=dbSNP:rs1802376

Top

SNVs in the skipped exons for SNX1

- 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.

SNX1_ESCA_exon_skip_122690_psi_boxplot.png
boxplot

SNX1_LIHC_exon_skip_122690_psi_boxplot.png
boxplot

- 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-DD-A1EG-01	exon_skip_122689 exon_skip_122680	64418278	64418419	64418316	64418316	Frame_Shift_Del	A	-	p.V183fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_122690	64423886	64424091	64423933	64423933	Frame_Shift_Del	G	-	p.G355fs
LUAD	TCGA-44-7671-01	exon_skip_122695	64426863	64427006	64426931	64426937	Frame_Shift_Del	GCGGGAG	-	p.K430fs
LUAD	TCGA-44-7671-01	exon_skip_122695	64426863	64427006	64426931	64426937	Frame_Shift_Del	GCGGGAG	-	p.KRE430fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_122698	64428529	64428609	64428588	64428588	Frame_Shift_Del	A	-	p.R427fs
LIHC	TCGA-DD-A3A0-01	exon_skip_122698	64428529	64428609	64428604	64428604	Frame_Shift_Del	T	-	p.F433fs
LUAD	TCGA-86-A4JF-01	exon_skip_122689 exon_skip_122680	64418278	64418419	64418397	64418398	Frame_Shift_Ins	-	C	p.PP210fs
KICH	TCGA-KL-8341-01	exon_skip_122695	64426863	64427006	64426911	64426912	Frame_Shift_Ins	-	A	p.Q424fs
COAD	TCGA-CM-6168-01	exon_skip_122681	64410987	64411053	64410999	64410999	Nonsense_Mutation	G	T	p.E138X
ESCA	TCGA-L5-A4OI-01	exon_skip_122690	64423886	64424091	64424092	64424092	Splice_Site	G	A	.
ESCA	TCGA-L5-A4OI-01	exon_skip_122690	64423886	64424091	64424092	64424092	Splice_Site	G	A	e11+1

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons	Mutation description
	Sample: TCGA-L5-A4OI-01
	Cancer type: ESCA
	ESID: exon_skip_122690
	Skipped exon start: 64423886
	Skipped exon end: 64424091
	Mutation start: 64424092
	Mutation end: 64424092
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: A
	AAchange: .
	Sample: TCGA-L5-A4OI-01
	Cancer type: ESCA
	ESID: exon_skip_122690
	Skipped exon start: 64423886
	Skipped exon end: 64424091
	Mutation start: 64424092
	Mutation end: 64424092
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: A
	AAchange: e11+1
exon_skip_112640_ESCA_TCGA-L5-A4OI-01.png
exon_skip_112965_ESCA_TCGA-L5-A4OI-01.png
exon_skip_122690_ESCA_TCGA-L5-A4OI-01.png
exon_skip_129706_ESCA_TCGA-L5-A4OI-01.png
exon_skip_135696_ESCA_TCGA-L5-A4OI-01.png
exon_skip_135704_ESCA_TCGA-L5-A4OI-01.png
exon_skip_135820_ESCA_TCGA-L5-A4OI-01.png
exon_skip_147024_ESCA_TCGA-L5-A4OI-01.png
exon_skip_149455_ESCA_TCGA-L5-A4OI-01.png
exon_skip_307491_ESCA_TCGA-L5-A4OI-01.png
exon_skip_308211_ESCA_TCGA-L5-A4OI-01.png
exon_skip_308974_ESCA_TCGA-L5-A4OI-01.png
exon_skip_309972_ESCA_TCGA-L5-A4OI-01.png
exon_skip_311841_ESCA_TCGA-L5-A4OI-01.png
exon_skip_328488_ESCA_TCGA-L5-A4OI-01.png
exon_skip_349475_ESCA_TCGA-L5-A4OI-01.png
exon_skip_352933_ESCA_TCGA-L5-A4OI-01.png
exon_skip_374468_ESCA_TCGA-L5-A4OI-01.png
exon_skip_374469_ESCA_TCGA-L5-A4OI-01.png
exon_skip_386802_ESCA_TCGA-L5-A4OI-01.png
exon_skip_423582_ESCA_TCGA-L5-A4OI-01.png
exon_skip_428975_ESCA_TCGA-L5-A4OI-01.png
exon_skip_434375_ESCA_TCGA-L5-A4OI-01.png
exon_skip_439047_ESCA_TCGA-L5-A4OI-01.png
exon_skip_439048_ESCA_TCGA-L5-A4OI-01.png
exon_skip_441654_ESCA_TCGA-L5-A4OI-01.png
exon_skip_443160_ESCA_TCGA-L5-A4OI-01.png
exon_skip_443161_ESCA_TCGA-L5-A4OI-01.png
exon_skip_457940_ESCA_TCGA-L5-A4OI-01.png
exon_skip_461524_ESCA_TCGA-L5-A4OI-01.png
exon_skip_470470_ESCA_TCGA-L5-A4OI-01.png
exon_skip_470694_ESCA_TCGA-L5-A4OI-01.png
exon_skip_474097_ESCA_TCGA-L5-A4OI-01.png
exon_skip_477308_ESCA_TCGA-L5-A4OI-01.png
exon_skip_487634_ESCA_TCGA-L5-A4OI-01.png
exon_skip_495456_ESCA_TCGA-L5-A4OI-01.png
exon_skip_502537_ESCA_TCGA-L5-A4OI-01.png
exon_skip_506535_ESCA_TCGA-L5-A4OI-01.png
exon_skip_55351_ESCA_TCGA-L5-A4OI-01.png
exon_skip_77217_ESCA_TCGA-L5-A4OI-01.png
exon_skip_91288_ESCA_TCGA-L5-A4OI-01.png

- 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
VMRCRCZ_KIDNEY	64423886	64424091	64423993	64423994	Frame_Shift_Ins	-	A	p.E375fs
HEC108_ENDOMETRIUM	64404772	64404883	64404881	64404881	Missense_Mutation	C	T	p.A90V
EN_ENDOMETRIUM	64423886	64424091	64423954	64423954	Missense_Mutation	G	A	p.A362T
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64423886	64424091	64424080	64424080	Missense_Mutation	G	A	p.A404T
SNU175_LARGE_INTESTINE	64426863	64427006	64426897	64426897	Missense_Mutation	G	A	p.R419H
RERFGC1B_STOMACH	64426863	64427006	64427004	64427004	Missense_Mutation	G	A	p.E455K
8305C_THYROID	64426863	64427006	64427004	64427004	Missense_Mutation	G	A	p.E455K
L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	64428529	64428609	64428565	64428565	Missense_Mutation	G	A	p.E468K
SNU1040_LARGE_INTESTINE	64428529	64428609	64428565	64428565	Missense_Mutation	G	A	p.E468K
IM95_STOMACH	64428529	64428609	64428600	64428600	Missense_Mutation	A	G	p.I479M
HEC251_ENDOMETRIUM	64404772	64404883	64404847	64404847	Nonsense_Mutation	G	T	p.E79*

Top

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SNX1

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
exon_skip_122689	15	64415701:64415745:64418277:64418419:64419372:64419451	64418277:64418419	ENST00000353874.4,ENST00000559844.1,ENST00000261889.5,ENST00000561026.1,ENST00000380285.3	KIRC	rs1130603	chr15:64418397	G/A	5.63e-04
exon_skip_122689	15	64415701:64415745:64418277:64418419:64419372:64419451	64418277:64418419	ENST00000353874.4,ENST00000559844.1,ENST00000261889.5,ENST00000561026.1,ENST00000380285.3	STAD	rs1130603	chr15:64418397	G/A	2.15e-04
exon_skip_122680	15	64404771:64404883:64418277:64418419:64419372:64419451	64418277:64418419	ENST00000560260.1	KIRC	rs1130603	chr15:64418397	G/A	5.63e-04
exon_skip_122680	15	64404771:64404883:64418277:64418419:64419372:64419451	64418277:64418419	ENST00000560260.1	STAD	rs1130603	chr15:64418397	G/A	2.15e-04

Top

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SNX1

Top

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SNX1

Top

RelatedDrugs for SNX1

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

Top

RelatedDiseases for SNX1

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

Home

Download

Statistics

Landscape

Help

Contact