ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for GBF1

Gene summary

Gene information	Gene symbol	GBF1
	Gene ID	8729
	Gene name	golgi brefeldin A resistant guanine nucleotide exchange factor 1
	Synonyms	ARF1GEF
	Cytomap	10q24.32
	Type of gene	protein-coding
	Description	Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1BFA-resistant GEF 1
	Modification date	20180522
	UniProtAcc	Q92538
	Context	PubMed: GBF1 [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 GBF1 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 GBF1

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 GBF1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_44627	10	104019806:104019873:104103807:104103939:104111012:104111131	104103807:104103939	ENSG00000107862.4	ENST00000369983.3
exon_skip_44629	10	104111599:104111708:104112214:104112275:104113356:104113411	104112214:104112275	ENSG00000107862.4	ENST00000369983.3
exon_skip_44634	10	104118262:104118486:104119026:104119192:104119940:104120152	104119026:104119192	ENSG00000107862.4	ENST00000369983.3
exon_skip_44637	10	104119026:104119192:104119940:104120152:104120778:104120877	104119940:104120152	ENSG00000107862.4	ENST00000369983.3
exon_skip_44639	10	104119940:104120152:104120778:104120877:104121474:104121669	104120778:104120877	ENSG00000107862.4	ENST00000369983.3
exon_skip_44643	10	104122231:104122421:104123012:104123153:104123466:104123555	104123012:104123153	ENSG00000107862.4	ENST00000369983.3
exon_skip_44644	10	104123012:104123153:104123466:104123555:104125153:104125356	104123466:104123555	ENSG00000107862.4	ENST00000369983.3
exon_skip_44645	10	104127234:104127317:104127974:104128211:104128495:104128589	104127974:104128211	ENSG00000107862.4	ENST00000369983.3
exon_skip_44649	10	104127974:104128211:104128495:104128589:104128967:104129144	104128495:104128589	ENSG00000107862.4	ENST00000369983.3
exon_skip_44651	10	104129467:104129532:104129617:104129741:104129930:104130002	104129617:104129741	ENSG00000107862.4	ENST00000369983.3
exon_skip_44654	10	104130463:104130617:104135115:104135341:104136028:104136189	104135115:104135341	ENSG00000107862.4	ENST00000369983.3
exon_skip_44658	10	104139277:104139408:104139609:104139711:104140005:104140119	104139609:104139711	ENSG00000107862.4	ENST00000369983.3
exon_skip_44662	10	104139609:104139711:104140005:104140119:104140262:104140443	104140005:104140119	ENSG00000107862.4	ENST00000369983.3
exon_skip_44667	10	104140262:104140443:104140883:104141012:104141812:104141967	104140883:104141012	ENSG00000107862.4	ENST00000369983.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for GBF1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_44627	10	104019806:104019873:104103807:104103939:104111012:104111131	104103807:104103939	ENSG00000107862.4	ENST00000369983.3
exon_skip_44629	10	104111599:104111708:104112214:104112275:104113356:104113411	104112214:104112275	ENSG00000107862.4	ENST00000369983.3
exon_skip_44634	10	104118262:104118486:104119026:104119192:104119940:104120152	104119026:104119192	ENSG00000107862.4	ENST00000369983.3
exon_skip_44637	10	104119026:104119192:104119940:104120152:104120778:104120877	104119940:104120152	ENSG00000107862.4	ENST00000369983.3
exon_skip_44639	10	104119940:104120152:104120778:104120877:104121474:104121669	104120778:104120877	ENSG00000107862.4	ENST00000369983.3
exon_skip_44643	10	104122231:104122421:104123012:104123153:104123466:104123555	104123012:104123153	ENSG00000107862.4	ENST00000369983.3
exon_skip_44644	10	104123012:104123153:104123466:104123555:104125153:104125356	104123466:104123555	ENSG00000107862.4	ENST00000369983.3
exon_skip_44645	10	104127234:104127317:104127974:104128211:104128495:104128589	104127974:104128211	ENSG00000107862.4	ENST00000369983.3
exon_skip_44649	10	104127974:104128211:104128495:104128589:104128967:104129144	104128495:104128589	ENSG00000107862.4	ENST00000369983.3
exon_skip_44651	10	104129467:104129532:104129617:104129741:104129930:104130002	104129617:104129741	ENSG00000107862.4	ENST00000369983.3
exon_skip_44654	10	104130463:104130617:104135115:104135341:104136028:104136189	104135115:104135341	ENSG00000107862.4	ENST00000369983.3
exon_skip_44658	10	104139277:104139408:104139609:104139711:104140005:104140119	104139609:104139711	ENSG00000107862.4	ENST00000369983.3
exon_skip_44662	10	104139609:104139711:104140005:104140119:104140262:104140443	104140005:104140119	ENSG00000107862.4	ENST00000369983.3
exon_skip_44667	10	104140262:104140443:104140883:104141012:104141812:104141967	104140883:104141012	ENSG00000107862.4	ENST00000369983.3

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 GBF1

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
ENST00000369983	104112214	104112275	Frame-shift
ENST00000369983	104119026	104119192	Frame-shift
ENST00000369983	104119940	104120152	Frame-shift
ENST00000369983	104123466	104123555	Frame-shift
ENST00000369983	104128495	104128589	Frame-shift
ENST00000369983	104129617	104129741	Frame-shift
ENST00000369983	104135115	104135341	Frame-shift
ENST00000369983	104103807	104103939	In-frame
ENST00000369983	104120778	104120877	In-frame
ENST00000369983	104123012	104123153	In-frame
ENST00000369983	104127974	104128211	In-frame
ENST00000369983	104139609	104139711	In-frame
ENST00000369983	104140005	104140119	In-frame
ENST00000369983	104140883	104141012	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
ENST00000369983	104112214	104112275	Frame-shift
ENST00000369983	104119026	104119192	Frame-shift
ENST00000369983	104119940	104120152	Frame-shift
ENST00000369983	104123466	104123555	Frame-shift
ENST00000369983	104128495	104128589	Frame-shift
ENST00000369983	104129617	104129741	Frame-shift
ENST00000369983	104135115	104135341	Frame-shift
ENST00000369983	104103807	104103939	In-frame
ENST00000369983	104120778	104120877	In-frame
ENST00000369983	104123012	104123153	In-frame
ENST00000369983	104127974	104128211	In-frame
ENST00000369983	104139609	104139711	In-frame
ENST00000369983	104140005	104140119	In-frame
ENST00000369983	104140883	104141012	In-frame

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Infer the effects of exon skipping event on protein functional features for GBF1

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
ENST00000369983	6420	1859	104103807	104103939	424	555	54	98
ENST00000369983	6420	1859	104120778	104120877	1650	1748	463	496
ENST00000369983	6420	1859	104123012	104123153	2134	2274	624	671
ENST00000369983	6420	1859	104127974	104128211	2900	3136	880	958
ENST00000369983	6420	1859	104139609	104139711	5034	5135	1591	1625
ENST00000369983	6420	1859	104140005	104140119	5136	5249	1625	1663
ENST00000369983	6420	1859	104140883	104141012	5431	5559	1723	1766

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
ENST00000369983	6420	1859	104103807	104103939	424	555	54	98
ENST00000369983	6420	1859	104120778	104120877	1650	1748	463	496
ENST00000369983	6420	1859	104123012	104123153	2134	2274	624	671
ENST00000369983	6420	1859	104127974	104128211	2900	3136	880	958
ENST00000369983	6420	1859	104139609	104139711	5034	5135	1591	1625
ENST00000369983	6420	1859	104140005	104140119	5136	5249	1625	1663
ENST00000369983	6420	1859	104140883	104141012	5431	5559	1723	1766

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
Q92538	54	98	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	54	98	1	380	Region	Note=Interaction with RAB1B;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17429068;Dbxref=PMID:17429068
Q92538	54	98	1	211	Region	Note=DCB%3B DCB:DCB domain and DCB:HUS domain interaction;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9R1D7
Q92538	463	496	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	624	671	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	624	671	662	662	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q92538	880	958	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	880	958	692	882	Domain	Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00189
Q92538	880	958	886	1370	Region	Note=Phosphatidylinositol-phosphate binding%3B required for translocation to the leading edge and for ARF1 activation upon GPCR signaling;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22573891;Dbxref=PMID:22573891
Q92538	1591	1625	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	1625	1663	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	1723	1766	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	1723	1766	1751	1854	Compositional bias	Note=Pro-rich

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
Q92538	54	98	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	54	98	1	380	Region	Note=Interaction with RAB1B;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17429068;Dbxref=PMID:17429068
Q92538	54	98	1	211	Region	Note=DCB%3B DCB:DCB domain and DCB:HUS domain interaction;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9R1D7
Q92538	463	496	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	624	671	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	624	671	662	662	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q92538	880	958	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	880	958	692	882	Domain	Note=SEC7;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00189
Q92538	880	958	886	1370	Region	Note=Phosphatidylinositol-phosphate binding%3B required for translocation to the leading edge and for ARF1 activation upon GPCR signaling;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22573891;Dbxref=PMID:22573891
Q92538	1591	1625	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	1625	1663	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	1723	1766	1	1859	Chain	ID=PRO_0000120210;Note=Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1
Q92538	1723	1766	1751	1854	Compositional bias	Note=Pro-rich

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SNVs in the skipped exons for GBF1

- 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-DD-A39Y-01	exon_skip_44634	104119027	104119192	104119043	104119043	Frame_Shift_Del	A	-	p.E343fs
KIRP	TCGA-MH-A560-01	exon_skip_44644	104123467	104123555	104123472	104123472	Frame_Shift_Del	A	-	p.D674fs
KIRP	TCGA-MH-A560-01	exon_skip_44644	104123467	104123555	104123472	104123472	Frame_Shift_Del	A	-	p.K674fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_44645	104127975	104128211	104128131	104128131	Frame_Shift_Del	C	-	p.G932fs
LGG	TCGA-DU-6392-01	exon_skip_44639	104120779	104120877	104120794	104120794	Nonsense_Mutation	C	T	p.R469*
THYM	TCGA-4V-A9QQ-01	exon_skip_44639	104120779	104120877	104120794	104120794	Nonsense_Mutation	C	T	p.R470X
ESCA	TCGA-L5-A8NJ-01	exon_skip_44639	104120779	104120877	104120821	104120821	Nonsense_Mutation	C	T	p.R479X
UCEC	TCGA-D1-A174-01	exon_skip_44639	104120779	104120877	104120821	104120821	Nonsense_Mutation	C	T	p.R478*
UCEC	TCGA-B5-A1MY-01	exon_skip_44639	104120779	104120877	104120878	104120878	Splice_Site	G	T	p.E496_splice
CHOL	TCGA-W5-AA34-01	exon_skip_44644	104123467	104123555	104123466	104123466	Splice_Site	G	T	.
BRCA	TCGA-A8-A084-01	exon_skip_44654	104135116	104135341	104135342	104135342	Splice_Site	G	A	e29+1
THCA	TCGA-DJ-A4UT-01	exon_skip_44662	104140006	104140119	104140004	104140004	Splice_Site	A	C	.

- 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
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104123013	104123153	104123150	104123150	Frame_Shift_Del	G	-	p.G671fs
HEC108_ENDOMETRIUM	104103808	104103939	104103838	104103838	Missense_Mutation	T	C	p.L65P
MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104112215	104112275	104112232	104112232	Missense_Mutation	G	A	p.A181T
CHAGOK1_LUNG	104112215	104112275	104112242	104112242	Missense_Mutation	C	T	p.T184I
SNU1_STOMACH	104112215	104112275	104112247	104112247	Missense_Mutation	G	A	p.V186I
NB1_AUTONOMIC_GANGLIA	104119027	104119192	104119047	104119047	Missense_Mutation	G	T	p.K344N
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104119027	104119192	104119145	104119145	Missense_Mutation	A	G	p.Y377C
PK45H_PANCREAS	104119027	104119192	104119157	104119157	Missense_Mutation	G	T	p.R381L
CAL27_UPPER_AERODIGESTIVE_TRACT	104119027	104119192	104119162	104119162	Missense_Mutation	G	A	p.V383M
HS695T_SKIN	104119941	104120152	104120078	104120078	Missense_Mutation	G	A	p.E439K
MET2B	104119941	104120152	104120117	104120117	Missense_Mutation	C	A	p.L452I
NCC010_KIDNEY	104119941	104120152	104120124	104120124	Missense_Mutation	A	T	p.K454M
SKMEL2_SKIN	104120779	104120877	104120816	104120816	Missense_Mutation	C	T	p.S476F
BICR18_UPPER_AERODIGESTIVE_TRACT	104123013	104123153	104123142	104123142	Missense_Mutation	T	G	p.V668G
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104123467	104123555	104123490	104123490	Missense_Mutation	C	T	p.P680S
HCC1171_LUNG	104127975	104128211	104127993	104127993	Missense_Mutation	G	A	p.M886I
KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104127975	104128211	104128022	104128022	Missense_Mutation	A	G	p.E896G
QIMRWIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104127975	104128211	104128046	104128046	Missense_Mutation	T	G	p.L904R
NCIH1105_LUNG	104127975	104128211	104128057	104128057	Missense_Mutation	G	A	p.A908T
OVK18_OVARY	104127975	104128211	104128068	104128068	Missense_Mutation	G	T	p.E911D
639V_URINARY_TRACT	104127975	104128211	104128082	104128082	Missense_Mutation	G	A	p.R916H
GP2D_LARGE_INTESTINE	104127975	104128211	104128100	104128100	Missense_Mutation	A	G	p.Y922C
KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104128496	104128589	104128530	104128530	Missense_Mutation	A	G	p.S971G
BICR18_UPPER_AERODIGESTIVE_TRACT	104129618	104129741	104129732	104129732	Missense_Mutation	G	C	p.E1109D
CORL321_PLEURA	104140884	104141012	104141006	104141006	Missense_Mutation	G	C	p.A1765P
COGAR359_SOFT_TISSUE	104135116	104135341	104135340	104135340	Splice_Site	C	T	p.A1294A

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GBF1

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 GBF1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GBF1

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RelatedDrugs for GBF1

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 GBF1

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 GBF1

Exon skipping events across known transcript of Ensembl for GBF1 from UCSC genome browser

Gene isoform structures and expression levels for GBF1

Exon skipping events with PSIs in TCGA for GBF1

Exon skipping events with PSIs in GTEx for GBF1

Open reading frame (ORF) annotation in the exon skipping event for GBF1

Infer the effects of exon skipping event on protein functional features for GBF1

SNVs in the skipped exons for GBF1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GBF1

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GBF1

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GBF1

RelatedDrugs for GBF1

RelatedDiseases for GBF1