ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ABI1

Gene summary

Gene information	Gene symbol	ABI1
	Gene ID	10006
	Gene name	abl interactor 1
	Synonyms	ABI-1\|ABLBP4\|E3B1\|NAP1BP\|SSH3BP\|SSH3BP1
	Cytomap	10p12.1
	Type of gene	protein-coding
	Description	abl interactor 1Abelson interactor 1Abl-interactor protein 1 longabl-binding protein 4eps8 SH3 domain-binding proteininteractor protein AblBP4nap1 binding proteinspectrin SH3 domain-binding protein 1
	Modification date	20180522
	UniProtAcc	Q8IZP0
	Context	PubMed: ABI1 [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
ABI1	GO:0018108	peptidyl-tyrosine phosphorylation	17101133

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Exon skipping events across known transcript of Ensembl for ABI1 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 ABI1

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 ABI1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_48294	10	27037498:27037674:27040526:27040712:27054146:27054247	27040526:27040712	ENSG00000136754.12	ENST00000536334.1,ENST00000490841.2
exon_skip_48296	10	27040526:27040712:27044583:27044670:27047990:27048164	27044583:27044670	ENSG00000136754.12	ENST00000376142.2,ENST00000376134.3,ENST00000359188.4,ENST00000376160.1,ENST00000355394.4,ENST00000376140.3,ENST00000376139.2
exon_skip_48299	10	27040526:27040712:27044583:27044670:27054146:27054247	27044583:27044670	ENSG00000136754.12	ENST00000376137.4
exon_skip_48302	10	27040526:27040712:27047990:27048164:27054146:27054247	27047990:27048164	ENSG00000136754.12	ENST00000376170.4,ENST00000376166.1
exon_skip_48303	10	27040526:27040712:27047990:27048167:27052808:27052889	27047990:27048167	ENSG00000136754.12	ENST00000346832.5
exon_skip_48305	10	27040526:27040712:27047990:27048167:27054146:27054247	27047990:27048167	ENSG00000136754.12	ENST00000376138.3
exon_skip_48311	10	27044583:27044670:27047990:27048164:27054146:27054247	27047990:27048164	ENSG00000136754.12	ENST00000359188.4,ENST00000376160.1
exon_skip_48312	10	27044583:27044670:27047990:27048167:27052808:27052889	27047990:27048167	ENSG00000136754.12	ENST00000376142.2,ENST00000355394.4
exon_skip_48313	10	27044583:27044670:27047990:27048167:27054146:27054247	27047990:27048167	ENSG00000136754.12	ENST00000376134.3,ENST00000376140.3,ENST00000376139.2
exon_skip_48320	10	27047990:27048167:27052808:27052889:27054146:27054247	27052808:27052889	ENSG00000136754.12	ENST00000376142.2,ENST00000346832.5,ENST00000355394.4
exon_skip_48322	10	27054146:27054247:27057780:27057921:27059173:27059274	27057780:27057921	ENSG00000136754.12	ENST00000376138.3,ENST00000376142.2,ENST00000376134.3,ENST00000359188.4,ENST00000536334.1,ENST00000376160.1,ENST00000490841.2,ENST00000346832.5,ENST00000355394.4,ENST00000376140.3,ENST00000376137.4,ENST00000376170.4,ENST00000376139.2,ENST00000376166.1
exon_skip_48327	10	27059173:27059274:27060003:27060018:27065993:27066170	27060003:27060018	ENSG00000136754.12	ENST00000376138.3,ENST00000376142.2,ENST00000359188.4,ENST00000346832.5,ENST00000376140.3,ENST00000376170.4
exon_skip_48328	10	27059173:27059274:27065993:27066170:27112066:27112219	27065993:27066170	ENSG00000136754.12	ENST00000376160.1,ENST00000376139.2,ENST00000376166.1
exon_skip_48331	10	27065993:27066170:27112066:27112234:27149675:27149792	27112066:27112234	ENSG00000136754.12	ENST00000376138.3,ENST00000376142.2,ENST00000376134.3,ENST00000359188.4,ENST00000536334.1,ENST00000376160.1,ENST00000355394.4,ENST00000376140.3,ENST00000376137.4,ENST00000376139.2,ENST00000376166.1
exon_skip_48334	10	27112066:27112234:27128661:27128712:27149675:27149792	27128661:27128712	ENSG00000136754.12	ENST00000346832.5

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ABI1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_48294	10	27037498:27037674:27040526:27040712:27054146:27054247	27040526:27040712	ENSG00000136754.12	ENST00000536334.1,ENST00000490841.2
exon_skip_48296	10	27040526:27040712:27044583:27044670:27047990:27048164	27044583:27044670	ENSG00000136754.12	ENST00000376142.2,ENST00000359188.4,ENST00000376139.2,ENST00000376160.1,ENST00000355394.4,ENST00000376134.3,ENST00000376140.3
exon_skip_48299	10	27040526:27040712:27044583:27044670:27054146:27054247	27044583:27044670	ENSG00000136754.12	ENST00000376137.4
exon_skip_48302	10	27040526:27040712:27047990:27048164:27054146:27054247	27047990:27048164	ENSG00000136754.12	ENST00000376170.4,ENST00000376166.1
exon_skip_48303	10	27040526:27040712:27047990:27048167:27052808:27052889	27047990:27048167	ENSG00000136754.12	ENST00000346832.5
exon_skip_48305	10	27040526:27040712:27047990:27048167:27054146:27054247	27047990:27048167	ENSG00000136754.12	ENST00000376138.3
exon_skip_48311	10	27044583:27044670:27047990:27048164:27054146:27054247	27047990:27048164	ENSG00000136754.12	ENST00000359188.4,ENST00000376160.1
exon_skip_48312	10	27044583:27044670:27047990:27048167:27052808:27052889	27047990:27048167	ENSG00000136754.12	ENST00000376142.2,ENST00000355394.4
exon_skip_48313	10	27044583:27044670:27047990:27048167:27054146:27054247	27047990:27048167	ENSG00000136754.12	ENST00000376139.2,ENST00000376134.3,ENST00000376140.3
exon_skip_48320	10	27047990:27048167:27052808:27052889:27054146:27054247	27052808:27052889	ENSG00000136754.12	ENST00000376142.2,ENST00000355394.4,ENST00000346832.5
exon_skip_48322	10	27054146:27054247:27057780:27057921:27059173:27059274	27057780:27057921	ENSG00000136754.12	ENST00000376170.4,ENST00000376142.2,ENST00000359188.4,ENST00000376139.2,ENST00000376160.1,ENST00000376166.1,ENST00000376138.3,ENST00000355394.4,ENST00000346832.5,ENST00000376134.3,ENST00000376137.4,ENST00000536334.1,ENST00000490841.2,ENST00000376140.3
exon_skip_48327	10	27059173:27059274:27060003:27060018:27065993:27066170	27060003:27060018	ENSG00000136754.12	ENST00000376170.4,ENST00000376142.2,ENST00000359188.4,ENST00000376138.3,ENST00000346832.5,ENST00000376140.3
exon_skip_48328	10	27059173:27059274:27065993:27066170:27112066:27112219	27065993:27066170	ENSG00000136754.12	ENST00000376139.2,ENST00000376160.1,ENST00000376166.1
exon_skip_48331	10	27065993:27066170:27112066:27112234:27149675:27149792	27112066:27112234	ENSG00000136754.12	ENST00000376142.2,ENST00000359188.4,ENST00000376139.2,ENST00000376160.1,ENST00000376166.1,ENST00000376138.3,ENST00000355394.4,ENST00000376134.3,ENST00000376137.4,ENST00000536334.1,ENST00000376140.3
exon_skip_48334	10	27112066:27112234:27128661:27128712:27149675:27149792	27128661:27128712	ENSG00000136754.12	ENST00000346832.5

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 ABI1

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
ENST00000376142	27044583	27044670	In-frame
ENST00000376142	27047990	27048167	In-frame
ENST00000376142	27052808	27052889	In-frame
ENST00000376142	27057780	27057921	In-frame
ENST00000376142	27060003	27060018	In-frame
ENST00000376142	27112066	27112234	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
ENST00000376142	27044583	27044670	In-frame
ENST00000376142	27047990	27048167	In-frame
ENST00000376142	27052808	27052889	In-frame
ENST00000376142	27057780	27057921	In-frame
ENST00000376142	27060003	27060018	In-frame
ENST00000376142	27112066	27112234	In-frame

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Infer the effects of exon skipping event on protein functional features for ABI1

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
ENST00000376142	3593	508	27112066	27112234	190	357	39	95
ENST00000376142	3593	508	27057780	27057921	651	791	193	239
ENST00000376142	3593	508	27052808	27052889	893	973	273	300
ENST00000376142	3593	508	27047990	27048167	974	1150	300	359
ENST00000376142	3593	508	27044583	27044670	1151	1237	359	388

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
ENST00000376142	3593	508	27112066	27112234	190	357	39	95
ENST00000376142	3593	508	27057780	27057921	651	791	193	239
ENST00000376142	3593	508	27052808	27052889	893	973	273	300
ENST00000376142	3593	508	27047990	27048167	974	1150	300	359
ENST00000376142	3593	508	27044583	27044670	1151	1237	359	388

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 ABI1

- 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.

ABI1_LUAD_exon_skip_48327_psi_boxplot.png
boxplot

ABI1_UCS_exon_skip_48320_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-A39Y-01	exon_skip_48294	27040527	27040712	27040546	27040546	Frame_Shift_Del	G	-	p.P445fs
LIHC	TCGA-DD-A39Y-01	exon_skip_48294	27040527	27040712	27040688	27040688	Frame_Shift_Del	G	-	p.P402fs
UCEC	TCGA-D1-A177-01	exon_skip_48299 exon_skip_48296	27044584	27044670	27044652	27044652	Frame_Shift_Del	G	-	p.P366fs
STAD	TCGA-VQ-A8P2-01	exon_skip_48311 exon_skip_48302	27047991	27048164	27048066	27048066	Nonsense_Mutation	G	A	p.R336*
STAD	TCGA-VQ-A8P2-01	exon_skip_48311 exon_skip_48302	27047991	27048164	27048066	27048066	Nonsense_Mutation	G	A	p.R352X
STAD	TCGA-VQ-A8P2-01	exon_skip_48312 exon_skip_48313 exon_skip_48305 exon_skip_48303	27047991	27048167	27048066	27048066	Nonsense_Mutation	G	A	p.R336*
STAD	TCGA-VQ-A8P2-01	exon_skip_48312 exon_skip_48313 exon_skip_48305 exon_skip_48303	27047991	27048167	27048066	27048066	Nonsense_Mutation	G	A	p.R352X
READ	TCGA-AG-A002-01	exon_skip_48311 exon_skip_48302	27047991	27048164	27048111	27048111	Nonsense_Mutation	G	A	p.R293X
READ	TCGA-AG-A002-01	exon_skip_48312 exon_skip_48313 exon_skip_48305 exon_skip_48303	27047991	27048167	27048111	27048111	Nonsense_Mutation	G	A	p.R293X
STAD	TCGA-BR-4362-01	exon_skip_48328	27065994	27066170	27066140	27066140	Nonsense_Mutation	G	A	p.R106*
STAD	TCGA-BR-4362-01	exon_skip_48328	27065994	27066170	27066140	27066140	Nonsense_Mutation	G	A	p.R123X
UCS	TCGA-ND-A4WC-01	exon_skip_48320	27052809	27052889	27052890	27052890	Splice_Site	C	A	.
LUAD	TCGA-49-6761-01	exon_skip_48327	27060004	27060018	27060003	27060003	Splice_Site	C	A	p.K159_splice

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-49-6761-01
	Cancer type: LUAD
	ESID: exon_skip_48327
	Skipped exon start: 27060004
	Skipped exon end: 27060018
	Mutation start: 27060003
	Mutation end: 27060003
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: A
	AAchange: p.K159_splice
exon_skip_48327_LUAD_TCGA-49-6761-01.png
	Sample: TCGA-ND-A4WC-01
	Cancer type: UCS
	ESID: exon_skip_48320
	Skipped exon start: 27052809
	Skipped exon end: 27052889
	Mutation start: 27052890
	Mutation end: 27052890
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: A
	AAchange: .
exon_skip_149665_UCS_TCGA-ND-A4WC-01.png
exon_skip_299626_UCS_TCGA-ND-A4WC-01.png
exon_skip_344918_UCS_TCGA-ND-A4WC-01.png
exon_skip_360263_UCS_TCGA-ND-A4WC-01.png
exon_skip_382353_UCS_TCGA-ND-A4WC-01.png
exon_skip_385882_UCS_TCGA-ND-A4WC-01.png
exon_skip_443509_UCS_TCGA-ND-A4WC-01.png
exon_skip_45962_UCS_TCGA-ND-A4WC-01.png
exon_skip_48320_UCS_TCGA-ND-A4WC-01.png
exon_skip_484856_UCS_TCGA-ND-A4WC-01.png
exon_skip_59444_UCS_TCGA-ND-A4WC-01.png
	Sample: TCGA-D1-A177-01
	Cancer type: UCEC
	ESID: exon_skip_48296
	Skipped exon start: 27044584
	Skipped exon end: 27044670
	Mutation start: 27044652
	Mutation end: 27044652
	Mutation type: Frame_Shift_Del
	Reference seq: G
	Mutation seq: -
	AAchange: p.P366fs
exon_skip_357723_UCEC_TCGA-D1-A177-01.png
exon_skip_357725_UCEC_TCGA-D1-A177-01.png
exon_skip_473467_UCEC_TCGA-D1-A177-01.png
exon_skip_473471_UCEC_TCGA-D1-A177-01.png
exon_skip_48296_UCEC_TCGA-D1-A177-01.png
exon_skip_48299_UCEC_TCGA-D1-A177-01.png
exon_skip_84515_UCEC_TCGA-D1-A177-01.png
exon_skip_9817_UCEC_TCGA-D1-A177-01.png
	Sample: TCGA-D1-A177-01
	Cancer type: UCEC
	ESID: exon_skip_48296
	Skipped exon start: 27044584
	Skipped exon end: 27044670
	Mutation start: 27044652
	Mutation end: 27044652
	Mutation type: Frame_Shift_Del
	Reference seq: G
	Mutation seq: -
	AAchange: p.P366fs
exon_skip_357723_UCEC_TCGA-D1-A177-01.png
exon_skip_357725_UCEC_TCGA-D1-A177-01.png
exon_skip_473467_UCEC_TCGA-D1-A177-01.png
exon_skip_473471_UCEC_TCGA-D1-A177-01.png
exon_skip_48296_UCEC_TCGA-D1-A177-01.png
exon_skip_48299_UCEC_TCGA-D1-A177-01.png
exon_skip_84515_UCEC_TCGA-D1-A177-01.png
exon_skip_9817_UCEC_TCGA-D1-A177-01.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
LS411N_LARGE_INTESTINE	27044584	27044670	27044586	27044586	Frame_Shift_Del	T	-	p.N388fs
HEC59_ENDOMETRIUM	27044584	27044670	27044652	27044652	Frame_Shift_Del	G	-	p.P368fs
HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	27057781	27057921	27057885	27057885	Frame_Shift_Del	T	-	p.K205fs
JHUEM7_ENDOMETRIUM	27040527	27040712	27040543	27040543	Missense_Mutation	C	A	p.K445N
HCC1954_BREAST	27040527	27040712	27040631	27040631	Missense_Mutation	G	A	p.P416L
HCC1954_MATCHED_NORMAL_TISSUE	27040527	27040712	27040631	27040631	Missense_Mutation	G	A	p.P416L
MKN7_STOMACH	27040527	27040712	27040710	27040710	Missense_Mutation	C	T	p.A390T
SCH_STOMACH	27047991	27048164	27048056	27048056	Missense_Mutation	G	C	p.S338C
SCH_STOMACH	27047991	27048167	27048056	27048056	Missense_Mutation	G	C	p.S338C
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	27047991	27048164	27048102	27048102	Missense_Mutation	A	G	p.S323P
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	27047991	27048167	27048102	27048102	Missense_Mutation	A	G	p.S323P
SW48_LARGE_INTESTINE	27047991	27048164	27048135	27048135	Missense_Mutation	C	T	p.G312S
SW48_LARGE_INTESTINE	27047991	27048167	27048135	27048135	Missense_Mutation	C	T	p.G312S
BICR18_UPPER_AERODIGESTIVE_TRACT	27047991	27048164	27048156	27048156	Missense_Mutation	A	C	p.S305A
BICR18_UPPER_AERODIGESTIVE_TRACT	27047991	27048167	27048156	27048156	Missense_Mutation	A	C	p.S305A
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	27047991	27048164	27048156	27048156	Missense_Mutation	A	C	p.S305A
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	27047991	27048167	27048156	27048156	Missense_Mutation	A	C	p.S305A
S117_SOFT_TISSUE	27047991	27048164	27048156	27048156	Missense_Mutation	A	C	p.S305A
S117_SOFT_TISSUE	27047991	27048167	27048156	27048156	Missense_Mutation	A	C	p.S305A
UMUC3_URINARY_TRACT	27057781	27057921	27057885	27057885	Missense_Mutation	T	G	p.K205N
LNCAPCLONEFGC_PROSTATE	27057781	27057921	27057919	27057919	Missense_Mutation	C	T	p.R194Q
T84_LARGE_INTESTINE	27065994	27066170	27065999	27065999	Missense_Mutation	C	A	p.V153F
SNU407_LARGE_INTESTINE	27065994	27066170	27066017	27066017	Missense_Mutation	C	A	p.D147Y
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	27065994	27066170	27066094	27066094	Missense_Mutation	G	T	p.T121N
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	27065994	27066170	27066139	27066139	Missense_Mutation	C	T	p.R106Q
JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	27112067	27112234	27112231	27112231	Missense_Mutation	T	C	p.T41A

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ABI1

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 ABI1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ABI1

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RelatedDrugs for ABI1

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 ABI1

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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