ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ARHGEF10L

Gene summary

Gene information	Gene symbol	ARHGEF10L
	Gene ID	55160
	Gene name	Rho guanine nucleotide exchange factor 10 like
	Synonyms	GrinchGEF
	Cytomap	1p36.13
	Type of gene	protein-coding
	Description	rho guanine nucleotide exchange factor 10-like proteinRho guanine nucleotide exchange factor (GEF) 10-like
	Modification date	20180523
	UniProtAcc	Q9HCE6
	Context	PubMed: ARHGEF10L [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 ARHGEF10L 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 ARHGEF10L

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 ARHGEF10L

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_2071	1	17930005:17930086:17934296:17934472:17942588:17942697	17934296:17934472	ENSG00000074964.12	ENST00000375415.1,ENST00000375420.3,ENST00000452522.1
exon_skip_2075	1	17934296:17934472:17939552:17939669:17942588:17942697	17939552:17939669	ENSG00000074964.12	ENST00000361221.3,ENST00000434513.1
exon_skip_2076	1	17934296:17934472:17942588:17942697:17945833:17945940	17942588:17942697	ENSG00000074964.12	ENST00000375415.1,ENST00000375420.3,ENST00000452522.1
exon_skip_2079	1	17942588:17942697:17945833:17945940:17948358:17948436	17945833:17945940	ENSG00000074964.12	ENST00000361221.3,ENST00000469726.1,ENST00000375415.1,ENST00000375420.3,ENST00000434513.1,ENST00000452522.1
exon_skip_2080	1	17945833:17945940:17948358:17948436:17949490:17949670	17948358:17948436	ENSG00000074964.12	ENST00000361221.3,ENST00000469726.1,ENST00000375415.1,ENST00000375408.3,ENST00000375420.3,ENST00000434513.1,ENST00000167825.4,ENST00000452522.1
exon_skip_2083	1	17949490:17949670:17950881:17950998:17952450:17952543	17950881:17950998	ENSG00000074964.12	ENST00000361221.3,ENST00000469726.1,ENST00000375415.1,ENST00000375408.3,ENST00000375420.3,ENST00000434513.1,ENST00000452522.1
exon_skip_2089	1	17950881:17950998:17952450:17952543:17953824:17953998	17952450:17952543	ENSG00000074964.12	ENST00000361221.3,ENST00000469726.1,ENST00000375415.1,ENST00000375408.3,ENST00000375420.3,ENST00000434513.1,ENST00000452522.1
exon_skip_2091	1	17958815:17958961:17961042:17961057:17961329:17961511	17961042:17961057	ENSG00000074964.12	ENST00000361221.3,ENST00000375415.1,ENST00000375420.3,ENST00000452522.1
exon_skip_2092	1	17958815:17958961:17961329:17961511:17964382:17964498	17961329:17961511	ENSG00000074964.12	ENST00000469726.1,ENST00000375408.3,ENST00000434513.1,ENST00000475356.1,ENST00000167825.4
exon_skip_2094	1	17961329:17961511:17964382:17964498:17965056:17965184	17964382:17964498	ENSG00000074964.12	ENST00000361221.3,ENST00000469726.1,ENST00000375415.1,ENST00000375408.3,ENST00000375420.3,ENST00000434513.1,ENST00000475356.1,ENST00000167825.4,ENST00000452522.1
exon_skip_2106	1	17966696:17966797:17975048:17975170:17981130:17981160	17975048:17975170	ENSG00000074964.12	ENST00000361221.3,ENST00000469726.1,ENST00000375415.1,ENST00000375408.3,ENST00000466782.1,ENST00000434513.1,ENST00000475356.1,ENST00000167825.4,ENST00000452522.1
exon_skip_2108	1	17975048:17975170:17981130:17981217:17982373:17982597	17981130:17981217	ENSG00000074964.12	ENST00000361221.3,ENST00000469726.1,ENST00000375415.1,ENST00000375408.3,ENST00000434513.1,ENST00000475356.1,ENST00000167825.4,ENST00000452522.1
exon_skip_2109	1	17983048:17983203:17990941:17991090:18014067:18014242	17990941:17991090	ENSG00000074964.12	ENST00000361221.3,ENST00000469726.1,ENST00000375415.1,ENST00000375408.3,ENST00000434513.1,ENST00000475356.1,ENST00000167825.4,ENST00000452522.1
exon_skip_2113	1	18014067:18014242:18017614:18017687:18021652:18021775	18017614:18017687	ENSG00000074964.12	ENST00000475356.1
exon_skip_2123	1	18014067:18014242:18021652:18021775:18023342:18024144	18021652:18021775	ENSG00000074964.12	ENST00000361221.3,ENST00000469726.1,ENST00000375415.1,ENST00000375408.3,ENST00000167825.4,ENST00000452522.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ARHGEF10L

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_2071	1	17930005:17930086:17934296:17934472:17942588:17942697	17934296:17934472	ENSG00000074964.12	ENST00000452522.1,ENST00000375415.1,ENST00000375420.3
exon_skip_2075	1	17934296:17934472:17939552:17939669:17942588:17942697	17939552:17939669	ENSG00000074964.12	ENST00000361221.3,ENST00000434513.1
exon_skip_2076	1	17934296:17934472:17942588:17942697:17945833:17945940	17942588:17942697	ENSG00000074964.12	ENST00000452522.1,ENST00000375415.1,ENST00000375420.3
exon_skip_2079	1	17942588:17942697:17945833:17945940:17948358:17948436	17945833:17945940	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000434513.1,ENST00000375415.1,ENST00000375420.3,ENST00000469726.1
exon_skip_2080	1	17945833:17945940:17948358:17948436:17949490:17949670	17948358:17948436	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000434513.1,ENST00000375415.1,ENST00000375420.3,ENST00000469726.1,ENST00000375408.3,ENST00000167825.4
exon_skip_2083	1	17949490:17949670:17950881:17950998:17952450:17952543	17950881:17950998	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000434513.1,ENST00000375415.1,ENST00000375420.3,ENST00000469726.1,ENST00000375408.3
exon_skip_2089	1	17950881:17950998:17952450:17952543:17953824:17953998	17952450:17952543	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000434513.1,ENST00000375415.1,ENST00000375420.3,ENST00000469726.1,ENST00000375408.3
exon_skip_2091	1	17958815:17958961:17961042:17961057:17961329:17961511	17961042:17961057	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000375415.1,ENST00000375420.3
exon_skip_2092	1	17958815:17958961:17961329:17961511:17964382:17964498	17961329:17961511	ENSG00000074964.12	ENST00000434513.1,ENST00000469726.1,ENST00000375408.3,ENST00000167825.4,ENST00000475356.1
exon_skip_2094	1	17961329:17961511:17964382:17964498:17965056:17965184	17964382:17964498	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000434513.1,ENST00000375415.1,ENST00000375420.3,ENST00000469726.1,ENST00000375408.3,ENST00000167825.4,ENST00000475356.1
exon_skip_2106	1	17966696:17966797:17975048:17975170:17981130:17981160	17975048:17975170	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000434513.1,ENST00000375415.1,ENST00000469726.1,ENST00000375408.3,ENST00000167825.4,ENST00000475356.1,ENST00000466782.1
exon_skip_2108	1	17975048:17975170:17981130:17981217:17982373:17982597	17981130:17981217	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000434513.1,ENST00000375415.1,ENST00000469726.1,ENST00000375408.3,ENST00000167825.4,ENST00000475356.1
exon_skip_2109	1	17983048:17983203:17990941:17991090:18014067:18014242	17990941:17991090	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000434513.1,ENST00000375415.1,ENST00000469726.1,ENST00000375408.3,ENST00000167825.4,ENST00000475356.1
exon_skip_2113	1	18014067:18014242:18017614:18017687:18021652:18021775	18017614:18017687	ENSG00000074964.12	ENST00000475356.1
exon_skip_2123	1	18014067:18014242:18021652:18021775:18023342:18024144	18021652:18021775	ENSG00000074964.12	ENST00000361221.3,ENST00000452522.1,ENST00000375415.1,ENST00000469726.1,ENST00000375408.3,ENST00000167825.4

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 ARHGEF10L

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
ENST00000361221	17945833	17945940	Frame-shift
ENST00000361221	17964382	17964498	Frame-shift
ENST00000361221	17975048	17975170	Frame-shift
ENST00000361221	17990941	17991090	Frame-shift
ENST00000361221	17939552	17939669	In-frame
ENST00000361221	17948358	17948436	In-frame
ENST00000361221	17950881	17950998	In-frame
ENST00000361221	17952450	17952543	In-frame
ENST00000361221	17961042	17961057	In-frame
ENST00000361221	17981130	17981217	In-frame
ENST00000361221	18021652	18021775	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
ENST00000361221	17945833	17945940	Frame-shift
ENST00000361221	17964382	17964498	Frame-shift
ENST00000361221	17975048	17975170	Frame-shift
ENST00000361221	17990941	17991090	Frame-shift
ENST00000361221	17939552	17939669	In-frame
ENST00000361221	17948358	17948436	In-frame
ENST00000361221	17950881	17950998	In-frame
ENST00000361221	17952450	17952543	In-frame
ENST00000361221	17961042	17961057	In-frame
ENST00000361221	17981130	17981217	In-frame
ENST00000361221	18021652	18021775	In-frame

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Infer the effects of exon skipping event on protein functional features for ARHGEF10L

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
ENST00000361221	4505	1279	17939552	17939669	769	885	203	242
ENST00000361221	4505	1279	17948358	17948436	1102	1179	314	340
ENST00000361221	4505	1279	17950881	17950998	1360	1476	400	439
ENST00000361221	4505	1279	17952450	17952543	1477	1569	439	470
ENST00000361221	4505	1279	17981130	17981217	2554	2640	798	827
ENST00000361221	4505	1279	18021652	18021775	3344	3466	1061	1102

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
ENST00000361221	4505	1279	17939552	17939669	769	885	203	242
ENST00000361221	4505	1279	17948358	17948436	1102	1179	314	340
ENST00000361221	4505	1279	17950881	17950998	1360	1476	400	439
ENST00000361221	4505	1279	17952450	17952543	1477	1569	439	470
ENST00000361221	4505	1279	17981130	17981217	2554	2640	798	827
ENST00000361221	4505	1279	18021652	18021775	3344	3466	1061	1102

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 ARHGEF10L

- 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-A3A0-01	exon_skip_2075	17939553	17939669	17939625	17939625	Frame_Shift_Del	G	-	p.G229fs
COAD	TCGA-A6-6781-01	exon_skip_2094	17964383	17964498	17964399	17964399	Frame_Shift_Del	C	-	p.G609fs
LIHC	TCGA-DD-A39Y-01	exon_skip_2094	17964383	17964498	17964399	17964399	Frame_Shift_Del	C	-	p.G648fs
LIHC	TCGA-DD-A1EG-01	exon_skip_2106	17975049	17975170	17975103	17975103	Frame_Shift_Del	C	-	p.A776fs
LIHC	TCGA-DD-A3A0-01	exon_skip_2108	17981131	17981217	17981164	17981164	Frame_Shift_Del	C	-	p.P810fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_2109	17990942	17991090	17990992	17990992	Frame_Shift_Del	C	-	p.P971fs
LIHC	TCGA-DD-A39Y-01	exon_skip_2123	18021653	18021775	18021704	18021704	Frame_Shift_Del	G	-	p.W1079fs
STAD	TCGA-BR-6802-01	exon_skip_2089	17952451	17952543	17952451	17952451	Nonsense_Mutation	C	T	p.R440*
STAD	TCGA-BR-6802-01	exon_skip_2089	17952451	17952543	17952451	17952451	Nonsense_Mutation	C	T	p.R440X
BLCA	TCGA-DK-AA75-01	exon_skip_2108	17981131	17981217	17981180	17981180	Nonsense_Mutation	C	G	p.S815*
LUSC	TCGA-56-1622-01	exon_skip_2109	17990942	17991090	17991036	17991036	Nonsense_Mutation	G	A	p.W985*
LUSC	TCGA-60-2710-01	exon_skip_2080	17948359	17948436	17948358	17948358	Splice_Site	G	T	p.V315_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
IM95_STOMACH	17964383	17964498	17964399	17964399	Frame_Shift_Del	C	-	p.G648fs
HEC1A_ENDOMETRIUM	17934297	17934472	17934337	17934338	Frame_Shift_Ins	-	G	p.G159fs
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM	17964383	17964498	17964398	17964399	Frame_Shift_Ins	-	C	p.GP648fs
EN_ENDOMETRIUM	17964383	17964498	17964398	17964399	Frame_Shift_Ins	-	C	p.GP648fs
639V_URINARY_TRACT	17964383	17964498	17964414	17964415	In_Frame_Ins	-	CAGGAGCTG	p.654_654Q>QELQ
JHESOAD1_OESOPHAGUS	17934297	17934472	17934434	17934434	Missense_Mutation	G	A	p.V191I
MEWO_SKIN	17939553	17939669	17939557	17939557	Missense_Mutation	C	T	p.S205F
BICR18_UPPER_AERODIGESTIVE_TRACT	17939553	17939669	17939590	17939590	Missense_Mutation	C	T	p.A216V
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	17939553	17939669	17939590	17939590	Missense_Mutation	C	T	p.A216V
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	17939553	17939669	17939590	17939590	Missense_Mutation	C	T	p.A216V
SNU1040_LARGE_INTESTINE	17939553	17939669	17939661	17939661	Missense_Mutation	G	A	p.D240N
SNGM_ENDOMETRIUM	17942589	17942697	17942610	17942610	Missense_Mutation	G	A	p.A250T
BICR18_UPPER_AERODIGESTIVE_TRACT	17942589	17942697	17942626	17942626	Missense_Mutation	A	G	p.K255R
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	17945834	17945940	17945876	17945876	Missense_Mutation	T	C	p.V293A
SNU1040_LARGE_INTESTINE	17945834	17945940	17945917	17945917	Missense_Mutation	C	T	p.P307S
BC3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	17945834	17945940	17945935	17945935	Missense_Mutation	C	A	p.Q313K
BHY_UPPER_AERODIGESTIVE_TRACT	17948359	17948436	17948432	17948432	Missense_Mutation	T	A	p.L339H
SW684_SOFT_TISSUE	17950882	17950998	17950892	17950892	Missense_Mutation	C	T	p.S404F
SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	17950882	17950998	17950940	17950940	Missense_Mutation	C	A	p.A420D
NCIH630_LARGE_INTESTINE	17950882	17950998	17950945	17950945	Missense_Mutation	T	C	p.S422P
SW684_SOFT_TISSUE	17950882	17950998	17950993	17950993	Missense_Mutation	C	A	p.L438I
ONS76_CENTRAL_NERVOUS_SYSTEM	17952451	17952543	17952487	17952487	Missense_Mutation	T	C	p.Y452H
PCI15A_UPPER_AERODIGESTIVE_TRACT	17961330	17961511	17961336	17961336	Missense_Mutation	G	T	p.Q584H
HCT15_LARGE_INTESTINE	17961330	17961511	17961415	17961415	Missense_Mutation	G	T	p.V611L
SKRC20_KIDNEY	17961330	17961511	17961434	17961434	Missense_Mutation	G	A	p.G617D
HEC265_ENDOMETRIUM	17964383	17964498	17964401	17964401	Missense_Mutation	C	A	p.P649H
JHUEM7_ENDOMETRIUM	17964383	17964498	17964406	17964406	Missense_Mutation	C	T	p.R651C
RHJT_SOFT_TISSUE	17964383	17964498	17964407	17964407	Missense_Mutation	G	A	p.R651H
HEC59_ENDOMETRIUM	17964383	17964498	17964431	17964431	Missense_Mutation	T	C	p.L659P
HCT116_LARGE_INTESTINE	17964383	17964498	17964448	17964448	Missense_Mutation	G	A	p.V665M
SNU119_OVARY	17975049	17975170	17975063	17975063	Missense_Mutation	C	A	p.P763T
MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	17981131	17981217	17981150	17981150	Missense_Mutation	G	A	p.S805N
HEC59_ENDOMETRIUM	17990942	17991090	17990950	17990950	Missense_Mutation	C	A	p.L957M
EFM19_BREAST	17990942	17991090	17990954	17990954	Missense_Mutation	G	C	p.W958S
SF295_CENTRAL_NERVOUS_SYSTEM	17990942	17991090	17990966	17990966	Missense_Mutation	G	A	p.S962N
SCH_STOMACH	17990942	17991090	17990995	17990995	Missense_Mutation	G	A	p.G972R
SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	18021653	18021775	18021748	18021748	Missense_Mutation	C	T	p.R1094W

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARHGEF10L

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 ARHGEF10L

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARHGEF10L

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RelatedDrugs for ARHGEF10L

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 ARHGEF10L

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 ARHGEF10L

Exon skipping events across known transcript of Ensembl for ARHGEF10L from UCSC genome browser

Gene isoform structures and expression levels for ARHGEF10L

Exon skipping events with PSIs in TCGA for ARHGEF10L

Exon skipping events with PSIs in GTEx for ARHGEF10L

Open reading frame (ORF) annotation in the exon skipping event for ARHGEF10L

Infer the effects of exon skipping event on protein functional features for ARHGEF10L

SNVs in the skipped exons for ARHGEF10L

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARHGEF10L

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARHGEF10L

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARHGEF10L

RelatedDrugs for ARHGEF10L

RelatedDiseases for ARHGEF10L