ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ARVCF

Gene summary

Gene information	Gene symbol	ARVCF
	Gene ID	421
	Gene name	ARVCF, delta catenin family member
	Synonyms	-
	Cytomap	22q11.21
	Type of gene	protein-coding
	Description	armadillo repeat protein deleted in velo-cardio-facial syndromearmadillo repeat gene deleted in velocardiofacial syndrome
	Modification date	20180523
	UniProtAcc	O00192
	Context	PubMed: ARVCF [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 ARVCF 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 ARVCF

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 ARVCF

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_367534	22	19957420:19958266:19958738:19958858:19959408:19959494	19958738:19958858	ENSG00000099889.9	ENST00000263207.3,ENST00000344269.3
exon_skip_367536	22	19959408:19959494:19959880:19959934:19960259:19960346	19959880:19959934	ENSG00000099889.9	ENST00000406522.1,ENST00000263207.3,ENST00000344269.3,ENST00000406259.1,ENST00000495096.1,ENST00000401994.1
exon_skip_367537	22	19960447:19960559:19960641:19960840:19961165:19961316	19960641:19960840	ENSG00000099889.9	ENST00000406522.1,ENST00000263207.3,ENST00000344269.3,ENST00000406259.1,ENST00000495096.1,ENST00000401994.1
exon_skip_367541	22	19960684:19960840:19961165:19961316:19961634:19961762	19961165:19961316	ENSG00000099889.9	ENST00000406522.1,ENST00000263207.3,ENST00000344269.3,ENST00000406259.1,ENST00000495096.1,ENST00000401994.1,ENST00000480792.1
exon_skip_367542	22	19961165:19961316:19961634:19961762:19963208:19963280	19961634:19961762	ENSG00000099889.9	ENST00000406522.1,ENST00000263207.3,ENST00000344269.3,ENST00000406259.1,ENST00000495096.1,ENST00000401994.1
exon_skip_367550	22	19963208:19963280:19964228:19964246:19964937:19965109	19964228:19964246	ENSG00000099889.9	ENST00000263207.3,ENST00000344269.3,ENST00000401994.1
exon_skip_367558	22	19966419:19966603:19967265:19967765:19968733:19969260	19967265:19967765	ENSG00000099889.9	ENST00000406522.1,ENST00000263207.3,ENST00000344269.3,ENST00000406259.1,ENST00000401994.1
exon_skip_367567	22	19969513:19969614:19974173:19974206:19974595:19974616	19974173:19974206	ENSG00000099889.9	ENST00000492625.1
exon_skip_367568	22	19969513:19969614:19978107:19978335:19997977:19998031	19978107:19978335	ENSG00000099889.9	ENST00000263207.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ARVCF

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_367534	22	19957420:19958266:19958738:19958858:19959408:19959494	19958738:19958858	ENSG00000099889.9	ENST00000263207.3,ENST00000344269.3
exon_skip_367536	22	19959408:19959494:19959880:19959934:19960259:19960346	19959880:19959934	ENSG00000099889.9	ENST00000263207.3,ENST00000495096.1,ENST00000344269.3,ENST00000401994.1,ENST00000406522.1,ENST00000406259.1
exon_skip_367537	22	19960447:19960559:19960641:19960840:19961165:19961316	19960641:19960840	ENSG00000099889.9	ENST00000263207.3,ENST00000495096.1,ENST00000344269.3,ENST00000401994.1,ENST00000406522.1,ENST00000406259.1
exon_skip_367541	22	19960684:19960840:19961165:19961316:19961634:19961762	19961165:19961316	ENSG00000099889.9	ENST00000263207.3,ENST00000495096.1,ENST00000344269.3,ENST00000401994.1,ENST00000406522.1,ENST00000406259.1,ENST00000480792.1
exon_skip_367542	22	19961165:19961316:19961634:19961762:19963208:19963280	19961634:19961762	ENSG00000099889.9	ENST00000263207.3,ENST00000495096.1,ENST00000344269.3,ENST00000401994.1,ENST00000406522.1,ENST00000406259.1
exon_skip_367543	22	19961165:19961316:19961634:19961801:19963208:19963280	19961634:19961801	ENSG00000099889.9	ENST00000480792.1
exon_skip_367550	22	19963208:19963280:19964228:19964246:19964937:19965109	19964228:19964246	ENSG00000099889.9	ENST00000263207.3,ENST00000344269.3,ENST00000401994.1
exon_skip_367558	22	19966419:19966603:19967265:19967765:19968733:19969260	19967265:19967765	ENSG00000099889.9	ENST00000263207.3,ENST00000344269.3,ENST00000401994.1,ENST00000406522.1,ENST00000406259.1
exon_skip_367567	22	19969513:19969614:19974173:19974206:19974595:19974616	19974173:19974206	ENSG00000099889.9	ENST00000492625.1
exon_skip_367568	22	19969513:19969614:19978107:19978335:19997977:19998031	19978107:19978335	ENSG00000099889.9	ENST00000263207.3

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 ARVCF

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
ENST00000263207	19978107	19978335	3UTR-3CDS
ENST00000263207	19958738	19958858	5CDS-5UTR
ENST00000263207	19960641	19960840	Frame-shift
ENST00000263207	19961165	19961316	Frame-shift
ENST00000263207	19961634	19961762	Frame-shift
ENST00000263207	19967265	19967765	Frame-shift
ENST00000263207	19959880	19959934	In-frame
ENST00000263207	19964228	19964246	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
ENST00000263207	19978107	19978335	3UTR-3CDS
ENST00000263207	19958738	19958858	5CDS-5UTR
ENST00000263207	19960641	19960840	Frame-shift
ENST00000263207	19961165	19961316	Frame-shift
ENST00000263207	19961634	19961762	Frame-shift
ENST00000263207	19967265	19967765	Frame-shift
ENST00000263207	19959880	19959934	In-frame
ENST00000263207	19964228	19964246	In-frame

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

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
ENST00000263207	4058	962	19959880	19959934	2934	2987	880	898

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
ENST00000263207	4058	962	19959880	19959934	2934	2987	880	898

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
O00192	880	898	1	962	Chain	ID=PRO_0000064294;Note=Armadillo repeat protein deleted in velo-cardio-facial syndrome

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
O00192	880	898	1	962	Chain	ID=PRO_0000064294;Note=Armadillo repeat protein deleted in velo-cardio-facial syndrome

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SNVs in the skipped exons for ARVCF

- 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
HNSC	TCGA-CV-6955-01	exon_skip_367534	19958739	19958858	19958829	19958829	Frame_Shift_Del	G	-	p.P937fs
LIHC	TCGA-DD-A1EG-01	exon_skip_367536	19959881	19959934	19959886	19959886	Frame_Shift_Del	C	-	p.G897fs
LIHC	TCGA-DD-AAVP-01	exon_skip_367537	19960642	19960840	19960689	19960692	Frame_Shift_Del	GAGC	-	p.797_798del
ESCA	TCGA-2H-A9GI-01	exon_skip_367537	19960642	19960840	19960775	19960775	Frame_Shift_Del	C	-	p.A769fs
LIHC	TCGA-DD-A3A1-01	exon_skip_367558	19967266	19967765	19967501	19967501	Frame_Shift_Del	A	-	p.F387fs
LIHC	TCGA-DD-A3A0-01	exon_skip_367558	19967266	19967765	19967543	19967543	Frame_Shift_Del	G	-	p.P373fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_367568	19978108	19978335	19978203	19978203	Frame_Shift_Del	G	-	p.L39fs

- 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
CW2_LARGE_INTESTINE	19960642	19960840	19960775	19960775	Frame_Shift_Del	C	-	p.A769fs
BICR18_UPPER_AERODIGESTIVE_TRACT	19978108	19978335	19978154	19978155	In_Frame_Ins	-	CCA	p.54_55insV
SNU1_STOMACH	19958739	19958858	19958789	19958789	Missense_Mutation	C	A	p.G951W
JHUEM1_ENDOMETRIUM	19958739	19958858	19958812	19958812	Missense_Mutation	G	A	p.A943V
KM12_LARGE_INTESTINE	19958739	19958858	19958848	19958848	Missense_Mutation	C	T	p.S931N
22RV1_PROSTATE	19959881	19959934	19959914	19959914	Missense_Mutation	G	A	p.R888W
SNU1272_KIDNEY	19959881	19959934	19959918	19959919	Missense_Mutation	GC	AA	p.G886V
SNU1272_KIDNEY	19959881	19959934	19959919	19959919	Missense_Mutation	C	A	p.G886V
SNU407_LARGE_INTESTINE	19960642	19960840	19960681	19960681	Missense_Mutation	G	T	p.A800E
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19960642	19960840	19960699	19960699	Missense_Mutation	G	A	p.A794V
HEC108_ENDOMETRIUM	19960642	19960840	19960700	19960700	Missense_Mutation	C	T	p.A794T
MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19960642	19960840	19960702	19960702	Missense_Mutation	T	C	p.N793S
KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19960642	19960840	19960715	19960715	Missense_Mutation	C	T	p.D789N
MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19960642	19960840	19960723	19960723	Missense_Mutation	A	G	p.I786T
TE8_OESOPHAGUS	19960642	19960840	19960771	19960771	Missense_Mutation	C	A	p.C770F
SNUC1_LARGE_INTESTINE	19961166	19961316	19961240	19961240	Missense_Mutation	G	C	p.T722S
PLCPRF5_LIVER	19961166	19961316	19961277	19961277	Missense_Mutation	C	A	p.G710W
MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19961166	19961316	19961279	19961279	Missense_Mutation	C	T	p.R709H
IHH4_THYROID	19961166	19961316	19961289	19961289	Missense_Mutation	G	A	p.R706C
HEC108_ENDOMETRIUM	19961166	19961316	19961291	19961291	Missense_Mutation	A	G	p.V705A
SKUT1_SOFT_TISSUE	19961166	19961316	19961291	19961291	Missense_Mutation	A	G	p.V705A
SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19961166	19961316	19961309	19961309	Missense_Mutation	G	A	p.T699M
SW48_LARGE_INTESTINE	19961635	19961762	19961646	19961646	Missense_Mutation	C	T	p.G693S
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19961635	19961762	19961646	19961646	Missense_Mutation	C	A	p.G693C
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19961635	19961762	19961678	19961678	Missense_Mutation	G	A	p.A682V
SNUC5_LARGE_INTESTINE	19961635	19961762	19961735	19961735	Missense_Mutation	A	G	p.V663A
COV644_OVARY	19961635	19961762	19961741	19961741	Missense_Mutation	G	T	p.P661H
NCIH650_LUNG	19967266	19967765	19967344	19967344	Missense_Mutation	G	A	p.R440W
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19967266	19967765	19967350	19967350	Missense_Mutation	C	T	p.A438T
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19967266	19967765	19967388	19967388	Missense_Mutation	C	T	p.R425H
TGBC11TKB_STOMACH	19967266	19967765	19967389	19967389	Missense_Mutation	G	A	p.R425C
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19967266	19967765	19967424	19967424	Missense_Mutation	C	T	p.R413Q
ACCMESO1_PLEURA	19967266	19967765	19967473	19967473	Missense_Mutation	G	A	p.R397W
RL952_ENDOMETRIUM	19967266	19967765	19967508	19967508	Missense_Mutation	A	G	p.L385P
MKN74_STOMACH	19967266	19967765	19967524	19967524	Missense_Mutation	C	T	p.A380T
SUIT2_PANCREAS	19967266	19967765	19967544	19967544	Missense_Mutation	G	A	p.P373L
EFO27_OVARY	19967266	19967765	19967564	19967564	Missense_Mutation	C	T	p.M366I
HEC108_ENDOMETRIUM	19967266	19967765	19967568	19967568	Missense_Mutation	G	A	p.A365V
DMS273_LUNG	19967266	19967765	19967589	19967589	Missense_Mutation	G	A	p.P358L
M00921_SKIN	19967266	19967765	19967601	19967601	Missense_Mutation	C	T	p.R354H
SKMEL28_SKIN	19967266	19967765	19967631	19967631	Missense_Mutation	G	A	p.P344L
SNU407_LARGE_INTESTINE	19967266	19967765	19967734	19967734	Missense_Mutation	C	T	p.E310K
HSC39_STOMACH	19967266	19967765	19967758	19967758	Missense_Mutation	C	T	p.E302K
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19978108	19978335	19978212	19978212	Missense_Mutation	G	A	p.H36Y
SNU245_BILIARY_TRACT	19978108	19978335	19978215	19978215	Missense_Mutation	G	A	p.R35C
HEC1A_ENDOMETRIUM	19978108	19978335	19978217	19978217	Missense_Mutation	C	A	p.R34L
HEC1_ENDOMETRIUM	19978108	19978335	19978217	19978217	Missense_Mutation	C	A	p.R34L
HEC1B_ENDOMETRIUM	19978108	19978335	19978217	19978217	Missense_Mutation	C	A	p.R34L

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

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 ARVCF

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

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RelatedDrugs for ARVCF

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 ARVCF

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
ARVCF	C0036341	Schizophrenia	4	PSYGENET
ARVCF	C0809983	Schizophrenia and related disorders	1	PSYGENET

	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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