ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ARMC6

Gene summary

Gene information	Gene symbol	ARMC6
	Gene ID	93436
	Gene name	armadillo repeat containing 6
	Synonyms	R30923_1
	Cytomap	19p13.11
	Type of gene	protein-coding
	Description	armadillo repeat-containing protein 6
	Modification date	20180523
	UniProtAcc	Q6NXE6
	Context	PubMed: ARMC6 [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 ARMC6 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 ARMC6

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 ARMC6

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_304139	19	19144631:19144739:19144939:19145047:19148360:19148516	19144939:19145047	ENSG00000105676.9	ENST00000539985.1
exon_skip_304142	19	19144631:19144739:19144939:19145047:19153519:19153588	19144939:19145047	ENSG00000105676.9	ENST00000535612.1
exon_skip_304143	19	19144631:19144739:19144939:19145047:19153524:19153686	19144939:19145047	ENSG00000105676.9	ENST00000540792.1
exon_skip_304145	19	19144631:19144739:19148360:19148516:19153519:19153588	19148360:19148516	ENSG00000105676.9	ENST00000537263.1
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENSG00000105676.9	ENST00000540707.1
exon_skip_304149	19	19144631:19144739:19153519:19153686:19162430:19162438	19153519:19153686	ENSG00000105676.9	ENST00000545091.1
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENSG00000105676.9	ENST00000538663.1
exon_skip_304163	19	19145009:19145047:19148360:19148516:19153519:19153588	19148360:19148516	ENSG00000105676.9	ENST00000539985.1
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENSG00000105676.9	ENST00000543877.1
exon_skip_304167	19	19145009:19145047:19151498:19151601:19153519:19153686	19151498:19151601	ENSG00000105676.9	ENST00000535758.1
exon_skip_304170	19	19153524:19153686:19154800:19154883:19162430:19162438	19154800:19154883	ENSG00000105676.9	ENST00000537263.1,ENST00000269932.6,ENST00000536098.1,ENST00000392336.3,ENST00000538663.1,ENST00000535612.1,ENST00000535758.1,ENST00000392335.2,ENST00000541898.1,ENST00000540792.1,ENST00000541725.1,ENST00000539985.1
exon_skip_304174	19	19166073:19166205:19166599:19166737:19168224:19168280	19166599:19166737	ENSG00000105676.9	ENST00000269932.6,ENST00000392336.3,ENST00000535612.1,ENST00000392335.2,ENST00000546344.1
exon_skip_304176	19	19166073:19166205:19166599:19166786:19168224:19168280	19166599:19166786	ENSG00000105676.9	ENST00000535795.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ARMC6

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_304139	19	19144631:19144739:19144939:19145047:19148360:19148516	19144939:19145047	ENSG00000105676.9	ENST00000539985.1
exon_skip_304140	19	19144631:19144739:19144939:19145047:19150130:19150223	19144939:19145047	ENSG00000105676.9	ENST00000543877.1
exon_skip_304142	19	19144631:19144739:19144939:19145047:19153519:19153588	19144939:19145047	ENSG00000105676.9	ENST00000535612.1
exon_skip_304143	19	19144631:19144739:19144939:19145047:19153524:19153686	19144939:19145047	ENSG00000105676.9	ENST00000540792.1
exon_skip_304145	19	19144631:19144739:19148360:19148516:19153519:19153588	19148360:19148516	ENSG00000105676.9	ENST00000537263.1
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENSG00000105676.9	ENST00000540707.1
exon_skip_304149	19	19144631:19144739:19153519:19153686:19162430:19162438	19153519:19153686	ENSG00000105676.9	ENST00000545091.1
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENSG00000105676.9	ENST00000538663.1
exon_skip_304163	19	19145009:19145047:19148360:19148516:19153519:19153588	19148360:19148516	ENSG00000105676.9	ENST00000539985.1
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENSG00000105676.9	ENST00000543877.1
exon_skip_304170	19	19153524:19153686:19154800:19154883:19162430:19162438	19154800:19154883	ENSG00000105676.9	ENST00000392335.2,ENST00000535612.1,ENST00000537263.1,ENST00000541725.1,ENST00000269932.6,ENST00000540792.1,ENST00000536098.1,ENST00000541898.1,ENST00000539985.1,ENST00000538663.1,ENST00000392336.3,ENST00000535758.1
exon_skip_304174	19	19166073:19166205:19166599:19166737:19168224:19168280	19166599:19166737	ENSG00000105676.9	ENST00000392335.2,ENST00000535612.1,ENST00000269932.6,ENST00000546344.1,ENST00000392336.3
exon_skip_304176	19	19166073:19166205:19166599:19166786:19168224:19168280	19166599:19166786	ENSG00000105676.9	ENST00000535795.1

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 ARMC6

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
ENST00000535612	19144939	19145047	5CDS-5UTR
ENST00000392336	19154800	19154883	Frame-shift
ENST00000535612	19154800	19154883	Frame-shift
ENST00000392336	19166599	19166737	In-frame
ENST00000535612	19166599	19166737	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
ENST00000535612	19144939	19145047	5CDS-5UTR
ENST00000392336	19154800	19154883	Frame-shift
ENST00000535612	19154800	19154883	Frame-shift
ENST00000392336	19166599	19166737	In-frame
ENST00000535612	19166599	19166737	In-frame

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Infer the effects of exon skipping event on protein functional features for ARMC6

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
ENST00000392336	1883	501	19166599	19166737	1263	1400	385	431
ENST00000535612	2505	501	19166599	19166737	1588	1725	385	431

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
ENST00000392336	1883	501	19166599	19166737	1263	1400	385	431
ENST00000535612	2505	501	19166599	19166737	1588	1725	385	431

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
Q6NXE6	385	431	1	501	Chain	ID=PRO_0000242660;Note=Armadillo repeat-containing protein 6
Q6NXE6	385	431	1	501	Chain	ID=PRO_0000242660;Note=Armadillo repeat-containing protein 6
Q6NXE6	385	431	370	412	Repeat	Note=ARM 4
Q6NXE6	385	431	370	412	Repeat	Note=ARM 4

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
Q6NXE6	385	431	1	501	Chain	ID=PRO_0000242660;Note=Armadillo repeat-containing protein 6
Q6NXE6	385	431	1	501	Chain	ID=PRO_0000242660;Note=Armadillo repeat-containing protein 6
Q6NXE6	385	431	370	412	Repeat	Note=ARM 4
Q6NXE6	385	431	370	412	Repeat	Note=ARM 4

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SNVs in the skipped exons for ARMC6

- 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.

ARMC6_HNSC_exon_skip_304176_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-A3A0-01	exon_skip_304170	19154801	19154883	19154855	19154855	Frame_Shift_Del	C	-	p.S84fs
HNSC	TCGA-CN-6992-01		19166600	19166737	19166617	19166617	Nonsense_Mutation	C	A	p.C391*
HNSC	TCGA-CN-6992-01		19166600	19166786	19166617	19166617	Nonsense_Mutation	C	A	p.C391*

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-CN-6992-01
	Cancer type: HNSC
	ESID:
	Skipped exon start: 19166600
	Skipped exon end: 19166786
	Mutation start: 19166617
	Mutation end: 19166617
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: A
	AAchange: p.C391*
	Sample: TCGA-CN-6992-01
	Cancer type: HNSC
	ESID:
	Skipped exon start: 19166600
	Skipped exon end: 19166737
	Mutation start: 19166617
	Mutation end: 19166617
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: A
	AAchange: p.C391*
exon_skip_304176_HNSC_TCGA-CN-6992-01.png
exon_skip_474679_HNSC_TCGA-CN-6992-01.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
HEC6_ENDOMETRIUM	19153520	19153686	19153540	19153540	Missense_Mutation	G	A	p.C17Y
SNU175_LARGE_INTESTINE	19153520	19153686	19153578	19153579	Missense_Mutation	CG	TA	p.R30Y
SNU175_LARGE_INTESTINE	19153520	19153686	19153578	19153578	Missense_Mutation	C	T	p.R30C
SNU1040_LARGE_INTESTINE	19153520	19153686	19153579	19153579	Missense_Mutation	G	A	p.R30H
SNU175_LARGE_INTESTINE	19153520	19153686	19153579	19153579	Missense_Mutation	G	A	p.R30H
KYSE270_OESOPHAGUS	19153520	19153686	19153611	19153611	Missense_Mutation	C	T	p.R41C
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	19153520	19153686	19153633	19153633	Missense_Mutation	C	T	p.A48V
HEC251_ENDOMETRIUM	19153520	19153686	19153681	19153681	Missense_Mutation	C	T	p.S64L
SW48_LARGE_INTESTINE	19153520	19153686	19153681	19153681	Missense_Mutation	C	T	p.S64L
SNU407_LARGE_INTESTINE	19166600	19166786	19166643	19166643	Missense_Mutation	G	A	p.R400H
SNU407_LARGE_INTESTINE	19166600	19166737	19166643	19166643	Missense_Mutation	G	A	p.R400H
SNU349_KIDNEY	19166600	19166786	19166702	19166702	Missense_Mutation	G	T	p.A420S
SNU349_KIDNEY	19166600	19166737	19166702	19166702	Missense_Mutation	G	T	p.A420S
HEC108_ENDOMETRIUM	19166600	19166786	19166733	19166733	Missense_Mutation	T	G	p.V430G
HEC108_ENDOMETRIUM	19166600	19166737	19166733	19166733	Missense_Mutation	T	G	p.V430G

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARMC6

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_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000543877.1	BRCA	rs12979565	chr19:19150183	C/T	1.92e-04
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000543877.1	BRCA	rs12979565	chr19:19150183	C/T	1.92e-04
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000543877.1	BRCA	rs12979565	chr19:19150183	C/T	3.96e-03
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000543877.1	KIRC	rs12979565	chr19:19150183	C/T	1.07e-03
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000543877.1	KIRC	rs12979565	chr19:19150183	C/T	1.07e-03
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000543877.1	LUSC	rs12979565	chr19:19150183	C/T	2.82e-04
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000543877.1	LUSC	rs12979565	chr19:19150183	C/T	2.83e-04
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000543877.1	THCA	rs12979565	chr19:19150183	C/T	3.66e-03
exon_skip_304166	19	19144939:19145047:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000543877.1	THCA	rs12979565	chr19:19150183	C/T	3.66e-03
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000538663.1	BRCA	rs12979565	chr19:19150183	C/T	1.92e-04
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000538663.1	BRCA	rs12979565	chr19:19150183	C/T	1.92e-04
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000538663.1	BRCA	rs12979565	chr19:19150183	C/T	3.96e-03
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000538663.1	KIRC	rs12979565	chr19:19150183	C/T	1.07e-03
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000538663.1	KIRC	rs12979565	chr19:19150183	C/T	1.07e-03
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000538663.1	LUSC	rs12979565	chr19:19150183	C/T	2.82e-04
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000538663.1	LUSC	rs12979565	chr19:19150183	C/T	2.83e-04
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000538663.1	THCA	rs12979565	chr19:19150183	C/T	3.66e-03
exon_skip_304160	19	19144720:19144822:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000538663.1	THCA	rs12979565	chr19:19150183	C/T	3.66e-03
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000540707.1	BRCA	rs12979565	chr19:19150183	C/T	1.92e-04
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000540707.1	BRCA	rs12979565	chr19:19150183	C/T	1.92e-04
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000540707.1	BRCA	rs12979565	chr19:19150183	C/T	3.96e-03
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000540707.1	KIRC	rs12979565	chr19:19150183	C/T	1.07e-03
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000540707.1	KIRC	rs12979565	chr19:19150183	C/T	1.07e-03
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000540707.1	LUSC	rs12979565	chr19:19150183	C/T	2.82e-04
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000540707.1	LUSC	rs12979565	chr19:19150183	C/T	2.83e-04
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000540707.1	THCA	rs12979565	chr19:19150183	C/T	3.66e-03
exon_skip_304148	19	19144631:19144739:19150130:19150223:19153519:19153588	19150130:19150223	ENST00000540707.1	THCA	rs12979565	chr19:19150183	C/T	3.66e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARMC6

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARMC6

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RelatedDrugs for ARMC6

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 ARMC6

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 ARMC6

Exon skipping events across known transcript of Ensembl for ARMC6 from UCSC genome browser

Gene isoform structures and expression levels for ARMC6

Exon skipping events with PSIs in TCGA for ARMC6

Exon skipping events with PSIs in GTEx for ARMC6

Open reading frame (ORF) annotation in the exon skipping event for ARMC6

Infer the effects of exon skipping event on protein functional features for ARMC6

SNVs in the skipped exons for ARMC6

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARMC6

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARMC6

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARMC6

RelatedDrugs for ARMC6

RelatedDiseases for ARMC6