ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for R3HDM2

Gene summary

Gene information	Gene symbol	R3HDM2
	Gene ID	22864
	Gene name	R3H domain containing 2
	Synonyms	CAG6\|PR01365
	Cytomap	12q13.3
	Type of gene	protein-coding
	Description	R3H domain-containing protein 2
	Modification date	20180519
	UniProtAcc	Q9Y2K5
	Context	PubMed: R3HDM2 [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 R3HDM2 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 R3HDM2

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 R3HDM2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_94117	12	57663534:57663777:57666235:57666337:57674140:57674313	57666235:57666337	ENSG00000179912.15	ENST00000441731.2,ENST00000403821.2
exon_skip_94118	12	57677606:57677839:57682639:57682693:57682791:57682823	57682639:57682693	ENSG00000179912.15	ENST00000403821.2,ENST00000347140.3,ENST00000358907.2
exon_skip_94121	12	57677606:57677839:57682791:57682823:57686354:57686450	57682791:57682823	ENSG00000179912.15	ENST00000402412.1,ENST00000429355.2
exon_skip_94122	12	57677606:57677839:57682791:57682823:57689181:57689290	57682791:57682823	ENSG00000179912.15	ENST00000547262.1
exon_skip_94123	12	57677606:57677839:57686354:57686450:57689181:57689290	57686354:57686450	ENSG00000179912.15	ENST00000547019.1
exon_skip_94124	12	57682791:57682823:57686354:57686450:57689181:57689290	57686354:57686450	ENSG00000179912.15	ENST00000402412.1
exon_skip_94127	12	57693877:57693964:57696958:57697000:57704046:57704234	57696958:57697000	ENSG00000179912.15	ENST00000403821.2,ENST00000402412.1,ENST00000551465.1,ENST00000347140.3,ENST00000358907.2
exon_skip_94132	12	57696958:57697000:57704046:57704246:57789531:57789601	57704046:57704246	ENSG00000179912.15	ENST00000402412.1,ENST00000347140.3
exon_skip_94138	12	57704122:57704246:57789531:57789601:57824502:57824573	57789531:57789601	ENSG00000179912.15	ENST00000402412.1,ENST00000347140.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for R3HDM2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_94117	12	57663534:57663777:57666235:57666337:57674140:57674313	57666235:57666337	ENSG00000179912.15	ENST00000441731.2,ENST00000403821.2
exon_skip_94118	12	57677606:57677839:57682639:57682693:57682791:57682823	57682639:57682693	ENSG00000179912.15	ENST00000347140.3,ENST00000358907.2,ENST00000403821.2
exon_skip_94121	12	57677606:57677839:57682791:57682823:57686354:57686450	57682791:57682823	ENSG00000179912.15	ENST00000402412.1,ENST00000429355.2
exon_skip_94122	12	57677606:57677839:57682791:57682823:57689181:57689290	57682791:57682823	ENSG00000179912.15	ENST00000547262.1
exon_skip_94123	12	57677606:57677839:57686354:57686450:57689181:57689290	57686354:57686450	ENSG00000179912.15	ENST00000547019.1
exon_skip_94124	12	57682791:57682823:57686354:57686450:57689181:57689290	57686354:57686450	ENSG00000179912.15	ENST00000402412.1
exon_skip_94127	12	57693877:57693964:57696958:57697000:57704046:57704234	57696958:57697000	ENSG00000179912.15	ENST00000347140.3,ENST00000402412.1,ENST00000358907.2,ENST00000403821.2,ENST00000551465.1
exon_skip_94132	12	57696958:57697000:57704046:57704246:57789531:57789601	57704046:57704246	ENSG00000179912.15	ENST00000347140.3,ENST00000402412.1
exon_skip_94138	12	57704122:57704246:57789531:57789601:57824502:57824573	57789531:57789601	ENSG00000179912.15	ENST00000347140.3,ENST00000402412.1

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 R3HDM2

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
ENST00000347140	57704046	57704246	3UTR-3CDS
ENST00000347140	57789531	57789601	3UTR-3UTR
ENST00000347140	57682639	57682693	In-frame
ENST00000358907	57682639	57682693	In-frame
ENST00000347140	57696958	57697000	In-frame
ENST00000358907	57696958	57697000	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
ENST00000347140	57704046	57704246	3UTR-3CDS
ENST00000347140	57789531	57789601	3UTR-3UTR
ENST00000347140	57682639	57682693	In-frame
ENST00000358907	57682639	57682693	In-frame
ENST00000347140	57696958	57697000	In-frame
ENST00000358907	57696958	57697000	In-frame

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Infer the effects of exon skipping event on protein functional features for R3HDM2

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
ENST00000347140	4348	976	57696958	57697000	557	598	55	69
ENST00000358907	3991	976	57696958	57697000	201	242	55	69
ENST00000347140	4348	976	57682639	57682693	1234	1287	281	298
ENST00000358907	3991	976	57682639	57682693	878	931	281	298

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
ENST00000347140	4348	976	57696958	57697000	557	598	55	69
ENST00000358907	3991	976	57696958	57697000	201	242	55	69
ENST00000347140	4348	976	57682639	57682693	1234	1287	281	298
ENST00000358907	3991	976	57682639	57682693	878	931	281	298

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
Q9Y2K5	55	69	1	339	Alternative sequence	ID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	55	69	1	339	Alternative sequence	ID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	55	69	1	295	Alternative sequence	ID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	55	69	1	295	Alternative sequence	ID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	55	69	1	976	Chain	ID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5	55	69	1	976	Chain	ID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5	281	298	1	339	Alternative sequence	ID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	1	339	Alternative sequence	ID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	1	295	Alternative sequence	ID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	1	295	Alternative sequence	ID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	296	298	Alternative sequence	ID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	296	298	Alternative sequence	ID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	1	976	Chain	ID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5	281	298	1	976	Chain	ID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5	281	298	288	369	Compositional bias	Note=Ser-rich
Q9Y2K5	281	298	288	369	Compositional bias	Note=Ser-rich
Q9Y2K5	281	298	233	310	Domain	Note=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01009
Q9Y2K5	281	298	233	310	Domain	Note=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01009

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
Q9Y2K5	55	69	1	339	Alternative sequence	ID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	55	69	1	339	Alternative sequence	ID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	55	69	1	295	Alternative sequence	ID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	55	69	1	295	Alternative sequence	ID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	55	69	1	976	Chain	ID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5	55	69	1	976	Chain	ID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5	281	298	1	339	Alternative sequence	ID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	1	339	Alternative sequence	ID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	1	295	Alternative sequence	ID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	1	295	Alternative sequence	ID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	296	298	Alternative sequence	ID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	296	298	Alternative sequence	ID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5	281	298	1	976	Chain	ID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5	281	298	1	976	Chain	ID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5	281	298	288	369	Compositional bias	Note=Ser-rich
Q9Y2K5	281	298	288	369	Compositional bias	Note=Ser-rich
Q9Y2K5	281	298	233	310	Domain	Note=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01009
Q9Y2K5	281	298	233	310	Domain	Note=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01009

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SNVs in the skipped exons for R3HDM2

- 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.

R3HDM2_CHOL_exon_skip_94118_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_94124 exon_skip_94123	57686355	57686450	57686381	57686381	Frame_Shift_Del	C	-	p.V294fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_94124 exon_skip_94123	57686355	57686450	57686384	57686384	Frame_Shift_Del	T	-	p.R293fs
LIHC	TCGA-DD-A3A0-01	exon_skip_94132	57704047	57704246	57704095	57704095	Frame_Shift_Del	T	-	p.E40fs
ESCA	TCGA-L5-A4OI-01	exon_skip_94132	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
ESCA	TCGA-L5-A4OI-01	exon_skip_94132	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.L21fs
LIHC	TCGA-DD-A3A0-01	exon_skip_94132	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
CHOL	TCGA-W5-AA39-01	exon_skip_94118	57682640	57682693	57682695	57682711	Splice_Site	TGTTGGTTAACATCAAA	-	.

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-W5-AA39-01
	Cancer type: CHOL
	ESID: exon_skip_94118
	Skipped exon start: 57682640
	Skipped exon end: 57682693
	Mutation start: 57682695
	Mutation end: 57682711
	Mutation type: Splice_Site
	Reference seq: TGTTGGTTAACATCAAA
	Mutation seq: -
	AAchange: .
exon_skip_148507_CHOL_TCGA-W5-AA39-01.png
exon_skip_26206_CHOL_TCGA-W5-AA39-01.png
exon_skip_300665_CHOL_TCGA-W5-AA39-01.png
exon_skip_94118_CHOL_TCGA-W5-AA39-01.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
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57682640	57682693	57682642	57682642	Frame_Shift_Del	A	-	p.F298fs
C33A_CERVIX	57704047	57704246	57704126	57704126	Frame_Shift_Del	T	-	p.N29fs
22RV1_PROSTATE	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
RKO_LARGE_INTESTINE	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
SNGM_ENDOMETRIUM	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
SNU1_STOMACH	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
GP2D_LARGE_INTESTINE	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
GP5D_LARGE_INTESTINE	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
HEC108_ENDOMETRIUM	57704047	57704246	57704152	57704152	Frame_Shift_Del	T	-	p.K20fs
SNU81_LARGE_INTESTINE	57682640	57682693	57682673	57682673	Missense_Mutation	G	T	p.S288Y
KM12_LARGE_INTESTINE	57704047	57704246	57704061	57704061	Missense_Mutation	G	A	p.R51C
NCIH2087_LUNG	57704047	57704246	57704086	57704086	Missense_Mutation	C	G	p.E42D
OSRC2_KIDNEY	57704047	57704246	57704193	57704193	Missense_Mutation	T	A	p.T7S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for R3HDM2

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 R3HDM2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for R3HDM2

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RelatedDrugs for R3HDM2

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 R3HDM2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
R3HDM2	C0023893	Liver Cirrhosis, Experimental	1	CTD_human
R3HDM2	C3495559	Juvenile arthritis	1	CTD_human

	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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