ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SMC5

Gene summary

Gene information	Gene symbol	SMC5
	Gene ID	23137
	Gene name	structural maintenance of chromosomes 5
	Synonyms	SMC5L1
	Cytomap	9q21.12
	Type of gene	protein-coding
	Description	structural maintenance of chromosomes protein 5SMC protein 5SMC-5SMC5 structural maintenance of chromosomes 5-like 1hSMC5
	Modification date	20180519
	UniProtAcc	Q8IY18
	Context	PubMed: SMC5 [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
SMC5	GO:0006974	cellular response to DNA damage stimulus	11408570\|25931565

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Exon skipping events across known transcript of Ensembl for SMC5 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 SMC5

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 SMC5

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_496403	9	72879219:72879361:72882838:72882891:72892225:72892388	72882838:72882891	ENSG00000198887.7	ENST00000361138.5
exon_skip_496406	9	72893406:72893541:72895674:72895815:72897337:72897499	72895674:72895815	ENSG00000198887.7	ENST00000361138.5
exon_skip_496407	9	72897337:72897499:72901115:72901187:72912881:72913137	72901115:72901187	ENSG00000198887.7	ENST00000361138.5
exon_skip_496409	9	72914961:72915116:72920162:72920276:72929657:72929752	72920162:72920276	ENSG00000198887.7	ENST00000361138.5
exon_skip_496411	9	72938936:72939059:72959059:72959185:72961520:72961565	72959059:72959185	ENSG00000198887.7	ENST00000361138.5
exon_skip_496416	9	72959059:72959185:72961520:72961565:72961981:72962077	72961520:72961565	ENSG00000198887.7	ENST00000361138.5
exon_skip_496418	9	72961981:72962077:72962528:72962633:72962834:72962954	72962528:72962633	ENSG00000198887.7	ENST00000471372.1,ENST00000361138.5
exon_skip_496419	9	72962528:72962633:72962834:72962954:72965029:72965209	72962834:72962954	ENSG00000198887.7	ENST00000471372.1,ENST00000361138.5
exon_skip_496421	9	72962834:72962954:72965029:72965209:72965291:72965387	72965029:72965209	ENSG00000198887.7	ENST00000471372.1,ENST00000361138.5
exon_skip_496425	9	72965029:72965209:72965291:72965387:72967106:72967161	72965291:72965387	ENSG00000198887.7	ENST00000471372.1,ENST00000361138.5

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SMC5

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_496403	9	72879219:72879361:72882838:72882891:72892225:72892388	72882838:72882891	ENSG00000198887.7	ENST00000361138.5
exon_skip_496406	9	72893406:72893541:72895674:72895815:72897337:72897499	72895674:72895815	ENSG00000198887.7	ENST00000361138.5
exon_skip_496407	9	72897337:72897499:72901115:72901187:72912881:72913137	72901115:72901187	ENSG00000198887.7	ENST00000361138.5
exon_skip_496409	9	72914961:72915116:72920162:72920276:72929657:72929752	72920162:72920276	ENSG00000198887.7	ENST00000361138.5
exon_skip_496411	9	72938936:72939059:72959059:72959185:72961520:72961565	72959059:72959185	ENSG00000198887.7	ENST00000361138.5
exon_skip_496416	9	72959059:72959185:72961520:72961565:72961981:72962077	72961520:72961565	ENSG00000198887.7	ENST00000361138.5
exon_skip_496418	9	72961981:72962077:72962528:72962633:72962834:72962954	72962528:72962633	ENSG00000198887.7	ENST00000361138.5,ENST00000471372.1
exon_skip_496419	9	72962528:72962633:72962834:72962954:72965029:72965209	72962834:72962954	ENSG00000198887.7	ENST00000361138.5,ENST00000471372.1
exon_skip_496421	9	72962834:72962954:72965029:72965209:72965291:72965387	72965029:72965209	ENSG00000198887.7	ENST00000361138.5,ENST00000471372.1
exon_skip_496425	9	72965029:72965209:72965291:72965387:72967106:72967161	72965291:72965387	ENSG00000198887.7	ENST00000361138.5,ENST00000471372.1

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 SMC5

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
ENST00000361138	72882838	72882891	Frame-shift
ENST00000361138	72895674	72895815	In-frame
ENST00000361138	72901115	72901187	In-frame
ENST00000361138	72920162	72920276	In-frame
ENST00000361138	72959059	72959185	In-frame
ENST00000361138	72961520	72961565	In-frame
ENST00000361138	72962528	72962633	In-frame
ENST00000361138	72962834	72962954	In-frame
ENST00000361138	72965029	72965209	In-frame
ENST00000361138	72965291	72965387	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
ENST00000361138	72882838	72882891	Frame-shift
ENST00000361138	72895674	72895815	In-frame
ENST00000361138	72901115	72901187	In-frame
ENST00000361138	72920162	72920276	In-frame
ENST00000361138	72959059	72959185	In-frame
ENST00000361138	72961520	72961565	In-frame
ENST00000361138	72962528	72962633	In-frame
ENST00000361138	72962834	72962954	In-frame
ENST00000361138	72965029	72965209	In-frame
ENST00000361138	72965291	72965387	In-frame

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Infer the effects of exon skipping event on protein functional features for SMC5

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
ENST00000361138	5938	1101	72895674	72895815	737	877	226	273
ENST00000361138	5938	1101	72901115	72901187	1040	1111	327	351
ENST00000361138	5938	1101	72920162	72920276	1523	1636	488	526
ENST00000361138	5938	1101	72959059	72959185	2456	2581	799	841
ENST00000361138	5938	1101	72961520	72961565	2582	2626	841	856
ENST00000361138	5938	1101	72962528	72962633	2723	2827	888	923
ENST00000361138	5938	1101	72962834	72962954	2828	2947	923	963
ENST00000361138	5938	1101	72965029	72965209	2948	3127	963	1023
ENST00000361138	5938	1101	72965291	72965387	3128	3223	1023	1055

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
ENST00000361138	5938	1101	72895674	72895815	737	877	226	273
ENST00000361138	5938	1101	72901115	72901187	1040	1111	327	351
ENST00000361138	5938	1101	72920162	72920276	1523	1636	488	526
ENST00000361138	5938	1101	72959059	72959185	2456	2581	799	841
ENST00000361138	5938	1101	72961520	72961565	2582	2626	841	856
ENST00000361138	5938	1101	72962528	72962633	2723	2827	888	923
ENST00000361138	5938	1101	72962834	72962954	2828	2947	923	963
ENST00000361138	5938	1101	72965029	72965209	2948	3127	963	1023
ENST00000361138	5938	1101	72965291	72965387	3128	3223	1023	1055

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
Q8IY18	226	273	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	226	273	207	445	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	327	351	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	327	351	207	445	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	488	526	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	488	526	446	646	Region	Note=Flexible hinge
Q8IY18	799	841	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	799	841	647	828	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	841	856	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	888	923	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	888	923	888	927	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	923	963	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	923	963	888	927	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	963	1023	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	963	1023	991	1026	Compositional bias	Note=Ala/Asp-rich (DA-box)
Q8IY18	1023	1055	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	1023	1055	991	1026	Compositional bias	Note=Ala/Asp-rich (DA-box)

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
Q8IY18	226	273	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	226	273	207	445	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	327	351	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	327	351	207	445	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	488	526	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	488	526	446	646	Region	Note=Flexible hinge
Q8IY18	799	841	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	799	841	647	828	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	841	856	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	888	923	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	888	923	888	927	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	923	963	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	923	963	888	927	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8IY18	963	1023	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	963	1023	991	1026	Compositional bias	Note=Ala/Asp-rich (DA-box)
Q8IY18	1023	1055	1	1101	Chain	ID=PRO_0000270951;Note=Structural maintenance of chromosomes protein 5
Q8IY18	1023	1055	991	1026	Compositional bias	Note=Ala/Asp-rich (DA-box)

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SNVs in the skipped exons for SMC5

- 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.

SMC5_STAD_exon_skip_496407_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-G3-A3CJ-01	exon_skip_496407	72901116	72901187	72901141	72901141	Frame_Shift_Del	A	-	p.Q336fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_496409	72920163	72920276	72920271	72920271	Frame_Shift_Del	A	-	p.K525fs
LIHC	TCGA-DD-A1EG-01	exon_skip_496416	72961521	72961565	72961559	72961559	Frame_Shift_Del	C	-	p.L854fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_496418	72962529	72962633	72962546	72962546	Frame_Shift_Del	A	-	p.T894fs
COAD	TCGA-A6-5665-01	exon_skip_496418	72962529	72962633	72962620	72962620	Frame_Shift_Del	A	-	p.E919fs
LIHC	TCGA-DD-A1EG-01	exon_skip_496419	72962835	72962954	72962875	72962875	Frame_Shift_Del	A	-	p.E937fs
LIHC	TCGA-DD-A39Y-01	exon_skip_496419	72962835	72962954	72962887	72962887	Frame_Shift_Del	A	-	p.E941fs
LIHC	TCGA-DD-A1EG-01	exon_skip_496419	72962835	72962954	72962900	72962900	Frame_Shift_Del	T	-	p.N945fs
UCEC	TCGA-B5-A0K2-01	exon_skip_496403	72882839	72882891	72882844	72882845	Frame_Shift_Ins	-	T	p.G111fs
UCEC	TCGA-B5-A0JZ-01	exon_skip_496406	72895675	72895815	72895705	72895705	Nonsense_Mutation	C	T	p.Q237*
BLCA	TCGA-DK-A6AW-01	exon_skip_496421	72965030	72965209	72965054	72965054	Nonsense_Mutation	C	T	p.R972*
COAD	TCGA-AZ-4315-01	exon_skip_496421	72965030	72965209	72965054	72965054	Nonsense_Mutation	C	T	p.R972X
COAD	TCGA-G4-6320-01	exon_skip_496421	72965030	72965209	72965054	72965054	Nonsense_Mutation	C	T	p.R972X
UCEC	TCGA-B5-A0JY-01	exon_skip_496421	72965030	72965209	72965054	72965054	Nonsense_Mutation	C	T	p.R972*
READ	TCGA-F5-6814-01	exon_skip_496421	72965030	72965209	72965072	72965072	Nonsense_Mutation	C	T	p.R978X
STAD	TCGA-BR-8680-01	exon_skip_496421	72965030	72965209	72965072	72965072	Nonsense_Mutation	C	T	p.R978*
STAD	TCGA-BR-8680-01	exon_skip_496421	72965030	72965209	72965072	72965072	Nonsense_Mutation	C	T	p.R978X
STAD	TCGA-BR-8591-01	exon_skip_496407	72901116	72901187	72901115	72901115	Splice_Site	G	T	.
STAD	TCGA-BR-8591-01	exon_skip_496407	72901116	72901187	72901115	72901115	Splice_Site	G	T	p.A328_splice
LUSC	TCGA-33-4532-01	exon_skip_496418	72962529	72962633	72962528	72962528	Splice_Site	G	C	p.I889_splice

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-BR-8591-01
	Cancer type: STAD
	ESID: exon_skip_496407
	Skipped exon start: 72901116
	Skipped exon end: 72901187
	Mutation start: 72901115
	Mutation end: 72901115
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: T
	AAchange: .
	Sample: TCGA-BR-8591-01
	Cancer type: STAD
	ESID: exon_skip_496407
	Skipped exon start: 72901116
	Skipped exon end: 72901187
	Mutation start: 72901115
	Mutation end: 72901115
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: T
	AAchange: p.A328_splice
exon_skip_139886_STAD_TCGA-BR-8591-01.png
exon_skip_22733_STAD_TCGA-BR-8591-01.png
exon_skip_344506_STAD_TCGA-BR-8591-01.png
exon_skip_344507_STAD_TCGA-BR-8591-01.png
exon_skip_347690_STAD_TCGA-BR-8591-01.png
exon_skip_461353_STAD_TCGA-BR-8591-01.png
exon_skip_462689_STAD_TCGA-BR-8591-01.png
exon_skip_463441_STAD_TCGA-BR-8591-01.png
exon_skip_468148_STAD_TCGA-BR-8591-01.png
exon_skip_468149_STAD_TCGA-BR-8591-01.png
exon_skip_487281_STAD_TCGA-BR-8591-01.png
exon_skip_496407_STAD_TCGA-BR-8591-01.png
exon_skip_508189_STAD_TCGA-BR-8591-01.png
exon_skip_84502_STAD_TCGA-BR-8591-01.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
COLO684_ENDOMETRIUM	72962835	72962954	72962900	72962900	Frame_Shift_Del	T	-	p.N945fs
CW2_LARGE_INTESTINE	72962835	72962954	72962874	72962875	Frame_Shift_Ins	-	A	p.E937fs
YD38_UPPER_AERODIGESTIVE_TRACT	72962835	72962954	72962899	72962900	Frame_Shift_Ins	-	T	p.NF945fs
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	72895675	72895815	72895694	72895694	Missense_Mutation	C	T	p.T233I
NCIH647_LUNG	72895675	72895815	72895696	72895696	Missense_Mutation	G	A	p.E234K
PACADD137_PANCREAS	72895675	72895815	72895730	72895730	Missense_Mutation	G	A	p.R245K
IOMMLEE_CENTRAL_NERVOUS_SYSTEM	72895675	72895815	72895763	72895763	Missense_Mutation	G	A	p.R256Q
SW1990_PANCREAS	72920163	72920276	72920185	72920185	Missense_Mutation	A	C	p.N496T
BICR18_UPPER_AERODIGESTIVE_TRACT	72920163	72920276	72920262	72920262	Missense_Mutation	G	A	p.V522I
BICR18_UPPER_AERODIGESTIVE_TRACT	72920163	72920276	72920272	72920272	Missense_Mutation	A	G	p.K525R
EGI1_BILIARY_TRACT	72959060	72959185	72959063	72959063	Missense_Mutation	C	G	p.H801D
ESO51_OESOPHAGUS	72959060	72959185	72959151	72959151	Missense_Mutation	G	A	p.G830D
BICR18_UPPER_AERODIGESTIVE_TRACT	72961521	72961565	72961549	72961549	Missense_Mutation	A	G	p.N851S
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	72961521	72961565	72961549	72961549	Missense_Mutation	A	G	p.N851S
BICR18_UPPER_AERODIGESTIVE_TRACT	72961521	72961565	72961558	72961558	Missense_Mutation	T	C	p.L854P
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	72961521	72961565	72961558	72961558	Missense_Mutation	T	C	p.L854P
SNU1040_LARGE_INTESTINE	72962529	72962633	72962613	72962613	Missense_Mutation	T	C	p.Y917H
RKO_LARGE_INTESTINE	72962835	72962954	72962853	72962853	Missense_Mutation	A	G	p.N930D
HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	72962835	72962954	72962866	72962866	Missense_Mutation	A	C	p.E934A
SNU81_LARGE_INTESTINE	72962835	72962954	72962905	72962905	Missense_Mutation	T	G	p.F947C
OC316_OVARY	72965030	72965209	72965073	72965073	Missense_Mutation	G	A	p.R978Q
OC314_OVARY	72965030	72965209	72965073	72965073	Missense_Mutation	G	A	p.R978Q
HEC108_ENDOMETRIUM	72965030	72965209	72965114	72965114	Missense_Mutation	A	C	p.S992R
RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	72965292	72965387	72965325	72965325	Missense_Mutation	G	A	p.E1035K
CALU6_LUNG	72965292	72965387	72965340	72965340	Missense_Mutation	A	T	p.T1040S
HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	72965292	72965387	72965356	72965356	Missense_Mutation	A	G	p.N1045S
HCC2998_LARGE_INTESTINE	72965030	72965209	72965054	72965054	Nonsense_Mutation	C	T	p.R972*
TK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	72965292	72965387	72965292	72965292	Splice_Site	G	C	p.G1024R

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMC5

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 SMC5

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMC5

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RelatedDrugs for SMC5

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 SMC5

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SMC5	C0023893	Liver Cirrhosis, Experimental	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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