ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for MRPS11

Gene summary

Gene information	Gene symbol	MRPS11
	Gene ID	64963
	Gene name	mitochondrial ribosomal protein S11
	Synonyms	HCC-2\|MRP-S11\|S11mt
	Cytomap	15q25.3
	Type of gene	protein-coding
	Description	28S ribosomal protein S11, mitochondrialcervical cancer proto-oncogene 2 proteinmitochondrial small ribosomal subunit protein uS11m
	Modification date	20180523
	UniProtAcc	P82912
	Context	PubMed: MRPS11 [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 MRPS11 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 MRPS11

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 MRPS11

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_124637	15	89011193:89011255:89015857:89015956:89018340:89018470	89015857:89015956	ENSG00000181991.11	ENST00000325844.4,ENST00000558406.1
exon_skip_124639	15	89011193:89011255:89015857:89015956:89018402:89018470	89015857:89015956	ENSG00000181991.11	ENST00000560708.1
exon_skip_124648	15	89011138:89012376:89015857:89015956:89018340:89018470	89015857:89015956	ENSG00000181991.11	ENST00000559323.1
exon_skip_124651	15	89015877:89015956:89018340:89018470:89020219:89020285	89018340:89018470	ENSG00000181991.11	ENST00000559323.1,ENST00000325844.4,ENST00000558406.1
exon_skip_124653	15	89015877:89015956:89018402:89018470:89020219:89020285	89018402:89018470	ENSG00000181991.11	ENST00000560708.1
exon_skip_124655	15	89018402:89018470:89020219:89020285:89021102:89021135	89020219:89020285	ENSG00000181991.11	ENST00000559323.1,ENST00000353598.6,ENST00000325844.4,ENST00000560708.1,ENST00000557974.1,ENST00000558406.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for MRPS11

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_124637	15	89011193:89011255:89015857:89015956:89018340:89018470	89015857:89015956	ENSG00000181991.11	ENST00000325844.4,ENST00000558406.1
exon_skip_124639	15	89011193:89011255:89015857:89015956:89018402:89018470	89015857:89015956	ENSG00000181991.11	ENST00000560708.1
exon_skip_124648	15	89011138:89012376:89015857:89015956:89018340:89018470	89015857:89015956	ENSG00000181991.11	ENST00000559323.1
exon_skip_124651	15	89015877:89015956:89018340:89018470:89020219:89020285	89018340:89018470	ENSG00000181991.11	ENST00000325844.4,ENST00000559323.1,ENST00000558406.1
exon_skip_124653	15	89015877:89015956:89018402:89018470:89020219:89020285	89018402:89018470	ENSG00000181991.11	ENST00000560708.1
exon_skip_124655	15	89018402:89018470:89020219:89020285:89021102:89021135	89020219:89020285	ENSG00000181991.11	ENST00000560708.1,ENST00000325844.4,ENST00000557974.1,ENST00000559323.1,ENST00000353598.6,ENST00000558406.1

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 MRPS11

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
ENST00000325844	89018340	89018470	Frame-shift
ENST00000325844	89015857	89015956	In-frame
ENST00000325844	89020219	89020285	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
ENST00000325844	89018340	89018470	Frame-shift
ENST00000325844	89015857	89015956	In-frame
ENST00000325844	89020219	89020285	In-frame

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Infer the effects of exon skipping event on protein functional features for MRPS11

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
ENST00000325844	1879	194	89015857	89015956	448	546	61	93
ENST00000325844	1879	194	89020219	89020285	677	742	137	159

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
ENST00000325844	1879	194	89015857	89015956	448	546	61	93
ENST00000325844	1879	194	89020219	89020285	677	742	137	159

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
P82912	61	93	62	94	Alternative sequence	ID=VSP_005720;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334

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
P82912	61	93	62	94	Alternative sequence	ID=VSP_005720;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334

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SNVs in the skipped exons for MRPS11

- 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-A39Y-01	exon_skip_124648 exon_skip_124639 exon_skip_124637	89015858	89015956	89015913	89015913	Frame_Shift_Del	T	-	p.F80fs
UCEC	TCGA-D1-A16Y-01	exon_skip_124655	89020220	89020285	89020250	89020250	Nonsense_Mutation	C	T	p.R148*
STAD	TCGA-BR-8363-01	exon_skip_124655	89020220	89020285	89020277	89020277	Nonsense_Mutation	G	T	p.G157*
BRCA	TCGA-C8-A137-01	exon_skip_124655	89020220	89020285	89020219	89020219	Splice_Site	G	A	e5-1

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-DD-A39Y-01
	Cancer type: LIHC
	ESID: exon_skip_124637
	Skipped exon start: 89015858
	Skipped exon end: 89015956
	Mutation start: 89015913
	Mutation end: 89015913
	Mutation type: Frame_Shift_Del
	Reference seq: T
	Mutation seq: -
	AAchange: p.F80fs
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- 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
OE21_OESOPHAGUS	89015858	89015956	89015880	89015880	Missense_Mutation	G	A	p.E69K
NCIH2087_LUNG	89015858	89015956	89015909	89015909	Missense_Mutation	G	C	p.K78N
769P_KIDNEY	89015858	89015956	89015954	89015954	Missense_Mutation	C	G	p.N93K
HCC2998_LARGE_INTESTINE	89018341	89018470	89018366	89018366	Missense_Mutation	A	G	p.S103G
HEC251_ENDOMETRIUM	89018341	89018470	89018411	89018411	Missense_Mutation	C	T	p.R118W
HEC251_ENDOMETRIUM	89018403	89018470	89018411	89018411	Missense_Mutation	C	T	p.R118W
SNU81_LARGE_INTESTINE	89018341	89018470	89018411	89018411	Missense_Mutation	C	T	p.R118W
SNU81_LARGE_INTESTINE	89018403	89018470	89018411	89018411	Missense_Mutation	C	T	p.R118W
HT115_LARGE_INTESTINE	89018341	89018470	89018466	89018466	Missense_Mutation	C	T	p.A136V
HT115_LARGE_INTESTINE	89018403	89018470	89018466	89018466	Missense_Mutation	C	T	p.A136V
GP2D_LARGE_INTESTINE	89020220	89020285	89020245	89020245	Missense_Mutation	A	G	p.H146R
GP5D_LARGE_INTESTINE	89020220	89020285	89020245	89020245	Missense_Mutation	A	G	p.H146R
HCT116_LARGE_INTESTINE	89020220	89020285	89020220	89020220	Splice_Site	A	G	p.R138G

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MRPS11

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 MRPS11

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MRPS11

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RelatedDrugs for MRPS11

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 MRPS11

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
MRPS11	C0038356	Stomach Neoplasms	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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