ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for MRC2

Gene summary

Gene information	Gene symbol	MRC2
	Gene ID	9902
	Gene name	mannose receptor C type 2
	Synonyms	CD280\|CLEC13E\|ENDO180\|UPARAP
	Cytomap	17q23.2
	Type of gene	protein-coding
	Description	C-type mannose receptor 2C-type lectin domain family 13 member EUPAR-associated proteinendocytic receptor (macrophage mannose receptor family)endocytic receptor 180macrophage mannose receptor 2urokinase-type plasminogen activator receptor-associated
	Modification date	20180523
	UniProtAcc	Q9UBG0
	Context	PubMed: MRC2 [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
MRC2	GO:0030574	collagen catabolic process	12972549

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Exon skipping events across known transcript of Ensembl for MRC2 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 MRC2

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 MRC2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_155147	17	60741908:60742310:60743454:60743628:60743815:60743980	60743454:60743628	ENSG00000011028.9	ENST00000303375.5,ENST00000584265.1
exon_skip_155151	17	60749083:60749198:60749358:60749513:60751423:60751531	60749358:60749513	ENSG00000011028.9	ENST00000303375.5,ENST00000584265.1
exon_skip_155159	17	60754629:60754847:60755864:60756007:60757160:60757263	60755864:60756007	ENSG00000011028.9	ENST00000303375.5
exon_skip_155160	17	60758160:60758321:60758422:60758490:60759197:60759298	60758422:60758490	ENSG00000011028.9	ENST00000303375.5,ENST00000583597.1
exon_skip_155165	17	60758422:60758490:60759197:60759298:60759595:60759684	60759197:60759298	ENSG00000011028.9	ENST00000303375.5,ENST00000583597.1
exon_skip_155167	17	60759595:60759738:60765649:60765764:60765861:60766025	60765649:60765764	ENSG00000011028.9	ENST00000303375.5,ENST00000583597.1,ENST00000446119.2
exon_skip_155169	17	60765649:60765764:60765861:60766025:60766212:60766321	60765861:60766025	ENSG00000011028.9	ENST00000303375.5,ENST00000583597.1,ENST00000446119.2
exon_skip_155173	17	60765861:60766025:60766212:60766321:60767254:60767294	60766212:60766321	ENSG00000011028.9	ENST00000446119.2
exon_skip_155176	17	60766238:60766321:60766731:60766798:60767254:60767294	60766731:60766798	ENSG00000011028.9	ENST00000580916.1
exon_skip_155178	17	60766238:60766321:60766882:60767121:60767254:60767294	60766882:60767121	ENSG00000011028.9	ENST00000303375.5,ENST00000583597.1
exon_skip_155181	17	60766218:60766321:60767254:60767423:60767516:60767666	60767254:60767423	ENSG00000011028.9	ENST00000446119.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for MRC2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_155147	17	60741908:60742310:60743454:60743628:60743815:60743980	60743454:60743628	ENSG00000011028.9	ENST00000303375.5,ENST00000584265.1
exon_skip_155151	17	60749083:60749198:60749358:60749513:60751423:60751531	60749358:60749513	ENSG00000011028.9	ENST00000303375.5,ENST00000584265.1
exon_skip_155159	17	60754629:60754847:60755864:60756007:60757160:60757263	60755864:60756007	ENSG00000011028.9	ENST00000303375.5
exon_skip_155165	17	60758422:60758490:60759197:60759298:60759595:60759684	60759197:60759298	ENSG00000011028.9	ENST00000303375.5,ENST00000583597.1
exon_skip_155167	17	60759595:60759738:60765649:60765764:60765861:60766025	60765649:60765764	ENSG00000011028.9	ENST00000303375.5,ENST00000583597.1,ENST00000446119.2
exon_skip_155169	17	60765649:60765764:60765861:60766025:60766212:60766321	60765861:60766025	ENSG00000011028.9	ENST00000303375.5,ENST00000583597.1,ENST00000446119.2
exon_skip_155173	17	60765861:60766025:60766212:60766321:60767254:60767294	60766212:60766321	ENSG00000011028.9	ENST00000446119.2
exon_skip_155176	17	60766238:60766321:60766731:60766798:60767254:60767294	60766731:60766798	ENSG00000011028.9	ENST00000580916.1
exon_skip_155178	17	60766238:60766321:60766882:60767121:60767254:60767294	60766882:60767121	ENSG00000011028.9	ENST00000303375.5,ENST00000583597.1
exon_skip_155181	17	60766218:60766321:60767254:60767423:60767516:60767666	60767254:60767423	ENSG00000011028.9	ENST00000446119.2

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 MRC2

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
ENST00000303375	60749358	60749513	Frame-shift
ENST00000303375	60755864	60756007	Frame-shift
ENST00000303375	60758422	60758490	Frame-shift
ENST00000303375	60759197	60759298	Frame-shift
ENST00000303375	60765649	60765764	Frame-shift
ENST00000303375	60765861	60766025	Frame-shift
ENST00000303375	60766882	60767121	Frame-shift
ENST00000303375	60743454	60743628	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
ENST00000303375	60749358	60749513	Frame-shift
ENST00000303375	60755864	60756007	Frame-shift
ENST00000303375	60759197	60759298	Frame-shift
ENST00000303375	60765649	60765764	Frame-shift
ENST00000303375	60765861	60766025	Frame-shift
ENST00000303375	60766882	60767121	Frame-shift
ENST00000303375	60743454	60743628	In-frame

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Infer the effects of exon skipping event on protein functional features for MRC2

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
ENST00000303375	6005	1479	60743454	60743628	923	1096	173	231

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
ENST00000303375	6005	1479	60743454	60743628	923	1096	173	231

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
Q9UBG0	173	231	189	193	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	196	200	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	212	218	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	225	227	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	31	1479	Chain	ID=PRO_0000046078;Note=C-type mannose receptor 2
Q9UBG0	173	231	187	213	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9UBG0	173	231	201	228	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9UBG0	173	231	182	230	Domain	Note=Fibronectin type-II;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00479
Q9UBG0	173	231	219	222	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	31	1414	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UBG0	173	231	180	184	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6

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
Q9UBG0	173	231	189	193	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	196	200	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	212	218	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	225	227	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	31	1479	Chain	ID=PRO_0000046078;Note=C-type mannose receptor 2
Q9UBG0	173	231	187	213	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9UBG0	173	231	201	228	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9UBG0	173	231	182	230	Domain	Note=Fibronectin type-II;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00479
Q9UBG0	173	231	219	222	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6
Q9UBG0	173	231	31	1414	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UBG0	173	231	180	184	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5EW6

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SNVs in the skipped exons for MRC2

- 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-G3-A3CJ-01	exon_skip_155147	60743455	60743628	60743474	60743474	Frame_Shift_Del	A	-	p.G180fs
LIHC	TCGA-DD-A39Y-01	exon_skip_155159	60755865	60756007	60755938	60755938	Frame_Shift_Del	C	-	p.A709fs
LIHC	TCGA-DD-A3A1-01	exon_skip_155165	60759198	60759298	60759250	60759250	Frame_Shift_Del	C	-	p.R919fs
COAD	TCGA-G4-6586-01	exon_skip_155167	60765650	60765764	60765652	60765652	Frame_Shift_Del	T	-	p.C983fs
LIHC	TCGA-DD-A1EG-01	exon_skip_155169	60765862	60766025	60765911	60765911	Frame_Shift_Del	C	-	p.G1037fs
LIHC	TCGA-DD-A1EG-01	exon_skip_155173	60766213	60766321	60766314	60766314	Frame_Shift_Del	G	-	p.K1109fs
SKCM	TCGA-FR-A3YO-06	exon_skip_155169	60765862	60766025	60765904	60765904	Nonsense_Mutation	G	A	p.W1035*
SKCM	TCGA-FR-A3YO-06	exon_skip_155169	60765862	60766025	60765904	60765904	Nonsense_Mutation	G	A	p.W1035X
BRCA	TCGA-A2-A0CL-01	exon_skip_155169	60765862	60766025	60765922	60765922	Nonsense_Mutation	C	A	p.S1041*
CESC	TCGA-C5-A3HE-01	exon_skip_155151	60749359	60749513	60749358	60749358	Splice_Site	G	A	e8-1
KIRP	TCGA-B3-3926-01	exon_skip_155173	60766213	60766321	60766323	60766323	Splice_Site	T	C	.
KIRP	TCGA-B3-3926-01	exon_skip_155173	60766213	60766321	60766323	60766323	Splice_Site	T	C	p.D1112_splice
STAD	TCGA-BR-8078-01	exon_skip_155181	60767255	60767423	60767425	60767425	Splice_Site	T	C	p.G1248_splice

- 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
SW48_LARGE_INTESTINE	60755865	60756007	60755933	60755933	Frame_Shift_Del	G	-	p.L707fs
SNUC5_LARGE_INTESTINE	60755865	60756007	60755933	60755933	Frame_Shift_Del	G	-	p.L707fs
OAW28_OVARY	60765862	60766025	60765940	60765949	Frame_Shift_Del	GGGTGGAGCA	-	p.WVEQ1047fs
IM95_STOMACH	60766213	60766321	60766236	60766236	Frame_Shift_Del	C	-	p.H1083fs
HEC108_ENDOMETRIUM	60767255	60767423	60767331	60767332	Frame_Shift_Ins	-	G	p.PG1217fs
NUGC3_STOMACH	60767255	60767423	60767331	60767332	Frame_Shift_Ins	-	G	p.PG1217fs
IPC298_SKIN	60743455	60743628	60743497	60743497	Missense_Mutation	C	T	p.T188I
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	60743455	60743628	60743592	60743592	Missense_Mutation	G	C	p.G220R
SNU349_KIDNEY	60749359	60749513	60749413	60749413	Missense_Mutation	A	G	p.E454G
NCIH1838_LUNG	60749359	60749513	60749419	60749419	Missense_Mutation	C	A	p.S456Y
T84_LARGE_INTESTINE	60749359	60749513	60749449	60749449	Missense_Mutation	G	T	p.W466L
BICR18_UPPER_AERODIGESTIVE_TRACT	60755865	60756007	60755891	60755891	Missense_Mutation	C	G	p.D693E
MDAPCA2B_PROSTATE	60758423	60758490	60758430	60758430	Missense_Mutation	G	A	p.R881Q
NCIBL2009_MATCHED_NORMAL_TISSUE	60758423	60758490	60758456	60758456	Missense_Mutation	G	A	p.G890S
ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	60758423	60758490	60758484	60758484	Missense_Mutation	G	A	p.R899H
SNU175_LARGE_INTESTINE	60759198	60759298	60759209	60759209	Missense_Mutation	G	A	p.G905D
SISO_CERVIX	60759198	60759298	60759280	60759280	Missense_Mutation	T	C	p.Y929H
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	60759198	60759298	60759280	60759280	Missense_Mutation	T	C	p.Y929H
BICR18_UPPER_AERODIGESTIVE_TRACT	60759198	60759298	60759296	60759296	Missense_Mutation	G	A	p.R934Q
DU145_PROSTATE	60765650	60765764	60765747	60765747	Missense_Mutation	C	T	p.T1015I
LNZTA3WT4_CENTRAL_NERVOUS_SYSTEM	60765862	60766025	60765960	60765960	Missense_Mutation	A	C	p.M1054L
LNZ308_CENTRAL_NERVOUS_SYSTEM	60765862	60766025	60765960	60765960	Missense_Mutation	A	C	p.M1054L
SISO_CERVIX	60765862	60766025	60765993	60765993	Missense_Mutation	G	A	p.G1065S
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	60765862	60766025	60765993	60765993	Missense_Mutation	G	A	p.G1065S
BICR18_UPPER_AERODIGESTIVE_TRACT	60766213	60766321	60766228	60766228	Missense_Mutation	G	A	p.V1081I
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	60766213	60766321	60766244	60766244	Missense_Mutation	C	T	p.S1086L
JHUEM7_ENDOMETRIUM	60766213	60766321	60766273	60766273	Missense_Mutation	C	T	p.R1096W
HEC1_ENDOMETRIUM	60766213	60766321	60766298	60766298	Missense_Mutation	G	A	p.G1104D
IM95_STOMACH	60766883	60767121	60766976	60766976	Missense_Mutation	C	A	p.P1143Q
CW2_LARGE_INTESTINE	60766883	60767121	60767006	60767006	Missense_Mutation	G	A	p.C1153Y
MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	60766883	60767121	60767047	60767047	Missense_Mutation	T	C	p.Y1167H
SNU1040_LARGE_INTESTINE	60766883	60767121	60767086	60767086	Missense_Mutation	C	T	p.R1180C
KYSE450_OESOPHAGUS	60766883	60767121	60767105	60767105	Missense_Mutation	G	T	p.G1186V
COLO679_SKIN	60767255	60767423	60767282	60767282	Missense_Mutation	G	A	p.E1201K
HCT15_LARGE_INTESTINE	60767255	60767423	60767297	60767297	Missense_Mutation	T	C	p.Y1206H
BFTC909_KIDNEY	60767255	60767423	60767328	60767328	Missense_Mutation	A	C	p.Q1216P
CW2_LARGE_INTESTINE	60767255	60767423	60767409	60767409	Missense_Mutation	G	A	p.C1243Y
CW2_LARGE_INTESTINE	60743455	60743628	60743455	60743455	Splice_Site	A	G	p.E174G
CP66MEL_SKIN	60765650	60765764	60765764	60765764	Splice_Site	G	A	p.A1021T

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MRC2

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 MRC2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MRC2

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RelatedDrugs for MRC2

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 MRC2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
MRC2	C0024667	Animal Mammary Neoplasms	1	CTD_human
MRC2	C0024668	Mammary Neoplasms, 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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