ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for MSR1

Gene summary

Gene information	Gene symbol	MSR1
	Gene ID	4481
	Gene name	macrophage scavenger receptor 1
	Synonyms	CD204\|SCARA1\|SR-A\|SR-AI\|SR-AII\|SR-AIII\|SRA\|phSR1\|phSR2
	Cytomap	8p22
	Type of gene	protein-coding
	Description	macrophage scavenger receptor types I and IImacrophage acetylated LDL receptor I and IImacrophage scavenger receptor type IIIscavenger receptor class A member 1
	Modification date	20180523
	UniProtAcc	P21757
	Context	PubMed: MSR1 [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 MSR1 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 MSR1

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 MSR1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_488337	8	15967593:15967727:15977926:15978115:16001066:16001120	15977926:15978115	ENSG00000038945.10	ENST00000445506.2,ENST00000262101.5
exon_skip_488338	8	15977926:15978115:16001066:16001120:16007739:16007820	16001066:16001120	ENSG00000038945.10	ENST00000445506.2,ENST00000262101.5
exon_skip_488339	8	16021573:16021760:16025966:16026379:16032695:16032809	16025966:16026379	ENSG00000038945.10	ENST00000445506.2,ENST00000355282.2,ENST00000381998.4,ENST00000350896.3,ENST00000262101.5
exon_skip_488342	8	16025966:16026379:16032695:16032809:16035394:16035497	16032695:16032809	ENSG00000038945.10	ENST00000445506.2,ENST00000355282.2,ENST00000381998.4,ENST00000350896.3,ENST00000262101.5
exon_skip_488347	8	16035394:16035501:16122681:16122840:16240787:16240836	16122681:16122840	ENSG00000038945.10	ENST00000518026.1
exon_skip_488354	8	16353301:16353455:16355382:16355493:16369355:16369419	16355382:16355493	ENSG00000038945.10	ENST00000518343.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for MSR1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_488337	8	15967593:15967727:15977926:15978115:16001066:16001120	15977926:15978115	ENSG00000038945.10	ENST00000262101.5,ENST00000445506.2
exon_skip_488338	8	15977926:15978115:16001066:16001120:16007739:16007820	16001066:16001120	ENSG00000038945.10	ENST00000262101.5,ENST00000445506.2
exon_skip_488339	8	16021573:16021760:16025966:16026379:16032695:16032809	16025966:16026379	ENSG00000038945.10	ENST00000350896.3,ENST00000262101.5,ENST00000445506.2,ENST00000355282.2,ENST00000381998.4
exon_skip_488342	8	16025966:16026379:16032695:16032809:16035394:16035497	16032695:16032809	ENSG00000038945.10	ENST00000350896.3,ENST00000262101.5,ENST00000445506.2,ENST00000355282.2,ENST00000381998.4
exon_skip_488347	8	16035394:16035501:16122681:16122840:16240787:16240836	16122681:16122840	ENSG00000038945.10	ENST00000518026.1
exon_skip_488354	8	16353301:16353455:16355382:16355493:16369355:16369419	16355382:16355493	ENSG00000038945.10	ENST00000518343.1

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 MSR1

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
ENST00000262101	16025966	16026379	Frame-shift
ENST00000262101	15977926	15978115	In-frame
ENST00000262101	16001066	16001120	In-frame
ENST00000262101	16032695	16032809	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
ENST00000262101	16025966	16026379	Frame-shift
ENST00000262101	15977926	15978115	In-frame
ENST00000262101	16001066	16001120	In-frame
ENST00000262101	16032695	16032809	In-frame

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Infer the effects of exon skipping event on protein functional features for MSR1

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
ENST00000262101	2149	451	16032695	16032809	226	339	34	72
ENST00000262101	2149	451	16001066	16001120	1102	1155	326	344
ENST00000262101	2149	451	15977926	15978115	1156	1344	344	407

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
ENST00000262101	2149	451	16032695	16032809	226	339	34	72
ENST00000262101	2149	451	16001066	16001120	1102	1155	326	344
ENST00000262101	2149	451	15977926	15978115	1156	1344	344	407

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
P21757	34	72	1	451	Chain	ID=PRO_0000181627;Note=Macrophage scavenger receptor types I and II
P21757	34	72	36	36	Natural variant	ID=VAR_066581;Note=Found in a family with prostate cancer. P->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12244320;Dbxref=dbSNP:rs749666450,PMID:12244320
P21757	34	72	41	41	Natural variant	ID=VAR_066582;Note=Found in patients with prostate cancer. S->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12244320;Dbxref=dbSNP:rs145597376,PMID:12244320
P21757	34	72	1	50	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21757	34	72	51	76	Transmembrane	Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21757	326	344	1	451	Chain	ID=PRO_0000181627;Note=Macrophage scavenger receptor types I and II
P21757	326	344	273	341	Domain	Note=Collagen-like
P21757	326	344	77	451	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21757	344	407	345	408	Alternative sequence	ID=VSP_036842;Note=In isoform III. TPFTKVRLVGGSGPHEGRVEILHSGQWGTICDDRWEVRVGQVVCRSLGYPGVQAVHKAAHFGQG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9548586;Dbxref=PMID:9548586
P21757	344	407	345	358	Alternative sequence	ID=VSP_006229;Note=In isoform II. TPFTKVRLVGGSGP->RPVQLTDHIRAGPS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:2251254;Dbxref=PMID:2251254
P21757	344	407	359	451	Alternative sequence	ID=VSP_006230;Note=In isoform II. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:2251254;Dbxref=PMID:2251254
P21757	344	407	1	451	Chain	ID=PRO_0000181627;Note=Macrophage scavenger receptor types I and II
P21757	344	407	375	439	Disulfide bond	Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255\|PROSITE-ProRule:PRU00196,ECO:0000269\|PubMed:8900177;Dbxref=PMID:8900177
P21757	344	407	388	449	Disulfide bond	Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255\|PROSITE-ProRule:PRU00196,ECO:0000269\|PubMed:8900177;Dbxref=PMID:8900177
P21757	344	407	350	450	Domain	Note=SRCR;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00196
P21757	344	407	369	369	Natural variant	ID=VAR_066586;Note=Found in a family with prostate cancer. G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12244320;Dbxref=dbSNP:rs776370129,PMID:12244320
P21757	344	407	77	451	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
P21757	34	72	1	451	Chain	ID=PRO_0000181627;Note=Macrophage scavenger receptor types I and II
P21757	34	72	36	36	Natural variant	ID=VAR_066581;Note=Found in a family with prostate cancer. P->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12244320;Dbxref=dbSNP:rs749666450,PMID:12244320
P21757	34	72	41	41	Natural variant	ID=VAR_066582;Note=Found in patients with prostate cancer. S->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12244320;Dbxref=dbSNP:rs145597376,PMID:12244320
P21757	34	72	1	50	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21757	34	72	51	76	Transmembrane	Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21757	326	344	1	451	Chain	ID=PRO_0000181627;Note=Macrophage scavenger receptor types I and II
P21757	326	344	273	341	Domain	Note=Collagen-like
P21757	326	344	77	451	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21757	344	407	345	408	Alternative sequence	ID=VSP_036842;Note=In isoform III. TPFTKVRLVGGSGPHEGRVEILHSGQWGTICDDRWEVRVGQVVCRSLGYPGVQAVHKAAHFGQG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9548586;Dbxref=PMID:9548586
P21757	344	407	345	358	Alternative sequence	ID=VSP_006229;Note=In isoform II. TPFTKVRLVGGSGP->RPVQLTDHIRAGPS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:2251254;Dbxref=PMID:2251254
P21757	344	407	359	451	Alternative sequence	ID=VSP_006230;Note=In isoform II. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:2251254;Dbxref=PMID:2251254
P21757	344	407	1	451	Chain	ID=PRO_0000181627;Note=Macrophage scavenger receptor types I and II
P21757	344	407	375	439	Disulfide bond	Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255\|PROSITE-ProRule:PRU00196,ECO:0000269\|PubMed:8900177;Dbxref=PMID:8900177
P21757	344	407	388	449	Disulfide bond	Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255\|PROSITE-ProRule:PRU00196,ECO:0000269\|PubMed:8900177;Dbxref=PMID:8900177
P21757	344	407	350	450	Domain	Note=SRCR;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00196
P21757	344	407	369	369	Natural variant	ID=VAR_066586;Note=Found in a family with prostate cancer. G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12244320;Dbxref=dbSNP:rs776370129,PMID:12244320
P21757	344	407	77	451	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for MSR1

- 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-A3A1-01	exon_skip_488337	15977927	15978115	15978066	15978066	Frame_Shift_Del	C	-	p.G361fs
LIHC	TCGA-DD-A1EG-01	exon_skip_488339	16025967	16026379	16025996	16025996	Frame_Shift_Del	T	-	p.I201fs
LUAD	TCGA-86-8674-01	exon_skip_488339	16025967	16026379	16026001	16026001	Frame_Shift_Del	C	-	p.G199fs
LIHC	TCGA-DD-A1EG-01	exon_skip_488339	16025967	16026379	16026141	16026141	Frame_Shift_Del	A	-	p.F152fs
SKCM	TCGA-FW-A3R5-06	exon_skip_488337	15977927	15978115	15978098	15978098	Nonsense_Mutation	G	A	p.R351*
SKCM	TCGA-FS-A1Z3-06	exon_skip_488339	16025967	16026379	16025993	16025993	Nonsense_Mutation	G	A	p.Q202*
SKCM	TCGA-FS-A1Z3-06	exon_skip_488339	16025967	16026379	16025993	16025993	Nonsense_Mutation	G	A	p.Q202X
COAD	TCGA-A6-6141-01	exon_skip_488339	16025967	16026379	16026014	16026014	Nonsense_Mutation	C	A	p.E195X
COAD	TCGA-CA-6717-01	exon_skip_488339	16025967	16026379	16026263	16026263	Nonsense_Mutation	C	A	p.E112X
LGG	TCGA-HT-7860-01	exon_skip_488339	16025967	16026379	16026364	16026364	Nonsense_Mutation	C	T	p.W78*
LGG	TCGA-HT-7860-01	exon_skip_488339	16025967	16026379	16026364	16026364	Nonsense_Mutation	C	T	p.W78X
LUAD	TCGA-86-8073-01	exon_skip_488342	16032696	16032809	16032708	16032708	Nonsense_Mutation	C	A	p.G69*
LUSC	TCGA-37-4133-01	exon_skip_488338	16001067	16001120	16001066	16001066	Splice_Site	C	T	p.T363_splice
SKCM	TCGA-GF-A3OT-06	exon_skip_488338	16001067	16001120	16001121	16001121	Splice_Site	C	T	.
KIRC	TCGA-DV-5573-01	exon_skip_488342	16032696	16032809	16032694	16032695	Splice_Site	-	C	.

- 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
EFO27_OVARY	16025967	16026379	16026009	16026010	Frame_Shift_Ins	-	T	p.N196fs
RH30_SOFT_TISSUE	15977927	15978115	15977957	15977957	Missense_Mutation	C	T	p.A398T
SJRH30_SOFT_TISSUE	15977927	15978115	15977957	15977957	Missense_Mutation	C	T	p.A398T
RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	15977927	15978115	15977959	15977959	Missense_Mutation	T	G	p.Q397P
SNUC4_LARGE_INTESTINE	15977927	15978115	15977966	15977966	Missense_Mutation	C	A	p.G395C
MIAPACA2_PANCREAS	15977927	15978115	15977976	15977976	Missense_Mutation	C	G	p.L391F
HEC59_ENDOMETRIUM	15977927	15978115	15977986	15977986	Missense_Mutation	C	T	p.C388Y
DMS79_LUNG	15977927	15978115	15978005	15978005	Missense_Mutation	G	T	p.R382S
SNU1040_LARGE_INTESTINE	15977927	15978115	15978005	15978005	Missense_Mutation	G	A	p.R382C
ONS76_CENTRAL_NERVOUS_SYSTEM	15977927	15978115	15978038	15978038	Missense_Mutation	A	G	p.W371R
NCIH1734_LUNG	15977927	15978115	15978048	15978048	Missense_Mutation	G	T	p.H367Q
SNU1040_LARGE_INTESTINE	15977927	15978115	15978057	15978057	Missense_Mutation	C	A	p.E364D
NCIH2141_LUNG	15977927	15978115	15978074	15978074	Missense_Mutation	G	A	p.H359Y
RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	15977927	15978115	15978089	15978089	Missense_Mutation	C	T	p.G354S
NCIH1770_LUNG	15977927	15978115	15978113	15978113	Missense_Mutation	G	A	p.P346S
SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	16001067	16001120	16001069	16001069	Missense_Mutation	A	G	p.L344S
U2OS_BONE	16001067	16001120	16001087	16001087	Missense_Mutation	T	G	p.K338T
CAKI2_KIDNEY	16001067	16001120	16001102	16001102	Missense_Mutation	C	A	p.G333V
CHSA8926_BONE	16025967	16026379	16025974	16025974	Missense_Mutation	T	C	p.Q208R
NB14_AUTONOMIC_GANGLIA	16025967	16026379	16025974	16025974	Missense_Mutation	T	C	p.Q208R
NCIH2122_LUNG	16025967	16026379	16026001	16026001	Missense_Mutation	C	A	p.G199V
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	16025967	16026379	16026020	16026020	Missense_Mutation	T	G	p.N193H
HAL01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	16025967	16026379	16026086	16026086	Missense_Mutation	T	C	p.N171D
KMOE2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	16025967	16026379	16026100	16026100	Missense_Mutation	A	T	p.V166D
SNU81_LARGE_INTESTINE	16025967	16026379	16026142	16026142	Missense_Mutation	A	C	p.F152C
SNU1197_LARGE_INTESTINE	16025967	16026379	16026145	16026145	Missense_Mutation	C	A	p.R151I
SNB75_CENTRAL_NERVOUS_SYSTEM	16025967	16026379	16026148	16026148	Missense_Mutation	T	G	p.Q150P
SLR26_KIDNEY	16025967	16026379	16026152	16026152	Missense_Mutation	C	A	p.D149Y
JHUEM7_ENDOMETRIUM	16025967	16026379	16026197	16026197	Missense_Mutation	T	C	p.N134D
INA6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	16025967	16026379	16026215	16026215	Missense_Mutation	T	C	p.I128V
D247MG_CENTRAL_NERVOUS_SYSTEM	16025967	16026379	16026224	16026224	Missense_Mutation	T	G	p.I125L
SNU81_LARGE_INTESTINE	16025967	16026379	16026226	16026226	Missense_Mutation	C	A	p.R124I
BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	16025967	16026379	16026295	16026295	Missense_Mutation	C	A	p.G101V
SNB75_CENTRAL_NERVOUS_SYSTEM	16025967	16026379	16026295	16026295	Missense_Mutation	C	T	p.G101E
IPC298_SKIN	16025967	16026379	16026301	16026301	Missense_Mutation	C	T	p.G99E
HT115_LARGE_INTESTINE	16025967	16026379	16026349	16026349	Missense_Mutation	C	T	p.C83Y
HEC6_ENDOMETRIUM	16025967	16026379	16026358	16026358	Missense_Mutation	G	A	p.T80M
MEWO_SKIN	16032696	16032809	16032806	16032807	Missense_Mutation	GG	AA	p.P36F
KNS81_CENTRAL_NERVOUS_SYSTEM	16032696	16032809	16032807	16032807	Missense_Mutation	G	A	p.P36S
KNS81FD_CENTRAL_NERVOUS_SYSTEM	16032696	16032809	16032807	16032807	Missense_Mutation	G	A	p.P36S
M980513_SKIN	16025967	16026379	16025993	16025993	Nonsense_Mutation	G	A	p.Q202*
OMC1_CERVIX	16025967	16026379	16026098	16026098	Nonsense_Mutation	G	A	p.Q167*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MSR1

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 MSR1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MSR1

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RelatedDrugs for MSR1

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 MSR1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
MSR1	C0022661	Kidney Failure, Chronic	1	CTD_human
MSR1	C0033578	Prostatic 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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