ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CSF1R

Gene summary

Gene information	Gene symbol	CSF1R
	Gene ID	1436
	Gene name	colony stimulating factor 1 receptor
	Synonyms	C-FMS\|CD115\|CSF-1R\|CSFR\|FIM2\|FMS\|HDLS\|M-CSF-R
	Cytomap	5q32
	Type of gene	protein-coding
	Description	macrophage colony-stimulating factor 1 receptorCD115 antigenCSF-1 receptorFMS proto-oncogeneMcDonough feline sarcoma viral (v-fms) oncogene homologmacrophage colony stimulating factor I receptorproto-oncogene c-Fms
	Modification date	20180527
	UniProtAcc	P07333
	Context	PubMed: CSF1R [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
CSF1R	GO:0018108	peptidyl-tyrosine phosphorylation	20504948
CSF1R	GO:0046777	protein autophosphorylation	20504948

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Exon skipping events across known transcript of Ensembl for CSF1R 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 CSF1R

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 CSF1R

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_445295	5	149433884:149433993:149434799:149434899:149435588:149435700	149434799:149434899	ENSG00000182578.9	ENST00000504875.1,ENST00000286301.3
exon_skip_445296	5	149435588:149435700:149435781:149435904:149436849:149436947	149435781:149435904	ENSG00000182578.9	ENST00000515068.1,ENST00000504875.1,ENST00000286301.3
exon_skip_445299	5	149437066:149437155:149437717:149437834:149440424:149440535	149437717:149437834	ENSG00000182578.9	ENST00000515068.1
exon_skip_445300	5	149437066:149437155:149439262:149439425:149440424:149440535	149439262:149439425	ENSG00000182578.9	ENST00000286301.3
exon_skip_445301	5	149440424:149440535:149441053:149441158:149441285:149441412	149441053:149441158	ENSG00000182578.9	ENST00000504875.1,ENST00000515239.1,ENST00000286301.3
exon_skip_445302	5	149450102:149450134:149452863:149453056:149456838:149456998	149452863:149453056	ENSG00000182578.9	ENST00000504875.1,ENST00000286301.3
exon_skip_445307	5	149460329:149460587:149465941:149466170:149492823:149492935	149465941:149466170	ENSG00000182578.9	ENST00000286301.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for CSF1R

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_445295	5	149433884:149433993:149434799:149434899:149435588:149435700	149434799:149434899	ENSG00000182578.9	ENST00000504875.1,ENST00000286301.3
exon_skip_445296	5	149435588:149435700:149435781:149435904:149436849:149436947	149435781:149435904	ENSG00000182578.9	ENST00000504875.1,ENST00000286301.3,ENST00000515068.1
exon_skip_445299	5	149437066:149437155:149437717:149437834:149440424:149440535	149437717:149437834	ENSG00000182578.9	ENST00000515068.1
exon_skip_445300	5	149437066:149437155:149439262:149439425:149440424:149440535	149439262:149439425	ENSG00000182578.9	ENST00000286301.3
exon_skip_445301	5	149440424:149440535:149441053:149441158:149441285:149441412	149441053:149441158	ENSG00000182578.9	ENST00000504875.1,ENST00000286301.3,ENST00000515239.1
exon_skip_445302	5	149450102:149450134:149452863:149453056:149456838:149456998	149452863:149453056	ENSG00000182578.9	ENST00000504875.1,ENST00000286301.3
exon_skip_445307	5	149460329:149460587:149465941:149466170:149492823:149492935	149465941:149466170	ENSG00000182578.9	ENST00000286301.3

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 CSF1R

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
ENST00000286301	149465941	149466170	3UTR-3CDS
ENST00000286301	149434799	149434899	Frame-shift
ENST00000286301	149439262	149439425	Frame-shift
ENST00000286301	149452863	149453056	Frame-shift
ENST00000286301	149435781	149435904	In-frame
ENST00000286301	149441053	149441158	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
ENST00000286301	149465941	149466170	3UTR-3CDS
ENST00000286301	149434799	149434899	Frame-shift
ENST00000286301	149439262	149439425	Frame-shift
ENST00000286301	149452863	149453056	Frame-shift
ENST00000286301	149435781	149435904	In-frame
ENST00000286301	149441053	149441158	In-frame

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Infer the effects of exon skipping event on protein functional features for CSF1R

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
ENST00000286301	4006	972	149441053	149441158	2046	2150	584	619
ENST00000286301	4006	972	149435781	149435904	2612	2734	773	814

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
ENST00000286301	4006	972	149441053	149441158	2046	2150	584	619
ENST00000286301	4006	972	149435781	149435904	2612	2734	773	814

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
P07333	584	619	307	972	Alternative sequence	ID=VSP_047758;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18593464;Dbxref=PMID:18593464
P07333	584	619	581	590	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	584	619	592	601	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	584	619	605	607	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	584	619	612	618	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	584	619	616	616	Binding site	Note=ATP;Ontology_term=ECO:0000305;evidence=ECO:0000305
P07333	584	619	20	972	Chain	ID=PRO_0000016765;Note=Macrophage colony-stimulating factor 1 receptor
P07333	584	619	582	910	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P07333	584	619	585	619	Natural variant	ID=VAR_067396;Note=In HDLS. GKTLGAGAFGKVVEATAFGLGKEDAVLKVAVKMLK->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=PMID:22197934
P07333	584	619	589	589	Natural variant	ID=VAR_067397;Note=In HDLS. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=dbSNP:rs281860268,PMID:22197934
P07333	584	619	588	596	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P07333	584	619	539	972	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P07333	773	814	778	778	Active site	Note=Proton acceptor;Ontology_term=ECO:0000255,ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159,ECO:0000255\|PROSITE-ProRule:PRU10028
P07333	773	814	307	972	Alternative sequence	ID=VSP_047758;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18593464;Dbxref=PMID:18593464
P07333	773	814	785	787	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	791	794	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	809	811	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	20	972	Chain	ID=PRO_0000016765;Note=Macrophage colony-stimulating factor 1 receptor
P07333	773	814	582	910	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P07333	773	814	781	783	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	788	790	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	798	800	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	803	805	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	809	809	Modified residue	Note=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20489731;Dbxref=PMID:20489731
P07333	773	814	802	802	Mutagenesis	Note=Constitutive kinase activity. Loss of inhibition by imatinib. D->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:10340379,ECO:0000269\|PubMed:16170366;Dbxref=PMID:10340379,PMID:16170366
P07333	773	814	809	809	Mutagenesis	Note=Reduced kinase activity. Reduced interaction with SRC%2C FYN and YES1. Y->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:7681396;Dbxref=PMID:7681396
P07333	773	814	774	814	Natural variant	ID=VAR_067403;Note=In HDLS. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=PMID:22197934
P07333	773	814	775	775	Natural variant	ID=VAR_067404;Note=In HDLS%3B impairs autophosphorylation upon stimulation with CSF1. I->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=dbSNP:rs281860273,PMID:22197934
P07333	773	814	794	794	Natural variant	ID=VAR_067405;Note=In HDLS. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=dbSNP:rs281860274,PMID:22197934
P07333	773	814	796	818	Region	Note=Activation loop
P07333	773	814	539	972	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P07333	773	814	806	808	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LCO

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
P07333	584	619	307	972	Alternative sequence	ID=VSP_047758;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18593464;Dbxref=PMID:18593464
P07333	584	619	581	590	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	584	619	592	601	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	584	619	605	607	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	584	619	612	618	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	584	619	616	616	Binding site	Note=ATP;Ontology_term=ECO:0000305;evidence=ECO:0000305
P07333	584	619	20	972	Chain	ID=PRO_0000016765;Note=Macrophage colony-stimulating factor 1 receptor
P07333	584	619	582	910	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P07333	584	619	585	619	Natural variant	ID=VAR_067396;Note=In HDLS. GKTLGAGAFGKVVEATAFGLGKEDAVLKVAVKMLK->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=PMID:22197934
P07333	584	619	589	589	Natural variant	ID=VAR_067397;Note=In HDLS. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=dbSNP:rs281860268,PMID:22197934
P07333	584	619	588	596	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P07333	584	619	539	972	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P07333	773	814	778	778	Active site	Note=Proton acceptor;Ontology_term=ECO:0000255,ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159,ECO:0000255\|PROSITE-ProRule:PRU10028
P07333	773	814	307	972	Alternative sequence	ID=VSP_047758;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18593464;Dbxref=PMID:18593464
P07333	773	814	785	787	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	791	794	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	809	811	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	20	972	Chain	ID=PRO_0000016765;Note=Macrophage colony-stimulating factor 1 receptor
P07333	773	814	582	910	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P07333	773	814	781	783	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	788	790	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	798	800	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	803	805	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I1M
P07333	773	814	809	809	Modified residue	Note=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20489731;Dbxref=PMID:20489731
P07333	773	814	802	802	Mutagenesis	Note=Constitutive kinase activity. Loss of inhibition by imatinib. D->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:10340379,ECO:0000269\|PubMed:16170366;Dbxref=PMID:10340379,PMID:16170366
P07333	773	814	809	809	Mutagenesis	Note=Reduced kinase activity. Reduced interaction with SRC%2C FYN and YES1. Y->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:7681396;Dbxref=PMID:7681396
P07333	773	814	774	814	Natural variant	ID=VAR_067403;Note=In HDLS. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=PMID:22197934
P07333	773	814	775	775	Natural variant	ID=VAR_067404;Note=In HDLS%3B impairs autophosphorylation upon stimulation with CSF1. I->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=dbSNP:rs281860273,PMID:22197934
P07333	773	814	794	794	Natural variant	ID=VAR_067405;Note=In HDLS. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22197934;Dbxref=dbSNP:rs281860274,PMID:22197934
P07333	773	814	796	818	Region	Note=Activation loop
P07333	773	814	539	972	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P07333	773	814	806	808	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LCO

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SNVs in the skipped exons for CSF1R

- 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-A1EG-01	exon_skip_445302	149452864	149453056	149452997	149452997	Frame_Shift_Del	C	-	p.E317fs
UCEC	TCGA-AX-A0J1-01	exon_skip_445296	149435782	149435904	149435906	149435906	Splice_Site	T	C	e17-2

- 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
CADOES1_BONE	149435782	149435904	149435850	149435850	Missense_Mutation	C	G	p.A792P
NCIH740_LUNG	149435782	149435904	149435882	149435882	Missense_Mutation	G	T	p.A781E
HEC59_ENDOMETRIUM	149435782	149435904	149435889	149435889	Missense_Mutation	C	T	p.V779M
CORL321_PLEURA	149439263	149439425	149439266	149439266	Missense_Mutation	C	T	p.R710H
MOGGUVW_CENTRAL_NERVOUS_SYSTEM	149439263	149439425	149439266	149439266	Missense_Mutation	C	T	p.R710H
S117_SOFT_TISSUE	149439263	149439425	149439295	149439295	Missense_Mutation	C	G	p.K700N
A253_SALIVARY_GLAND	149439263	149439425	149439315	149439315	Missense_Mutation	C	T	p.E694K
NCIH810_LUNG	149439263	149439425	149439327	149439327	Missense_Mutation	C	T	p.G690S
NCIH2342_LUNG	149439263	149439425	149439404	149439404	Missense_Mutation	T	C	p.E664G
HT115_LARGE_INTESTINE	149439263	149439425	149439419	149439419	Missense_Mutation	A	G	p.V659A
KYSE410_OESOPHAGUS	149441054	149441158	149441146	149441146	Missense_Mutation	C	T	p.G589E
KYSE410_OESOPHAGUS	149452864	149453056	149452874	149452874	Missense_Mutation	C	T	p.D358N
HS944T_SKIN	149452864	149453056	149452875	149452875	Missense_Mutation	C	A	p.K357N
TE4_OESOPHAGUS	149452864	149453056	149453003	149453003	Missense_Mutation	C	A	p.V315L

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CSF1R

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 CSF1R

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CSF1R

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RelatedDrugs for CSF1R

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
	P07333	DB00619	Imatinib	Macrophage colony-stimulating factor 1 receptor	small molecule	approved
	P07333	DB01268	Sunitinib	Macrophage colony-stimulating factor 1 receptor	small molecule	approved\|investigational
	P07333	DB12010	Fostamatinib	Macrophage colony-stimulating factor 1 receptor	small molecule	approved\|investigational

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RelatedDiseases for CSF1R

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
CSF1R	C3711381	Hereditary Diffuse Leukoencephalopathy with Spheroids	2	ORPHANET;UNIPROT
CSF1R	C0023467	Leukemia, Myelocytic, Acute	1	CTD_human
CSF1R	C0023893	Liver Cirrhosis, Experimental	1	CTD_human
CSF1R	C0027627	Neoplasm Metastasis	1	CTD_human
CSF1R	C0270612	Leukoencephalopathies	1	CTD_human;HPO
CSF1R	C1458155	Mammary 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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