ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CELF4

Gene summary

Gene information	Gene symbol	CELF4
	Gene ID	56853
	Gene name	CUGBP Elav-like family member 4
	Synonyms	BRUNOL4\|CELF-4
	Cytomap	18q12.2
	Type of gene	protein-coding
	Description	CUGBP Elav-like family member 4CUG-BP- and ETR-3-like factor 4LYST-interacting protein LIP9RNA-binding protein BRUNOL4bruno-like 4, RNA binding proteinbruno-like protein 4
	Modification date	20180523
	UniProtAcc	Q9BZC1
	Context	PubMed: CELF4 [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
CELF4	GO:0000380	alternative mRNA splicing, via spliceosome	19720736
CELF4	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	11158314\|19720736
CELF4	GO:0048026	positive regulation of mRNA splicing, via spliceosome	15009664

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Exon skipping events across known transcript of Ensembl for CELF4 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 CELF4

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 CELF4

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_298949	18	34824966:34825160:34827148:34827233:34833729:34833901	34827148:34827233	ENSG00000101489.14	ENST00000587911.1
exon_skip_298952	18	34833817:34833901:34839083:34839227:34844636:34844717	34839083:34839227	ENSG00000101489.14	ENST00000589386.1
exon_skip_298958	18	34833817:34833901:34839143:34839227:34844636:34844717	34839143:34839227	ENSG00000101489.14	ENST00000591287.1,ENST00000361795.5,ENST00000412753.1,ENST00000603232.1,ENST00000420428.2,ENST00000591282.1,ENST00000590112.1,ENST00000601019.1
exon_skip_298961	18	34833817:34833901:34844636:34844717:34846495:34846556	34844636:34844717	ENSG00000101489.14	ENST00000593271.1
exon_skip_298963	18	34833817:34833901:34844636:34844720:34846495:34846556	34844636:34844720	ENSG00000101489.14	ENST00000588591.1,ENST00000334919.5
exon_skip_298970	18	34839143:34839227:34844636:34844717:34846495:34846556	34844636:34844717	ENSG00000101489.14	ENST00000588597.1
exon_skip_298971	18	34839143:34839227:34844636:34844720:34846495:34846556	34844636:34844720	ENSG00000101489.14	ENST00000361795.5,ENST00000412753.1,ENST00000603232.1,ENST00000420428.2,ENST00000591282.1,ENST00000590112.1,ENST00000589386.1,ENST00000601019.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for CELF4

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_298949	18	34824966:34825160:34827148:34827233:34833729:34833901	34827148:34827233	ENSG00000101489.14	ENST00000587911.1
exon_skip_298952	18	34833817:34833901:34839083:34839227:34844636:34844717	34839083:34839227	ENSG00000101489.14	ENST00000589386.1
exon_skip_298958	18	34833817:34833901:34839143:34839227:34844636:34844717	34839143:34839227	ENSG00000101489.14	ENST00000591287.1,ENST00000420428.2,ENST00000412753.1,ENST00000590112.1,ENST00000601019.1,ENST00000361795.5,ENST00000603232.1,ENST00000591282.1
exon_skip_298961	18	34833817:34833901:34844636:34844717:34846495:34846556	34844636:34844717	ENSG00000101489.14	ENST00000593271.1
exon_skip_298963	18	34833817:34833901:34844636:34844720:34846495:34846556	34844636:34844720	ENSG00000101489.14	ENST00000588591.1,ENST00000334919.5
exon_skip_298970	18	34839143:34839227:34844636:34844717:34846495:34846556	34844636:34844717	ENSG00000101489.14	ENST00000588597.1
exon_skip_298971	18	34839143:34839227:34844636:34844720:34846495:34846556	34844636:34844720	ENSG00000101489.14	ENST00000420428.2,ENST00000412753.1,ENST00000590112.1,ENST00000601019.1,ENST00000361795.5,ENST00000603232.1,ENST00000591282.1,ENST00000589386.1

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 CELF4

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
ENST00000420428	34839143	34839227	In-frame
ENST00000591282	34839143	34839227	In-frame
ENST00000420428	34844636	34844720	In-frame
ENST00000591282	34844636	34844720	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
ENST00000420428	34839143	34839227	In-frame
ENST00000591282	34839143	34839227	In-frame
ENST00000420428	34844636	34844720	In-frame
ENST00000591282	34844636	34844720	In-frame

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Infer the effects of exon skipping event on protein functional features for CELF4

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
ENST00000420428	4069	486	34844636	34844720	1562	1645	388	416
ENST00000591282	1478	486	34844636	34844720	1166	1249	388	416
ENST00000420428	4069	486	34839143	34839227	1646	1729	416	444
ENST00000591282	1478	486	34839143	34839227	1250	1333	416	444

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
ENST00000420428	4069	486	34844636	34844720	1562	1645	388	416
ENST00000591282	1478	486	34844636	34844720	1166	1249	388	416
ENST00000420428	4069	486	34839143	34839227	1646	1729	416	444
ENST00000591282	1478	486	34839143	34839227	1250	1333	416	444

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
Q9BZC1	388	416	388	389	Alternative sequence	ID=VSP_026831;Note=In isoform 2. GP->A;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9BZC1	388	416	388	389	Alternative sequence	ID=VSP_026831;Note=In isoform 2. GP->A;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9BZC1	388	416	1	486	Chain	ID=PRO_0000295221;Note=CUGBP Elav-like family member 4
Q9BZC1	388	416	1	486	Chain	ID=PRO_0000295221;Note=CUGBP Elav-like family member 4
Q9BZC1	388	416	404	479	Domain	Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9BZC1	388	416	404	479	Domain	Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9BZC1	388	416	388	388	Natural variant	ID=VAR_052203;Note=G->S;Dbxref=dbSNP:rs12458669
Q9BZC1	388	416	388	388	Natural variant	ID=VAR_052203;Note=G->S;Dbxref=dbSNP:rs12458669
Q9BZC1	416	444	417	444	Alternative sequence	ID=VSP_026832;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10893231,ECO:0000303\|PubMed:15489334;Dbxref=PMID:10893231,PMID:15489334
Q9BZC1	416	444	417	444	Alternative sequence	ID=VSP_026832;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10893231,ECO:0000303\|PubMed:15489334;Dbxref=PMID:10893231,PMID:15489334
Q9BZC1	416	444	1	486	Chain	ID=PRO_0000295221;Note=CUGBP Elav-like family member 4
Q9BZC1	416	444	1	486	Chain	ID=PRO_0000295221;Note=CUGBP Elav-like family member 4
Q9BZC1	416	444	404	479	Domain	Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9BZC1	416	444	404	479	Domain	Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176

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
Q9BZC1	388	416	388	389	Alternative sequence	ID=VSP_026831;Note=In isoform 2. GP->A;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9BZC1	388	416	388	389	Alternative sequence	ID=VSP_026831;Note=In isoform 2. GP->A;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9BZC1	388	416	1	486	Chain	ID=PRO_0000295221;Note=CUGBP Elav-like family member 4
Q9BZC1	388	416	1	486	Chain	ID=PRO_0000295221;Note=CUGBP Elav-like family member 4
Q9BZC1	388	416	404	479	Domain	Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9BZC1	388	416	404	479	Domain	Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9BZC1	388	416	388	388	Natural variant	ID=VAR_052203;Note=G->S;Dbxref=dbSNP:rs12458669
Q9BZC1	388	416	388	388	Natural variant	ID=VAR_052203;Note=G->S;Dbxref=dbSNP:rs12458669
Q9BZC1	416	444	417	444	Alternative sequence	ID=VSP_026832;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10893231,ECO:0000303\|PubMed:15489334;Dbxref=PMID:10893231,PMID:15489334
Q9BZC1	416	444	417	444	Alternative sequence	ID=VSP_026832;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10893231,ECO:0000303\|PubMed:15489334;Dbxref=PMID:10893231,PMID:15489334
Q9BZC1	416	444	1	486	Chain	ID=PRO_0000295221;Note=CUGBP Elav-like family member 4
Q9BZC1	416	444	1	486	Chain	ID=PRO_0000295221;Note=CUGBP Elav-like family member 4
Q9BZC1	416	444	404	479	Domain	Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176
Q9BZC1	416	444	404	479	Domain	Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00176

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SNVs in the skipped exons for CELF4

- 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.

CELF4_LUAD_exon_skip_298952_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
COAD	TCGA-AD-6889-01	exon_skip_298961 exon_skip_298970	34844637	34844717	34844652	34844652	Frame_Shift_Del	G	-	p.Q402fs
COAD	TCGA-AD-6889-01	exon_skip_298963 exon_skip_298971	34844637	34844720	34844652	34844652	Frame_Shift_Del	G	-	p.Q402fs
LUAD	TCGA-86-8358-01	exon_skip_298952	34839084	34839227	34839128	34839128	Nonsense_Mutation	G	T	p.S438*
LUSC	TCGA-22-5472-01	exon_skip_298952	34839084	34839227	34839189	34839189	Nonsense_Mutation	G	A	p.Q430*
LUSC	TCGA-22-5472-01	exon_skip_298958	34839144	34839227	34839189	34839189	Nonsense_Mutation	G	A	p.Q430*

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-86-8358-01
	Cancer type: LUAD
	ESID: exon_skip_298952
	Skipped exon start: 34839084
	Skipped exon end: 34839227
	Mutation start: 34839128
	Mutation end: 34839128
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: T
	AAchange: p.S438*
exon_skip_298952_LUAD_TCGA-86-8358-01.png
exon_skip_78168_LUAD_TCGA-86-8358-01.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
BICR18_UPPER_AERODIGESTIVE_TRACT	34839144	34839227	34839207	34839207	Missense_Mutation	A	G	p.F424L
BICR18_UPPER_AERODIGESTIVE_TRACT	34839084	34839227	34839207	34839207	Missense_Mutation	A	G	p.F424L
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34839144	34839227	34839207	34839207	Missense_Mutation	A	G	p.F424L
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34839084	34839227	34839207	34839207	Missense_Mutation	A	G	p.F424L
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34839144	34839227	34839207	34839207	Missense_Mutation	A	G	p.F424L
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34839084	34839227	34839207	34839207	Missense_Mutation	A	G	p.F424L
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34839144	34839227	34839207	34839207	Missense_Mutation	A	G	p.F424L
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34839084	34839227	34839207	34839207	Missense_Mutation	A	G	p.F424L
CP66MEL_SKIN	34844637	34844717	34844676	34844676	Missense_Mutation	G	A	p.P404S
CP66MEL_SKIN	34844637	34844720	34844676	34844676	Missense_Mutation	G	A	p.P404S
A549_LUNG	34844637	34844717	34844685	34844685	Nonsense_Mutation	G	A	p.Q401*
A549_LUNG	34844637	34844720	34844685	34844685	Nonsense_Mutation	G	A	p.Q401*
HGC27_STOMACH	34844637	34844717	34844685	34844685	Nonsense_Mutation	G	A	p.Q401*
HGC27_STOMACH	34844637	34844720	34844685	34844685	Nonsense_Mutation	G	A	p.Q401*
OC316_OVARY	34839144	34839227	34839144	34839144	Splice_Site	C	T	p.G445S
OC316_OVARY	34839084	34839227	34839144	34839144	Splice_Site	C	T	p.G445S
OC314_OVARY	34839144	34839227	34839144	34839144	Splice_Site	C	T	p.G445S
OC314_OVARY	34839084	34839227	34839144	34839144	Splice_Site	C	T	p.G445S
MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34839144	34839227	34839227	34839227	Splice_Site	C	A	p.G417V
MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34839084	34839227	34839227	34839227	Splice_Site	C	A	p.G417V

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CELF4

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 CELF4

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CELF4

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RelatedDrugs for CELF4

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 CELF4

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	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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