ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CEP164

Gene summary

Gene information	Gene symbol	CEP164
	Gene ID	22897
	Gene name	centrosomal protein 164
	Synonyms	NPHP15
	Cytomap	11q23.3
	Type of gene	protein-coding
	Description	centrosomal protein of 164 kDacentrosomal protein 164kDa
	Modification date	20180523
	UniProtAcc	Q9UPV0
	Context	PubMed: CEP164 [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 CEP164 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 CEP164

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 CEP164

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_65368	11	117198570:117198620:117206320:117206396:117209281:117209384	117206320:117206396	ENSG00000110274.10	ENST00000278935.3
exon_skip_65371	11	117198818:117198924:117206320:117206396:117209281:117209384	117206320:117206396	ENSG00000110274.10	ENST00000527609.1
exon_skip_65372	11	117198818:117198924:117206320:117206396:117214881:117214993	117206320:117206396	ENSG00000110274.10	ENST00000525416.1
exon_skip_65373	11	117198818:117198924:117209281:117209384:117214881:117214993	117209281:117209384	ENSG00000110274.10	ENST00000533570.1
exon_skip_65374	11	117206320:117206396:117209281:117209384:117214881:117214993	117209281:117209384	ENSG00000110274.10	ENST00000278935.3,ENST00000525734.1,ENST00000527609.1
exon_skip_65379	11	117233119:117233254:117234144:117234222:117241795:117242182	117234144:117234222	ENSG00000110274.10	ENST00000278935.3,ENST00000533675.1
exon_skip_65381	11	117241795:117242182:117244466:117244547:117246423:117246507	117244466:117244547	ENSG00000110274.10	ENST00000533706.1,ENST00000278935.3,ENST00000533675.1
exon_skip_65384	11	117252416:117252584:117253511:117253658:117257918:117258128	117253511:117253658	ENSG00000110274.10	ENST00000533706.1,ENST00000278935.3
exon_skip_65386	11	117252416:117252584:117257918:117258128:117261492:117261624	117257918:117258128	ENSG00000110274.10	ENST00000533675.1
exon_skip_65387	11	117253511:117253658:117257918:117258128:117261492:117261624	117257918:117258128	ENSG00000110274.10	ENST00000533706.1,ENST00000278935.3
exon_skip_65390	11	117261492:117261624:117261714:117261931:117262941:117263019	117261714:117261931	ENSG00000110274.10	ENST00000533223.1,ENST00000533706.1,ENST00000278935.3,ENST00000533675.1
exon_skip_65392	11	117263211:117263343:117263719:117263842:117265065:117265209	117263719:117263842	ENSG00000110274.10	ENST00000533223.1,ENST00000533706.1,ENST00000278935.3,ENST00000533675.1
exon_skip_65394	11	117265065:117265209:117265635:117265719:117265838:117265907	117265635:117265719	ENSG00000110274.10	ENST00000533223.1,ENST00000533706.1,ENST00000278935.3
exon_skip_65396	11	117265635:117265719:117265838:117265907:117266262:117266438	117265838:117265907	ENSG00000110274.10	ENST00000533223.1,ENST00000533706.1,ENST00000278935.3
exon_skip_65398	11	117265838:117265907:117266262:117266438:117266769:117266896	117266262:117266438	ENSG00000110274.10	ENST00000533223.1,ENST00000533706.1,ENST00000278935.3,ENST00000533675.1
exon_skip_65400	11	117278640:117278748:117279241:117279471:117279605:117279720	117279241:117279471	ENSG00000110274.10	ENST00000533706.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for CEP164

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_65368	11	117198570:117198620:117206320:117206396:117209281:117209384	117206320:117206396	ENSG00000110274.10	ENST00000278935.3
exon_skip_65371	11	117198818:117198924:117206320:117206396:117209281:117209384	117206320:117206396	ENSG00000110274.10	ENST00000527609.1
exon_skip_65372	11	117198818:117198924:117206320:117206396:117214881:117214993	117206320:117206396	ENSG00000110274.10	ENST00000525416.1
exon_skip_65373	11	117198818:117198924:117209281:117209384:117214881:117214993	117209281:117209384	ENSG00000110274.10	ENST00000533570.1
exon_skip_65374	11	117206320:117206396:117209281:117209384:117214881:117214993	117209281:117209384	ENSG00000110274.10	ENST00000525734.1,ENST00000278935.3,ENST00000527609.1
exon_skip_65379	11	117233119:117233254:117234144:117234222:117241795:117242182	117234144:117234222	ENSG00000110274.10	ENST00000278935.3,ENST00000533675.1
exon_skip_65381	11	117241795:117242182:117244466:117244547:117246423:117246507	117244466:117244547	ENSG00000110274.10	ENST00000278935.3,ENST00000533675.1,ENST00000533706.1
exon_skip_65384	11	117252416:117252584:117253511:117253658:117257918:117258128	117253511:117253658	ENSG00000110274.10	ENST00000278935.3,ENST00000533706.1
exon_skip_65386	11	117252416:117252584:117257918:117258128:117261492:117261624	117257918:117258128	ENSG00000110274.10	ENST00000533675.1
exon_skip_65387	11	117253511:117253658:117257918:117258128:117261492:117261624	117257918:117258128	ENSG00000110274.10	ENST00000278935.3,ENST00000533706.1
exon_skip_65390	11	117261492:117261624:117261714:117261931:117262941:117263019	117261714:117261931	ENSG00000110274.10	ENST00000278935.3,ENST00000533675.1,ENST00000533706.1,ENST00000533223.1
exon_skip_65392	11	117263211:117263343:117263719:117263842:117265065:117265209	117263719:117263842	ENSG00000110274.10	ENST00000278935.3,ENST00000533675.1,ENST00000533706.1,ENST00000533223.1
exon_skip_65394	11	117265065:117265209:117265635:117265719:117265838:117265907	117265635:117265719	ENSG00000110274.10	ENST00000278935.3,ENST00000533706.1,ENST00000533223.1
exon_skip_65396	11	117265635:117265719:117265838:117265907:117266262:117266438	117265838:117265907	ENSG00000110274.10	ENST00000278935.3,ENST00000533706.1,ENST00000533223.1
exon_skip_65398	11	117265838:117265907:117266262:117266438:117266769:117266896	117266262:117266438	ENSG00000110274.10	ENST00000278935.3,ENST00000533675.1,ENST00000533706.1,ENST00000533223.1
exon_skip_65400	11	117278640:117278748:117279241:117279471:117279605:117279720	117279241:117279471	ENSG00000110274.10	ENST00000533706.1

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 CEP164

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
ENST00000278935	117209281	117209384	5CDS-5UTR
ENST00000278935	117206320	117206396	5UTR-5UTR
ENST00000278935	117261714	117261931	Frame-shift
ENST00000278935	117266262	117266438	Frame-shift
ENST00000278935	117234144	117234222	In-frame
ENST00000278935	117244466	117244547	In-frame
ENST00000278935	117253511	117253658	In-frame
ENST00000278935	117257918	117258128	In-frame
ENST00000278935	117263719	117263842	In-frame
ENST00000278935	117265635	117265719	In-frame
ENST00000278935	117265838	117265907	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
ENST00000278935	117209281	117209384	5CDS-5UTR
ENST00000278935	117206320	117206396	5UTR-5UTR
ENST00000278935	117261714	117261931	Frame-shift
ENST00000278935	117266262	117266438	Frame-shift
ENST00000278935	117234144	117234222	In-frame
ENST00000278935	117244466	117244547	In-frame
ENST00000278935	117253511	117253658	In-frame
ENST00000278935	117257918	117258128	In-frame
ENST00000278935	117263719	117263842	In-frame
ENST00000278935	117265635	117265719	In-frame
ENST00000278935	117265838	117265907	In-frame

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Infer the effects of exon skipping event on protein functional features for CEP164

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
ENST00000278935	5647	1460	117234144	117234222	835	912	229	255
ENST00000278935	5647	1460	117244466	117244547	1300	1380	384	411
ENST00000278935	5647	1460	117253511	117253658	1725	1871	526	574
ENST00000278935	5647	1460	117257918	117258128	1872	2081	575	644
ENST00000278935	5647	1460	117263719	117263842	2641	2763	831	872
ENST00000278935	5647	1460	117265635	117265719	2908	2991	920	948
ENST00000278935	5647	1460	117265838	117265907	2992	3060	948	971

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
ENST00000278935	5647	1460	117234144	117234222	835	912	229	255
ENST00000278935	5647	1460	117244466	117244547	1300	1380	384	411
ENST00000278935	5647	1460	117253511	117253658	1725	1871	526	574
ENST00000278935	5647	1460	117257918	117258128	1872	2081	575	644
ENST00000278935	5647	1460	117263719	117263842	2641	2763	831	872
ENST00000278935	5647	1460	117265635	117265719	2908	2991	920	948
ENST00000278935	5647	1460	117265838	117265907	2992	3060	948	971

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
Q9UPV0	229	255	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	384	411	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	526	574	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	526	574	468	955	Compositional bias	Note=Glu-rich
Q9UPV0	526	574	566	566	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q9UPV0	575	644	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	575	644	468	955	Compositional bias	Note=Glu-rich
Q9UPV0	831	872	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	831	872	468	955	Compositional bias	Note=Glu-rich
Q9UPV0	920	948	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	920	948	468	955	Compositional bias	Note=Glu-rich
Q9UPV0	948	971	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	948	971	468	955	Compositional bias	Note=Glu-rich

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
Q9UPV0	229	255	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	384	411	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	526	574	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	526	574	468	955	Compositional bias	Note=Glu-rich
Q9UPV0	526	574	566	566	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q9UPV0	575	644	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	575	644	468	955	Compositional bias	Note=Glu-rich
Q9UPV0	831	872	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	831	872	468	955	Compositional bias	Note=Glu-rich
Q9UPV0	920	948	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	920	948	468	955	Compositional bias	Note=Glu-rich
Q9UPV0	948	971	1	1460	Chain	ID=PRO_0000312494;Note=Centrosomal protein of 164 kDa
Q9UPV0	948	971	468	955	Compositional bias	Note=Glu-rich

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SNVs in the skipped exons for CEP164

- 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-A3A0-01	exon_skip_65379	117234145	117234222	117234201	117234201	Frame_Shift_Del	G	-	p.L248fs
STAD	TCGA-HU-A4GX-01	exon_skip_65390	117261715	117261931	117261750	117261751	Frame_Shift_Del	AA	-	p.704_704del
STAD	TCGA-HU-A4GX-01	exon_skip_65390	117261715	117261931	117261750	117261751	Frame_Shift_Del	AA	-	p.E701fs
LIHC	TCGA-DD-A3A0-01	exon_skip_65392	117263720	117263842	117263759	117263759	Frame_Shift_Del	G	-	p.G845fs
LIHC	TCGA-DD-A39Y-01	exon_skip_65398	117266263	117266438	117266387	117266387	Frame_Shift_Del	C	-	p.S1013fs
COAD	TCGA-A6-6780-01	exon_skip_65379	117234145	117234222	117234192	117234193	Frame_Shift_Ins	-	G	p.I245fs
LUAD	TCGA-J2-A4AD-01	exon_skip_65379	117234145	117234222	117234158	117234158	Nonsense_Mutation	C	G	p.S234*
THYM	TCGA-XM-A8RG-01	exon_skip_65379	117234145	117234222	117234214	117234214	Nonsense_Mutation	G	T	p.E253X
LUSC	TCGA-39-5028-01	exon_skip_65381	117244467	117244547	117244507	117244507	Nonsense_Mutation	C	G	p.S398*
UCEC	TCGA-AP-A056-01	exon_skip_65390	117261715	117261931	117261929	117261929	Nonsense_Mutation	G	T	p.E761*
UCEC	TCGA-B5-A0JY-01	exon_skip_65390	117261715	117261931	117261929	117261929	Nonsense_Mutation	G	T	p.E761*
CESC	TCGA-LP-A7HU-01	exon_skip_65398	117266263	117266438	117266344	117266344	Nonsense_Mutation	G	T	p.E999*
READ	TCGA-F5-6814-01	exon_skip_65398	117266263	117266438	117266344	117266344	Nonsense_Mutation	G	T	p.E999X

- 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
SW1573_LUNG	117263720	117263842	117263784	117263785	Frame_Shift_Del	AG	-	p.K853fs
RKO_LARGE_INTESTINE	117234145	117234222	117234152	117234152	Missense_Mutation	A	G	p.H232R
HCT15_LARGE_INTESTINE	117234145	117234222	117234153	117234153	Missense_Mutation	C	G	p.H232Q
GI1_CENTRAL_NERVOUS_SYSTEM	117234145	117234222	117234192	117234192	Missense_Mutation	T	G	p.I245M
NCIH810_LUNG	117234145	117234222	117234194	117234194	Missense_Mutation	G	T	p.G246V
INA6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117253512	117253658	117253557	117253557	Missense_Mutation	G	T	p.E541D
RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117253512	117253658	117253639	117253639	Missense_Mutation	C	T	p.P569S
RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117253512	117253658	117253639	117253640	Missense_Mutation	CC	TT	p.P569L
RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117253512	117253658	117253640	117253640	Missense_Mutation	C	T	p.P569L
A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117257919	117258128	117257965	117257965	Missense_Mutation	G	T	p.A591S
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117257919	117258128	117258058	117258058	Missense_Mutation	C	T	p.R622W
SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117257919	117258128	117258116	117258116	Missense_Mutation	A	T	p.E641V
HT115_LARGE_INTESTINE	117261715	117261931	117261856	117261856	Missense_Mutation	G	T	p.E736D
PCI38_UPPER_AERODIGESTIVE_TRACT	117261715	117261931	117261871	117261871	Missense_Mutation	T	A	p.N741K
K2_SKIN	117261715	117261931	117261885	117261885	Missense_Mutation	A	C	p.K746T
EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117261715	117261931	117261929	117261929	Missense_Mutation	G	C	p.E761Q
SNU407_LARGE_INTESTINE	117263720	117263842	117263744	117263744	Missense_Mutation	C	T	p.R840C
P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117263720	117263842	117263745	117263745	Missense_Mutation	G	A	p.R840H
SNU1040_LARGE_INTESTINE	117263720	117263842	117263764	117263764	Missense_Mutation	G	T	p.E846D
NCIH810_LUNG	117263720	117263842	117263788	117263788	Missense_Mutation	G	A	p.M854I
NCIH2882_LUNG	117266263	117266438	117266278	117266278	Missense_Mutation	C	T	p.H977Y
WIL2NS_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117266263	117266438	117266297	117266297	Missense_Mutation	C	T	p.A983V
LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	117263720	117263842	117263756	117263756	Nonsense_Mutation	G	T	p.E844*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CEP164

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 CEP164

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CEP164

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RelatedDrugs for CEP164

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 CEP164

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
CEP164	C3541853	NEPHRONOPHTHISIS 15	1	UNIPROT

	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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