ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CALCOCO1

Gene summary

Gene information	Gene symbol	CALCOCO1
	Gene ID	57658
	Gene name	calcium binding and coiled-coil domain 1
	Synonyms	Cocoa\|PP13275\|calphoglin
	Cytomap	12q13.13
	Type of gene	protein-coding
	Description	calcium-binding and coiled-coil domain-containing protein 1coiled-coil coactivator proteincoiled-coil leucine zipper coactivator 1inorganic pyrophosphatase activatorsarcoma antigen NY-SAR-3
	Modification date	20180522
	UniProtAcc	Q9P1Z2
	Context	PubMed: CALCOCO1 [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
CALCOCO1	GO:0010628	positive regulation of gene expression	16344550

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Exon skipping events across known transcript of Ensembl for CALCOCO1 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 CALCOCO1

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 CALCOCO1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_92844	12	54105573:54105905:54106558:54106630:54106883:54106987	54106558:54106630	ENSG00000012822.11	ENST00000546443.1
exon_skip_92852	12	54108381:54108477:54108983:54109109:54109576:54109831	54108983:54109109	ENSG00000012822.11	ENST00000549613.1,ENST00000262059.4,ENST00000550804.1,ENST00000430117.2,ENST00000548263.1,ENST00000549935.2
exon_skip_92854	12	54108983:54109109:54109576:54109831:54110043:54110199	54109576:54109831	ENSG00000012822.11	ENST00000262059.4,ENST00000550804.1,ENST00000548263.1,ENST00000549935.2
exon_skip_92856	12	54109576:54109831:54110043:54110199:54113522:54113613	54110043:54110199	ENSG00000012822.11	ENST00000262059.4,ENST00000550804.1,ENST00000552282.1,ENST00000548263.1,ENST00000549935.2
exon_skip_92857	12	54115947:54115967:54116683:54116720:54117376:54117391	54116683:54116720	ENSG00000012822.11	ENST00000547949.2
exon_skip_92860	12	54117512:54117567:54118368:54118531:54118870:54119042	54118368:54118531	ENSG00000012822.11	ENST00000549173.1
exon_skip_92861	12	54117512:54117567:54118428:54118531:54118870:54119042	54118428:54118531	ENSG00000012822.11	ENST00000549349.1,ENST00000552623.1,ENST00000549784.1,ENST00000262059.4,ENST00000553154.1,ENST00000550804.1,ENST00000548177.1,ENST00000549688.1,ENST00000546619.1,ENST00000551900.1,ENST00000547949.2,ENST00000548263.1
exon_skip_92862	12	54118870:54119050:54119473:54119543:54120027:54120118	54119473:54119543	ENSG00000012822.11	ENST00000549349.1,ENST00000552623.1
exon_skip_92863	12	54118870:54119050:54119473:54119543:54121187:54121212	54119473:54119543	ENSG00000012822.11	ENST00000549784.1
exon_skip_92864	12	54118870:54119050:54120027:54120118:54121187:54121212	54120027:54120118	ENSG00000012822.11	ENST00000548177.1
exon_skip_92866	12	54119473:54119543:54120027:54120118:54121187:54121212	54120027:54120118	ENSG00000012822.11	ENST00000549349.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for CALCOCO1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_92844	12	54105573:54105905:54106558:54106630:54106883:54106987	54106558:54106630	ENSG00000012822.11	ENST00000546443.1
exon_skip_92852	12	54108381:54108477:54108983:54109109:54109576:54109831	54108983:54109109	ENSG00000012822.11	ENST00000430117.2,ENST00000262059.4,ENST00000548263.1,ENST00000550804.1,ENST00000549935.2,ENST00000549613.1
exon_skip_92854	12	54108983:54109109:54109576:54109831:54110043:54110199	54109576:54109831	ENSG00000012822.11	ENST00000262059.4,ENST00000548263.1,ENST00000550804.1,ENST00000549935.2
exon_skip_92856	12	54109576:54109831:54110043:54110199:54113522:54113613	54110043:54110199	ENSG00000012822.11	ENST00000262059.4,ENST00000548263.1,ENST00000550804.1,ENST00000549935.2,ENST00000552282.1
exon_skip_92857	12	54115947:54115967:54116683:54116720:54117376:54117391	54116683:54116720	ENSG00000012822.11	ENST00000547949.2
exon_skip_92860	12	54117512:54117567:54118368:54118531:54118870:54119042	54118368:54118531	ENSG00000012822.11	ENST00000549173.1
exon_skip_92861	12	54117512:54117567:54118428:54118531:54118870:54119042	54118428:54118531	ENSG00000012822.11	ENST00000262059.4,ENST00000548263.1,ENST00000550804.1,ENST00000551900.1,ENST00000546619.1,ENST00000547949.2,ENST00000553154.1,ENST00000549784.1,ENST00000548177.1,ENST00000552623.1,ENST00000549349.1,ENST00000549688.1
exon_skip_92862	12	54118870:54119050:54119473:54119543:54120027:54120118	54119473:54119543	ENSG00000012822.11	ENST00000552623.1,ENST00000549349.1
exon_skip_92863	12	54118870:54119050:54119473:54119543:54121187:54121212	54119473:54119543	ENSG00000012822.11	ENST00000549784.1
exon_skip_92864	12	54118870:54119050:54120027:54120118:54121187:54121212	54120027:54120118	ENSG00000012822.11	ENST00000548177.1
exon_skip_92866	12	54119473:54119543:54120027:54120118:54121187:54121212	54120027:54120118	ENSG00000012822.11	ENST00000549349.1

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 CALCOCO1

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
ENST00000550804	54118428	54118531	Frame-shift
ENST00000550804	54108983	54109109	In-frame
ENST00000550804	54109576	54109831	In-frame
ENST00000550804	54110043	54110199	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
ENST00000550804	54118428	54118531	Frame-shift
ENST00000550804	54108983	54109109	In-frame
ENST00000550804	54109576	54109831	In-frame
ENST00000550804	54110043	54110199	In-frame

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Infer the effects of exon skipping event on protein functional features for CALCOCO1

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
ENST00000550804	2308	691	54110043	54110199	911	1066	283	335
ENST00000550804	2308	691	54109576	54109831	1067	1321	335	420
ENST00000550804	2308	691	54108983	54109109	1322	1447	420	462

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
ENST00000550804	2308	691	54110043	54110199	911	1066	283	335
ENST00000550804	2308	691	54109576	54109831	1067	1321	335	420
ENST00000550804	2308	691	54108983	54109109	1322	1447	420	462

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
Q9P1Z2	283	335	287	338	Alternative sequence	ID=VSP_041472;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9P1Z2	283	335	1	691	Chain	ID=PRO_0000308899;Note=Calcium-binding and coiled-coil domain-containing protein 1
Q9P1Z2	283	335	232	339	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9P1Z2	335	420	287	338	Alternative sequence	ID=VSP_041472;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9P1Z2	335	420	1	691	Chain	ID=PRO_0000308899;Note=Calcium-binding and coiled-coil domain-containing protein 1
Q9P1Z2	335	420	232	339	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9P1Z2	335	420	417	514	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9P1Z2	335	420	367	372	Compositional bias	Note=Poly-Ala
Q9P1Z2	335	420	393	393	Natural variant	ID=VAR_036881;Note=R->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14702039;Dbxref=dbSNP:rs3741659,PMID:14702039
Q9P1Z2	335	420	381	381	Sequence conflict	Note=H->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9P1Z2	420	462	1	691	Chain	ID=PRO_0000308899;Note=Calcium-binding and coiled-coil domain-containing protein 1
Q9P1Z2	420	462	417	514	Coiled coil	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
Q9P1Z2	283	335	287	338	Alternative sequence	ID=VSP_041472;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9P1Z2	283	335	1	691	Chain	ID=PRO_0000308899;Note=Calcium-binding and coiled-coil domain-containing protein 1
Q9P1Z2	283	335	232	339	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9P1Z2	335	420	287	338	Alternative sequence	ID=VSP_041472;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9P1Z2	335	420	1	691	Chain	ID=PRO_0000308899;Note=Calcium-binding and coiled-coil domain-containing protein 1
Q9P1Z2	335	420	232	339	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9P1Z2	335	420	417	514	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9P1Z2	335	420	367	372	Compositional bias	Note=Poly-Ala
Q9P1Z2	335	420	393	393	Natural variant	ID=VAR_036881;Note=R->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14702039;Dbxref=dbSNP:rs3741659,PMID:14702039
Q9P1Z2	335	420	381	381	Sequence conflict	Note=H->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9P1Z2	420	462	1	691	Chain	ID=PRO_0000308899;Note=Calcium-binding and coiled-coil domain-containing protein 1
Q9P1Z2	420	462	417	514	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for CALCOCO1

- 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
STAD	TCGA-BR-4191-01	exon_skip_92852	54108984	54109109	54108990	54108991	Frame_Shift_Del	AG	-	p.S460fs
BRCA	TCGA-A2-A0CX-01	exon_skip_92852	54108984	54109109	54109013	54109013	Nonsense_Mutation	C	A	p.E453*
LUAD	TCGA-55-A48Y-01	exon_skip_92852	54108984	54109109	54109067	54109067	Nonsense_Mutation	G	A	p.R435*
SKCM	TCGA-WE-A8JZ-06	exon_skip_92854	54109577	54109831	54109801	54109801	Nonsense_Mutation	G	A	p.R346*
LUAD	TCGA-05-4417-01	exon_skip_92856	54110044	54110199	54110043	54110043	Splice_Site	C	T	p.V335_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
MDAPCA2B_PROSTATE	54108984	54109109	54109054	54109054	Missense_Mutation	G	A	p.A439V
639V_URINARY_TRACT	54109577	54109831	54109675	54109675	Missense_Mutation	C	T	p.A388T
CP66MEL_SKIN	54109577	54109831	54109819	54109819	Missense_Mutation	G	T	p.P340T
SNU349_KIDNEY	54110044	54110199	54110048	54110048	Missense_Mutation	C	T	p.R334Q
HEC251_ENDOMETRIUM	54110044	54110199	54110049	54110049	Missense_Mutation	G	A	p.R334W
SEKI_SKIN	54118369	54118531	54118510	54118510	Missense_Mutation	C	G	p.D60H
SEKI_SKIN	54118429	54118531	54118510	54118510	Missense_Mutation	C	G	p.D60H
KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	54110044	54110199	54110103	54110103	Nonsense_Mutation	G	A	p.R316*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CALCOCO1

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
exon_skip_92854	12	54108983:54109109:54109576:54109831:54110043:54110199	54109576:54109831	ENST00000262059.4,ENST00000550804.1,ENST00000548263.1,ENST00000549935.2	LIHC	rs3741658	chr12:54109733	A/G	1.04e-08
exon_skip_92854	12	54108983:54109109:54109576:54109831:54110043:54110199	54109576:54109831	ENST00000262059.4,ENST00000550804.1,ENST00000548263.1,ENST00000549935.2	LIHC	rs3741659	chr12:54109659	C/T	2.22e-07
exon_skip_92854	12	54108983:54109109:54109576:54109831:54110043:54110199	54109576:54109831	ENST00000262059.4,ENST00000550804.1,ENST00000548263.1,ENST00000549935.2	LUSC	rs3741659	chr12:54109659	C/T	2.26e-03
exon_skip_92854	12	54108983:54109109:54109576:54109831:54110043:54110199	54109576:54109831	ENST00000262059.4,ENST00000550804.1,ENST00000548263.1,ENST00000549935.2	STAD	rs3741658	chr12:54109733	A/G	4.77e-07
exon_skip_92854	12	54108983:54109109:54109576:54109831:54110043:54110199	54109576:54109831	ENST00000262059.4,ENST00000550804.1,ENST00000548263.1,ENST00000549935.2	THCA	rs3741659	chr12:54109659	C/T	2.17e-03
exon_skip_92856	12	54109576:54109831:54110043:54110199:54113522:54113613	54110043:54110199	ENST00000262059.4,ENST00000550804.1,ENST00000552282.1,ENST00000548263.1,ENST00000549935.2	CESC	rs2277369	chr12:54110197	C/T	6.07e-20
exon_skip_92856	12	54109576:54109831:54110043:54110199:54113522:54113613	54110043:54110199	ENST00000262059.4,ENST00000550804.1,ENST00000552282.1,ENST00000548263.1,ENST00000549935.2	ESCA	rs2277369	chr12:54110197	C/T	8.61e-25
exon_skip_92856	12	54109576:54109831:54110043:54110199:54113522:54113613	54110043:54110199	ENST00000262059.4,ENST00000550804.1,ENST00000552282.1,ENST00000548263.1,ENST00000549935.2	LIHC	rs2277369	chr12:54110197	C/T	5.66e-27
exon_skip_92856	12	54109576:54109831:54110043:54110199:54113522:54113613	54110043:54110199	ENST00000262059.4,ENST00000550804.1,ENST00000552282.1,ENST00000548263.1,ENST00000549935.2	THYM	rs2277369	chr12:54110197	C/T	5.50e-10
exon_skip_92856	12	54109576:54109831:54110043:54110199:54113522:54113613	54110043:54110199	ENST00000262059.4,ENST00000550804.1,ENST00000552282.1,ENST00000548263.1,ENST00000549935.2	THCA	rs2277369	chr12:54110197	C/T	1.13e-40
exon_skip_92856	12	54109576:54109831:54110043:54110199:54113522:54113613	54110043:54110199	ENST00000262059.4,ENST00000550804.1,ENST00000552282.1,ENST00000548263.1,ENST00000549935.2	UCS	rs2277369	chr12:54110197	C/T	3.95e-07

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CALCOCO1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CALCOCO1

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RelatedDrugs for CALCOCO1

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 CALCOCO1

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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