ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CALR

Gene summary

Gene information	Gene symbol	CALR
	Gene ID	811
	Gene name	calreticulin
	Synonyms	CRT\|HEL-S-99n\|RO\|SSA\|cC1qR
	Cytomap	19p13.13
	Type of gene	protein-coding
	Description	calreticulinCRP55ERp60HACBPSicca syndrome antigen A (autoantigen Ro; calreticulin)calregulinendoplasmic reticulum resident protein 60epididymis secretory sperm binding protein Li 99ngrp60
	Modification date	20180527
	UniProtAcc	P27797
	Context	PubMed: CALR [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
CALR	GO:0000122	negative regulation of transcription by RNA polymerase II	8107809
CALR	GO:0006611	protein export from nucleus	11149926
CALR	GO:0017148	negative regulation of translation	14726956
CALR	GO:0033144	negative regulation of intracellular steroid hormone receptor signaling pathway	8107809
CALR	GO:0034504	protein localization to nucleus	15998798
CALR	GO:0045665	negative regulation of neuron differentiation	8107809
CALR	GO:0045892	negative regulation of transcription, DNA-templated	8107809
CALR	GO:0048387	negative regulation of retinoic acid receptor signaling pathway	8107809

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Exon skipping events across known transcript of Ensembl for CALR 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 CALR

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 CALR

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_302705	19	13049458:13049584:13049947:13050049:13050241:13050445	13049947:13050049	ENSG00000179218.9	ENST00000316448.5,ENST00000590325.1
exon_skip_302710	19	13050011:13050049:13050241:13050445:13050866:13050961	13050241:13050445	ENSG00000179218.9	ENST00000316448.5,ENST00000590325.1
exon_skip_302713	19	13051405:13051468:13051557:13051701:13054350:13054443	13051557:13051701	ENSG00000179218.9	ENST00000316448.5,ENST00000586760.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for CALR

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_302705	19	13049458:13049584:13049947:13050049:13050241:13050445	13049947:13050049	ENSG00000179218.9	ENST00000316448.5,ENST00000590325.1
exon_skip_302710	19	13050011:13050049:13050241:13050445:13050866:13050961	13050241:13050445	ENSG00000179218.9	ENST00000316448.5,ENST00000590325.1
exon_skip_302713	19	13051405:13051468:13051557:13051701:13054350:13054443	13051557:13051701	ENSG00000179218.9	ENST00000316448.5,ENST00000586760.1

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 CALR

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
ENST00000316448	13049947	13050049	In-frame
ENST00000316448	13050241	13050445	In-frame
ENST00000316448	13051557	13051701	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
ENST00000316448	13049947	13050049	In-frame
ENST00000316448	13050241	13050445	In-frame
ENST00000316448	13051557	13051701	In-frame

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

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
ENST00000316448	1920	417	13049947	13050049	165	266	30	64
ENST00000316448	1920	417	13050241	13050445	267	470	64	132
ENST00000316448	1920	417	13051557	13051701	890	1033	272	320

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
ENST00000316448	1920	417	13049947	13050049	165	266	30	64
ENST00000316448	1920	417	13050241	13050445	267	470	64	132
ENST00000316448	1920	417	13051557	13051701	890	1033	272	320

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
P27797	30	64	37	39	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	30	64	42	44	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	30	64	49	52	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	30	64	18	417	Chain	ID=PRO_0000004173;Note=Calreticulin
P27797	30	64	30	35	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	30	64	62	62	Metal binding	Note=Calcium%3B via carbonyl oxygen
P27797	30	64	64	64	Metal binding	Note=Calcium%3B via carbonyl oxygen
P27797	30	64	48	48	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P27797	30	64	18	197	Region	Note=N-domain
P27797	30	64	60	63	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	65	68	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	70	84	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	91	98	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	104	107	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	110	113	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	129	138	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	109	109	Binding site	Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
P27797	64	132	111	111	Binding site	Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
P27797	64	132	128	128	Binding site	Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
P27797	64	132	18	417	Chain	ID=PRO_0000004173;Note=Calreticulin
P27797	64	132	105	137	Disulfide bond	Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11322874,ECO:0000269\|PubMed:21423620;Dbxref=PMID:11322874,PMID:21423620
P27797	64	132	119	121	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	64	64	Metal binding	Note=Calcium%3B via carbonyl oxygen
P27797	64	132	18	197	Region	Note=N-domain
P27797	272	320	311	322	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	272	320	317	317	Binding site	Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
P27797	272	320	18	417	Chain	ID=PRO_0000004173;Note=Calreticulin
P27797	272	320	198	308	Region	Note=P-domain
P27797	272	320	259	297	Region	Note=3 X approximate repeats
P27797	272	320	309	417	Region	Note=C-domain
P27797	272	320	273	283	Repeat	Note=2-2
P27797	272	320	287	297	Repeat	Note=2-3
P27797	272	320	303	306	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LK5

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
P27797	30	64	37	39	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	30	64	42	44	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	30	64	49	52	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	30	64	18	417	Chain	ID=PRO_0000004173;Note=Calreticulin
P27797	30	64	30	35	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	30	64	62	62	Metal binding	Note=Calcium%3B via carbonyl oxygen
P27797	30	64	64	64	Metal binding	Note=Calcium%3B via carbonyl oxygen
P27797	30	64	48	48	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P27797	30	64	18	197	Region	Note=N-domain
P27797	30	64	60	63	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	65	68	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	70	84	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	91	98	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	104	107	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	110	113	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	129	138	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	109	109	Binding site	Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
P27797	64	132	111	111	Binding site	Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
P27797	64	132	128	128	Binding site	Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
P27797	64	132	18	417	Chain	ID=PRO_0000004173;Note=Calreticulin
P27797	64	132	105	137	Disulfide bond	Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11322874,ECO:0000269\|PubMed:21423620;Dbxref=PMID:11322874,PMID:21423620
P27797	64	132	119	121	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	64	132	64	64	Metal binding	Note=Calcium%3B via carbonyl oxygen
P27797	64	132	18	197	Region	Note=N-domain
P27797	272	320	311	322	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3POW
P27797	272	320	317	317	Binding site	Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
P27797	272	320	18	417	Chain	ID=PRO_0000004173;Note=Calreticulin
P27797	272	320	198	308	Region	Note=P-domain
P27797	272	320	259	297	Region	Note=3 X approximate repeats
P27797	272	320	309	417	Region	Note=C-domain
P27797	272	320	273	283	Repeat	Note=2-2
P27797	272	320	287	297	Repeat	Note=2-3
P27797	272	320	303	306	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LK5

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SNVs in the skipped exons for CALR

- 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
LUSC	TCGA-66-2727-01	exon_skip_302713	13051558	13051701	13051633	13051633	Nonsense_Mutation	G	T	p.E298*

- 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
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	13049948	13050049	13049975	13049975	Missense_Mutation	C	T	p.S40F
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	13049948	13050049	13049989	13049989	Missense_Mutation	G	T	p.D45Y
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	13050242	13050445	13050319	13050319	Missense_Mutation	C	A	p.L91M
D502MG_CENTRAL_NERVOUS_SYSTEM	13050242	13050445	13050388	13050388	Missense_Mutation	C	T	p.P114S
TT_THYROID	13050242	13050445	13050434	13050434	Missense_Mutation	A	T	p.N129I
639V_URINARY_TRACT	13051558	13051701	13051578	13051578	Missense_Mutation	G	T	p.Q279H
JHUEM7_ENDOMETRIUM	13051558	13051701	13051623	13051623	Missense_Mutation	T	G	p.I294M
SKMM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	13051558	13051701	13051645	13051645	Missense_Mutation	G	A	p.D302N

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

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 CALR

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

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RelatedDrugs for CALR

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
	P27797	DB00031	Tenecteplase	Calreticulin	biotech	approved
	P27797	DB11348	Calcium Phosphate	Calreticulin	small molecule	approved
	P27797	DB00025	Antihemophilic factor, human recombinant	Calreticulin	biotech	approved\|investigational
	P27797	DB11093	Calcium Citrate	Calreticulin	small molecule	approved\|investigational
	P27797	DB01065	Melatonin	Calreticulin	small molecule	approved\|nutraceutical\|vet_approved

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RelatedDiseases for CALR

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
CALR	C0033975	Psychotic Disorders	2	PSYGENET
CALR	C0036337	Schizoaffective Disorder	2	PSYGENET
CALR	C0349204	Nonorganic psychosis	2	PSYGENET
CALR	C0005586	Bipolar Disorder	1	PSYGENET
CALR	C0009404	Colorectal Neoplasms	1	CTD_human
CALR	C0025205	Melanoma, Experimental	1	CTD_human
CALR	C0027626	Neoplasm Invasiveness	1	CTD_human
CALR	C0033578	Prostatic Neoplasms	1	CTD_human
CALR	C0033937	Psychoses, Drug	1	PSYGENET
CALR	C0036349	Paranoid Schizophrenia	1	PSYGENET
CALR	C0036939	Shared Paranoid Disorder	1	PSYGENET
CALR	C0151744	Myocardial Ischemia	1	CTD_human
CALR	C0279626	Squamous cell carcinoma of esophagus	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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