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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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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 | 20200329 | |
| UniProtAcc | ||
| Context |
| 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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Gene structures and expression levels for CALR |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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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ENSG00000179218
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | DOWN | ENST00000586967.1 | CALR-204:nonsense_mediated_decay:CALR | 5.169115e+01 | -1.451827e+00 | 2.146768e-17 | 2.765639e-14 |
| TC | DOWN | ENST00000586967.1 | CALR-204:nonsense_mediated_decay:CALR | 4.725628e+01 | -1.662009e+00 | 1.609274e-17 | 2.515515e-14 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CALR |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_247716 | chr19 | 12939134:12939235:12939428:12939631:12940053:12940147 | 12939428:12939631 |
| exon_skip_256589 | chr19 | 12938645:12938770:12939134:12939235:12939428:12939631 | 12939134:12939235 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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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 ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000316448 | 12939428 | 12939631 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000316448 | 12939428 | 12939631 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000316448 | 12939134 | 12939235 | In-frame |
| ENST00000316448 | 12939428 | 12939631 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CALR |
p-ENSG00000179218_img4.png |
| Loci of skipped exons in ROSMAP 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 | 12939428 | 12939631 | 268 | 470 | 65 | 132 |
| Loci of skipped exons in MSBB 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 | 12939428 | 12939631 | 268 | 470 | 65 | 132 |
| Loci of skipped exons in Mayo 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 | 12939134 | 12939235 | 166 | 266 | 31 | 64 |
| ENST00000316448 | 1920 | 417 | 12939428 | 12939631 | 268 | 470 | 65 | 132 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| 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 | 65 | 132 | 65 | 68 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 70 | 84 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 91 | 98 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 104 | 107 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 110 | 113 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 129 | 138 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 109 | 109 | Binding site | Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P27797 | 65 | 132 | 111 | 111 | Binding site | Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P27797 | 65 | 132 | 128 | 128 | Binding site | Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P27797 | 65 | 132 | 18 | 417 | Chain | ID=PRO_0000004173;Note=Calreticulin |
| P27797 | 65 | 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 | 65 | 132 | 119 | 121 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 18 | 197 | Region | Note=N-domain |
| Lost protein functional features of individual exon skipping events in MSBB. |
| 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 | 65 | 132 | 65 | 68 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 70 | 84 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 91 | 98 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 104 | 107 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 110 | 113 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 129 | 138 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 109 | 109 | Binding site | Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P27797 | 65 | 132 | 111 | 111 | Binding site | Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P27797 | 65 | 132 | 128 | 128 | Binding site | Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P27797 | 65 | 132 | 18 | 417 | Chain | ID=PRO_0000004173;Note=Calreticulin |
| P27797 | 65 | 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 | 65 | 132 | 119 | 121 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 18 | 197 | Region | Note=N-domain |
| Lost protein functional features of individual exon skipping events in Mayo. |
| 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 | 31 | 64 | 37 | 39 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 31 | 64 | 42 | 44 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 31 | 64 | 49 | 52 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 31 | 64 | 18 | 417 | Chain | ID=PRO_0000004173;Note=Calreticulin |
| P27797 | 31 | 64 | 30 | 35 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 31 | 64 | 62 | 62 | Metal binding | Note=Calcium%3B via carbonyl oxygen |
| P27797 | 31 | 64 | 64 | 64 | Metal binding | Note=Calcium%3B via carbonyl oxygen |
| P27797 | 31 | 64 | 48 | 48 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P27797 | 31 | 64 | 18 | 197 | Region | Note=N-domain |
| P27797 | 31 | 64 | 60 | 63 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 65 | 68 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 70 | 84 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 91 | 98 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 104 | 107 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 110 | 113 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 129 | 138 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 109 | 109 | Binding site | Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P27797 | 65 | 132 | 111 | 111 | Binding site | Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P27797 | 65 | 132 | 128 | 128 | Binding site | Note=Carbohydrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P27797 | 65 | 132 | 18 | 417 | Chain | ID=PRO_0000004173;Note=Calreticulin |
| P27797 | 65 | 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 | 65 | 132 | 119 | 121 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3POW |
| P27797 | 65 | 132 | 18 | 197 | Region | Note=N-domain |
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3'-UTR located exon skipping events that lost miRNA binding sites in CALR |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for CALR |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
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AD stage-associated exon skippint events for CALR |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CALR |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for CALR |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for CALR |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P27797 | approved|investigational | DB00025 | Antihemophilic factor, human recombinant | biotech | P27797 |
| P27797 | approved | DB00031 | Tenecteplase | biotech | P27797 |
| P27797 | approved|nutraceutical|vet_approved | DB01065 | Melatonin | small molecule | P27797 |
| P27797 | approved|investigational | DB11093 | Calcium Citrate | small molecule | P27797 |
| P27797 | approved | DB11348 | Calcium Phosphate | small molecule | P27797 |
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RelatedDiseases for CALR |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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