|
||||||
|
 | |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| 3'-UTR located exon skipping events lost miRNA binding sites |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| |
| |
|
Gene summary for CALCOCO2 |
 Gene summary |
| Gene information | Gene symbol | CALCOCO2 | Gene ID | 10241 |
| Gene name | calcium binding and coiled-coil domain 2 | |
| Synonyms | NDP52 | |
| Cytomap | 17q21.32 | |
| Type of gene | protein-coding | |
| Description | calcium-binding and coiled-coil domain-containing protein 2antigen nuclear dot 52 kDa proteinnuclear domain 10 protein 52nuclear domain 10 protein NDP52nuclear dot protein 52 | |
| Modification date | 20200327 | |
| 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 |
| CALCOCO2 | GO:0034341 | response to interferon-gamma | 9230084 |
Top |
Gene structures and expression levels for CALCOCO2 |
| 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. |
 |
ENSG00000136436
| 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. |
 |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | UP | ENST00000508679.5 | CALCOCO2-211:protein_coding:CALCOCO2 | 6.541165e+01 | 1.162688e+00 | 2.852964e-04 | 5.912186e-03 |
| PG | UP | ENST00000416445.6 | CALCOCO2-203:protein_coding:CALCOCO2 | 9.030350e+00 | 2.150517e+00 | 3.358425e-03 | 3.453511e-02 |
| CB | UP | ENST00000509112.1 | CALCOCO2-213:retained_intron:CALCOCO2 | 1.172444e+01 | 8.484894e-01 | 3.059190e-07 | 5.469080e-06 |
| TC | UP | ENST00000502761.1 | CALCOCO2-205:protein_coding:CALCOCO2 | 1.293429e+01 | 8.930897e-01 | 1.294078e-04 | 1.985188e-03 |
| TC | UP | ENST00000448105.6 | CALCOCO2-204:protein_coding:CALCOCO2 | 1.428703e+02 | 8.958295e-01 | 4.372518e-03 | 3.028073e-02 |
| TC | UP | ENST00000513119.5 | CALCOCO2-221:protein_coding:CALCOCO2 | 5.042102e+01 | 1.118647e+00 | 6.872598e-03 | 4.243691e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CALCOCO2 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
 |
| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_102335 | chr17 | 48848322:48848455:48849252:48849377:48851089:48851177 | 48849252:48849377 |
| exon_skip_104726 | chr17 | 48851603:48851628:48852506:48852628:48852926:48853012 | 48852506:48852628 |
| exon_skip_12814 | chr17 | 48841698:48841887:48846443:48846514:48848064:48848166 | 48846443:48846514 |
| exon_skip_153651 | chr17 | 48848322:48848455:48849252:48849377:48851089:48851124 | 48849252:48849377 |
| exon_skip_153959 | chr17 | 48856101:48856187:48860314:48860449:48862276:48862304 | 48860314:48860449 |
| exon_skip_153960 | chr17 | 48856092:48856187:48860314:48860449:48862276:48862304 | 48860314:48860449 |
| exon_skip_163757 | chr17 | 48848322:48848455:48848801:48848827:48849252:48849269 | 48848801:48848827 |
| exon_skip_164680 | chr17 | 48852961:48853012:48856092:48856187:48860314:48860360 | 48856092:48856187 |
| exon_skip_177165 | chr17 | 48831056:48831078:48841698:48841887:48848064:48848082 | 48841698:48841887 |
| exon_skip_191981 | chr17 | 48856101:48856187:48856579:48856616:48860314:48860360 | 48856579:48856616 |
| exon_skip_196698 | chr17 | 48841774:48841887:48843903:48844026:48848064:48848166 | 48843903:48844026 |
| exon_skip_19772 | chr17 | 48856579:48856616:48860314:48860449:48862276:48862304 | 48860314:48860449 |
| exon_skip_203096 | chr17 | 48831056:48831078:48841774:48841887:48848064:48848082 | 48841774:48841887 |
| exon_skip_210143 | chr17 | 48841774:48841887:48843903:48844026:48848064:48848082 | 48843903:48844026 |
| exon_skip_239237 | chr17 | 48841698:48841887:48843903:48844026:48848064:48848082 | 48843903:48844026 |
| exon_skip_24264 | chr17 | 48841698:48841887:48843903:48844026:48848064:48848166 | 48843903:48844026 |
| exon_skip_272653 | chr17 | 48831056:48831078:48839376:48839511:48841698:48841887 | 48839376:48839511 |
| exon_skip_282301 | chr17 | 48848335:48848455:48849252:48849377:48851089:48851124 | 48849252:48849377 |
| exon_skip_39098 | chr17 | 48848335:48848455:48848801:48848827:48849252:48849269 | 48848801:48848827 |
| exon_skip_92739 | chr17 | 48852506:48852628:48852926:48853012:48856092:48856174 | 48852926:48853012 |
| 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 |
| exon_skip_191981 | MSBB_PG | 1.522917e-01 | 2.565455e-01 | -1.042538e-01 | 2.831365e-05 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CALCOCO2 |
| 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 |
| ENST00000258947 | 48860314 | 48860449 | Frame-shift |
| ENST00000258947 | 48849252 | 48849377 | In-frame |
| ENST00000258947 | 48852506 | 48852628 | In-frame |
| ENST00000258947 | 48852926 | 48853012 | In-frame |
| ENST00000258947 | 48856092 | 48856187 | 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 |
| ENST00000258947 | 48860314 | 48860449 | Frame-shift |
| ENST00000258947 | 48849252 | 48849377 | In-frame |
| ENST00000258947 | 48852506 | 48852628 | In-frame |
| ENST00000258947 | 48856092 | 48856187 | 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 |
| ENST00000258947 | 48860314 | 48860449 | Frame-shift |
| ENST00000258947 | 48849252 | 48849377 | In-frame |
| ENST00000258947 | 48852506 | 48852628 | In-frame |
| ENST00000258947 | 48852926 | 48853012 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for CALCOCO2 |
p-ENSG00000136436_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 |
| ENST00000258947 | 3699 | 446 | 48849252 | 48849377 | 520 | 644 | 139 | 181 |
| ENST00000258947 | 3699 | 446 | 48852506 | 48852628 | 805 | 926 | 234 | 275 |
| ENST00000258947 | 3699 | 446 | 48852926 | 48853012 | 928 | 1013 | 275 | 304 |
| ENST00000258947 | 3699 | 446 | 48856092 | 48856187 | 1015 | 1109 | 304 | 336 |
| 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 |
| ENST00000258947 | 3699 | 446 | 48849252 | 48849377 | 520 | 644 | 139 | 181 |
| ENST00000258947 | 3699 | 446 | 48852506 | 48852628 | 805 | 926 | 234 | 275 |
| ENST00000258947 | 3699 | 446 | 48856092 | 48856187 | 1015 | 1109 | 304 | 336 |
| 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 |
| ENST00000258947 | 3699 | 446 | 48849252 | 48849377 | 520 | 644 | 139 | 181 |
| ENST00000258947 | 3699 | 446 | 48852506 | 48852628 | 805 | 926 | 234 | 275 |
| ENST00000258947 | 3699 | 446 | 48852926 | 48853012 | 928 | 1013 | 275 | 304 |
| 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 |
| Q13137 | 139 | 181 | 139 | 180 | Alternative sequence | ID=VSP_044728;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q13137 | 139 | 181 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 139 | 181 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13137 | 139 | 181 | 140 | 140 | Natural variant | ID=VAR_037489;Note=G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14702039;Dbxref=dbSNP:rs550510,PMID:14702039 |
| Q13137 | 234 | 275 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 234 | 275 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13137 | 234 | 275 | 248 | 248 | Natural variant | ID=VAR_037491;Note=V->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:14702039,ECO:0000269|Ref.3;Dbxref=dbSNP:rs2303015,PMID:14702039 |
| Q13137 | 234 | 275 | 273 | 273 | Natural variant | ID=VAR_037492;Note=T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs17849804,PMID:15489334 |
| Q13137 | 275 | 304 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 275 | 304 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13137 | 304 | 336 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 304 | 336 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13137 | 304 | 336 | 313 | 313 | Sequence conflict | Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q13137 | 139 | 181 | 139 | 180 | Alternative sequence | ID=VSP_044728;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q13137 | 139 | 181 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 139 | 181 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13137 | 139 | 181 | 140 | 140 | Natural variant | ID=VAR_037489;Note=G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14702039;Dbxref=dbSNP:rs550510,PMID:14702039 |
| Q13137 | 234 | 275 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 234 | 275 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13137 | 234 | 275 | 248 | 248 | Natural variant | ID=VAR_037491;Note=V->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:14702039,ECO:0000269|Ref.3;Dbxref=dbSNP:rs2303015,PMID:14702039 |
| Q13137 | 234 | 275 | 273 | 273 | Natural variant | ID=VAR_037492;Note=T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs17849804,PMID:15489334 |
| Q13137 | 304 | 336 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 304 | 336 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13137 | 304 | 336 | 313 | 313 | Sequence conflict | Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q13137 | 139 | 181 | 139 | 180 | Alternative sequence | ID=VSP_044728;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q13137 | 139 | 181 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 139 | 181 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13137 | 139 | 181 | 140 | 140 | Natural variant | ID=VAR_037489;Note=G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14702039;Dbxref=dbSNP:rs550510,PMID:14702039 |
| Q13137 | 234 | 275 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 234 | 275 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13137 | 234 | 275 | 248 | 248 | Natural variant | ID=VAR_037491;Note=V->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:14702039,ECO:0000269|Ref.3;Dbxref=dbSNP:rs2303015,PMID:14702039 |
| Q13137 | 234 | 275 | 273 | 273 | Natural variant | ID=VAR_037492;Note=T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs17849804,PMID:15489334 |
| Q13137 | 275 | 304 | 1 | 446 | Chain | ID=PRO_0000312337;Note=Calcium-binding and coiled-coil domain-containing protein 2 |
| Q13137 | 275 | 304 | 137 | 349 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in CALCOCO2 |
| 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 |
Top |
SNVs in the skipped exons for CALCOCO2 |
| - 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 |
Top |
AD stage-associated exon skippint events for CALCOCO2 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CALCOCO2 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for CALCOCO2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RALYL | exon_skip_191981 | 4.325209e-01 | 1.244863e-08 |
| DLPFC | RALYL | exon_skip_191981 | 4.122287e-01 | 1.836643e-15 |
| FL | SRSF2 | exon_skip_191981 | 4.335565e-01 | 4.145515e-10 |
| FL | SRSF11 | exon_skip_191981 | 4.723360e-01 | 5.979396e-12 |
| FL | ILF2 | exon_skip_191981 | 4.401746e-01 | 2.087279e-10 |
| FL | RBM24 | exon_skip_191981 | 5.042627e-01 | 1.194639e-13 |
| FL | RALYL | exon_skip_191981 | 5.491930e-01 | 2.314511e-16 |
| FL | SRSF9 | exon_skip_191981 | 4.173874e-01 | 2.085168e-09 |
| FL | EIF4B | exon_skip_191981 | 4.207472e-01 | 1.501056e-09 |
| IFG | RBM24 | exon_skip_191981 | 5.109592e-01 | 5.459159e-03 |
| IFG | RALYL | exon_skip_191981 | 6.402744e-01 | 2.428402e-04 |
| IFG | ESRP1 | exon_skip_191981 | 4.801388e-01 | 9.713995e-03 |
| PCC | SAMD4A | exon_skip_191981 | -4.991139e-01 | 6.049751e-15 |
| PCC | RALYL | exon_skip_191981 | 4.713786e-01 | 2.720404e-13 |
| PG | RBM24 | exon_skip_191981 | 4.588219e-01 | 9.395316e-12 |
| PG | RALYL | exon_skip_191981 | 5.558730e-01 | 1.560766e-17 |
| STG | RBM24 | exon_skip_191981 | 4.284638e-01 | 2.803492e-05 |
| STG | RALYL | exon_skip_191981 | 5.450900e-01 | 3.333016e-08 |
| TC | SRSF2 | exon_skip_191981 | 4.715923e-01 | 3.083942e-10 |
| TC | SAMD4A | exon_skip_191981 | -4.094796e-01 | 7.591419e-08 |
| TC | ILF2 | exon_skip_191981 | 4.394658e-01 | 6.106392e-09 |
| TC | RBM24 | exon_skip_191981 | 7.376040e-01 | 9.673613e-29 |
| TC | RALYL | exon_skip_191981 | 8.582235e-01 | 1.267187e-47 |
| TC | ESRP1 | exon_skip_191981 | 6.066003e-01 | 1.875366e-17 |
Top |
RelatedDrugs for CALCOCO2 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for CALCOCO2 |
| 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)
|