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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 CBWD3 |
 Gene summary |
| Gene information | Gene symbol | CBWD3 | Gene ID | 445571 |
| Gene name | COBW domain containing 3 | |
| Synonyms | bA561O23.1 | |
| Cytomap | 9q21.11 | |
| Type of gene | protein-coding | |
| Description | COBW domain-containing protein 3cobalamin synthase W domain-containing protein 3cobalamin synthetase W domain-containing protein 3 | |
| Modification date | 20200313 | |
| 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 |
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Gene structures and expression levels for CBWD3 |
| 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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ENSG00000196873
| 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 | ENST00000612050.4 | CBWD3-208:nonsense_mediated_decay:CBWD3 | 3.497138e+00 | -1.370534e+00 | 4.386725e-03 | 1.767592e-02 |
| 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 CBWD3 |
| 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_118730 | chr9 | 68269600:68269722:68274882:68274938:68285989:68286040 | 68274882:68274938 |
| exon_skip_122500 | chr9 | 68269600:68269722:68269852:68269896:68270302:68270385 | 68269852:68269896 |
| exon_skip_12271 | chr9 | 68264468:68264514:68266220:68266306:68268934:68268978 | 68266220:68266306 |
| exon_skip_157451 | chr9 | 68248821:68248897:68256921:68256980:68258532:68258569 | 68256921:68256980 |
| exon_skip_160212 | chr9 | 68264468:68264514:68266220:68266306:68268934:68268977 | 68266220:68266306 |
| exon_skip_162586 | chr9 | 68241989:68242185:68245213:68245299:68247613:68247709 | 68245213:68245299 |
| exon_skip_165611 | chr9 | 68285989:68286040:68297580:68297648:68297752:68297817 | 68297580:68297648 |
| exon_skip_174159 | chr9 | 68258532:68258569:68264468:68264514:68266220:68266306 | 68264468:68264514 |
| exon_skip_182979 | chr9 | 68248806:68248897:68256921:68256980:68258532:68258569 | 68256921:68256980 |
| exon_skip_18850 | chr9 | 68235000:68235128:68245213:68245299:68247613:68247709 | 68245213:68245299 |
| exon_skip_18968 | chr9 | 68232437:68232495:68235000:68235128:68245213:68245299 | 68235000:68235128 |
| exon_skip_190333 | chr9 | 68259347:68259434:68264468:68264514:68266220:68266306 | 68264468:68264514 |
| exon_skip_201876 | chr9 | 68259347:68259434:68260857:68260996:68264468:68264514 | 68260857:68260996 |
| exon_skip_227287 | chr9 | 68258532:68258569:68259347:68259434:68264468:68264514 | 68259347:68259434 |
| exon_skip_232649 | chr9 | 68264468:68264514:68268934:68268978:68285989:68286040 | 68268934:68268978 |
| exon_skip_24156 | chr9 | 68270302:68270385:68272992:68273197:68274882:68274938 | 68272992:68273197 |
| exon_skip_243071 | chr9 | 68258532:68258569:68259347:68259434:68260857:68261001 | 68259347:68259434 |
| exon_skip_256617 | chr9 | 68266220:68266306:68268934:68268978:68285989:68286040 | 68268934:68268978 |
| exon_skip_262395 | chr9 | 68268934:68268978:68285989:68286040:68297580:68297648 | 68285989:68286040 |
| exon_skip_264708 | chr9 | 68264478:68264514:68266220:68266306:68268934:68268978 | 68266220:68266306 |
| exon_skip_283938 | chr9 | 68297752:68297817:68298964:68299093:68299481:68299644 | 68298964:68299093 |
| exon_skip_284529 | chr9 | 68268934:68268978:68270302:68270518:68274882:68274938 | 68270302:68270518 |
| exon_skip_48014 | chr9 | 68268934:68268978:68274882:68274938:68285989:68286040 | 68274882:68274938 |
| exon_skip_5927 | chr9 | 68241985:68242185:68243183:68243280:68245213:68245299 | 68243183:68243280 |
| exon_skip_79485 | chr9 | 68258532:68258569:68260857:68261001:68264468:68264514 | 68260857:68261001 |
| exon_skip_8642 | chr9 | 68241989:68242185:68243183:68243280:68245213:68245299 | 68243183:68243280 |
| exon_skip_958 | chr9 | 68268934:68268978:68269600:68269722:68274882:68274938 | 68269600:68269722 |
| exon_skip_97415 | chr9 | 68266220:68266306:68268934:68268978:68274882:68274938 | 68268934:68268978 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_227287 | Mayo_TC | 5.998734e-01 | 7.496970e-01 | -1.498236e-01 | 2.365324e-06 |
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Open reading frame (ORF) annotation in the exon skipping event for CBWD3 |
| 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 |
| ENST00000360171 | 68298964 | 68299093 | Frame-shift |
| ENST00000360171 | 68245213 | 68245299 | In-frame |
| ENST00000360171 | 68256921 | 68256980 | In-frame |
| ENST00000360171 | 68266220 | 68266306 | In-frame |
| ENST00000360171 | 68268934 | 68268978 | In-frame |
| ENST00000360171 | 68274882 | 68274938 | 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 |
| ENST00000360171 | 68264468 | 68264514 | Frame-shift |
| ENST00000360171 | 68256921 | 68256980 | In-frame |
| ENST00000360171 | 68266220 | 68266306 | In-frame |
| ENST00000360171 | 68274882 | 68274938 | 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 |
| ENST00000360171 | 68298964 | 68299093 | Frame-shift |
| ENST00000360171 | 68256921 | 68256980 | In-frame |
| ENST00000360171 | 68266220 | 68266306 | In-frame |
| ENST00000360171 | 68274882 | 68274938 | In-frame |
| ENST00000360171 | 68297580 | 68297648 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CBWD3 |
p-ENSG00000196873_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 |
| ENST00000360171 | 2182 | 395 | 68245213 | 68245299 | 707 | 792 | 52 | 80 |
| ENST00000360171 | 2182 | 395 | 68256921 | 68256980 | 983 | 1041 | 144 | 163 |
| ENST00000360171 | 2182 | 395 | 68266220 | 68266306 | 1128 | 1213 | 192 | 220 |
| ENST00000360171 | 2182 | 395 | 68268934 | 68268978 | 1215 | 1258 | 221 | 235 |
| ENST00000360171 | 2182 | 395 | 68274882 | 68274938 | 1260 | 1315 | 236 | 254 |
| 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 |
| ENST00000360171 | 2182 | 395 | 68256921 | 68256980 | 983 | 1041 | 144 | 163 |
| ENST00000360171 | 2182 | 395 | 68266220 | 68266306 | 1128 | 1213 | 192 | 220 |
| ENST00000360171 | 2182 | 395 | 68274882 | 68274938 | 1260 | 1315 | 236 | 254 |
| 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 |
| ENST00000360171 | 2182 | 395 | 68256921 | 68256980 | 983 | 1041 | 144 | 163 |
| ENST00000360171 | 2182 | 395 | 68266220 | 68266306 | 1128 | 1213 | 192 | 220 |
| ENST00000360171 | 2182 | 395 | 68274882 | 68274938 | 1260 | 1315 | 236 | 254 |
| ENST00000360171 | 2182 | 395 | 68297580 | 68297648 | 1369 | 1436 | 272 | 295 |
| 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 |
| Q5JTY5 | 52 | 80 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 52 | 80 | 49 | 56 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5JTY5 | 144 | 163 | 145 | 164 | Alternative sequence | ID=VSP_055975;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5JTY5 | 144 | 163 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 192 | 220 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 192 | 220 | 203 | 206 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5JTY5 | 221 | 235 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 236 | 254 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| 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 |
| Q5JTY5 | 144 | 163 | 145 | 164 | Alternative sequence | ID=VSP_055975;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5JTY5 | 144 | 163 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 192 | 220 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 192 | 220 | 203 | 206 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5JTY5 | 236 | 254 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| 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 |
| Q5JTY5 | 144 | 163 | 145 | 164 | Alternative sequence | ID=VSP_055975;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5JTY5 | 144 | 163 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 192 | 220 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 192 | 220 | 203 | 206 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5JTY5 | 236 | 254 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 272 | 295 | 1 | 395 | Chain | ID=PRO_0000317238;Note=COBW domain-containing protein 3 |
| Q5JTY5 | 272 | 295 | 274 | 377 | Domain | Note=CobW C-terminal |
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3'-UTR located exon skipping events that lost miRNA binding sites in CBWD3 |
| 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 CBWD3 |
| - 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 CBWD3 |
| 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 CBWD3 |
| 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 CBWD3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | PCBP4 | exon_skip_227287 | 5.272122e-01 | 1.820415e-12 |
| CB | TRA2A | exon_skip_227287 | -4.285895e-01 | 2.643182e-08 |
| DLPFC | PCBP4 | exon_skip_227287 | 4.747315e-01 | 6.927218e-19 |
| TC | RBM47 | exon_skip_227287 | -4.043790e-01 | 4.550223e-07 |
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RelatedDrugs for CBWD3 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for CBWD3 |
| 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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