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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 CSMD3 |
 Gene summary |
| Gene information | Gene symbol | CSMD3 | Gene ID | 114788 |
| Gene name | CUB and Sushi multiple domains 3 | |
| Synonyms | - | |
| Cytomap | 8q23.3 | |
| Type of gene | protein-coding | |
| Description | CUB and sushi domain-containing protein 3CUB and sushi multiple domains 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 CSMD3 |
| 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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ENSG00000164796
| 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 |
| 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 CSMD3 |
| 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_106744 | chr8 | 112947790:112947877:112954684:112954761:113019067:113019179 | 112954684:112954761 |
| exon_skip_11642 | chr8 | 113278592:113278704:113314571:113314793:113436677:113436790 | 113314571:113314793 |
| exon_skip_156161 | chr8 | 112237190:112237348:112241720:112241785:112244394:112244573 | 112241720:112241785 |
| exon_skip_158086 | chr8 | 112954684:112954761:112975837:112976148:113019067:113019179 | 112975837:112976148 |
| exon_skip_15824 | chr8 | 112406524:112406727:112408318:112408413:112408919:112409032 | 112408318:112408413 |
| exon_skip_167358 | chr8 | 112650161:112650349:112656154:112656341:112666277:112666415 | 112656154:112656341 |
| exon_skip_169946 | chr8 | 112947790:112947877:112954684:112954761:112975837:112976148 | 112954684:112954761 |
| exon_skip_213262 | chr8 | 113098756:113098963:113173722:113173916:113278592:113278704 | 113173722:113173916 |
| exon_skip_216298 | chr8 | 112228756:112228891:112231545:112231632:112234365:112234477 | 112231545:112231632 |
| exon_skip_223901 | chr8 | 113278605:113278704:113314571:113314793:113436677:113436790 | 113314571:113314793 |
| exon_skip_66814 | chr8 | 112947790:112947877:112954684:112954761:112975837:112976012 | 112954684:112954761 |
| 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 CSMD3 |
| 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 |
| ENST00000297405 | 113314571 | 113314793 | Frame-shift |
| ENST00000297405 | 112241720 | 112241785 | In-frame |
| ENST00000297405 | 112408318 | 112408413 | In-frame |
| ENST00000297405 | 112954684 | 112954761 | In-frame |
| ENST00000297405 | 112975837 | 112976148 | 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 |
| ENST00000297405 | 112656154 | 112656341 | Frame-shift |
| ENST00000297405 | 113314571 | 113314793 | Frame-shift |
| ENST00000297405 | 112408318 | 112408413 | In-frame |
| ENST00000297405 | 112954684 | 112954761 | In-frame |
| ENST00000297405 | 112975837 | 112976148 | In-frame |
| ENST00000297405 | 113173722 | 113173916 | 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 |
| ENST00000297405 | 112231545 | 112231632 | Frame-shift |
| ENST00000297405 | 112241720 | 112241785 | In-frame |
| ENST00000297405 | 112408318 | 112408413 | In-frame |
| ENST00000297405 | 112954684 | 112954761 | In-frame |
| ENST00000297405 | 112975837 | 112976148 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CSMD3 |
p-ENSG00000164796_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 |
| ENST00000297405 | 13229 | 3707 | 112975837 | 112976148 | 1276 | 1586 | 343 | 447 |
| ENST00000297405 | 13229 | 3707 | 112954684 | 112954761 | 1588 | 1664 | 447 | 473 |
| ENST00000297405 | 13229 | 3707 | 112408318 | 112408413 | 5755 | 5849 | 1836 | 1868 |
| ENST00000297405 | 13229 | 3707 | 112241720 | 112241785 | 10648 | 10712 | 3467 | 3489 |
| 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 |
| ENST00000297405 | 13229 | 3707 | 113173722 | 113173916 | 760 | 953 | 171 | 236 |
| ENST00000297405 | 13229 | 3707 | 112975837 | 112976148 | 1276 | 1586 | 343 | 447 |
| ENST00000297405 | 13229 | 3707 | 112954684 | 112954761 | 1588 | 1664 | 447 | 473 |
| ENST00000297405 | 13229 | 3707 | 112408318 | 112408413 | 5755 | 5849 | 1836 | 1868 |
| 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 |
| ENST00000297405 | 13229 | 3707 | 112975837 | 112976148 | 1276 | 1586 | 343 | 447 |
| ENST00000297405 | 13229 | 3707 | 112954684 | 112954761 | 1588 | 1664 | 447 | 473 |
| ENST00000297405 | 13229 | 3707 | 112408318 | 112408413 | 5755 | 5849 | 1836 | 1868 |
| ENST00000297405 | 13229 | 3707 | 112241720 | 112241785 | 10648 | 10712 | 3467 | 3489 |
| 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 |
| Q7Z407 | 343 | 447 | 344 | 447 | Alternative sequence | ID=VSP_009048;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12906867;Dbxref=PMID:12906867 |
| Q7Z407 | 343 | 447 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 343 | 447 | 241 | 345 | Domain | Note=CUB 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00059 |
| Q7Z407 | 343 | 447 | 361 | 361 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 343 | 447 | 409 | 409 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 343 | 447 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 447 | 473 | 344 | 447 | Alternative sequence | ID=VSP_009048;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12906867;Dbxref=PMID:12906867 |
| Q7Z407 | 447 | 473 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 447 | 473 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 1836 | 1868 | 1799 | 1868 | Alternative sequence | ID=VSP_009050;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11572484;Dbxref=PMID:11572484 |
| Q7Z407 | 1836 | 1868 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 1836 | 1868 | 1762 | 1870 | Domain | Note=CUB 10;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00059 |
| Q7Z407 | 1836 | 1868 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 3467 | 3489 | 2676 | 3707 | Alternative sequence | ID=VSP_009052;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q7Z407 | 3467 | 3489 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 3467 | 3489 | 3409 | 3468 | Domain | Note=Sushi 28;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00302 |
| Q7Z407 | 3467 | 3489 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q7Z407 | 171 | 236 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 171 | 236 | 178 | 218 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q7Z407 | 171 | 236 | 204 | 235 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q7Z407 | 171 | 236 | 65 | 173 | Domain | Note=CUB 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00059 |
| Q7Z407 | 171 | 236 | 176 | 237 | Domain | Note=Sushi 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00302 |
| Q7Z407 | 171 | 236 | 219 | 219 | Natural variant | ID=VAR_017404;Note=I->M;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12943675;Dbxref=dbSNP:rs2219898,PMID:12943675 |
| Q7Z407 | 171 | 236 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 343 | 447 | 344 | 447 | Alternative sequence | ID=VSP_009048;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12906867;Dbxref=PMID:12906867 |
| Q7Z407 | 343 | 447 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 343 | 447 | 241 | 345 | Domain | Note=CUB 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00059 |
| Q7Z407 | 343 | 447 | 361 | 361 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 343 | 447 | 409 | 409 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 343 | 447 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 447 | 473 | 344 | 447 | Alternative sequence | ID=VSP_009048;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12906867;Dbxref=PMID:12906867 |
| Q7Z407 | 447 | 473 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 447 | 473 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 1836 | 1868 | 1799 | 1868 | Alternative sequence | ID=VSP_009050;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11572484;Dbxref=PMID:11572484 |
| Q7Z407 | 1836 | 1868 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 1836 | 1868 | 1762 | 1870 | Domain | Note=CUB 10;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00059 |
| Q7Z407 | 1836 | 1868 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q7Z407 | 343 | 447 | 344 | 447 | Alternative sequence | ID=VSP_009048;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12906867;Dbxref=PMID:12906867 |
| Q7Z407 | 343 | 447 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 343 | 447 | 241 | 345 | Domain | Note=CUB 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00059 |
| Q7Z407 | 343 | 447 | 361 | 361 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 343 | 447 | 409 | 409 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 343 | 447 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 447 | 473 | 344 | 447 | Alternative sequence | ID=VSP_009048;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12906867;Dbxref=PMID:12906867 |
| Q7Z407 | 447 | 473 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 447 | 473 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 1836 | 1868 | 1799 | 1868 | Alternative sequence | ID=VSP_009050;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11572484;Dbxref=PMID:11572484 |
| Q7Z407 | 1836 | 1868 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 1836 | 1868 | 1762 | 1870 | Domain | Note=CUB 10;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00059 |
| Q7Z407 | 1836 | 1868 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7Z407 | 3467 | 3489 | 2676 | 3707 | Alternative sequence | ID=VSP_009052;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q7Z407 | 3467 | 3489 | 1 | 3707 | Chain | ID=PRO_0000021027;Note=CUB and sushi domain-containing protein 3 |
| Q7Z407 | 3467 | 3489 | 3409 | 3468 | Domain | Note=Sushi 28;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00302 |
| Q7Z407 | 3467 | 3489 | 64 | 3630 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CSMD3 |
| 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 CSMD3 |
| - 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 CSMD3 |
| 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 CSMD3 |
| 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 CSMD3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | TARDBP | exon_skip_158086 | -5.840763e-01 | 1.101184e-03 |
| IFG | RBMS3 | exon_skip_158086 | -5.707242e-01 | 1.516535e-03 |
| IFG | PABPN1 | exon_skip_158086 | -4.571747e-01 | 1.444951e-02 |
| IFG | ZNF638 | exon_skip_158086 | -6.742505e-01 | 8.347738e-05 |
| IFG | RBM6 | exon_skip_158086 | -6.024400e-01 | 6.929200e-04 |
| IFG | CNOT4 | exon_skip_158086 | -5.499044e-01 | 2.433737e-03 |
| IFG | IGF2BP3 | exon_skip_158086 | -4.452836e-01 | 1.757096e-02 |
| IFG | RBM3 | exon_skip_158086 | 5.095250e-01 | 5.614111e-03 |
| IFG | UNK | exon_skip_158086 | -5.594086e-01 | 1.968557e-03 |
| IFG | TRA2A | exon_skip_158086 | -7.043999e-01 | 2.867111e-05 |
| IFG | PCBP2 | exon_skip_158086 | -4.237363e-01 | 2.463755e-02 |
| IFG | RC3H1 | exon_skip_158086 | -4.889686e-01 | 8.279127e-03 |
| IFG | SNRPA | exon_skip_158086 | -4.327439e-01 | 2.144445e-02 |
| IFG | SF1 | exon_skip_158086 | -6.737023e-01 | 8.501962e-05 |
| IFG | ENOX1 | exon_skip_158086 | -4.552313e-01 | 1.492566e-02 |
| IFG | RBM45 | exon_skip_158086 | -5.464895e-01 | 2.622533e-03 |
| IFG | PTBP1 | exon_skip_158086 | -6.189699e-01 | 4.455533e-04 |
| IFG | PABPC5 | exon_skip_158086 | -5.862072e-01 | 1.045021e-03 |
| IFG | SRSF1 | exon_skip_158086 | -4.760866e-01 | 1.043910e-02 |
| IFG | RBM41 | exon_skip_158086 | -4.095399e-01 | 3.044757e-02 |
| PCC | RBMS3 | exon_skip_158086 | -4.605668e-01 | 4.757994e-11 |
| PCC | UNK | exon_skip_158086 | -4.023230e-01 | 1.502765e-08 |
| PCC | KHDRBS2 | exon_skip_158086 | -4.065929e-01 | 1.021815e-08 |
| PCC | RBM45 | exon_skip_158086 | -4.296144e-01 | 1.160420e-09 |
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RelatedDrugs for CSMD3 |
| 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 CSMD3 |
| 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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