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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for CCDC42 |
 Gene summary |
| Gene information | Gene symbol | CCDC42 | Gene ID | 146849 |
| Gene name | coiled-coil domain containing 42 | |
| Synonyms | CCDC42A | |
| Cytomap | 17p13.1 | |
| Type of gene | protein-coding | |
| Description | coiled-coil domain-containing protein 42coiled-coil domain-containing protein 42A | |
| Modification date | 20180519 | |
| UniProtAcc | Q96M95 | |
| Context | PubMed: CCDC42 [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 |
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Exon skipping events across known transcript of Ensembl for CCDC42 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 CCDC42 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for CCDC42 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_286604 | 17 | 8638413:8638572:8638707:8638929:8644791:8644989 | 8638707:8638929 | ENSG00000161973.6 | ENST00000293845.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CCDC42 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_286604 | 17 | 8638413:8638572:8638707:8638929:8644791:8644989 | 8638707:8638929 | ENSG00000161973.6 | ENST00000293845.3 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for CCDC42 |
| 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 |
| ENST00000293845 | 8638707 | 8638929 | 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 |
| ENST00000293845 | 8638707 | 8638929 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CCDC42 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 |
| ENST00000293845 | 1391 | 316 | 8638707 | 8638929 | 720 | 941 | 164 | 238 |
| 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 |
| ENST00000293845 | 1391 | 316 | 8638707 | 8638929 | 720 | 941 | 164 | 238 |
| 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 |
| Q96M95 | 164 | 238 | 165 | 238 | Alternative sequence | ID=VSP_055651;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96M95 | 164 | 238 | 1 | 316 | Chain | ID=PRO_0000234498;Note=Coiled-coil domain-containing protein 42 |
| Q96M95 | 164 | 238 | 178 | 232 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q96M95 | 164 | 238 | 165 | 238 | Alternative sequence | ID=VSP_055651;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96M95 | 164 | 238 | 1 | 316 | Chain | ID=PRO_0000234498;Note=Coiled-coil domain-containing protein 42 |
| Q96M95 | 164 | 238 | 178 | 232 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for CCDC42 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - 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 |
| SKCM | TCGA-FR-A726-01 | exon_skip_286604 | 8638708 | 8638929 | 8638781 | 8638785 | Frame_Shift_Del | ATCTC | - | p.EI213fs |
| BRCA | TCGA-BH-A1F8-01 | exon_skip_286604 | 8638708 | 8638929 | 8638833 | 8638833 | Nonsense_Mutation | C | A | p.E197* |
| - 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 |
| NCIH513_PLEURA | 8638708 | 8638929 | 8638758 | 8638758 | Missense_Mutation | C | G | p.A222P |
| HCC827_LUNG | 8638708 | 8638929 | 8638791 | 8638791 | Missense_Mutation | C | T | p.D211N |
| LU65_LUNG | 8638708 | 8638929 | 8638792 | 8638792 | Missense_Mutation | C | G | p.K210N |
| SNU1040_LARGE_INTESTINE | 8638708 | 8638929 | 8638811 | 8638811 | Missense_Mutation | G | A | p.A204V |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CCDC42 |
| 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 CCDC42 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CCDC42 |
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RelatedDrugs for CCDC42 |
| 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 |
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RelatedDiseases for CCDC42 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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