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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 CCDC38 |
 Gene summary |
| Gene information | Gene symbol | CCDC38 | Gene ID | 120935 |
| Gene name | coiled-coil domain containing 38 | |
| Synonyms | - | |
| Cytomap | 12q23.1 | |
| Type of gene | protein-coding | |
| Description | coiled-coil domain-containing protein 38 | |
| Modification date | 20180329 | |
| UniProtAcc | Q502W7 | |
| Context | PubMed: CCDC38 [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 CCDC38 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 CCDC38 |
| 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 CCDC38 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_95481 | 12 | 96266139:96266238:96271988:96272124:96273421:96273449 | 96271988:96272124 | ENSG00000165972.8 | ENST00000549876.1,ENST00000344280.3 |
| exon_skip_95482 | 12 | 96275262:96275332:96282235:96282284:96284609:96284708 | 96282235:96282284 | ENSG00000165972.8 | ENST00000344280.3 |
| exon_skip_95483 | 12 | 96284609:96284708:96288766:96288924:96292162:96292243 | 96288766:96288924 | ENSG00000165972.8 | ENST00000344280.3 |
| exon_skip_95484 | 12 | 96292162:96292243:96292345:96292509:96300164:96300229 | 96292345:96292509 | ENSG00000165972.8 | ENST00000344280.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CCDC38 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_95481 | 12 | 96266139:96266238:96271988:96272124:96273421:96273449 | 96271988:96272124 | ENSG00000165972.8 | ENST00000549876.1,ENST00000344280.3 |
| exon_skip_95482 | 12 | 96275262:96275332:96282235:96282284:96284609:96284708 | 96282235:96282284 | ENSG00000165972.8 | ENST00000344280.3 |
| exon_skip_95483 | 12 | 96284609:96284708:96288766:96288924:96292162:96292243 | 96288766:96288924 | ENSG00000165972.8 | ENST00000344280.3 |
| exon_skip_95484 | 12 | 96292162:96292243:96292345:96292509:96300164:96300229 | 96292345:96292509 | ENSG00000165972.8 | ENST00000344280.3 |
| exon_skip_95485 | 12 | 96312657:96312754:96313216:96313401:96330250:96330301 | 96313216:96313401 | ENSG00000165972.8 | ENST00000546803.1 |
| exon_skip_95486 | 12 | 96312719:96312754:96313216:96313435:96330250:96330301 | 96313216:96313435 | ENSG00000165972.8 | ENST00000549752.1 |
| exon_skip_95487 | 12 | 96312653:96312754:96313331:96313401:96330250:96330301 | 96313331:96313401 | ENSG00000165972.8 | ENST00000546947.1 |
| 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 CCDC38 |
| 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 |
| ENST00000344280 | 96271988 | 96272124 | Frame-shift |
| ENST00000344280 | 96282235 | 96282284 | Frame-shift |
| ENST00000344280 | 96288766 | 96288924 | Frame-shift |
| ENST00000344280 | 96292345 | 96292509 | Frame-shift |
| 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 |
| ENST00000344280 | 96271988 | 96272124 | Frame-shift |
| ENST00000344280 | 96282235 | 96282284 | Frame-shift |
| ENST00000344280 | 96288766 | 96288924 | Frame-shift |
| ENST00000344280 | 96292345 | 96292509 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for CCDC38 |
| 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 |
| 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 |
| 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 |
| 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 |
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SNVs in the skipped exons for CCDC38 |
| - 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-FW-A3R5-06 | exon_skip_95482 | 96282236 | 96282284 | 96282260 | 96282260 | Frame_Shift_Del | C | - | p.R299fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_95483 | 96288767 | 96288924 | 96288803 | 96288803 | Frame_Shift_Del | T | - | p.S246fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_95483 | 96288767 | 96288924 | 96288860 | 96288860 | Frame_Shift_Del | T | - | p.M227fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_95483 | 96288767 | 96288924 | 96288870 | 96288870 | Frame_Shift_Del | A | - | p.F223fs |
| STAD | TCGA-HU-A4GU-01 | exon_skip_95483 | 96288767 | 96288924 | 96288870 | 96288870 | Frame_Shift_Del | A | - | p.F223fs |
| STAD | TCGA-HU-A4GU-01 | exon_skip_95483 | 96288767 | 96288924 | 96288870 | 96288870 | Frame_Shift_Del | A | - | p.L224fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.K149fs |
| STAD | TCGA-BR-4361-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.A150fs |
| STAD | TCGA-BR-8360-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.A150fs |
| STAD | TCGA-CG-4442-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.A150fs |
| STAD | TCGA-CG-5733-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.A150fs |
| STAD | TCGA-HU-A4GT-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.A150fs |
| STAD | TCGA-R5-A7ZI-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.A150fs |
| STAD | TCGA-R5-A7ZI-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.K149fs |
| UCEC | TCGA-D1-A17M-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.K149fs |
| UCEC | TCGA-DI-A0WH-01 | exon_skip_95484 | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.K149fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_95484 | 96292346 | 96292509 | 96292465 | 96292465 | Frame_Shift_Del | T | - | p.D139fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_95484 | 96292346 | 96292509 | 96292465 | 96292465 | Frame_Shift_Del | T | - | p.K138fs |
| ESCA | TCGA-L5-A43J-01 | exon_skip_95481 | 96271989 | 96272124 | 96271999 | 96271999 | Nonsense_Mutation | G | T | p.S423* |
| ESCA | TCGA-L5-A43J-01 | exon_skip_95481 | 96271989 | 96272124 | 96271999 | 96271999 | Nonsense_Mutation | G | T | p.S423X |
| ESCA | TCGA-LN-A4MQ-01 | exon_skip_95481 | 96271989 | 96272124 | 96271999 | 96271999 | Nonsense_Mutation | G | C | p.S423X |
| SKCM | TCGA-EE-A3JD-06 | exon_skip_95481 | 96271989 | 96272124 | 96272009 | 96272009 | Nonsense_Mutation | C | A | p.E420* |
| SKCM | TCGA-EE-A3JD-06 | exon_skip_95481 | 96271989 | 96272124 | 96272009 | 96272009 | Nonsense_Mutation | C | A | p.E420X |
| HNSC | TCGA-CQ-5329-01 | exon_skip_95483 | 96288767 | 96288924 | 96288808 | 96288808 | Nonsense_Mutation | G | T | p.S244* |
| LUAD | TCGA-05-4424-01 | exon_skip_95484 | 96292346 | 96292509 | 96292380 | 96292380 | Nonsense_Mutation | C | A | p.E167* |
| SKCM | TCGA-EB-A5UM-01 | exon_skip_95484 | 96292346 | 96292509 | 96292383 | 96292383 | Nonsense_Mutation | G | A | p.R166* |
| - 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 |
| OVK18_OVARY | 96288767 | 96288924 | 96288821 | 96288821 | Frame_Shift_Del | T | - | p.R240fs |
| NCIH740_LUNG | 96288767 | 96288924 | 96288821 | 96288821 | Frame_Shift_Del | T | - | p.R240fs |
| OC316_OVARY | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.K149fs |
| RKO_LARGE_INTESTINE | 96292346 | 96292509 | 96292432 | 96292432 | Frame_Shift_Del | T | - | p.K149fs |
| LS411N_LARGE_INTESTINE | 96271989 | 96272124 | 96271994 | 96271994 | Missense_Mutation | C | T | p.A425T |
| TE11_OESOPHAGUS | 96288767 | 96288924 | 96288820 | 96288820 | Missense_Mutation | C | G | p.R240T |
| CW2_LARGE_INTESTINE | 96288767 | 96288924 | 96288862 | 96288862 | Missense_Mutation | T | C | p.Q226R |
| HT115_LARGE_INTESTINE | 96288767 | 96288924 | 96288877 | 96288877 | Missense_Mutation | C | T | p.G221D |
| MET2B | 96288767 | 96288924 | 96288885 | 96288885 | Missense_Mutation | C | T | p.M218I |
| MDAMB361_BREAST | 96292346 | 96292509 | 96292449 | 96292449 | Nonsense_Mutation | C | A | p.E144* |
| LS180_LARGE_INTESTINE | 96292346 | 96292509 | 96292509 | 96292509 | Splice_Site | A | G | p.Y124H |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CCDC38 |
| 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 |
| exon_skip_95483 | 12 | 96284609:96284708:96288766:96288924:96292162:96292243 | 96288766:96288924 | ENST00000344280.3 | LIHC | rs10859974 | chr12:96288860 | A/G | 5.88e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CCDC38 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CCDC38 |
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RelatedDrugs for CCDC38 |
| 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 CCDC38 |
| 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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