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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 CCDC39 |
 Gene summary |
| Gene information | Gene symbol | CCDC39 | Gene ID | 339829 |
| Gene name | coiled-coil domain containing 39 | |
| Synonyms | CILD14|FAP59 | |
| Cytomap | 3q26.33 | |
| Type of gene | protein-coding | |
| Description | coiled-coil domain-containing protein 39 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9UFE4 | |
| Context | PubMed: CCDC39 [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 CCDC39 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 CCDC39 |
| 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 CCDC39 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_390283 | 3 | 180331601:180331652:180332783:180332865:180334068:180334151 | 180332783:180332865 | ENSG00000145075.7 | ENST00000473854.1 |
| exon_skip_390284 | 3 | 180332783:180332865:180334068:180334151:180334303:180334405 | 180334068:180334151 | ENSG00000145075.7 | ENST00000442201.2,ENST00000476379.1,ENST00000273654.4 |
| exon_skip_390285 | 3 | 180337046:180337153:180337598:180337758:180349256:180349380 | 180337598:180337758 | ENSG00000145075.7 | ENST00000442201.2 |
| exon_skip_390286 | 3 | 180369950:180370054:180372549:180372741:180377239:180377368 | 180372549:180372741 | ENSG00000145075.7 | ENST00000442201.2,ENST00000476379.1,ENST00000273654.4 |
| exon_skip_390287 | 3 | 180377239:180377368:180377464:180377557:180378357:180378516 | 180377464:180377557 | ENSG00000145075.7 | ENST00000442201.2,ENST00000476379.1,ENST00000273654.4 |
| exon_skip_390288 | 3 | 180381654:180381774:180397078:180397170:180397395:180397587 | 180397078:180397170 | ENSG00000145075.7 | ENST00000476379.1,ENST00000273654.4 |
| exon_skip_390290 | 3 | 180443302:180443361:180451266:180451470:180452274:180452394 | 180451266:180451470 | ENSG00000145075.7 | ENST00000485055.1 |
| exon_skip_390295 | 3 | 180499771:180499912:180528197:180528258:180565294:180565412 | 180528197:180528258 | ENSG00000145075.7 | ENST00000485055.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CCDC39 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_390283 | 3 | 180331601:180331652:180332783:180332865:180334068:180334151 | 180332783:180332865 | ENSG00000145075.7 | ENST00000473854.1 |
| exon_skip_390284 | 3 | 180332783:180332865:180334068:180334151:180334303:180334405 | 180334068:180334151 | ENSG00000145075.7 | ENST00000476379.1,ENST00000273654.4,ENST00000442201.2 |
| exon_skip_390285 | 3 | 180337046:180337153:180337598:180337758:180349256:180349380 | 180337598:180337758 | ENSG00000145075.7 | ENST00000442201.2 |
| exon_skip_390286 | 3 | 180369950:180370054:180372549:180372741:180377239:180377368 | 180372549:180372741 | ENSG00000145075.7 | ENST00000476379.1,ENST00000273654.4,ENST00000442201.2 |
| exon_skip_390287 | 3 | 180377239:180377368:180377464:180377557:180378357:180378516 | 180377464:180377557 | ENSG00000145075.7 | ENST00000476379.1,ENST00000273654.4,ENST00000442201.2 |
| exon_skip_390288 | 3 | 180381654:180381774:180397078:180397170:180397395:180397587 | 180397078:180397170 | ENSG00000145075.7 | ENST00000476379.1,ENST00000273654.4 |
| exon_skip_390290 | 3 | 180443302:180443361:180451266:180451470:180452274:180452394 | 180451266:180451470 | ENSG00000145075.7 | ENST00000485055.1 |
| exon_skip_390294 | 3 | 180455280:180455602:180465667:180465831:180466033:180466104 | 180465667:180465831 | ENSG00000145075.7 | ENST00000485055.1 |
| exon_skip_390295 | 3 | 180499771:180499912:180528197:180528258:180565294:180565412 | 180528197:180528258 | ENSG00000145075.7 | ENST00000485055.1 |
| 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 CCDC39 |
| 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 |
| 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 |
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Infer the effects of exon skipping event on protein functional features for CCDC39 |
| 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 CCDC39 |
| - 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 |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_390284 | 180334069 | 180334151 | 180334106 | 180334106 | Frame_Shift_Del | T | - | p.S879fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_390286 | 180372550 | 180372741 | 180372604 | 180372604 | Frame_Shift_Del | T | - | p.K376fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_390286 | 180372550 | 180372741 | 180372636 | 180372636 | Frame_Shift_Del | T | - | p.R366fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_390286 | 180372550 | 180372741 | 180372658 | 180372658 | Frame_Shift_Del | C | - | p.G358fs |
| HNSC | TCGA-BA-6869-01 | exon_skip_390286 | 180372550 | 180372741 | 180372672 | 180372672 | Frame_Shift_Del | C | - | p.E270fs |
| HNSC | TCGA-BA-6869-01 | exon_skip_390286 | 180372550 | 180372741 | 180372672 | 180372672 | Frame_Shift_Del | C | - | p.E354fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_390286 | 180372550 | 180372741 | 180372674 | 180372674 | Frame_Shift_Del | A | - | p.L353fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_390286 | 180372550 | 180372741 | 180372698 | 180372698 | Frame_Shift_Del | A | - | p.L345fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_390286 | 180372550 | 180372741 | 180372706 | 180372706 | Frame_Shift_Del | T | - | p.K342fs |
| COAD | TCGA-CA-6718-01 | exon_skip_390286 | 180372550 | 180372741 | 180372579 | 180372579 | Nonsense_Mutation | C | A | p.E301X |
| LUAD | TCGA-44-7671-01 | exon_skip_390286 | 180372550 | 180372741 | 180372601 | 180372601 | Nonsense_Mutation | A | T | p.C293* |
| LUAD | TCGA-44-7671-01 | exon_skip_390286 | 180372550 | 180372741 | 180372601 | 180372601 | Nonsense_Mutation | A | T | p.C377* |
| BLCA | TCGA-KQ-A41P-01 | exon_skip_390287 | 180377465 | 180377557 | 180377515 | 180377515 | Nonsense_Mutation | G | A | p.Q271* |
| HNSC | TCGA-CV-A45X-01 | exon_skip_390287 | 180377465 | 180377557 | 180377524 | 180377524 | Nonsense_Mutation | C | A | p.E268* |
| OV | TCGA-13-0887-01 | exon_skip_390287 | 180377465 | 180377557 | 180377524 | 180377524 | Nonsense_Mutation | C | A | p.E184* |
| STAD | TCGA-BR-4191-01 | exon_skip_390288 | 180397079 | 180397170 | 180397081 | 180397081 | Nonsense_Mutation | G | A | p.Q30* |
| STAD | TCGA-BR-4191-01 | exon_skip_390288 | 180397079 | 180397170 | 180397081 | 180397081 | Nonsense_Mutation | G | A | p.Q30X |
| BLCA | TCGA-E5-A4U1-01 | exon_skip_390288 | 180397079 | 180397170 | 180397136 | 180397136 | Nonsense_Mutation | C | T | p.W95* |
| - 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 |
| LS180_LARGE_INTESTINE | 180337599 | 180337758 | 180337714 | 180337717 | Frame_Shift_Del | CAAA | - | p.CL680fs |
| PC3_PROSTATE | 180332784 | 180332865 | 180332844 | 180332849 | In_Frame_Del | TGTACT | - | p.ST898del |
| PC3JPC3_LUNG | 180332784 | 180332865 | 180332844 | 180332849 | In_Frame_Del | TGTACT | - | p.ST898del |
| NCIH847_LUNG | 180332784 | 180332865 | 180332830 | 180332830 | Missense_Mutation | G | T | p.S902Y |
| KYSE270_OESOPHAGUS | 180332784 | 180332865 | 180332836 | 180332836 | Missense_Mutation | G | C | p.S900C |
| CW2_LARGE_INTESTINE | 180332784 | 180332865 | 180332852 | 180332852 | Missense_Mutation | T | C | p.T895A |
| K5_THYROID | 180334069 | 180334151 | 180334135 | 180334135 | Missense_Mutation | G | A | p.P868L |
| MDAMB361_BREAST | 180334069 | 180334151 | 180334142 | 180334142 | Missense_Mutation | C | T | p.E866K |
| HEC251_ENDOMETRIUM | 180372550 | 180372741 | 180372569 | 180372569 | Missense_Mutation | C | T | p.R304K |
| NCIH1568_LUNG | 180372550 | 180372741 | 180372585 | 180372585 | Missense_Mutation | C | A | p.D299Y |
| SNUC1_LARGE_INTESTINE | 180377465 | 180377557 | 180377511 | 180377511 | Missense_Mutation | T | G | p.K188T |
| VMCUB1_URINARY_TRACT | 180397079 | 180397170 | 180397084 | 180397084 | Missense_Mutation | C | T | p.D29N |
| HUH1_LIVER | 180397079 | 180397170 | 180397121 | 180397122 | Missense_Mutation | GG | TT | p.A16E |
| HCC2998_LARGE_INTESTINE | 180397079 | 180397170 | 180397156 | 180397156 | Missense_Mutation | A | C | p.F5V |
| LNCAPCLONEFGC_PROSTATE | 180337599 | 180337758 | 180337678 | 180337678 | Nonsense_Mutation | G | C | p.Y693* |
| GP2D_LARGE_INTESTINE | 180334069 | 180334151 | 180334069 | 180334069 | Splice_Site | C | T | p.R890K |
| RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 180337599 | 180337758 | 180337599 | 180337599 | Splice_Site | T | C | p.S720G |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CCDC39 |
| 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 CCDC39 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CCDC39 |
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RelatedDrugs for CCDC39 |
| 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 CCDC39 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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