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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 CCDC47 |
 Gene summary |
| Gene information | Gene symbol | CCDC47 | Gene ID | 57003 |
| Gene name | coiled-coil domain containing 47 | |
| Synonyms | GK001|MSTP041 | |
| Cytomap | 17q23.3 | |
| Type of gene | protein-coding | |
| Description | coiled-coil domain-containing protein 47Calumin | |
| Modification date | 20180523 | |
| UniProtAcc | Q96A33 | |
| Context | PubMed: CCDC47 [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 CCDC47 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 CCDC47 |
| 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 CCDC47 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_292339 | 17 | 61830139:61830159:61831792:61831878:61833599:61833710 | 61831792:61831878 | ENSG00000108588.9 | ENST00000403162.3,ENST00000225726.5,ENST00000582331.2,ENST00000582252.1 |
| exon_skip_292342 | 17 | 61833599:61833710:61833828:61833930:61838273:61838339 | 61833828:61833930 | ENSG00000108588.9 | ENST00000403162.3,ENST00000225726.5,ENST00000582331.2,ENST00000582252.1 |
| exon_skip_292343 | 17 | 61841375:61841550:61842099:61842207:61843271:61843554 | 61842099:61842207 | ENSG00000108588.9 | ENST00000403162.3,ENST00000225726.5,ENST00000582252.1 |
| exon_skip_292345 | 17 | 61843478:61843554:61850136:61850223:61850771:61850924 | 61850136:61850223 | ENSG00000108588.9 | ENST00000403162.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CCDC47 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_292339 | 17 | 61830139:61830159:61831792:61831878:61833599:61833710 | 61831792:61831878 | ENSG00000108588.9 | ENST00000225726.5,ENST00000403162.3,ENST00000582252.1,ENST00000582331.2 |
| exon_skip_292342 | 17 | 61833599:61833710:61833828:61833930:61838273:61838339 | 61833828:61833930 | ENSG00000108588.9 | ENST00000225726.5,ENST00000403162.3,ENST00000582252.1,ENST00000582331.2 |
| exon_skip_292343 | 17 | 61841375:61841550:61842099:61842207:61843271:61843554 | 61842099:61842207 | ENSG00000108588.9 | ENST00000225726.5,ENST00000403162.3,ENST00000582252.1 |
| exon_skip_292345 | 17 | 61843478:61843554:61850136:61850223:61850771:61850924 | 61850136:61850223 | ENSG00000108588.9 | ENST00000403162.3 |
| 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 CCDC47 |
| 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 |
| ENST00000403162 | 61850136 | 61850223 | 3UTR-3UTR |
| ENST00000225726 | 61831792 | 61831878 | Frame-shift |
| ENST00000403162 | 61831792 | 61831878 | Frame-shift |
| ENST00000225726 | 61833828 | 61833930 | In-frame |
| ENST00000403162 | 61833828 | 61833930 | In-frame |
| ENST00000225726 | 61842099 | 61842207 | In-frame |
| ENST00000403162 | 61842099 | 61842207 | 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 |
| ENST00000403162 | 61850136 | 61850223 | 3UTR-3UTR |
| ENST00000225726 | 61831792 | 61831878 | Frame-shift |
| ENST00000403162 | 61831792 | 61831878 | Frame-shift |
| ENST00000225726 | 61833828 | 61833930 | In-frame |
| ENST00000403162 | 61833828 | 61833930 | In-frame |
| ENST00000225726 | 61842099 | 61842207 | In-frame |
| ENST00000403162 | 61842099 | 61842207 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CCDC47 |
| 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 |
| ENST00000225726 | 3483 | 483 | 61842099 | 61842207 | 648 | 755 | 88 | 124 |
| ENST00000403162 | 2212 | 483 | 61842099 | 61842207 | 530 | 637 | 88 | 124 |
| ENST00000225726 | 3483 | 483 | 61833828 | 61833930 | 1119 | 1220 | 245 | 279 |
| ENST00000403162 | 2212 | 483 | 61833828 | 61833930 | 1001 | 1102 | 245 | 279 |
| 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 |
| ENST00000225726 | 3483 | 483 | 61842099 | 61842207 | 648 | 755 | 88 | 124 |
| ENST00000403162 | 2212 | 483 | 61842099 | 61842207 | 530 | 637 | 88 | 124 |
| ENST00000225726 | 3483 | 483 | 61833828 | 61833930 | 1119 | 1220 | 245 | 279 |
| ENST00000403162 | 2212 | 483 | 61833828 | 61833930 | 1001 | 1102 | 245 | 279 |
| 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 |
| Q96A33 | 88 | 124 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
| Q96A33 | 88 | 124 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
| Q96A33 | 245 | 279 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
| Q96A33 | 245 | 279 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
| 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 |
| Q96A33 | 88 | 124 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
| Q96A33 | 88 | 124 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
| Q96A33 | 245 | 279 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
| Q96A33 | 245 | 279 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
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SNVs in the skipped exons for CCDC47 |
| - 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_292339 | 61831793 | 61831878 | 61831827 | 61831827 | Frame_Shift_Del | A | - | p.S334fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_292339 | 61831793 | 61831878 | 61831827 | 61831827 | Frame_Shift_Del | A | - | p.S334fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_292339 | 61831793 | 61831878 | 61831827 | 61831827 | Frame_Shift_Del | A | - | p.S334X |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_292339 | 61831793 | 61831878 | 61831827 | 61831827 | Frame_Shift_Del | A | - | p.S334fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_292342 | 61833829 | 61833930 | 61833865 | 61833865 | Frame_Shift_Del | T | - | p.K267fs |
| COAD | TCGA-CM-4746-01 | 61842100 | 61842207 | 61842124 | 61842125 | Frame_Shift_Ins | - | T | p.N116fs | |
| LUSC | TCGA-60-2698-01 | 61842100 | 61842207 | 61842099 | 61842099 | Splice_Site | C | G | p.D124_splice |
| - 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 |
| HCC1954_BREAST | 61842100 | 61842207 | 61842196 | 61842198 | In_Frame_Del | AGT | - | p.T92del |
| HCC1954_MATCHED_NORMAL_TISSUE | 61842100 | 61842207 | 61842196 | 61842198 | In_Frame_Del | AGT | - | p.T92del |
| OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 61831793 | 61831878 | 61831840 | 61831840 | Missense_Mutation | T | G | p.E329D |
| JHUEM7_ENDOMETRIUM | 61833829 | 61833930 | 61833865 | 61833865 | Missense_Mutation | T | A | p.K267N |
| BIN67_OVARY | 61833829 | 61833930 | 61833870 | 61833870 | Missense_Mutation | G | A | p.R266W |
| HCC1438_LUNG | 61833829 | 61833930 | 61833878 | 61833878 | Missense_Mutation | A | C | p.V263G |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CCDC47 |
| 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 CCDC47 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CCDC47 |
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RelatedDrugs for CCDC47 |
| 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 CCDC47 |
| 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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