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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for CCDC47 |
Gene summary |
Gene information | Gene symbol | CCDC47 | Gene ID | 57003 |
Gene name | coiled-coil domain containing 47 | |
Synonyms | GK001|MSTP041|THNS | |
Cytomap | 17q23.3 | |
Type of gene | protein-coding | |
Description | coiled-coil domain-containing protein 47Calumin | |
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 CCDC47 |
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. |
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 CCDC47 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_12517 | chr17 | 63764016:63764190:63764740:63764847:63765912:63766194 | 63764740:63764847 |
exon_skip_243283 | chr17 | 63766119:63766194:63772777:63772863:63773412:63773570 | 63772777:63772863 |
exon_skip_56192 | chr17 | 63752780:63752799:63754433:63754518:63756240:63756266 | 63754433:63754518 |
exon_skip_76581 | chr17 | 63766119:63766194:63772777:63772863:63773412:63773564 | 63772777:63772863 |
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 CCDC47 |
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 |
ENST00000403162 | 63772777 | 63772863 | 3UTR-3UTR |
ENST00000225726 | 63754433 | 63754518 | Frame-shift |
ENST00000403162 | 63754433 | 63754518 | Frame-shift |
ENST00000225726 | 63764740 | 63764847 | In-frame |
ENST00000403162 | 63764740 | 63764847 | 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 |
ENST00000225726 | 63754433 | 63754518 | Frame-shift |
ENST00000403162 | 63754433 | 63754518 | Frame-shift |
ENST00000225726 | 63764740 | 63764847 | In-frame |
ENST00000403162 | 63764740 | 63764847 | 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 |
ENST00000403162 | 63772777 | 63772863 | 3UTR-3UTR |
ENST00000225726 | 63754433 | 63754518 | Frame-shift |
ENST00000403162 | 63754433 | 63754518 | Frame-shift |
ENST00000225726 | 63764740 | 63764847 | In-frame |
ENST00000403162 | 63764740 | 63764847 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CCDC47 |
p-ENSG00000108588_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 |
ENST00000225726 | 3483 | 483 | 63764740 | 63764847 | 648 | 754 | 88 | 123 |
ENST00000403162 | 2212 | 483 | 63764740 | 63764847 | 530 | 636 | 88 | 123 |
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 |
ENST00000225726 | 3483 | 483 | 63764740 | 63764847 | 648 | 754 | 88 | 123 |
ENST00000403162 | 2212 | 483 | 63764740 | 63764847 | 530 | 636 | 88 | 123 |
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 |
ENST00000225726 | 3483 | 483 | 63764740 | 63764847 | 648 | 754 | 88 | 123 |
ENST00000403162 | 2212 | 483 | 63764740 | 63764847 | 530 | 636 | 88 | 123 |
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 |
Q96A33 | 88 | 123 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
Q96A33 | 88 | 123 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
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 |
Q96A33 | 88 | 123 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
Q96A33 | 88 | 123 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
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 |
Q96A33 | 88 | 123 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
Q96A33 | 88 | 123 | 21 | 483 | Chain | ID=PRO_0000235797;Note=Coiled-coil domain-containing protein 47 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CCDC47 |
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 |
Mayo | ENST00000403162 | 63772777 | 63772863 | hsa-miR-146b-5p | chr17:63772815-63772822 | 8mer-1a | chr17:63772800-63772822 | 172.00 | -28.79 |
Mayo | ENST00000403162 | 63772777 | 63772863 | hsa-miR-4483 | chr17:63772843-63772850 | 8mer-1a | chr17:63772826-63772850 | 174.00 | -39.79 |
Mayo | ENST00000403162 | 63772777 | 63772863 | hsa-miR-1293 | chr17:63772843-63772850 | 8mer-1a | chr17:63772826-63772850 | 174.00 | -39.79 |
Mayo | ENST00000403162 | 63772777 | 63772863 | hsa-miR-7153-5p | chr17:63772815-63772822 | 8mer-1a | chr17:63772800-63772822 | 172.00 | -28.79 |
Mayo | ENST00000403162 | 63772777 | 63772863 | hsa-miR-3128 | chr17:63772836-63772843 | 8mer-1a | chr17:63772826-63772850 | 174.00 | -39.79 |
Mayo | ENST00000403162 | 63772777 | 63772863 | hsa-miR-6809-5p | chr17:63772834-63772841 | 8mer-1a | chr17:63772826-63772850 | 174.00 | -39.79 |
Mayo | ENST00000403162 | 63772777 | 63772863 | hsa-miR-146a-5p | chr17:63772815-63772822 | 8mer-1a | chr17:63772800-63772822 | 172.00 | -28.79 |
ROSMAP | ENST00000403162 | 63772777 | 63772863 | hsa-miR-146b-5p | chr17:63772815-63772822 | 8mer-1a | chr17:63772800-63772822 | 172.00 | -28.79 |
ROSMAP | ENST00000403162 | 63772777 | 63772863 | hsa-miR-4483 | chr17:63772843-63772850 | 8mer-1a | chr17:63772826-63772850 | 174.00 | -39.79 |
ROSMAP | ENST00000403162 | 63772777 | 63772863 | hsa-miR-1293 | chr17:63772843-63772850 | 8mer-1a | chr17:63772826-63772850 | 174.00 | -39.79 |
ROSMAP | ENST00000403162 | 63772777 | 63772863 | hsa-miR-7153-5p | chr17:63772815-63772822 | 8mer-1a | chr17:63772800-63772822 | 172.00 | -28.79 |
ROSMAP | ENST00000403162 | 63772777 | 63772863 | hsa-miR-3128 | chr17:63772836-63772843 | 8mer-1a | chr17:63772826-63772850 | 174.00 | -39.79 |
ROSMAP | ENST00000403162 | 63772777 | 63772863 | hsa-miR-6809-5p | chr17:63772834-63772841 | 8mer-1a | chr17:63772826-63772850 | 174.00 | -39.79 |
ROSMAP | ENST00000403162 | 63772777 | 63772863 | hsa-miR-146a-5p | chr17:63772815-63772822 | 8mer-1a | chr17:63772800-63772822 | 172.00 | -28.79 |
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SNVs in the skipped exons for CCDC47 |
- 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 CCDC47 |
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 CCDC47 |
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 CCDC47 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for CCDC47 |
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 CCDC47 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |