|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for CCDC28B |
 Gene summary |
| Gene information | Gene symbol | CCDC28B | Gene ID | 79140 |
| Gene name | coiled-coil domain containing 28B | |
| Synonyms | - | |
| Cytomap | 1p35.2 | |
| Type of gene | protein-coding | |
| Description | coiled-coil domain-containing protein 28B | |
| Modification date | 20180523 | |
| UniProtAcc | Q9BUN5 | |
| Context | PubMed: CCDC28B [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 |
Top |
Exon skipping events across known transcript of Ensembl for CCDC28B 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. |
 |
Top |
Gene isoform structures and expression levels for CCDC28B |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for CCDC28B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_3910 | 1 | 32669484:32669646:32669786:32669980:32670198:32670221 | 32669786:32669980 | ENSG00000160050.10 | ENST00000373602.5,ENST00000421922.2 |
| exon_skip_3911 | 1 | 32669484:32669646:32669833:32669980:32670198:32670221 | 32669833:32669980 | ENSG00000160050.10 | ENST00000461819.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for CCDC28B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_3910 | 1 | 32669484:32669646:32669786:32669980:32670198:32670221 | 32669786:32669980 | ENSG00000160050.10 | ENST00000373602.5,ENST00000421922.2 |
| exon_skip_3911 | 1 | 32669484:32669646:32669833:32669980:32670198:32670221 | 32669833:32669980 | ENSG00000160050.10 | ENST00000461819.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CCDC28B |
| 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 |
| ENST00000373602 | 32669786 | 32669980 | 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 |
| ENST00000373602 | 32669786 | 32669980 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for CCDC28B |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| 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 |
Top |
SNVs in the skipped exons for CCDC28B |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - 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 |
| BLCA | TCGA-SY-A9G5-01 | exon_skip_3910 | 32669787 | 32669980 | 32669915 | 32669915 | Nonsense_Mutation | G | T | p.E154* |
| BLCA | TCGA-SY-A9G5-01 | exon_skip_3911 | 32669834 | 32669980 | 32669915 | 32669915 | Nonsense_Mutation | G | T | p.E154* |
| LUSC | TCGA-43-2578-01 | exon_skip_3910 | 32669787 | 32669980 | 32669966 | 32669966 | Nonsense_Mutation | C | T | p.Q171* |
| LUSC | TCGA-43-2578-01 | exon_skip_3911 | 32669834 | 32669980 | 32669966 | 32669966 | Nonsense_Mutation | C | T | p.Q171* |
| - 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 |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32669787 | 32669980 | 32669852 | 32669852 | Missense_Mutation | C | T | p.H133Y |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32669834 | 32669980 | 32669852 | 32669852 | Missense_Mutation | C | T | p.H133Y |
| LNCAPCLONEFGC_PROSTATE | 32669787 | 32669980 | 32669859 | 32669859 | Missense_Mutation | G | A | p.S135N |
| LNCAPCLONEFGC_PROSTATE | 32669834 | 32669980 | 32669859 | 32669859 | Missense_Mutation | G | A | p.S135N |
| MEWO_SKIN | 32669787 | 32669980 | 32669882 | 32669882 | Missense_Mutation | G | A | p.E143K |
| MEWO_SKIN | 32669834 | 32669980 | 32669882 | 32669882 | Missense_Mutation | G | A | p.E143K |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32669787 | 32669980 | 32669907 | 32669907 | Missense_Mutation | G | T | p.G151V |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32669834 | 32669980 | 32669907 | 32669907 | Missense_Mutation | G | T | p.G151V |
| HUO9_BONE | 32669787 | 32669980 | 32669913 | 32669913 | Missense_Mutation | C | G | p.T153S |
| HUO9_BONE | 32669834 | 32669980 | 32669913 | 32669913 | Missense_Mutation | C | G | p.T153S |
| HUCCT1_BILIARY_TRACT | 32669787 | 32669980 | 32669951 | 32669951 | Missense_Mutation | G | T | p.D166Y |
| HUCCT1_BILIARY_TRACT | 32669834 | 32669980 | 32669951 | 32669951 | Missense_Mutation | G | T | p.D166Y |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CCDC28B |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CCDC28B |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CCDC28B |
Top |
RelatedDrugs for CCDC28B |
| 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 |
Top |
RelatedDiseases for CCDC28B |
| 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)
|