|
||||||
|
 | |
| |
| |
| |
| 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 DKK3 |
 Gene summary |
| Gene information | Gene symbol | DKK3 | Gene ID | 27122 |
| Gene name | dickkopf WNT signaling pathway inhibitor 3 | |
| Synonyms | REIC|RIG | |
| Cytomap | 11p15.3 | |
| Type of gene | protein-coding | |
| Description | dickkopf-related protein 3RIG-like 5-6RIG-like 7-1dickkopf 3 homologdickkopf homolog 3dickkopf-3dkk-3hDkk-3regulated in glioma | |
| Modification date | 20180523 | |
| UniProtAcc | Q9UBP4 | |
| Context | PubMed: DKK3 [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 |
| DKK3 | GO:0032348 | negative regulation of aldosterone biosynthetic process | 16981135 |
| DKK3 | GO:0045892 | negative regulation of transcription, DNA-templated | 16981135 |
| DKK3 | GO:0090090 | negative regulation of canonical Wnt signaling pathway | 12857724 |
| DKK3 | GO:2000065 | negative regulation of cortisol biosynthetic process | 16981135 |
Top |
Exon skipping events across known transcript of Ensembl for DKK3 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 DKK3 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for DKK3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_69295 | 11 | 11986161:11986233:11987355:11987512:11988500:11988645 | 11987355:11987512 | ENSG00000050165.13 | ENST00000528188.1,ENST00000326932.4,ENST00000396505.2,ENST00000450094.2 |
| exon_skip_69302 | 11 | 11989989:11990034:12020242:12020326:12023846:12023973 | 12020242:12020326 | ENSG00000050165.13 | ENST00000525493.1,ENST00000533813.1,ENST00000532873.1,ENST00000326932.4,ENST00000396505.2 |
| exon_skip_69307 | 11 | 12023846:12023984:12029916:12030155:12030416:12030444 | 12029916:12030155 | ENSG00000050165.13 | ENST00000396505.2 |
| exon_skip_69308 | 11 | 12023846:12023984:12029916:12030155:12030718:12030759 | 12029916:12030155 | ENSG00000050165.13 | ENST00000534479.1,ENST00000326932.4,ENST00000533900.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for DKK3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_69295 | 11 | 11986161:11986233:11987355:11987512:11988500:11988645 | 11987355:11987512 | ENSG00000050165.13 | ENST00000396505.2,ENST00000326932.4,ENST00000450094.2,ENST00000528188.1 |
| exon_skip_69302 | 11 | 11989989:11990034:12020242:12020326:12023846:12023973 | 12020242:12020326 | ENSG00000050165.13 | ENST00000396505.2,ENST00000326932.4,ENST00000525493.1,ENST00000532873.1,ENST00000533813.1 |
| exon_skip_69307 | 11 | 12023846:12023984:12029916:12030155:12030416:12030444 | 12029916:12030155 | ENSG00000050165.13 | ENST00000396505.2 |
| exon_skip_69308 | 11 | 12023846:12023984:12029916:12030155:12030718:12030759 | 12029916:12030155 | ENSG00000050165.13 | ENST00000326932.4,ENST00000534479.1,ENST00000533900.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for DKK3 |
| 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 |
| ENST00000326932 | 12029916 | 12030155 | 3UTR-3CDS |
| ENST00000396505 | 12029916 | 12030155 | 3UTR-3CDS |
| ENST00000326932 | 11987355 | 11987512 | Frame-shift |
| ENST00000396505 | 11987355 | 11987512 | Frame-shift |
| ENST00000326932 | 12020242 | 12020326 | In-frame |
| ENST00000396505 | 12020242 | 12020326 | 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 |
| ENST00000326932 | 12029916 | 12030155 | 3UTR-3CDS |
| ENST00000396505 | 12029916 | 12030155 | 3UTR-3CDS |
| ENST00000326932 | 11987355 | 11987512 | Frame-shift |
| ENST00000396505 | 11987355 | 11987512 | Frame-shift |
| ENST00000326932 | 12020242 | 12020326 | In-frame |
| ENST00000396505 | 12020242 | 12020326 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for DKK3 |
| 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 |
| ENST00000326932 | 2653 | 350 | 12020242 | 12020326 | 577 | 660 | 117 | 145 |
| ENST00000396505 | 2667 | 350 | 12020242 | 12020326 | 591 | 674 | 117 | 145 |
| 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 |
| ENST00000326932 | 2653 | 350 | 12020242 | 12020326 | 577 | 660 | 117 | 145 |
| ENST00000396505 | 2667 | 350 | 12020242 | 12020326 | 591 | 674 | 117 | 145 |
| 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 |
| Q9UBP4 | 117 | 145 | 22 | 350 | Chain | ID=PRO_0000007222;Note=Dickkopf-related protein 3 |
| Q9UBP4 | 117 | 145 | 22 | 350 | Chain | ID=PRO_0000007222;Note=Dickkopf-related protein 3 |
| Q9UBP4 | 117 | 145 | 121 | 121 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UBP4 | 117 | 145 | 121 | 121 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q9UBP4 | 117 | 145 | 22 | 350 | Chain | ID=PRO_0000007222;Note=Dickkopf-related protein 3 |
| Q9UBP4 | 117 | 145 | 22 | 350 | Chain | ID=PRO_0000007222;Note=Dickkopf-related protein 3 |
| Q9UBP4 | 117 | 145 | 121 | 121 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UBP4 | 117 | 145 | 121 | 121 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
SNVs in the skipped exons for DKK3 |
| - 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 |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_69295 | 11987356 | 11987512 | 11987473 | 11987473 | Frame_Shift_Del | C | - | p.G238fs |
| BLCA | TCGA-GV-A3QI-01 | exon_skip_69295 | 11987356 | 11987512 | 11987391 | 11987391 | Nonsense_Mutation | G | T | p.C265* |
| - 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 |
| A375_SKIN | 11987356 | 11987512 | 11987486 | 11987486 | Frame_Shift_Del | G | - | p.L234fs |
| OVK18_OVARY | 11987356 | 11987512 | 11987422 | 11987423 | Frame_Shift_Ins | - | C | p.E255fs |
| SNU1040_LARGE_INTESTINE | 12020243 | 12020326 | 12020318 | 12020319 | Frame_Shift_Ins | - | T | p.N120fs |
| REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 11987356 | 11987512 | 11987453 | 11987453 | Missense_Mutation | C | T | p.A245T |
| MM370_SKIN | 12020243 | 12020326 | 12020264 | 12020264 | Missense_Mutation | G | C | p.D138E |
| MFE319_ENDOMETRIUM | 12020243 | 12020326 | 12020268 | 12020268 | Missense_Mutation | C | G | p.G137A |
| SW48_LARGE_INTESTINE | 12029917 | 12030155 | 12029934 | 12029934 | Missense_Mutation | G | A | p.R66C |
| SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 12029917 | 12030155 | 12030047 | 12030047 | Missense_Mutation | G | A | p.T28I |
| KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 12029917 | 12030155 | 12030051 | 12030051 | Missense_Mutation | C | T | p.A27T |
| OV7_OVARY | 12029917 | 12030155 | 12030075 | 12030075 | Missense_Mutation | T | G | p.T19P |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 11987356 | 11987512 | 11987471 | 11987471 | Nonsense_Mutation | C | A | p.E239* |
| SYO1_SOFT_TISSUE | 12020243 | 12020326 | 12020243 | 12020243 | Splice_Site | G | A | p.H145H |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for DKK3 |
| 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 DKK3 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for DKK3 |
Top |
RelatedDrugs for DKK3 |
| 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 DKK3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| DKK3 | C0036341 | Schizophrenia | 1 | PSYGENET |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|