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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 SDC1 |
 Gene summary |
| Gene information | Gene symbol | SDC1 | Gene ID | 6382 |
| Gene name | syndecan 1 | |
| Synonyms | CD138|SDC|SYND1|syndecan | |
| Cytomap | 2p24.1 | |
| Type of gene | protein-coding | |
| Description | syndecan-1CD138 antigenheparan sulfate proteoglycan fibroblast growth factor receptorsyndecan proteoglycan 1 | |
| Modification date | 20180527 | |
| UniProtAcc | P18827 | |
| Context | PubMed: SDC1 [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 SDC1 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 SDC1 |
| 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 SDC1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_337158 | 2 | 20403912:20404052:20405103:20405185:20424562:20424847 | 20405103:20405185 | ENSG00000115884.6 | ENST00000381150.1,ENST00000403076.1 |
| exon_skip_337172 | 2 | 20405109:20405185:20422963:20423039:20424562:20424847 | 20422963:20423039 | ENSG00000115884.6 | ENST00000447124.1 |
| exon_skip_337176 | 2 | 20405109:20405185:20424562:20424847:20425022:20425194 | 20424562:20424847 | ENSG00000115884.6 | ENST00000381150.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SDC1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_337158 | 2 | 20403912:20404052:20405103:20405185:20424562:20424847 | 20405103:20405185 | ENSG00000115884.6 | ENST00000381150.1,ENST00000403076.1 |
| exon_skip_337172 | 2 | 20405109:20405185:20422963:20423039:20424562:20424847 | 20422963:20423039 | ENSG00000115884.6 | ENST00000447124.1 |
| exon_skip_337176 | 2 | 20405109:20405185:20424562:20424847:20425022:20425194 | 20424562:20424847 | ENSG00000115884.6 | ENST00000381150.1 |
| 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 SDC1 |
| 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 |
| ENST00000381150 | 20424562 | 20424847 | 3UTR-3CDS |
| ENST00000381150 | 20405103 | 20405185 | 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 |
| ENST00000381150 | 20424562 | 20424847 | 3UTR-3CDS |
| ENST00000381150 | 20405103 | 20405185 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SDC1 |
| 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 SDC1 |
| - 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-G3-A3CJ-01 | exon_skip_337158 | 20405104 | 20405185 | 20405160 | 20405160 | Frame_Shift_Del | G | - | p.P31fs |
| BLCA | TCGA-FD-A3SP-01 | exon_skip_337158 | 20405104 | 20405185 | 20405159 | 20405160 | Frame_Shift_Ins | - | G | p.P31fs |
| HNSC | TCGA-CR-7380-01 | exon_skip_337158 | 20405104 | 20405185 | 20405159 | 20405160 | Frame_Shift_Ins | - | G | p.P31fs |
| HNSC | TCGA-CR-7380-01 | exon_skip_337158 | 20405104 | 20405185 | 20405159 | 20405160 | Frame_Shift_Ins | - | G | p.R31fs |
| - 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 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SDC1 |
| 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 SDC1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SDC1 |
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RelatedDrugs for SDC1 |
| 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 SDC1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SDC1 | C0345967 | Malignant mesothelioma | 1 | CTD_human |
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