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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 SYTL1 |
 Gene summary |
| Gene information | Gene symbol | SYTL1 | Gene ID | 84958 |
| Gene name | synaptotagmin like 1 | |
| Synonyms | JFC1|SLP1 | |
| Cytomap | 1p36.11 | |
| Type of gene | protein-coding | |
| Description | synaptotagmin-like protein 1NADPH oxidase-related, C2 domain-containing proteinexophilin-7 | |
| Modification date | 20180523 | |
| UniProtAcc | Q8IYJ3 | |
| Context | PubMed: SYTL1 [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 |
| SYTL1 | GO:0006887 | exocytosis | 18266782 |
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Exon skipping events across known transcript of Ensembl for SYTL1 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 SYTL1 |
| 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 SYTL1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_3083 | 1 | 27675888:27675989:27676142:27676256:27676462:27676623 | 27676142:27676256 | ENSG00000142765.13 | ENST00000543823.1,ENST00000318074.5 |
| exon_skip_3087 | 1 | 27676237:27676256:27676462:27676623:27676879:27676976 | 27676462:27676623 | ENSG00000142765.13 | ENST00000543823.1,ENST00000496001.1,ENST00000318074.5 |
| exon_skip_3096 | 1 | 27676879:27676976:27677284:27677443:27677748:27677827 | 27677284:27677443 | ENSG00000142765.13 | ENST00000483926.1,ENST00000485269.1,ENST00000543823.1,ENST00000496001.1,ENST00000318074.5 |
| exon_skip_3118 | 1 | 27677299:27677443:27677748:27677827:27677946:27678036 | 27677748:27677827 | ENSG00000142765.13 | ENST00000483926.1,ENST00000485269.1,ENST00000543823.1,ENST00000496001.1,ENST00000318074.5 |
| exon_skip_3123 | 1 | 27677748:27677827:27677946:27678046:27679773:27679979 | 27677946:27678046 | ENSG00000142765.13 | ENST00000483926.1,ENST00000543823.1,ENST00000490170.1,ENST00000318074.5 |
| exon_skip_3126 | 1 | 27677946:27678046:27679773:27679979:27680203:27680421 | 27679773:27679979 | ENSG00000142765.13 | ENST00000483926.1,ENST00000543823.1,ENST00000490170.1,ENST00000318074.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SYTL1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_3083 | 1 | 27675888:27675989:27676142:27676256:27676462:27676623 | 27676142:27676256 | ENSG00000142765.13 | ENST00000318074.5,ENST00000543823.1 |
| exon_skip_3087 | 1 | 27676237:27676256:27676462:27676623:27676879:27676976 | 27676462:27676623 | ENSG00000142765.13 | ENST00000318074.5,ENST00000543823.1,ENST00000496001.1 |
| exon_skip_3096 | 1 | 27676879:27676976:27677284:27677443:27677748:27677827 | 27677284:27677443 | ENSG00000142765.13 | ENST00000318074.5,ENST00000483926.1,ENST00000543823.1,ENST00000496001.1,ENST00000485269.1 |
| exon_skip_3118 | 1 | 27677299:27677443:27677748:27677827:27677946:27678036 | 27677748:27677827 | ENSG00000142765.13 | ENST00000318074.5,ENST00000483926.1,ENST00000543823.1,ENST00000496001.1,ENST00000485269.1 |
| exon_skip_3123 | 1 | 27677748:27677827:27677946:27678046:27679773:27679979 | 27677946:27678046 | ENSG00000142765.13 | ENST00000318074.5,ENST00000483926.1,ENST00000543823.1,ENST00000490170.1 |
| exon_skip_3126 | 1 | 27677946:27678046:27679773:27679979:27680203:27680421 | 27679773:27679979 | ENSG00000142765.13 | ENST00000318074.5,ENST00000483926.1,ENST00000543823.1,ENST00000490170.1 |
| 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 SYTL1 |
| 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 |
| ENST00000543823 | 27676462 | 27676623 | Frame-shift |
| ENST00000543823 | 27677748 | 27677827 | Frame-shift |
| ENST00000543823 | 27677946 | 27678046 | Frame-shift |
| ENST00000543823 | 27679773 | 27679979 | Frame-shift |
| ENST00000543823 | 27676142 | 27676256 | In-frame |
| ENST00000543823 | 27677284 | 27677443 | 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 |
| ENST00000543823 | 27676462 | 27676623 | Frame-shift |
| ENST00000543823 | 27677748 | 27677827 | Frame-shift |
| ENST00000543823 | 27677946 | 27678046 | Frame-shift |
| ENST00000543823 | 27679773 | 27679979 | Frame-shift |
| ENST00000543823 | 27676142 | 27676256 | In-frame |
| ENST00000543823 | 27677284 | 27677443 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SYTL1 |
| 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 |
| ENST00000543823 | 2246 | 562 | 27676142 | 27676256 | 1096 | 1209 | 211 | 249 |
| ENST00000543823 | 2246 | 562 | 27677284 | 27677443 | 1468 | 1626 | 335 | 388 |
| 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 |
| ENST00000543823 | 2246 | 562 | 27676142 | 27676256 | 1096 | 1209 | 211 | 249 |
| ENST00000543823 | 2246 | 562 | 27677284 | 27677443 | 1468 | 1626 | 335 | 388 |
| 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 |
| Q8IYJ3 | 211 | 249 | 1 | 562 | Chain | ID=PRO_0000190211;Note=Synaptotagmin-like protein 1 |
| Q8IYJ3 | 211 | 249 | 237 | 258 | Compositional bias | Note=Ser-rich |
| Q8IYJ3 | 211 | 249 | 216 | 216 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q8IYJ3 | 335 | 388 | 1 | 562 | Chain | ID=PRO_0000190211;Note=Synaptotagmin-like protein 1 |
| Q8IYJ3 | 335 | 388 | 268 | 368 | Domain | Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00041 |
| 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 |
| Q8IYJ3 | 211 | 249 | 1 | 562 | Chain | ID=PRO_0000190211;Note=Synaptotagmin-like protein 1 |
| Q8IYJ3 | 211 | 249 | 237 | 258 | Compositional bias | Note=Ser-rich |
| Q8IYJ3 | 211 | 249 | 216 | 216 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q8IYJ3 | 335 | 388 | 1 | 562 | Chain | ID=PRO_0000190211;Note=Synaptotagmin-like protein 1 |
| Q8IYJ3 | 335 | 388 | 268 | 368 | Domain | Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00041 |
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SNVs in the skipped exons for SYTL1 |
| - 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_3096 | 27677285 | 27677443 | 27677346 | 27677346 | Frame_Shift_Del | A | - | p.E356fs |
| BLCA | TCGA-GU-AATP-01 | exon_skip_3118 | 27677749 | 27677827 | 27677811 | 27677811 | Frame_Shift_Del | C | - | p.V409fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_3123 | 27677947 | 27678046 | 27677983 | 27677983 | Frame_Shift_Del | G | - | p.W427fs |
| BRCA | TCGA-AR-A24S-01 | exon_skip_3126 | 27679774 | 27679979 | 27679789 | 27679807 | Frame_Shift_Del | TGACAGCCAGGCCAGCCGC | - | p.D442fs |
| LUAD | TCGA-86-8673-01 | exon_skip_3096 | 27677285 | 27677443 | 27677309 | 27677309 | Nonsense_Mutation | C | T | p.Q344* |
| LUAD | TCGA-95-7039-01 | exon_skip_3096 | 27677285 | 27677443 | 27677381 | 27677381 | Nonsense_Mutation | G | T | p.E368* |
| SKCM | TCGA-EE-A29M-06 | exon_skip_3126 | 27679774 | 27679979 | 27679920 | 27679920 | Nonsense_Mutation | G | A | p.W485X |
| SKCM | TCGA-EE-A29M-06 | exon_skip_3126 | 27679774 | 27679979 | 27679920 | 27679920 | Nonsense_Mutation | G | A | p.W497* |
| - 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 |
| REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 27676143 | 27676256 | 27676149 | 27676149 | Missense_Mutation | G | A | p.A214T |
| HEC1A_ENDOMETRIUM | 27676143 | 27676256 | 27676152 | 27676152 | Missense_Mutation | G | A | p.A215T |
| KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 27676463 | 27676623 | 27676514 | 27676514 | Missense_Mutation | C | T | p.R267C |
| HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 27676463 | 27676623 | 27676556 | 27676556 | Missense_Mutation | G | T | p.A281S |
| SNU1041_UPPER_AERODIGESTIVE_TRACT | 27677285 | 27677443 | 27677289 | 27677289 | Missense_Mutation | C | G | p.S337C |
| LIM1215_LARGE_INTESTINE | 27677285 | 27677443 | 27677316 | 27677316 | Missense_Mutation | G | A | p.R346H |
| 2313287_STOMACH | 27679774 | 27679979 | 27679838 | 27679838 | Missense_Mutation | A | G | p.S470G |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 27679774 | 27679979 | 27679862 | 27679862 | Missense_Mutation | G | A | p.V478M |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 27679774 | 27679979 | 27679880 | 27679880 | Missense_Mutation | C | T | p.P484S |
| KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 27679774 | 27679979 | 27679944 | 27679944 | Missense_Mutation | G | A | p.R505H |
| OVTOKO_OVARY | 27679774 | 27679979 | 27679956 | 27679956 | Missense_Mutation | G | A | p.G509D |
| SNU1196_BILIARY_TRACT | 27679774 | 27679979 | 27679962 | 27679962 | Missense_Mutation | G | A | p.R511H |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 27679774 | 27679979 | 27679895 | 27679895 | Nonsense_Mutation | C | T | p.Q489* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SYTL1 |
| 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 |
| exon_skip_3126 | 1 | 27677946:27678046:27679773:27679979:27680203:27680421 | 27679773:27679979 | ENST00000483926.1,ENST00000543823.1,ENST00000490170.1,ENST00000318074.5 | THCA | rs3813795 | chr1:27679797 | A/G | 5.55e-04 |
| exon_skip_3126 | 1 | 27677946:27678046:27679773:27679979:27680203:27680421 | 27679773:27679979 | ENST00000483926.1,ENST00000543823.1,ENST00000490170.1,ENST00000318074.5 | THCA | rs3813795 | chr1:27679797 | A/G | 1.44e-03 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SYTL1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SYTL1 |
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RelatedDrugs for SYTL1 |
| 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 SYTL1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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