|
||||||
|
 | |
| |
| |
| |
| 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 SYNPO2 |
 Gene summary |
| Gene information | Gene symbol | SYNPO2 | Gene ID | 171024 |
| Gene name | synaptopodin 2 | |
| Synonyms | - | |
| Cytomap | 4q26 | |
| Type of gene | protein-coding | |
| Description | synaptopodin-2genethonin-2myopodin | |
| Modification date | 20180523 | |
| UniProtAcc | Q9UMS6 | |
| Context | PubMed: SYNPO2 [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 SYNPO2 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 SYNPO2 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for SYNPO2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_425907 | 4 | 119944625:119944736:119947781:119948593:119950999:119953008 | 119947781:119948593 | ENSG00000172403.6 | ENST00000434046.2,ENST00000307142.4,ENST00000504178.1,ENST00000429713.2 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for SYNPO2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_425907 | 4 | 119944625:119944736:119947781:119948593:119950999:119953008 | 119947781:119948593 | ENSG00000172403.6 | ENST00000307142.4,ENST00000429713.2,ENST00000434046.2,ENST00000504178.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SYNPO2 |
| 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 |
| ENST00000429713 | 119947781 | 119948593 | 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 |
| ENST00000429713 | 119947781 | 119948593 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for SYNPO2 |
| 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 SYNPO2 |
| - 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-DD-A1EG-01 | exon_skip_425907 | 119947782 | 119948593 | 119948337 | 119948337 | Frame_Shift_Del | C | - | p.I271fs |
| UCEC | TCGA-A5-A0GP-01 | exon_skip_425907 | 119947782 | 119948593 | 119947885 | 119947885 | Nonsense_Mutation | C | T | p.R121* |
| UCEC | TCGA-BS-A0UV-01 | exon_skip_425907 | 119947782 | 119948593 | 119947992 | 119947992 | Nonsense_Mutation | G | T | p.E108* |
| BLCA | TCGA-DK-A6AW-01 | exon_skip_425907 | 119947782 | 119948593 | 119947996 | 119947996 | Nonsense_Mutation | G | T | p.E158* |
| GBM | TCGA-28-2514-01 | exon_skip_425907 | 119947782 | 119948593 | 119948017 | 119948017 | Nonsense_Mutation | C | T | p.Q165* |
| LUAD | TCGA-78-7149-01 | exon_skip_425907 | 119947782 | 119948593 | 119948362 | 119948362 | Nonsense_Mutation | G | T | p.G280* |
| - 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 |
| MAC2A_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 119947782 | 119948593 | 119947816 | 119947816 | Missense_Mutation | G | A | p.E98K |
| EFO27_OVARY | 119947782 | 119948593 | 119948032 | 119948032 | Missense_Mutation | A | T | p.M170L |
| OC316_OVARY | 119947782 | 119948593 | 119948056 | 119948056 | Missense_Mutation | G | A | p.V178M |
| NCIH358_LUNG | 119947782 | 119948593 | 119948068 | 119948068 | Missense_Mutation | C | A | p.L182M |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 119947782 | 119948593 | 119948144 | 119948144 | Missense_Mutation | G | A | p.R207K |
| T173_FIBROBLAST | 119947782 | 119948593 | 119948150 | 119948150 | Missense_Mutation | A | T | p.K209M |
| YD8_UPPER_AERODIGESTIVE_TRACT | 119947782 | 119948593 | 119948183 | 119948183 | Missense_Mutation | G | A | p.G220E |
| HEC251_ENDOMETRIUM | 119947782 | 119948593 | 119948248 | 119948248 | Missense_Mutation | A | C | p.N242H |
| HT115_LARGE_INTESTINE | 119947782 | 119948593 | 119948252 | 119948252 | Missense_Mutation | C | T | p.S243L |
| MELJUSO_SKIN | 119947782 | 119948593 | 119948266 | 119948266 | Missense_Mutation | G | A | p.E248K |
| NCIH2009_LUNG | 119947782 | 119948593 | 119948328 | 119948328 | Missense_Mutation | G | C | p.L268F |
| SKNMC_BONE | 119947782 | 119948593 | 119948443 | 119948443 | Missense_Mutation | T | C | p.C307R |
| MCIXC_AUTONOMIC_GANGLIA | 119947782 | 119948593 | 119948443 | 119948443 | Missense_Mutation | T | C | p.C307R |
| UMUC3_URINARY_TRACT | 119947782 | 119948593 | 119948521 | 119948521 | Missense_Mutation | A | G | p.T333A |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 119947782 | 119948593 | 119948584 | 119948584 | Missense_Mutation | C | T | p.R354W |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SYNPO2 |
| 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 SYNPO2 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SYNPO2 |
Top |
RelatedDrugs for SYNPO2 |
| 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 SYNPO2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SYNPO2 | C0677886 | Epithelial ovarian cancer | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|