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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 SPDEF |
 Gene summary |
| Gene information | Gene symbol | SPDEF | Gene ID | 25803 |
| Gene name | SAM pointed domain containing ETS transcription factor | |
| Synonyms | PDEF|bA375E1.3 | |
| Cytomap | 6p21.31 | |
| Type of gene | protein-coding | |
| Description | SAM pointed domain-containing Ets transcription factorprostate epithelium-specific Ets transcription factorprostate-derived Ets factorprostate-specific Ets | |
| Modification date | 20180527 | |
| UniProtAcc | O95238 | |
| Context | PubMed: SPDEF [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 |
| SPDEF | GO:0000122 | negative regulation of transcription by RNA polymerase II | 21656828 |
| SPDEF | GO:0043065 | positive regulation of apoptotic process | 21656828 |
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Exon skipping events across known transcript of Ensembl for SPDEF 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 SPDEF |
| 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 SPDEF |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_458730 | 6 | 34505767:34506229:34507026:34507173:34507291:34507339 | 34507026:34507173 | ENSG00000124664.6 | ENST00000374037.3 |
| exon_skip_458731 | 6 | 34505767:34506229:34507026:34507173:34508760:34508958 | 34507026:34507173 | ENSG00000124664.6 | ENST00000544425.1 |
| exon_skip_458742 | 6 | 34507026:34507173:34507291:34507339:34508760:34508851 | 34507291:34507339 | ENSG00000124664.6 | ENST00000374037.3 |
| exon_skip_458758 | 6 | 34507026:34507173:34508760:34508958:34511796:34512261 | 34508760:34508958 | ENSG00000124664.6 | ENST00000544425.1 |
| exon_skip_458768 | 6 | 34507291:34507339:34508760:34508958:34511796:34511939 | 34508760:34508958 | ENSG00000124664.6 | ENST00000374037.3 |
| exon_skip_458809 | 6 | 34508760:34508958:34511796:34512261:34523705:34523843 | 34511796:34512261 | ENSG00000124664.6 | ENST00000544425.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SPDEF |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_458730 | 6 | 34505767:34506229:34507026:34507173:34507291:34507339 | 34507026:34507173 | ENSG00000124664.6 | ENST00000374037.3 |
| exon_skip_458742 | 6 | 34507026:34507173:34507291:34507339:34508760:34508851 | 34507291:34507339 | ENSG00000124664.6 | ENST00000374037.3 |
| exon_skip_458768 | 6 | 34507291:34507339:34508760:34508958:34511796:34511939 | 34508760:34508958 | ENSG00000124664.6 | ENST00000374037.3 |
| exon_skip_458809 | 6 | 34508760:34508958:34511796:34512261:34523705:34523843 | 34511796:34512261 | ENSG00000124664.6 | ENST00000544425.1 |
| 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 SPDEF |
| 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 |
| ENST00000374037 | 34507026 | 34507173 | In-frame |
| ENST00000374037 | 34507291 | 34507339 | In-frame |
| ENST00000374037 | 34508760 | 34508958 | 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 |
| ENST00000374037 | 34507026 | 34507173 | In-frame |
| ENST00000374037 | 34507291 | 34507339 | In-frame |
| ENST00000374037 | 34508760 | 34508958 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SPDEF |
| 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 |
| ENST00000374037 | 1912 | 335 | 34508760 | 34508958 | 852 | 1049 | 145 | 211 |
| ENST00000374037 | 1912 | 335 | 34507291 | 34507339 | 1050 | 1097 | 211 | 227 |
| ENST00000374037 | 1912 | 335 | 34507026 | 34507173 | 1098 | 1244 | 227 | 276 |
| 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 |
| ENST00000374037 | 1912 | 335 | 34508760 | 34508958 | 852 | 1049 | 145 | 211 |
| ENST00000374037 | 1912 | 335 | 34507291 | 34507339 | 1050 | 1097 | 211 | 227 |
| ENST00000374037 | 1912 | 335 | 34507026 | 34507173 | 1098 | 1244 | 227 | 276 |
| 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 |
| O95238 | 145 | 211 | 196 | 198 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 1 | 335 | Chain | ID=PRO_0000223958;Note=SAM pointed domain-containing Ets transcription factor |
| O95238 | 145 | 211 | 129 | 213 | Domain | Note=PNT;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00762 |
| O95238 | 145 | 211 | 147 | 149 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 155 | 165 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 172 | 175 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 180 | 185 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 188 | 194 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 200 | 213 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 211 | 227 | 212 | 227 | Alternative sequence | ID=VSP_044722;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O95238 | 211 | 227 | 1 | 335 | Chain | ID=PRO_0000223958;Note=SAM pointed domain-containing Ets transcription factor |
| O95238 | 211 | 227 | 129 | 213 | Domain | Note=PNT;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00762 |
| O95238 | 211 | 227 | 200 | 213 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 227 | 276 | 212 | 227 | Alternative sequence | ID=VSP_044722;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O95238 | 227 | 276 | 269 | 273 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
| O95238 | 227 | 276 | 1 | 335 | Chain | ID=PRO_0000223958;Note=SAM pointed domain-containing Ets transcription factor |
| O95238 | 227 | 276 | 249 | 332 | DNA binding | Note=ETS;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00237 |
| O95238 | 227 | 276 | 251 | 260 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
| O95238 | 227 | 276 | 262 | 265 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
| O95238 | 227 | 276 | 266 | 268 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
| O95238 | 227 | 276 | 274 | 277 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
| 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 |
| O95238 | 145 | 211 | 196 | 198 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 1 | 335 | Chain | ID=PRO_0000223958;Note=SAM pointed domain-containing Ets transcription factor |
| O95238 | 145 | 211 | 129 | 213 | Domain | Note=PNT;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00762 |
| O95238 | 145 | 211 | 147 | 149 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 155 | 165 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 172 | 175 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 180 | 185 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 188 | 194 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 145 | 211 | 200 | 213 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 211 | 227 | 212 | 227 | Alternative sequence | ID=VSP_044722;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O95238 | 211 | 227 | 1 | 335 | Chain | ID=PRO_0000223958;Note=SAM pointed domain-containing Ets transcription factor |
| O95238 | 211 | 227 | 129 | 213 | Domain | Note=PNT;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00762 |
| O95238 | 211 | 227 | 200 | 213 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DKX |
| O95238 | 227 | 276 | 212 | 227 | Alternative sequence | ID=VSP_044722;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O95238 | 227 | 276 | 269 | 273 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
| O95238 | 227 | 276 | 1 | 335 | Chain | ID=PRO_0000223958;Note=SAM pointed domain-containing Ets transcription factor |
| O95238 | 227 | 276 | 249 | 332 | DNA binding | Note=ETS;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00237 |
| O95238 | 227 | 276 | 251 | 260 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
| O95238 | 227 | 276 | 262 | 265 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
| O95238 | 227 | 276 | 266 | 268 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
| O95238 | 227 | 276 | 274 | 277 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1YO5 |
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SNVs in the skipped exons for SPDEF |
| - 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_458730 exon_skip_458731 | 34507027 | 34507173 | 34507069 | 34507069 | Frame_Shift_Del | G | - | p.H263fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_458742 | 34507292 | 34507339 | 34507307 | 34507307 | Frame_Shift_Del | C | - | p.A223fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_458809 | 34511797 | 34512261 | 34512000 | 34512000 | Frame_Shift_Del | G | - | p.P78fs |
| THYM | TCGA-ZB-A964-01 | exon_skip_458809 | 34511797 | 34512261 | 34512194 | 34512194 | Frame_Shift_Del | G | - | p.P13fs |
| UCEC | TCGA-AP-A0LV-01 | exon_skip_458809 | 34511797 | 34512261 | 34512172 | 34512173 | Frame_Shift_Ins | - | G | p.P20fs |
| LUSC | TCGA-34-2596-01 | exon_skip_458768 exon_skip_458758 | 34508761 | 34508958 | 34508830 | 34508830 | Nonsense_Mutation | C | A | p.E189* |
| STAD | TCGA-BR-6564-01 | exon_skip_458768 exon_skip_458758 | 34508761 | 34508958 | 34508912 | 34508912 | Nonsense_Mutation | C | T | p.W161* |
| STAD | TCGA-BR-6564-01 | exon_skip_458768 exon_skip_458758 | 34508761 | 34508958 | 34508912 | 34508912 | Nonsense_Mutation | C | T | p.W161X |
| HNSC | TCGA-CV-7568-01 | exon_skip_458809 | 34511797 | 34512261 | 34512014 | 34512014 | Nonsense_Mutation | C | T | p.W73* |
| - 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 |
| HCT116_LARGE_INTESTINE | 34511797 | 34512261 | 34512130 | 34512130 | Frame_Shift_Del | C | - | p.A35fs |
| AN3CA_ENDOMETRIUM | 34511797 | 34512261 | 34512173 | 34512173 | Frame_Shift_Del | G | - | p.P20fs |
| HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 34511797 | 34512261 | 34512228 | 34512228 | Frame_Shift_Del | C | - | p.G2fs |
| JHUEM1_ENDOMETRIUM | 34508761 | 34508958 | 34508799 | 34508799 | Missense_Mutation | C | A | p.G199V |
| NCIH1944_LUNG | 34508761 | 34508958 | 34508814 | 34508814 | Missense_Mutation | C | T | p.R194H |
| SNU878_LIVER | 34508761 | 34508958 | 34508842 | 34508842 | Missense_Mutation | C | T | p.A185T |
| 5637_URINARY_TRACT | 34508761 | 34508958 | 34508896 | 34508896 | Missense_Mutation | G | A | p.R167W |
| HMY1_SKIN | 34508761 | 34508958 | 34508942 | 34508942 | Missense_Mutation | G | T | p.S151R |
| NCIH1963_LUNG | 34511797 | 34512261 | 34511928 | 34511928 | Missense_Mutation | G | A | p.A102V |
| ES1_BONE | 34511797 | 34512261 | 34512019 | 34512019 | Missense_Mutation | T | C | p.S72G |
| G361_SKIN | 34511797 | 34512261 | 34512073 | 34512073 | Missense_Mutation | C | T | p.G54S |
| PSN1_PANCREAS | 34511797 | 34512261 | 34512166 | 34512166 | Missense_Mutation | C | T | p.V23M |
| TOV21G_OVARY | 34507027 | 34507173 | 34507100 | 34507100 | Nonsense_Mutation | C | T | p.W252* |
| GP5D_LARGE_INTESTINE | 34508761 | 34508958 | 34508946 | 34508946 | Nonsense_Mutation | C | T | p.W150* |
| HUH6CLONE5_LIVER | 34507292 | 34507339 | 34507293 | 34507293 | Splice_Site | A | G | p.C227C |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPDEF |
| 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 SPDEF |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SPDEF |
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RelatedDrugs for SPDEF |
| 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 SPDEF |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SPDEF | C0919267 | ovarian neoplasm | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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