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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 SEPHS1 |
 Gene summary |
| Gene information | Gene symbol | SEPHS1 | Gene ID | 22929 |
| Gene name | selenophosphate synthetase 1 | |
| Synonyms | SELD|SPS|SPS1 | |
| Cytomap | 10p13 | |
| Type of gene | protein-coding | |
| Description | selenide, water dikinase 1selenium donor protein 1selenophosphate synthase 1selenophosphate synthetase 1 +E9selenophosphate synthetase 1 +E9aselenophosphate synthetase 1 delta E2selenophosphate synthetase 1 delta E8selenophosphate synthetase 1 majo | |
| Modification date | 20180523 | |
| UniProtAcc | P49903 | |
| Context | PubMed: SEPHS1 [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 SEPHS1 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 SEPHS1 |
| 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 SEPHS1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_47766 | 10 | 13361171:13361356:13363973:13364065:13364834:13365041 | 13363973:13364065 | ENSG00000086475.10 | ENST00000545675.1 |
| exon_skip_47771 | 10 | 13361171:13361356:13364834:13365047:13370350:13370450 | 13364834:13365047 | ENSG00000086475.10 | ENST00000327347.5,ENST00000537130.1 |
| exon_skip_47774 | 10 | 13371697:13371788:13375816:13375971:13378242:13378350 | 13375816:13375971 | ENSG00000086475.10 | ENST00000327347.5,ENST00000545675.1,ENST00000378614.4,ENST00000537130.1 |
| exon_skip_47776 | 10 | 13375900:13375971:13378242:13378350:13380704:13380808 | 13378242:13378350 | ENSG00000086475.10 | ENST00000327347.5,ENST00000545675.1,ENST00000413411.1,ENST00000378614.4,ENST00000537130.1,ENST00000425947.1 |
| exon_skip_47777 | 10 | 13378242:13378350:13380704:13380808:13386757:13387028 | 13380704:13380808 | ENSG00000086475.10 | ENST00000327347.5,ENST00000545675.1,ENST00000413411.1,ENST00000378614.4 |
| exon_skip_47781 | 10 | 13380715:13380808:13386757:13387028:13389999:13390030 | 13386757:13387028 | ENSG00000086475.10 | ENST00000545675.1,ENST00000378614.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SEPHS1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_47766 | 10 | 13361171:13361356:13363973:13364065:13364834:13365041 | 13363973:13364065 | ENSG00000086475.10 | ENST00000545675.1 |
| exon_skip_47771 | 10 | 13361171:13361356:13364834:13365047:13370350:13370450 | 13364834:13365047 | ENSG00000086475.10 | ENST00000327347.5,ENST00000537130.1 |
| exon_skip_47774 | 10 | 13371697:13371788:13375816:13375971:13378242:13378350 | 13375816:13375971 | ENSG00000086475.10 | ENST00000327347.5,ENST00000378614.4,ENST00000545675.1,ENST00000537130.1 |
| exon_skip_47776 | 10 | 13375900:13375971:13378242:13378350:13380704:13380808 | 13378242:13378350 | ENSG00000086475.10 | ENST00000327347.5,ENST00000378614.4,ENST00000545675.1,ENST00000537130.1,ENST00000413411.1,ENST00000425947.1 |
| exon_skip_47777 | 10 | 13378242:13378350:13380704:13380808:13386757:13387028 | 13380704:13380808 | ENSG00000086475.10 | ENST00000327347.5,ENST00000378614.4,ENST00000545675.1,ENST00000413411.1 |
| exon_skip_47781 | 10 | 13380715:13380808:13386757:13387028:13389999:13390030 | 13386757:13387028 | ENSG00000086475.10 | ENST00000378614.4,ENST00000545675.1 |
| 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 SEPHS1 |
| 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 |
| ENST00000327347 | 13375816 | 13375971 | Frame-shift |
| ENST00000327347 | 13380704 | 13380808 | Frame-shift |
| ENST00000327347 | 13364834 | 13365047 | In-frame |
| ENST00000327347 | 13378242 | 13378350 | 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 |
| ENST00000327347 | 13375816 | 13375971 | Frame-shift |
| ENST00000327347 | 13380704 | 13380808 | Frame-shift |
| ENST00000327347 | 13364834 | 13365047 | In-frame |
| ENST00000327347 | 13378242 | 13378350 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SEPHS1 |
| 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 |
| ENST00000327347 | 3290 | 392 | 13378242 | 13378350 | 674 | 781 | 99 | 135 |
| ENST00000327347 | 3290 | 392 | 13364834 | 13365047 | 1128 | 1340 | 250 | 321 |
| 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 |
| ENST00000327347 | 3290 | 392 | 13378242 | 13378350 | 674 | 781 | 99 | 135 |
| ENST00000327347 | 3290 | 392 | 13364834 | 13365047 | 1128 | 1340 | 250 | 321 |
| 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 |
| P49903 | 99 | 135 | 120 | 129 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 99 | 135 | 110 | 110 | Binding site | Note=ATP |
| P49903 | 99 | 135 | 2 | 392 | Chain | ID=PRO_0000127648;Note=Selenide%2C water dikinase 1 |
| P49903 | 99 | 135 | 96 | 113 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 99 | 135 | 134 | 154 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 251 | 321 | Alternative sequence | ID=VSP_046702;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:20471958;Dbxref=PMID:20471958 |
| P49903 | 250 | 321 | 262 | 265 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 283 | 296 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 2 | 392 | Chain | ID=PRO_0000127648;Note=Selenide%2C water dikinase 1 |
| P49903 | 250 | 321 | 249 | 257 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 270 | 279 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 299 | 305 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 312 | 314 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 268 | 268 | Mutagenesis | Note=No change in ATP-binding. G->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 270 | 270 | Mutagenesis | Note=No change in ATP-binding. G->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 273 | 273 | Mutagenesis | Note=Loss of ATP-binding. G->A%2CD%2CV;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 274 | 274 | Mutagenesis | Note=Reduced ATP-binding. H->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 274 | 274 | Mutagenesis | Note=Increased ATP-binding. H->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 267 | 273 | Nucleotide binding | Note=ATP |
| P49903 | 250 | 321 | 260 | 260 | Sequence conflict | Note=A->T;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P49903 | 250 | 321 | 306 | 308 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| 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 |
| P49903 | 99 | 135 | 120 | 129 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 99 | 135 | 110 | 110 | Binding site | Note=ATP |
| P49903 | 99 | 135 | 2 | 392 | Chain | ID=PRO_0000127648;Note=Selenide%2C water dikinase 1 |
| P49903 | 99 | 135 | 96 | 113 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 99 | 135 | 134 | 154 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 251 | 321 | Alternative sequence | ID=VSP_046702;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:20471958;Dbxref=PMID:20471958 |
| P49903 | 250 | 321 | 262 | 265 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 283 | 296 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 2 | 392 | Chain | ID=PRO_0000127648;Note=Selenide%2C water dikinase 1 |
| P49903 | 250 | 321 | 249 | 257 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 270 | 279 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 299 | 305 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 312 | 314 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
| P49903 | 250 | 321 | 268 | 268 | Mutagenesis | Note=No change in ATP-binding. G->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 270 | 270 | Mutagenesis | Note=No change in ATP-binding. G->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 273 | 273 | Mutagenesis | Note=Loss of ATP-binding. G->A%2CD%2CV;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 274 | 274 | Mutagenesis | Note=Reduced ATP-binding. H->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 274 | 274 | Mutagenesis | Note=Increased ATP-binding. H->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7665581;Dbxref=PMID:7665581 |
| P49903 | 250 | 321 | 267 | 273 | Nucleotide binding | Note=ATP |
| P49903 | 250 | 321 | 260 | 260 | Sequence conflict | Note=A->T;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P49903 | 250 | 321 | 306 | 308 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3FD5 |
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SNVs in the skipped exons for SEPHS1 |
| - 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 |
| KIRC | TCGA-BP-4976-01 | exon_skip_47781 | 13386758 | 13387028 | 13386847 | 13386848 | Frame_Shift_Ins | - | G | p.Q35fs |
| KIRC | TCGA-BP-4976-01 | exon_skip_47781 | 13386758 | 13387028 | 13386847 | 13386848 | Frame_Shift_Ins | - | G | p.R35fs |
| UCS | TCGA-ND-A4WC-01 | exon_skip_47774 | 13375817 | 13375971 | 13375827 | 13375827 | Nonsense_Mutation | C | A | p.E184* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_47774 | 13375817 | 13375971 | 13375827 | 13375827 | Nonsense_Mutation | C | A | p.E184X |
| SKCM | TCGA-DA-A1I0-06 | exon_skip_47781 | 13386758 | 13387028 | 13386800 | 13386800 | Nonsense_Mutation | G | A | p.Q51* |
| LUSC | TCGA-21-5787-01 | exon_skip_47776 | 13378243 | 13378350 | 13378352 | 13378352 | Splice_Site | T | - | p.G100_splice |
| - 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 |
| OC316_OVARY | 13364835 | 13365047 | 13364840 | 13364840 | Missense_Mutation | G | C | p.T320S |
| OC314_OVARY | 13364835 | 13365047 | 13364840 | 13364840 | Missense_Mutation | G | C | p.T320S |
| HEC1A_ENDOMETRIUM | 13364835 | 13365047 | 13364895 | 13364895 | Missense_Mutation | C | T | p.V302M |
| HEC1_ENDOMETRIUM | 13364835 | 13365047 | 13364895 | 13364895 | Missense_Mutation | C | T | p.V302M |
| HEC1B_ENDOMETRIUM | 13364835 | 13365047 | 13364895 | 13364895 | Missense_Mutation | C | T | p.V302M |
| SNU175_LARGE_INTESTINE | 13364835 | 13365047 | 13364999 | 13364999 | Missense_Mutation | G | A | p.T267M |
| KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 13375817 | 13375971 | 13375826 | 13375826 | Missense_Mutation | T | C | p.E184G |
| A704_KIDNEY | 13375817 | 13375971 | 13375839 | 13375839 | Missense_Mutation | A | C | p.C180G |
| DMS53_LUNG | 13375817 | 13375971 | 13375851 | 13375851 | Missense_Mutation | C | G | p.A176P |
| HCT15_LARGE_INTESTINE | 13375817 | 13375971 | 13375877 | 13375877 | Missense_Mutation | T | G | p.N167T |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 13375817 | 13375971 | 13375907 | 13375907 | Missense_Mutation | G | A | p.T157I |
| NCIH2135_LUNG | 13375817 | 13375971 | 13375923 | 13375923 | Missense_Mutation | C | T | p.A152T |
| KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 13375817 | 13375971 | 13375926 | 13375926 | Missense_Mutation | C | T | p.A151T |
| MCC13_SKIN | 13375817 | 13375971 | 13375967 | 13375967 | Missense_Mutation | C | T | p.R137K |
| SNU1040_LARGE_INTESTINE | 13378243 | 13378350 | 13378284 | 13378284 | Missense_Mutation | T | C | p.M122V |
| SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 13386758 | 13387028 | 13386851 | 13386851 | Missense_Mutation | G | A | p.P34S |
| COLO792_SKIN | 13375817 | 13375971 | 13375890 | 13375890 | Nonsense_Mutation | G | A | p.Q163* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SEPHS1 |
| 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_47771 | 10 | 13361171:13361356:13364834:13365047:13370350:13370450 | 13364834:13365047 | ENST00000327347.5,ENST00000537130.1 | LIHC | rs62641685 | chr10:13364914 | C/G | 8.25e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SEPHS1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SEPHS1 |
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RelatedDrugs for SEPHS1 |
| 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 SEPHS1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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