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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 SEPSECS |
Gene summary |
Gene information | Gene symbol | SEPSECS | Gene ID | 51091 |
Gene name | Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase | |
Synonyms | LP|PCH2D|SLA|SLA/LP | |
Cytomap | 4p15.2 | |
Type of gene | protein-coding | |
Description | O-phosphoseryl-tRNA(Sec) selenium transferaseSLA-p35SLA/LP autoantigenUGA suppressor tRNA-associated proteinliver-pancreas antigensoluble liver antigensoluble liver antigen/liver pancreas antigentRNA(Ser/Sec)-associated antigenic protein | |
Modification date | 20180520 | |
UniProtAcc | Q9HD40 | |
Context | PubMed: SEPSECS [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 SEPSECS 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 SEPSECS |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for SEPSECS |
Information of exkip skipping event in TCGA. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_428892 | 4 | 25127315:25127406:25128885:25128979:25146395:25146487 | 25128885:25128979 | ENSG00000109618.7 | ENST00000302922.3,ENST00000514585.1,ENST00000382103.2,ENST00000358971.3 |
exon_skip_428894 | 4 | 25146395:25146487:25146625:25146755:25153581:25153684 | 25146625:25146755 | ENSG00000109618.7 | ENST00000302922.3,ENST00000514585.1,ENST00000382103.2,ENST00000358971.3 |
exon_skip_428897 | 4 | 25146625:25146755:25153581:25153684:25156619:25156773 | 25153581:25153684 | ENSG00000109618.7 | ENST00000302922.3,ENST00000514585.1,ENST00000382103.2,ENST00000358971.3 |
exon_skip_428898 | 4 | 25158477:25158596:25160574:25160729:25161877:25162016 | 25160574:25160729 | ENSG00000109618.7 | ENST00000382103.2 |
exon_skip_428901 | 4 | 25160574:25160729:25161131:25161386:25161877:25162016 | 25161131:25161386 | ENSG00000109618.7 | ENST00000513285.1 |
exon_skip_428903 | 4 | 25160574:25160729:25161249:25161386:25161877:25162016 | 25161249:25161386 | ENSG00000109618.7 | ENST00000358971.3 |
PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SEPSECS |
Information of exkip skipping event in GTEx |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_428892 | 4 | 25127315:25127406:25128885:25128979:25146395:25146487 | 25128885:25128979 | ENSG00000109618.7 | ENST00000302922.3,ENST00000382103.2,ENST00000358971.3,ENST00000514585.1 |
exon_skip_428894 | 4 | 25146395:25146487:25146625:25146755:25153581:25153684 | 25146625:25146755 | ENSG00000109618.7 | ENST00000302922.3,ENST00000382103.2,ENST00000358971.3,ENST00000514585.1 |
exon_skip_428897 | 4 | 25146625:25146755:25153581:25153684:25156619:25156773 | 25153581:25153684 | ENSG00000109618.7 | ENST00000302922.3,ENST00000382103.2,ENST00000358971.3,ENST00000514585.1 |
exon_skip_428898 | 4 | 25158477:25158596:25160574:25160729:25161877:25162016 | 25160574:25160729 | ENSG00000109618.7 | ENST00000382103.2 |
exon_skip_428901 | 4 | 25160574:25160729:25161131:25161386:25161877:25162016 | 25161131:25161386 | ENSG00000109618.7 | ENST00000513285.1 |
exon_skip_428903 | 4 | 25160574:25160729:25161249:25161386:25161877:25162016 | 25161249:25161386 | ENSG00000109618.7 | ENST00000358971.3 |
PSI values of skipped exons in GTEx. |
* Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for SEPSECS |
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 |
ENST00000382103 | 25128885 | 25128979 | Frame-shift |
ENST00000382103 | 25146625 | 25146755 | Frame-shift |
ENST00000382103 | 25153581 | 25153684 | Frame-shift |
ENST00000382103 | 25160574 | 25160729 | 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 |
ENST00000382103 | 25128885 | 25128979 | Frame-shift |
ENST00000382103 | 25146625 | 25146755 | Frame-shift |
ENST00000382103 | 25153581 | 25153684 | Frame-shift |
ENST00000382103 | 25160574 | 25160729 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SEPSECS |
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 |
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SNVs in the skipped exons for SEPSECS |
- 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-A3A0-01 | exon_skip_428892 | 25128886 | 25128979 | 25128952 | 25128952 | Frame_Shift_Del | T | - | p.I352fs |
LIHC | TCGA-DD-A3A0-01 | exon_skip_428894 | 25146626 | 25146755 | 25146666 | 25146666 | Frame_Shift_Del | A | - | p.F298fs |
LIHC | TCGA-DD-A3A0-01 | exon_skip_428894 | 25146626 | 25146755 | 25146706 | 25146706 | Frame_Shift_Del | T | - | p.N285fs |
LIHC | TCGA-DD-A3A0-01 | exon_skip_428898 | 25160575 | 25160729 | 25160641 | 25160641 | Frame_Shift_Del | C | - | p.G68fs |
BLCA | TCGA-ZF-A9RN-01 | exon_skip_428894 | 25146626 | 25146755 | 25146650 | 25146650 | Nonsense_Mutation | G | A | p.Q304* |
LUSC | TCGA-22-5478-01 | exon_skip_428894 | 25146626 | 25146755 | 25146715 | 25146715 | Nonsense_Mutation | A | T | p.L282* |
- 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 |
BICR18_UPPER_AERODIGESTIVE_TRACT | 25146626 | 25146755 | 25146645 | 25146645 | Missense_Mutation | T | G | p.E305D |
BICR18_UPPER_AERODIGESTIVE_TRACT | 25146626 | 25146755 | 25146659 | 25146659 | Missense_Mutation | A | G | p.S301P |
RERFLCKJ_LUNG | 25146626 | 25146755 | 25146748 | 25146748 | Missense_Mutation | C | T | p.R271Q |
HCC2998_LARGE_INTESTINE | 25153582 | 25153684 | 25153662 | 25153662 | Missense_Mutation | A | C | p.C242G |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SEPSECS |
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 SEPSECS |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SEPSECS |
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RelatedDrugs for SEPSECS |
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 |
Q9HD40 | DB00114 | Pyridoxal phosphate | O-phosphoseryl-tRNA(Sec) selenium transferase | small molecule | approved|investigational|nutraceutical |
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RelatedDiseases for SEPSECS |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |
SEPSECS | C3151140 | PONTOCEREBELLAR HYPOPLASIA, TYPE 2D | 2 | UNIPROT |
SEPSECS | C0043094 | Weight Gain | 1 | CTD_human |