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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 SPCS1 |
 Gene summary |
| Gene information | Gene symbol | SPCS1 | Gene ID | 28972 |
| Gene name | signal peptidase complex subunit 1 | |
| Synonyms | HSPC033|SPC1|SPC12|YJR010C-A | |
| Cytomap | 3p21.1 | |
| Type of gene | protein-coding | |
| Description | signal peptidase complex subunit 1SPase 12 kDa subunitmicrosomal signal peptidase 12 kDa subunitsignal peptidase 12kDasignal peptidase complex 12 kDa subunitsignal peptidase complex subunit 1 homolog | |
| Modification date | 20180523 | |
| UniProtAcc | Q9Y6A9 | |
| Context | PubMed: SPCS1 [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 SPCS1 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 SPCS1 |
| 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 SPCS1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_375123 | 3 | 52740659:52740719:52740808:52740895:52741702:52742035 | 52740808:52740895 | ENSG00000114902.9 | ENST00000602728.1,ENST00000423431.1,ENST00000233025.7,ENST00000474945.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SPCS1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_375123 | 3 | 52740659:52740719:52740808:52740895:52741702:52742035 | 52740808:52740895 | ENSG00000114902.9 | ENST00000423431.1,ENST00000233025.7,ENST00000602728.1,ENST00000474945.1 |
| 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 SPCS1 |
| 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 |
| ENST00000602728 | 52740808 | 52740895 | 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 |
| ENST00000602728 | 52740808 | 52740895 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SPCS1 |
| 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 |
| ENST00000602728 | 849 | 102 | 52740808 | 52740895 | 266 | 352 | 32 | 61 |
| 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 |
| ENST00000602728 | 849 | 102 | 52740808 | 52740895 | 266 | 352 | 32 | 61 |
| 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 |
| Q9Y6A9 | 32 | 61 | 1 | 102 | Chain | ID=PRO_0000215154;Note=Signal peptidase complex subunit 1 |
| Q9Y6A9 | 32 | 61 | 61 | 61 | Sequence conflict | Note=L->LAQ;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y6A9 | 32 | 61 | 48 | 48 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y6A9 | 32 | 61 | 27 | 47 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y6A9 | 32 | 61 | 49 | 69 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q9Y6A9 | 32 | 61 | 1 | 102 | Chain | ID=PRO_0000215154;Note=Signal peptidase complex subunit 1 |
| Q9Y6A9 | 32 | 61 | 61 | 61 | Sequence conflict | Note=L->LAQ;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y6A9 | 32 | 61 | 48 | 48 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y6A9 | 32 | 61 | 27 | 47 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y6A9 | 32 | 61 | 49 | 69 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for SPCS1 |
| - 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. |
SPCS1_HNSC_exon_skip_375123_psi_boxplot.png |
| - 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 |
| HNSC | TCGA-CN-A498-01 | exon_skip_375123 | 52740809 | 52740895 | 52740832 | 52740832 | Nonsense_Mutation | C | A | p.Y107* |
| HNSC | TCGA-F7-A624-01 | exon_skip_375123 | 52740809 | 52740895 | 52740853 | 52740853 | Nonsense_Mutation | G | A | p.W114* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-CN-A498-01 |
| Cancer type: HNSC | |
| ESID: exon_skip_375123 | |
| Skipped exon start: 52740809 | |
| Skipped exon end: 52740895 | |
| Mutation start: 52740832 | |
| Mutation end: 52740832 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: A | |
| AAchange: p.Y107* | |
exon_skip_375123_HNSC_TCGA-CN-A498-01.png | |
| - 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 |
| PATU8902_PANCREAS | 52740809 | 52740895 | 52740882 | 52740883 | Frame_Shift_Ins | - | T | p.AF57fs |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPCS1 |
| 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 SPCS1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SPCS1 |
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RelatedDrugs for SPCS1 |
| 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 SPCS1 |
| 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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