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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 SPTLC2 |
 Gene summary |
| Gene information | Gene symbol | SPTLC2 | Gene ID | 9517 |
| Gene name | serine palmitoyltransferase long chain base subunit 2 | |
| Synonyms | HSN1C|LCB2|LCB2A|NSAN1C|SPT2|hLCB2a | |
| Cytomap | 14q24.3 | |
| Type of gene | protein-coding | |
| Description | serine palmitoyltransferase 2LCB 2SPT 2long chain base biosynthesis protein 2aserine palmitoyltransferase, subunit IIserine-palmitoyl-CoA transferase 2 | |
| Modification date | 20180519 | |
| UniProtAcc | O15270 | |
| Context | PubMed: SPTLC2 [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 |
| SPTLC2 | GO:0030148 | sphingolipid biosynthetic process | 25332431 |
| SPTLC2 | GO:0046513 | ceramide biosynthetic process | 25691431 |
| SPTLC2 | GO:1904504 | positive regulation of lipophagy | 25332431 |
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Exon skipping events across known transcript of Ensembl for SPTLC2 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 SPTLC2 |
| 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 SPTLC2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_114759 | 14 | 77978683:77978746:77984380:77984510:77987788:77987924 | 77984380:77984510 | ENSG00000100596.2 | ENST00000216484.2,ENST00000556607.1 |
| exon_skip_114760 | 14 | 78023383:78023489:78028738:78028832:78036726:78036851 | 78028738:78028832 | ENSG00000100596.2 | ENST00000216484.2,ENST00000554901.1 |
| exon_skip_114764 | 14 | 78028738:78028832:78036726:78036851:78043109:78043258 | 78036726:78036851 | ENSG00000100596.2 | ENST00000216484.2,ENST00000554901.1 |
| exon_skip_114766 | 14 | 78043109:78043258:78045297:78045452:78063528:78063664 | 78045297:78045452 | ENSG00000100596.2 | ENST00000216484.2,ENST00000554901.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SPTLC2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_114759 | 14 | 77978683:77978746:77984380:77984510:77987788:77987924 | 77984380:77984510 | ENSG00000100596.2 | ENST00000216484.2,ENST00000556607.1 |
| exon_skip_114760 | 14 | 78023383:78023489:78028738:78028832:78036726:78036851 | 78028738:78028832 | ENSG00000100596.2 | ENST00000216484.2,ENST00000554901.1 |
| exon_skip_114764 | 14 | 78028738:78028832:78036726:78036851:78043109:78043258 | 78036726:78036851 | ENSG00000100596.2 | ENST00000216484.2,ENST00000554901.1 |
| 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 SPTLC2 |
| 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 |
| ENST00000216484 | 77984380 | 77984510 | Frame-shift |
| ENST00000216484 | 78028738 | 78028832 | Frame-shift |
| ENST00000216484 | 78036726 | 78036851 | Frame-shift |
| ENST00000216484 | 78045297 | 78045452 | 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 |
| ENST00000216484 | 77984380 | 77984510 | Frame-shift |
| ENST00000216484 | 78028738 | 78028832 | Frame-shift |
| ENST00000216484 | 78036726 | 78036851 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SPTLC2 |
| 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 |
| 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 SPTLC2 |
| - 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-A3A0-01 | exon_skip_114759 | 77984381 | 77984510 | 77984426 | 77984426 | Frame_Shift_Del | G | - | p.A508fs |
| CESC | TCGA-FU-A23L-01 | exon_skip_114766 | 78045298 | 78045452 | 78045373 | 78045385 | Frame_Shift_Del | CGATTCCAGTTGT | - | p.DNWNR132fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_114766 | 78045298 | 78045452 | 78045421 | 78045421 | Frame_Shift_Del | T | - | p.N120fs |
| - 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 |
| HCT15_LARGE_INTESTINE | 77984381 | 77984510 | 77984470 | 77984470 | Missense_Mutation | C | T | p.V494I |
| HEC1A_ENDOMETRIUM | 77984381 | 77984510 | 77984485 | 77984485 | Missense_Mutation | G | A | p.R489W |
| HEC1_ENDOMETRIUM | 77984381 | 77984510 | 77984485 | 77984485 | Missense_Mutation | G | A | p.R489W |
| HEC1B_ENDOMETRIUM | 77984381 | 77984510 | 77984485 | 77984485 | Missense_Mutation | G | A | p.R489W |
| SNU1040_LARGE_INTESTINE | 78028739 | 78028832 | 78028781 | 78028781 | Missense_Mutation | C | T | p.A270T |
| RH36_SOFT_TISSUE | 78036727 | 78036851 | 78036807 | 78036807 | Missense_Mutation | A | G | p.F226L |
| SNGM_ENDOMETRIUM | 78036727 | 78036851 | 78036809 | 78036809 | Missense_Mutation | C | A | p.R225M |
| KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 78045298 | 78045452 | 78045389 | 78045389 | Missense_Mutation | T | C | p.R131G |
| CW2_LARGE_INTESTINE | 78045298 | 78045452 | 78045409 | 78045409 | Missense_Mutation | C | T | p.R124K |
| SNU349_KIDNEY | 78045298 | 78045452 | 78045419 | 78045419 | Missense_Mutation | A | G | p.F121L |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPTLC2 |
| 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 SPTLC2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SPTLC2 |
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RelatedDrugs for SPTLC2 |
| 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 |
| O15270 | DB00114 | Pyridoxal phosphate | Serine palmitoyltransferase 2 | small molecule | approved|investigational|nutraceutical |
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RelatedDiseases for SPTLC2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SPTLC2 | C3150896 | NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IC | 2 | CTD_human;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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