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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 SLC38A2 |
 Gene summary |
| Gene information | Gene symbol | SLC38A2 | Gene ID | 54407 |
| Gene name | solute carrier family 38 member 2 | |
| Synonyms | ATA2|PRO1068|SAT2|SNAT2 | |
| Cytomap | 12q13.11 | |
| Type of gene | protein-coding | |
| Description | sodium-coupled neutral amino acid transporter 2amino acid transporter 2amino acid transporter A2protein 40-9-1system A amino acid transporter 2system A transporter 1system N amino acid transporter 2 | |
| Modification date | 20180523 | |
| UniProtAcc | Q96QD8 | |
| Context | PubMed: SLC38A2 [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 SLC38A2 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 SLC38A2 |
| 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 SLC38A2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_91360 | 12 | 46756276:46756421:46756803:46756928:46757508:46757609 | 46756803:46756928 | ENSG00000134294.9 | ENST00000256689.5,ENST00000551374.1,ENST00000548236.1,ENST00000549258.1 |
| exon_skip_91361 | 12 | 46757706:46757786:46758171:46758339:46758426:46758485 | 46758171:46758339 | ENSG00000134294.9 | ENST00000256689.5,ENST00000551374.1,ENST00000548236.1,ENST00000549258.1 |
| exon_skip_91363 | 12 | 46758426:46758485:46758889:46758972:46760646:46760728 | 46758889:46758972 | ENSG00000134294.9 | ENST00000256689.5,ENST00000547252.1,ENST00000549258.1,ENST00000548870.1 |
| exon_skip_91369 | 12 | 46758889:46758972:46760646:46760728:46760858:46760951 | 46760646:46760728 | ENSG00000134294.9 | ENST00000256689.5,ENST00000547252.1,ENST00000549258.1,ENST00000548870.1 |
| exon_skip_91372 | 12 | 46761049:46761123:46764294:46764410:46764558:46764629 | 46764294:46764410 | ENSG00000134294.9 | ENST00000256689.5,ENST00000547252.1 |
| exon_skip_91373 | 12 | 46764558:46764640:46764960:46765162:46766291:46766554 | 46764960:46765162 | ENSG00000134294.9 | ENST00000549258.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SLC38A2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_91360 | 12 | 46756276:46756421:46756803:46756928:46757508:46757609 | 46756803:46756928 | ENSG00000134294.9 | ENST00000256689.5,ENST00000549258.1,ENST00000551374.1,ENST00000548236.1 |
| exon_skip_91361 | 12 | 46757706:46757786:46758171:46758339:46758426:46758485 | 46758171:46758339 | ENSG00000134294.9 | ENST00000256689.5,ENST00000549258.1,ENST00000551374.1,ENST00000548236.1 |
| exon_skip_91363 | 12 | 46758426:46758485:46758889:46758972:46760646:46760728 | 46758889:46758972 | ENSG00000134294.9 | ENST00000256689.5,ENST00000549258.1,ENST00000548870.1,ENST00000547252.1 |
| exon_skip_91369 | 12 | 46758889:46758972:46760646:46760728:46760858:46760951 | 46760646:46760728 | ENSG00000134294.9 | ENST00000256689.5,ENST00000549258.1,ENST00000548870.1,ENST00000547252.1 |
| exon_skip_91372 | 12 | 46761049:46761123:46764294:46764410:46764558:46764629 | 46764294:46764410 | ENSG00000134294.9 | ENST00000256689.5,ENST00000547252.1 |
| exon_skip_91373 | 12 | 46764558:46764640:46764960:46765162:46766291:46766554 | 46764960:46765162 | ENSG00000134294.9 | ENST00000549258.1 |
| 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 SLC38A2 |
| 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 |
| ENST00000256689 | 46756803 | 46756928 | Frame-shift |
| ENST00000256689 | 46758889 | 46758972 | Frame-shift |
| ENST00000256689 | 46760646 | 46760728 | Frame-shift |
| ENST00000256689 | 46764294 | 46764410 | Frame-shift |
| ENST00000256689 | 46758171 | 46758339 | 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 |
| ENST00000256689 | 46756803 | 46756928 | Frame-shift |
| ENST00000256689 | 46758889 | 46758972 | Frame-shift |
| ENST00000256689 | 46760646 | 46760728 | Frame-shift |
| ENST00000256689 | 46764294 | 46764410 | Frame-shift |
| ENST00000256689 | 46758171 | 46758339 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SLC38A2 |
| 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 |
| ENST00000256689 | 4905 | 506 | 46758171 | 46758339 | 1151 | 1318 | 235 | 291 |
| 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 |
| ENST00000256689 | 4905 | 506 | 46758171 | 46758339 | 1151 | 1318 | 235 | 291 |
| 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 |
| Q96QD8 | 235 | 291 | 1 | 506 | Chain | ID=PRO_0000311369;Note=Sodium-coupled neutral amino acid transporter 2 |
| Q96QD8 | 235 | 291 | 245 | 281 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00114 |
| Q96QD8 | 235 | 291 | 258 | 258 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QD8 | 235 | 291 | 274 | 274 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QD8 | 235 | 291 | 273 | 273 | Sequence conflict | Note=H->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96QD8 | 235 | 291 | 239 | 292 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QD8 | 235 | 291 | 218 | 238 | 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 |
| Q96QD8 | 235 | 291 | 1 | 506 | Chain | ID=PRO_0000311369;Note=Sodium-coupled neutral amino acid transporter 2 |
| Q96QD8 | 235 | 291 | 245 | 281 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00114 |
| Q96QD8 | 235 | 291 | 258 | 258 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QD8 | 235 | 291 | 274 | 274 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QD8 | 235 | 291 | 273 | 273 | Sequence conflict | Note=H->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96QD8 | 235 | 291 | 239 | 292 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QD8 | 235 | 291 | 218 | 238 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for SLC38A2 |
| - 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_91369 | 46760647 | 46760728 | 46760671 | 46760671 | Frame_Shift_Del | A | - | p.L180fs |
| BLCA | TCGA-XF-A9ST-01 | exon_skip_91372 | 46764295 | 46764410 | 46764395 | 46764395 | Frame_Shift_Del | A | - | p.S72fs |
| STAD | TCGA-CG-5721-01 | exon_skip_91361 | 46758172 | 46758339 | 46758170 | 46758170 | Splice_Site | A | T | . |
| STAD | TCGA-CG-5721-01 | exon_skip_91361 | 46758172 | 46758339 | 46758170 | 46758170 | Splice_Site | A | T | p.Q291_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 |
| OVK18_OVARY | 46756804 | 46756928 | 46756836 | 46756836 | Missense_Mutation | C | T | p.V383M |
| GMEL_SKIN | 46756804 | 46756928 | 46756883 | 46756883 | Missense_Mutation | C | T | p.G367E |
| COLO699_LUNG | 46756804 | 46756928 | 46756926 | 46756926 | Missense_Mutation | G | A | p.H353Y |
| KPNRTBM1_AUTONOMIC_GANGLIA | 46758172 | 46758339 | 46758206 | 46758206 | Missense_Mutation | G | A | p.S280F |
| HGC27_STOMACH | 46758172 | 46758339 | 46758206 | 46758206 | Missense_Mutation | G | A | p.S280F |
| HTCC3_THYROID | 46758172 | 46758339 | 46758206 | 46758206 | Missense_Mutation | G | A | p.S280F |
| RCM1_LARGE_INTESTINE | 46758172 | 46758339 | 46758206 | 46758206 | Missense_Mutation | G | A | p.S280F |
| CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 46758172 | 46758339 | 46758222 | 46758222 | Missense_Mutation | C | T | p.V275M |
| HEC59_ENDOMETRIUM | 46758172 | 46758339 | 46758224 | 46758224 | Missense_Mutation | T | C | p.N274S |
| J82_URINARY_TRACT | 46758172 | 46758339 | 46758243 | 46758243 | Missense_Mutation | C | G | p.V268L |
| DL40_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 46758172 | 46758339 | 46758257 | 46758257 | Missense_Mutation | T | C | p.Q263R |
| KM12_LARGE_INTESTINE | 46758172 | 46758339 | 46758275 | 46758275 | Missense_Mutation | A | G | p.I257T |
| HCC2998_LARGE_INTESTINE | 46758172 | 46758339 | 46758282 | 46758282 | Missense_Mutation | C | T | p.E255K |
| IGR1_SKIN | 46758172 | 46758339 | 46758308 | 46758308 | Missense_Mutation | G | A | p.P246L |
| EW7_BONE | 46758172 | 46758339 | 46758320 | 46758320 | Missense_Mutation | T | A | p.Q242L |
| YD38_UPPER_AERODIGESTIVE_TRACT | 46758890 | 46758972 | 46758969 | 46758969 | Missense_Mutation | C | G | p.L189F |
| HEC251_ENDOMETRIUM | 46760647 | 46760728 | 46760657 | 46760657 | Missense_Mutation | C | A | p.D185Y |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 46760647 | 46760728 | 46760678 | 46760678 | Missense_Mutation | G | T | p.Q178K |
| NCIH2085_LUNG | 46764961 | 46765162 | 46765048 | 46765048 | Missense_Mutation | C | A | p.S10I |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC38A2 |
| 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 SLC38A2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC38A2 |
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RelatedDrugs for SLC38A2 |
| 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 SLC38A2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SLC38A2 | C0036341 | Schizophrenia | 1 | PSYGENET |
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