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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 SLC38A1 |
 Gene summary |
| Gene information | Gene symbol | SLC38A1 | Gene ID | 81539 |
| Gene name | solute carrier family 38 member 1 | |
| Synonyms | ATA1|NAT2|SAT1|SNAT1 | |
| Cytomap | 12q13.11 | |
| Type of gene | protein-coding | |
| Description | sodium-coupled neutral amino acid transporter 1N-system amino acid transporter 2amino acid transporter A1amino acid transporter system A1system A amino acid transporter 1system N amino acid transporter 1 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9H2H9 | |
| Context | PubMed: SLC38A1 [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 SLC38A1 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 SLC38A1 |
| 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 SLC38A1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_91313 | 12 | 46592510:46592526:46594880:46594981:46596792:46596872 | 46594880:46594981 | ENSG00000111371.11 | ENST00000398637.5,ENST00000546893.1,ENST00000552197.1,ENST00000549049.1,ENST00000549633.1,ENST00000439706.1 |
| exon_skip_91315 | 12 | 46594880:46594981:46596792:46596872:46598083:46598200 | 46596792:46596872 | ENSG00000111371.11 | ENST00000398637.5,ENST00000546893.1,ENST00000552197.1,ENST00000549049.1,ENST00000549633.1,ENST00000439706.1 |
| exon_skip_91318 | 12 | 46623346:46623422:46633461:46633676:46636982:46637097 | 46633461:46633676 | ENSG00000111371.11 | ENST00000398637.5,ENST00000546893.1,ENST00000552197.1,ENST00000439706.1 |
| exon_skip_91320 | 12 | 46623346:46623422:46633461:46633676:46662308:46662589 | 46633461:46633676 | ENSG00000111371.11 | ENST00000549049.1 |
| exon_skip_91321 | 12 | 46623346:46623422:46633461:46633676:46662647:46662826 | 46633461:46633676 | ENSG00000111371.11 | ENST00000550173.1 |
| exon_skip_91336 | 12 | 46633461:46633676:46636982:46637097:46662647:46662826 | 46636982:46637097 | ENSG00000111371.11 | ENST00000546893.1 |
| exon_skip_91346 | 12 | 46636982:46637097:46648596:46648719:46662308:46662589 | 46648596:46648719 | ENSG00000111371.11 | ENST00000439706.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SLC38A1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_91313 | 12 | 46592510:46592526:46594880:46594981:46596792:46596872 | 46594880:46594981 | ENSG00000111371.11 | ENST00000398637.5,ENST00000549049.1,ENST00000439706.1,ENST00000546893.1,ENST00000552197.1,ENST00000549633.1 |
| exon_skip_91315 | 12 | 46594880:46594981:46596792:46596872:46598083:46598200 | 46596792:46596872 | ENSG00000111371.11 | ENST00000398637.5,ENST00000549049.1,ENST00000439706.1,ENST00000546893.1,ENST00000552197.1,ENST00000549633.1 |
| exon_skip_91318 | 12 | 46623346:46623422:46633461:46633676:46636982:46637097 | 46633461:46633676 | ENSG00000111371.11 | ENST00000398637.5,ENST00000439706.1,ENST00000546893.1,ENST00000552197.1 |
| exon_skip_91320 | 12 | 46623346:46623422:46633461:46633676:46662308:46662589 | 46633461:46633676 | ENSG00000111371.11 | ENST00000549049.1 |
| exon_skip_91321 | 12 | 46623346:46623422:46633461:46633676:46662647:46662826 | 46633461:46633676 | ENSG00000111371.11 | ENST00000550173.1 |
| exon_skip_91336 | 12 | 46633461:46633676:46636982:46637097:46662647:46662826 | 46636982:46637097 | ENSG00000111371.11 | ENST00000546893.1 |
| exon_skip_91346 | 12 | 46636982:46637097:46648596:46648719:46662308:46662589 | 46648596:46648719 | ENSG00000111371.11 | ENST00000439706.1 |
| 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 SLC38A1 |
| 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 |
| ENST00000398637 | 46633461 | 46633676 | 3UTR-3CDS |
| ENST00000439706 | 46633461 | 46633676 | 3UTR-3CDS |
| ENST00000546893 | 46633461 | 46633676 | 3UTR-3CDS |
| ENST00000549049 | 46633461 | 46633676 | 3UTR-3CDS |
| ENST00000546893 | 46636982 | 46637097 | 3UTR-3UTR |
| ENST00000439706 | 46648596 | 46648719 | 3UTR-3UTR |
| ENST00000398637 | 46594880 | 46594981 | Frame-shift |
| ENST00000439706 | 46594880 | 46594981 | Frame-shift |
| ENST00000546893 | 46594880 | 46594981 | Frame-shift |
| ENST00000549049 | 46594880 | 46594981 | Frame-shift |
| ENST00000398637 | 46596792 | 46596872 | Frame-shift |
| ENST00000439706 | 46596792 | 46596872 | Frame-shift |
| ENST00000546893 | 46596792 | 46596872 | Frame-shift |
| ENST00000549049 | 46596792 | 46596872 | 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 |
| ENST00000398637 | 46633461 | 46633676 | 3UTR-3CDS |
| ENST00000439706 | 46633461 | 46633676 | 3UTR-3CDS |
| ENST00000546893 | 46633461 | 46633676 | 3UTR-3CDS |
| ENST00000549049 | 46633461 | 46633676 | 3UTR-3CDS |
| ENST00000546893 | 46636982 | 46637097 | 3UTR-3UTR |
| ENST00000439706 | 46648596 | 46648719 | 3UTR-3UTR |
| ENST00000398637 | 46594880 | 46594981 | Frame-shift |
| ENST00000439706 | 46594880 | 46594981 | Frame-shift |
| ENST00000546893 | 46594880 | 46594981 | Frame-shift |
| ENST00000549049 | 46594880 | 46594981 | Frame-shift |
| ENST00000398637 | 46596792 | 46596872 | Frame-shift |
| ENST00000439706 | 46596792 | 46596872 | Frame-shift |
| ENST00000546893 | 46596792 | 46596872 | Frame-shift |
| ENST00000549049 | 46596792 | 46596872 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SLC38A1 |
| 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 SLC38A1 |
| - 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-A39Y-01 | exon_skip_91313 | 46594881 | 46594981 | 46594900 | 46594900 | Frame_Shift_Del | A | - | p.F328fs |
| HNSC | TCGA-CV-A45U-01 | exon_skip_91313 | 46594881 | 46594981 | 46594952 | 46594952 | Nonsense_Mutation | G | C | p.S311* |
| - 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 |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 46594881 | 46594981 | 46594965 | 46594965 | Frame_Shift_Del | T | - | p.M307fs |
| SNU1040_LARGE_INTESTINE | 46594881 | 46594981 | 46594964 | 46594965 | Frame_Shift_Ins | - | T | p.M307fs |
| MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 46596793 | 46596872 | 46596826 | 46596826 | Missense_Mutation | G | A | p.P290L |
| SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 46596793 | 46596872 | 46596853 | 46596853 | Missense_Mutation | G | C | p.T281S |
| SNU349_KIDNEY | 46596793 | 46596872 | 46596866 | 46596866 | Missense_Mutation | A | G | p.Y277H |
| PACADD137_PANCREAS | 46633462 | 46633676 | 46633487 | 46633487 | Missense_Mutation | C | T | p.E33K |
| MELJUSO_SKIN | 46633462 | 46633676 | 46633569 | 46633569 | Missense_Mutation | T | A | p.K5N |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC38A1 |
| 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 SLC38A1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC38A1 |
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RelatedDrugs for SLC38A1 |
| 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 SLC38A1 |
| 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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