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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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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 | 20200313 | |
| UniProtAcc | ||
| Context |
| 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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Gene structures and expression levels for SLC38A1 |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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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ENSG00000111371
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000551506.1 | SLC38A1-209:lncRNA:SLC38A1 | 2.168064e+00 | 1.259172e+00 | 1.496389e-06 | 2.112319e-05 |
| TC | UP | ENST00000439706.5 | SLC38A1-202:protein_coding:SLC38A1 | 1.414088e+00 | 1.318173e+00 | 7.830594e-04 | 8.178779e-03 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SLC38A1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_139804 | chr12 | 46198728:46198743:46201098:46201198:46203010:46203089 | 46201098:46201198 |
| exon_skip_172363 | chr12 | 46201098:46201198:46203010:46203089:46204301:46204417 | 46203010:46203089 |
| exon_skip_19357 | chr12 | 46229564:46229639:46239679:46239893:46268526:46268806 | 46239679:46239893 |
| exon_skip_213125 | chr12 | 46229564:46229639:46239679:46239893:46268865:46269043 | 46239679:46239893 |
| exon_skip_213286 | chr12 | 46243200:46243314:46254814:46254936:46268526:46268806 | 46254814:46254936 |
| exon_skip_32091 | chr12 | 46239679:46239893:46243200:46243314:46268865:46269130 | 46243200:46243314 |
| exon_skip_37489 | chr12 | 46243200:46243314:46254814:46254936:46268526:46268997 | 46254814:46254936 |
| exon_skip_49006 | chr12 | 46239679:46239893:46243200:46243314:46268865:46269043 | 46243200:46243314 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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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 ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000549049 | 46239679 | 46239893 | 3UTR-3CDS |
| ENST00000546893 | 46243200 | 46243314 | 3UTR-3UTR |
| ENST00000439706 | 46254814 | 46254936 | 3UTR-3UTR |
| ENST00000398637 | 46203010 | 46203089 | Frame-shift |
| ENST00000439706 | 46203010 | 46203089 | Frame-shift |
| ENST00000546893 | 46203010 | 46203089 | Frame-shift |
| ENST00000549049 | 46203010 | 46203089 | Frame-shift |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000546893 | 46243200 | 46243314 | 3UTR-3UTR |
| ENST00000439706 | 46254814 | 46254936 | 3UTR-3UTR |
| ENST00000398637 | 46203010 | 46203089 | Frame-shift |
| ENST00000439706 | 46203010 | 46203089 | Frame-shift |
| ENST00000546893 | 46203010 | 46203089 | Frame-shift |
| ENST00000549049 | 46203010 | 46203089 | Frame-shift |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000549049 | 46239679 | 46239893 | 3UTR-3CDS |
| ENST00000546893 | 46243200 | 46243314 | 3UTR-3UTR |
| ENST00000439706 | 46254814 | 46254936 | 3UTR-3UTR |
| ENST00000398637 | 46201098 | 46201198 | Frame-shift |
| ENST00000439706 | 46201098 | 46201198 | Frame-shift |
| ENST00000546893 | 46201098 | 46201198 | Frame-shift |
| ENST00000549049 | 46201098 | 46201198 | Frame-shift |
| ENST00000398637 | 46203010 | 46203089 | Frame-shift |
| ENST00000439706 | 46203010 | 46203089 | Frame-shift |
| ENST00000546893 | 46203010 | 46203089 | Frame-shift |
| ENST00000549049 | 46203010 | 46203089 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SLC38A1 |
p-ENSG00000111371_img4.png |
| Loci of skipped exons in ROSMAP 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 MSBB 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 Mayo 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 ROSMAP. |
| 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 MSBB. |
| 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 Mayo. |
| 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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3'-UTR located exon skipping events that lost miRNA binding sites in SLC38A1 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
| Mayo | ENST00000439706 | 46254814 | 46254936 | hsa-miR-8068 | chr12:46254852-46254859 | 8mer-1a | chr12:46254838-46254859 | 140.00 | -10.38 |
| Mayo | ENST00000439706 | 46254814 | 46254936 | hsa-miR-548l | chr12:46254885-46254892 | 8mer-1a | chr12:46254875-46254896 | 149.00 | -9.68 |
| Mayo | ENST00000439706 | 46254814 | 46254936 | hsa-miR-4495 | chr12:46254889-46254896 | 8mer-1a | chr12:46254875-46254896 | 149.00 | -9.68 |
| Mayo | ENST00000546893 | 46243200 | 46243314 | hsa-miR-5586-3p | chr12:46243225-46243232 | 8mer-1a | chr12:46243219-46243241 | 164.00 | -10.36 |
| Mayo | ENST00000546893 | 46243200 | 46243314 | hsa-miR-3529-3p | chr12:46243239-46243246 | 8mer-1a | chr12:46243233-46243254 | 150.00 | -12.41 |
| Mayo | ENST00000546893 | 46243200 | 46243314 | hsa-miR-6790-5p | chr12:46243300-46243307 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| Mayo | ENST00000439706 | 46254814 | 46254936 | hsa-miR-2355-5p | chr12:46254830-46254837 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| Mayo | ENST00000546893 | 46243200 | 46243314 | hsa-miR-4755-3p | chr12:46243284-46243291 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| Mayo | ENST00000439706 | 46254814 | 46254936 | hsa-miR-6830-5p | chr12:46254927-46254934 | 8mer-1a | chr12:46254911-46254935 | 146.00 | -11.99 |
| Mayo | ENST00000439706 | 46254814 | 46254936 | hsa-miR-6833-3p | chr12:46254846-46254853 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| Mayo | ENST00000439706 | 46254814 | 46254936 | hsa-miR-6873-3p | chr12:46254845-46254852 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| Mayo | ENST00000546893 | 46243200 | 46243314 | hsa-miR-4658 | chr12:46243300-46243307 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| Mayo | ENST00000439706 | 46254814 | 46254936 | hsa-miR-8055 | chr12:46254917-46254924 | 8mer-1a | chr12:46254909-46254932 | 147.00 | -17.76 |
| Mayo | ENST00000439706 | 46254814 | 46254936 | hsa-miR-4768-5p | chr12:46254846-46254853 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| Mayo | ENST00000546893 | 46243200 | 46243314 | hsa-miR-934 | chr12:46243295-46243302 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| Mayo | ENST00000546893 | 46243200 | 46243314 | hsa-miR-892a | chr12:46243291-46243298 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| MSBB | ENST00000439706 | 46254814 | 46254936 | hsa-miR-8068 | chr12:46254852-46254859 | 8mer-1a | chr12:46254838-46254859 | 140.00 | -10.38 |
| MSBB | ENST00000439706 | 46254814 | 46254936 | hsa-miR-548l | chr12:46254885-46254892 | 8mer-1a | chr12:46254875-46254896 | 149.00 | -9.68 |
| MSBB | ENST00000439706 | 46254814 | 46254936 | hsa-miR-4495 | chr12:46254889-46254896 | 8mer-1a | chr12:46254875-46254896 | 149.00 | -9.68 |
| MSBB | ENST00000546893 | 46243200 | 46243314 | hsa-miR-5586-3p | chr12:46243225-46243232 | 8mer-1a | chr12:46243219-46243241 | 164.00 | -10.36 |
| MSBB | ENST00000546893 | 46243200 | 46243314 | hsa-miR-3529-3p | chr12:46243239-46243246 | 8mer-1a | chr12:46243233-46243254 | 150.00 | -12.41 |
| MSBB | ENST00000546893 | 46243200 | 46243314 | hsa-miR-6790-5p | chr12:46243300-46243307 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| MSBB | ENST00000439706 | 46254814 | 46254936 | hsa-miR-2355-5p | chr12:46254830-46254837 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| MSBB | ENST00000546893 | 46243200 | 46243314 | hsa-miR-4755-3p | chr12:46243284-46243291 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| MSBB | ENST00000439706 | 46254814 | 46254936 | hsa-miR-6830-5p | chr12:46254927-46254934 | 8mer-1a | chr12:46254911-46254935 | 146.00 | -11.99 |
| MSBB | ENST00000439706 | 46254814 | 46254936 | hsa-miR-6833-3p | chr12:46254846-46254853 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| MSBB | ENST00000439706 | 46254814 | 46254936 | hsa-miR-6873-3p | chr12:46254845-46254852 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| MSBB | ENST00000546893 | 46243200 | 46243314 | hsa-miR-4658 | chr12:46243300-46243307 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| MSBB | ENST00000439706 | 46254814 | 46254936 | hsa-miR-8055 | chr12:46254917-46254924 | 8mer-1a | chr12:46254909-46254932 | 147.00 | -17.76 |
| MSBB | ENST00000439706 | 46254814 | 46254936 | hsa-miR-4768-5p | chr12:46254846-46254853 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| MSBB | ENST00000546893 | 46243200 | 46243314 | hsa-miR-934 | chr12:46243295-46243302 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| MSBB | ENST00000546893 | 46243200 | 46243314 | hsa-miR-892a | chr12:46243291-46243298 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| ROSMAP | ENST00000439706 | 46254814 | 46254936 | hsa-miR-8068 | chr12:46254852-46254859 | 8mer-1a | chr12:46254838-46254859 | 140.00 | -10.38 |
| ROSMAP | ENST00000439706 | 46254814 | 46254936 | hsa-miR-548l | chr12:46254885-46254892 | 8mer-1a | chr12:46254875-46254896 | 149.00 | -9.68 |
| ROSMAP | ENST00000439706 | 46254814 | 46254936 | hsa-miR-4495 | chr12:46254889-46254896 | 8mer-1a | chr12:46254875-46254896 | 149.00 | -9.68 |
| ROSMAP | ENST00000546893 | 46243200 | 46243314 | hsa-miR-5586-3p | chr12:46243225-46243232 | 8mer-1a | chr12:46243219-46243241 | 164.00 | -10.36 |
| ROSMAP | ENST00000546893 | 46243200 | 46243314 | hsa-miR-3529-3p | chr12:46243239-46243246 | 8mer-1a | chr12:46243233-46243254 | 150.00 | -12.41 |
| ROSMAP | ENST00000546893 | 46243200 | 46243314 | hsa-miR-6790-5p | chr12:46243300-46243307 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| ROSMAP | ENST00000439706 | 46254814 | 46254936 | hsa-miR-2355-5p | chr12:46254830-46254837 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| ROSMAP | ENST00000546893 | 46243200 | 46243314 | hsa-miR-4755-3p | chr12:46243284-46243291 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| ROSMAP | ENST00000439706 | 46254814 | 46254936 | hsa-miR-6830-5p | chr12:46254927-46254934 | 8mer-1a | chr12:46254911-46254935 | 146.00 | -11.99 |
| ROSMAP | ENST00000439706 | 46254814 | 46254936 | hsa-miR-6833-3p | chr12:46254846-46254853 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| ROSMAP | ENST00000439706 | 46254814 | 46254936 | hsa-miR-6873-3p | chr12:46254845-46254852 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| ROSMAP | ENST00000546893 | 46243200 | 46243314 | hsa-miR-4658 | chr12:46243300-46243307 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| ROSMAP | ENST00000439706 | 46254814 | 46254936 | hsa-miR-8055 | chr12:46254917-46254924 | 8mer-1a | chr12:46254909-46254932 | 147.00 | -17.76 |
| ROSMAP | ENST00000439706 | 46254814 | 46254936 | hsa-miR-4768-5p | chr12:46254846-46254853 | 8mer-1a | chr12:46254830-46254853 | 161.00 | -26.41 |
| ROSMAP | ENST00000546893 | 46243200 | 46243314 | hsa-miR-934 | chr12:46243295-46243302 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
| ROSMAP | ENST00000546893 | 46243200 | 46243314 | hsa-miR-892a | chr12:46243291-46243298 | 8mer-1a | chr12:46243283-46243307 | 155.00 | -21.70 |
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SNVs in the skipped exons for SLC38A1 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
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AD stage-associated exon skippint events for SLC38A1 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC38A1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| PCC | exon_skip_213286 | rs7967767 | chr12:46174105 | 9.587312e-05 | 1.672709e-02 |
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Correlation with RNA binding proteins (RBPs) for SLC38A1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | ELAVL1 | exon_skip_172363 | -5.407496e-01 | 2.202564e-12 |
| CB | PCBP4 | exon_skip_172363 | 5.304581e-01 | 6.775948e-12 |
| CB | FUBP1 | exon_skip_172363 | -5.520866e-01 | 6.106395e-13 |
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RelatedDrugs for SLC38A1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| 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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