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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 SLC39A13 |
 Gene summary |
| Gene information | Gene symbol | SLC39A13 | Gene ID | 91252 |
| Gene name | solute carrier family 39 member 13 | |
| Synonyms | EDSSPD3|LZT-Hs9|SCDEDS|ZIP13 | |
| Cytomap | 11p11.2 | |
| Type of gene | protein-coding | |
| Description | zinc transporter ZIP13LIV-1 subfamily of ZIP zinc transporter 9solute carrier family 39 (metal ion transporter), member 13solute carrier family 39 (zinc transporter), member 13zrt- and Irt-like protein 13 | |
| 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 |
| SLC39A13 | GO:0006882 | cellular zinc ion homeostasis | 21917916 |
| SLC39A13 | GO:0071577 | zinc ion transmembrane transport | 21917916 |
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Gene structures and expression levels for SLC39A13 |
| 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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ENSG00000165915
| 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. |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| 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 SLC39A13 |
| 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_103337 | chr11 | 47413597:47413686:47414425:47414475:47414777:47414901 | 47414425:47414475 |
| exon_skip_12653 | chr11 | 47412346:47412467:47413400:47413507:47413597:47413685 | 47413400:47413507 |
| exon_skip_143523 | chr11 | 47415062:47415159:47415288:47415496:47416325:47416495 | 47415288:47415496 |
| exon_skip_148269 | chr11 | 47414437:47414475:47414777:47414905:47415060:47415159 | 47414777:47414905 |
| exon_skip_196937 | chr11 | 47415060:47415159:47415288:47415496:47416325:47416495 | 47415288:47415496 |
| exon_skip_208419 | chr11 | 47411926:47412039:47412346:47412467:47413400:47413507 | 47412346:47412467 |
| exon_skip_235648 | chr11 | 47414437:47414475:47414777:47414909:47415060:47415159 | 47414777:47414909 |
| exon_skip_237166 | chr11 | 47413602:47413686:47414425:47414475:47414777:47414901 | 47414425:47414475 |
| exon_skip_36467 | chr11 | 47412346:47412467:47413400:47413507:47413597:47413686 | 47413400:47413507 |
| exon_skip_42770 | chr11 | 47412346:47412467:47413400:47413507:47413597:47413640 | 47413400:47413507 |
| exon_skip_52272 | chr11 | 47412346:47412467:47413400:47413507:47413597:47413674 | 47413400:47413507 |
| exon_skip_54159 | chr11 | 47411926:47412039:47412346:47412467:47413597:47413686 | 47412346:47412467 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_12653 | Mayo_CB | 6.036585e-01 | 7.083117e-01 | -1.046532e-01 | 2.409165e-03 |
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Open reading frame (ORF) annotation in the exon skipping event for SLC39A13 |
| 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 |
| ENST00000362021 | 47413400 | 47413507 | In-frame |
| ENST00000362021 | 47414425 | 47414475 | In-frame |
| 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 |
| ENST00000362021 | 47413400 | 47413507 | In-frame |
| 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 |
| ENST00000362021 | 47412346 | 47412467 | Frame-shift |
| ENST00000362021 | 47413400 | 47413507 | In-frame |
| ENST00000362021 | 47414425 | 47414475 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SLC39A13 |
p-ENSG00000165915_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 |
| ENST00000362021 | 2313 | 371 | 47413400 | 47413507 | 581 | 687 | 179 | 215 |
| ENST00000362021 | 2313 | 371 | 47414425 | 47414475 | 779 | 828 | 245 | 262 |
| 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 |
| ENST00000362021 | 2313 | 371 | 47413400 | 47413507 | 581 | 687 | 179 | 215 |
| 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 |
| ENST00000362021 | 2313 | 371 | 47413400 | 47413507 | 581 | 687 | 179 | 215 |
| ENST00000362021 | 2313 | 371 | 47414425 | 47414475 | 779 | 828 | 245 | 262 |
| 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 |
| Q96H72 | 179 | 215 | 1 | 371 | Chain | ID=PRO_0000312309;Note=Zinc transporter ZIP13 |
| Q96H72 | 179 | 215 | 187 | 191 | Compositional bias | Note=Poly-Ala |
| Q96H72 | 179 | 215 | 171 | 235 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96H72 | 245 | 262 | 1 | 371 | Chain | ID=PRO_0000312309;Note=Zinc transporter ZIP13 |
| Q96H72 | 245 | 262 | 257 | 262 | Motif | Note=XEXPHE-motif |
| Q96H72 | 245 | 262 | 257 | 278 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96H72 | 245 | 262 | 236 | 256 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q96H72 | 179 | 215 | 1 | 371 | Chain | ID=PRO_0000312309;Note=Zinc transporter ZIP13 |
| Q96H72 | 179 | 215 | 187 | 191 | Compositional bias | Note=Poly-Ala |
| Q96H72 | 179 | 215 | 171 | 235 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q96H72 | 179 | 215 | 1 | 371 | Chain | ID=PRO_0000312309;Note=Zinc transporter ZIP13 |
| Q96H72 | 179 | 215 | 187 | 191 | Compositional bias | Note=Poly-Ala |
| Q96H72 | 179 | 215 | 171 | 235 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96H72 | 245 | 262 | 1 | 371 | Chain | ID=PRO_0000312309;Note=Zinc transporter ZIP13 |
| Q96H72 | 245 | 262 | 257 | 262 | Motif | Note=XEXPHE-motif |
| Q96H72 | 245 | 262 | 257 | 278 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96H72 | 245 | 262 | 236 | 256 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SLC39A13 |
| 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 |
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SNVs in the skipped exons for SLC39A13 |
| - 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 SLC39A13 |
| 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 SLC39A13 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| CB | exon_skip_12653 | rs12292911 | chr11:47427521 | 9.261519e-07 | 3.316603e-04 |
| CB | exon_skip_12653 | rs896817 | chr11:47372754 | 4.606146e-06 | 1.331412e-03 |
| TC | exon_skip_52272 | rs896817 | chr11:47372754 | 2.533126e-07 | 9.928162e-05 |
| TC | exon_skip_52272 | rs12292911 | chr11:47427521 | 2.661881e-07 | 1.033131e-04 |
| TC | exon_skip_52272 | rs7105122 | chr11:47427993 | 3.767314e-05 | 7.426448e-03 |
| TC | exon_skip_52272 | rs10742805 | chr11:47433150 | 3.767314e-05 | 7.426448e-03 |
| HCC | exon_skip_36467 | rs1534576 | chr11:47398112 | 6.380767e-10 | 1.972251e-07 |
| HCC | exon_skip_36467 | rs12292911 | chr11:47427521 | 6.380767e-10 | 1.972251e-07 |
| HCC | exon_skip_36467 | rs896817 | chr11:47372754 | 8.929435e-09 | 2.213541e-06 |
| HCC | exon_skip_36467 | rs10838703 | chr11:47401310 | 2.013481e-08 | 4.638729e-06 |
| HCC | exon_skip_36467 | rs11039212 | chr11:47371752 | 8.733255e-05 | 8.126539e-03 |
| HCC | exon_skip_36467 | rs4992357 | chr11:47372087 | 9.403717e-05 | 8.650838e-03 |
| HCC | exon_skip_36467 | rs3781626 | chr11:47421342 | 1.134977e-04 | 1.019146e-02 |
| HCC | exon_skip_36467 | rs11605672 | chr11:47392182 | 1.292220e-04 | 1.135928e-02 |
| PCC | exon_skip_36467 | rs1534576 | chr11:47398112 | 2.196317e-06 | 6.815143e-04 |
| PCC | exon_skip_36467 | rs12292911 | chr11:47427521 | 2.402330e-06 | 7.363119e-04 |
| PCC | exon_skip_36467 | rs10838703 | chr11:47401310 | 2.199009e-05 | 5.018916e-03 |
| PCC | exon_skip_36467 | rs896817 | chr11:47372754 | 4.298546e-05 | 8.751912e-03 |
| DLPFC | exon_skip_42770 | rs10838703 | chr11:47401310 | 1.769568e-08 | 3.935328e-06 |
| DLPFC | exon_skip_42770 | rs12292911 | chr11:47427521 | 9.906717e-08 | 1.855210e-05 |
| DLPFC | exon_skip_42770 | rs1534576 | chr11:47398112 | 1.578440e-07 | 2.793086e-05 |
| DLPFC | exon_skip_42770 | rs896817 | chr11:47372754 | 1.095871e-06 | 1.594612e-04 |
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Correlation with RNA binding proteins (RBPs) for SLC39A13 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | SFPQ | exon_skip_36467 | -4.950296e-01 | 8.658716e-03 |
| IFG | CNOT4 | exon_skip_36467 | -5.319062e-01 | 4.295803e-03 |
| IFG | PCBP2 | exon_skip_36467 | -4.494428e-01 | 1.867627e-02 |
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RelatedDrugs for SLC39A13 |
| 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 SLC39A13 |
| 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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