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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 SLC39A6 |
 Gene summary |
| Gene information | Gene symbol | SLC39A6 | Gene ID | 25800 |
| Gene name | solute carrier family 39 member 6 | |
| Synonyms | LIV-1|ZIP6 | |
| Cytomap | 18q12.2 | |
| Type of gene | protein-coding | |
| Description | zinc transporter ZIP6LIV-1 protein, estrogen regulatedZIP-6estrogen-regulated protein LIV-1solute carrier family 39 (metal ion transporter), member 6solute carrier family 39 (zinc transporter), member 6zrt- and Irt-like protein 6 | |
| Modification date | 20180523 | |
| UniProtAcc | Q13433 | |
| Context | PubMed: SLC39A6 [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 |
| SLC39A6 | GO:0006882 | cellular zinc ion homeostasis | 15642354 |
| SLC39A6 | GO:0071578 | zinc ion import across plasma membrane | 15642354 |
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Exon skipping events across known transcript of Ensembl for SLC39A6 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 SLC39A6 |
| 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 SLC39A6 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_298858 | 18 | 33689655:33689708:33691021:33691212:33692463:33692544 | 33691021:33691212 | ENSG00000141424.8 | ENST00000269187.5,ENST00000590986.1 |
| exon_skip_298860 | 18 | 33696636:33696742:33702014:33702233:33703457:33703627 | 33702014:33702233 | ENSG00000141424.8 | ENST00000269187.5,ENST00000590986.1,ENST00000440549.2 |
| exon_skip_298862 | 18 | 33702014:33702233:33703457:33703627:33704482:33704663 | 33703457:33703627 | ENSG00000141424.8 | ENST00000269187.5,ENST00000590986.1,ENST00000440549.2 |
| exon_skip_298881 | 18 | 33704482:33704663:33706181:33706979:33709063:33709344 | 33706181:33706979 | ENSG00000141424.8 | ENST00000590986.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SLC39A6 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_298858 | 18 | 33689655:33689708:33691021:33691212:33692463:33692544 | 33691021:33691212 | ENSG00000141424.8 | ENST00000269187.5,ENST00000590986.1 |
| exon_skip_298862 | 18 | 33702014:33702233:33703457:33703627:33704482:33704663 | 33703457:33703627 | ENSG00000141424.8 | ENST00000269187.5,ENST00000590986.1,ENST00000440549.2 |
| exon_skip_298881 | 18 | 33704482:33704663:33706181:33706979:33709063:33709344 | 33706181:33706979 | ENSG00000141424.8 | ENST00000590986.1 |
| 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 SLC39A6 |
| 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 |
| ENST00000590986 | 33706181 | 33706979 | 3UTR-3CDS |
| ENST00000269187 | 33691021 | 33691212 | Frame-shift |
| ENST00000590986 | 33691021 | 33691212 | Frame-shift |
| ENST00000269187 | 33703457 | 33703627 | Frame-shift |
| ENST00000590986 | 33703457 | 33703627 | Frame-shift |
| ENST00000269187 | 33702014 | 33702233 | In-frame |
| ENST00000590986 | 33702014 | 33702233 | 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 |
| ENST00000590986 | 33706181 | 33706979 | 3UTR-3CDS |
| ENST00000269187 | 33691021 | 33691212 | Frame-shift |
| ENST00000590986 | 33691021 | 33691212 | Frame-shift |
| ENST00000269187 | 33703457 | 33703627 | Frame-shift |
| ENST00000590986 | 33703457 | 33703627 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SLC39A6 |
| 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 |
| ENST00000269187 | 3560 | 755 | 33702014 | 33702233 | 1355 | 1573 | 380 | 453 |
| ENST00000590986 | 3020 | 755 | 33702014 | 33702233 | 1431 | 1649 | 380 | 453 |
| 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 |
| Q13433 | 380 | 453 | 29 | 755 | Chain | ID=PRO_0000041650;Note=Zinc transporter ZIP6 |
| Q13433 | 380 | 453 | 29 | 755 | Chain | ID=PRO_0000041650;Note=Zinc transporter ZIP6 |
| Q13433 | 380 | 453 | 376 | 391 | Compositional bias | Note=His-rich |
| Q13433 | 380 | 453 | 376 | 391 | Compositional bias | Note=His-rich |
| Q13433 | 380 | 453 | 448 | 453 | Compositional bias | Note=Poly-Lys |
| Q13433 | 380 | 453 | 448 | 453 | Compositional bias | Note=Poly-Lys |
| Q13433 | 380 | 453 | 377 | 423 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13433 | 380 | 453 | 377 | 423 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13433 | 380 | 453 | 445 | 657 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13433 | 380 | 453 | 445 | 657 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13433 | 380 | 453 | 424 | 444 | Transmembrane | Note=Helical%3B Name%3D3;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13433 | 380 | 453 | 424 | 444 | Transmembrane | Note=Helical%3B Name%3D3;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 |
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SNVs in the skipped exons for SLC39A6 |
| - 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_298858 | 33691022 | 33691212 | 33691205 | 33691205 | Frame_Shift_Del | A | - | p.F644fs |
| OV | TCGA-25-1316-01 | exon_skip_298860 | 33702015 | 33702233 | 33702138 | 33702139 | Frame_Shift_Del | TA | - | p.I412fs |
| LIHC | TCGA-DD-A3A1-01 | exon_skip_298860 | 33702015 | 33702233 | 33702176 | 33702176 | Frame_Shift_Del | T | - | p.R400fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_298881 | 33706182 | 33706979 | 33706229 | 33706229 | Frame_Shift_Del | G | - | p.R248fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_298881 | 33706182 | 33706979 | 33706229 | 33706229 | Frame_Shift_Del | G | - | p.R248fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_298881 | 33706182 | 33706979 | 33706771 | 33706771 | Frame_Shift_Del | T | - | p.N68fs |
| HNSC | TCGA-QK-A6VB-01 | exon_skip_298881 | 33706182 | 33706979 | 33706880 | 33706880 | Frame_Shift_Del | G | - | p.Q31fs |
| LUAD | TCGA-NJ-A4YI-01 | exon_skip_298858 | 33691022 | 33691212 | 33691066 | 33691067 | Frame_Shift_Ins | - | AA | p.T691fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_298881 | 33706182 | 33706979 | 33706788 | 33706789 | Frame_Shift_Ins | - | A | p.L61fs |
| LUAD | TCGA-44-8120-01 | exon_skip_298881 | 33706182 | 33706979 | 33706235 | 33706235 | Nonsense_Mutation | C | A | p.E246* |
| UCEC | TCGA-AP-A051-01 | exon_skip_298881 | 33706182 | 33706979 | 33706379 | 33706379 | Nonsense_Mutation | C | A | p.G198* |
| ACC | TCGA-OR-A5LB-01 | exon_skip_298881 | 33706182 | 33706979 | 33706547 | 33706547 | Nonsense_Mutation | G | A | p.R142* |
| ACC | TCGA-OR-A5LB-01 | exon_skip_298881 | 33706182 | 33706979 | 33706547 | 33706547 | Nonsense_Mutation | G | A | p.R142X |
| LUAD | TCGA-50-5930-01 | exon_skip_298881 | 33706182 | 33706979 | 33706778 | 33706778 | Nonsense_Mutation | C | A | p.G65* |
| - 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 |
| HEC6_ENDOMETRIUM | 33703458 | 33703627 | 33703474 | 33703474 | Frame_Shift_Del | A | - | p.L375fs |
| SNUC5_LARGE_INTESTINE | 33706182 | 33706979 | 33706600 | 33706617 | In_Frame_Del | GAGTGATGCTCGTGCTCT | - | p.118_124SEHEHHS>S |
| HEC1A_ENDOMETRIUM | 33691022 | 33691212 | 33691056 | 33691056 | Missense_Mutation | G | A | p.A694V |
| HEC1_ENDOMETRIUM | 33691022 | 33691212 | 33691056 | 33691056 | Missense_Mutation | G | A | p.A694V |
| HEC1B_ENDOMETRIUM | 33691022 | 33691212 | 33691056 | 33691056 | Missense_Mutation | G | A | p.A694V |
| MDAMB157_BREAST | 33691022 | 33691212 | 33691104 | 33691104 | Missense_Mutation | A | G | p.I678T |
| FU97_STOMACH | 33702015 | 33702233 | 33702019 | 33702019 | Missense_Mutation | T | C | p.K452R |
| CW2_LARGE_INTESTINE | 33702015 | 33702233 | 33702035 | 33702035 | Missense_Mutation | A | T | p.F447I |
| HEC251_ENDOMETRIUM | 33702015 | 33702233 | 33702183 | 33702183 | Missense_Mutation | T | G | p.E397D |
| DMS79_LUNG | 33702015 | 33702233 | 33702201 | 33702201 | Missense_Mutation | A | T | p.H391Q |
| NCIH1623_LUNG | 33702015 | 33702233 | 33702204 | 33702205 | Missense_Mutation | GC | AA | p.S390I |
| NCIH1623_LUNG | 33702015 | 33702233 | 33702205 | 33702205 | Missense_Mutation | C | A | p.S390I |
| NCIH1623_LUNG | 33702015 | 33702233 | 33702226 | 33702226 | Missense_Mutation | G | T | p.A383E |
| HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 33703458 | 33703627 | 33703502 | 33703502 | Missense_Mutation | C | T | p.V366I |
| IGROV1_OVARY | 33703458 | 33703627 | 33703523 | 33703523 | Missense_Mutation | T | G | p.S359R |
| SLR26_KIDNEY | 33706182 | 33706979 | 33706243 | 33706243 | Missense_Mutation | G | C | p.S243C |
| NKL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 33706182 | 33706979 | 33706325 | 33706325 | Missense_Mutation | T | C | p.K216E |
| SW684_SOFT_TISSUE | 33706182 | 33706979 | 33706390 | 33706390 | Missense_Mutation | G | A | p.T194I |
| MCC13_SKIN | 33706182 | 33706979 | 33706498 | 33706498 | Missense_Mutation | G | A | p.P158L |
| SNU46_UPPER_AERODIGESTIVE_TRACT | 33706182 | 33706979 | 33706510 | 33706510 | Missense_Mutation | G | A | p.S154L |
| SNU1040_LARGE_INTESTINE | 33706182 | 33706979 | 33706723 | 33706723 | Missense_Mutation | C | T | p.G83D |
| HCC2998_LARGE_INTESTINE | 33706182 | 33706979 | 33706765 | 33706765 | Missense_Mutation | G | T | p.S69Y |
| SNU475_LIVER | 33706182 | 33706979 | 33706840 | 33706840 | Missense_Mutation | A | G | p.I44T |
| NCIH1930_LUNG | 33706182 | 33706979 | 33706858 | 33706858 | Missense_Mutation | G | C | p.P38R |
| IGROV1_OVARY | 33702015 | 33702233 | 33702016 | 33702016 | Splice_Site | T | C | p.K453R |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC39A6 |
| 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 SLC39A6 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC39A6 |
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RelatedDrugs for SLC39A6 |
| 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 SLC39A6 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SLC39A6 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| SLC39A6 | C0027627 | Neoplasm Metastasis | 1 | CTD_human |
| SLC39A6 | C0279626 | Squamous cell carcinoma of esophagus | 1 | CTD_human |
| SLC39A6 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
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