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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 ALK |
 Gene summary |
| Gene information | Gene symbol | ALK | Gene ID | 238 |
| Gene name | ALK receptor tyrosine kinase | |
| Synonyms | CD246|NBLST3 | |
| Cytomap | 2p23.2-p23.1 | |
| Type of gene | protein-coding | |
| Description | ALK tyrosine kinase receptorCD246 antigenanaplastic lymphoma receptor tyrosine kinasemutant anaplastic lymphoma kinase | |
| Modification date | 20180527 | |
| UniProtAcc | Q9UM73 | |
| Context | PubMed: ALK [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 |
| ALK | GO:0016310 | phosphorylation | 9174053 |
| ALK | GO:0046777 | protein autophosphorylation | 9174053 |
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Exon skipping events across known transcript of Ensembl for ALK 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 ALK |
| 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 ALK |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_338031 | 2 | 29419635:29419726:29420407:29420542:29430036:29430138 | 29420407:29420542 | ENSG00000171094.11 | ENST00000389048.3 |
| exon_skip_338032 | 2 | 29436849:29436947:29443571:29443701:29445209:29445274 | 29443571:29443701 | ENSG00000171094.11 | ENST00000389048.3 |
| exon_skip_338034 | 2 | 29754780:29754982:29917715:29917880:29940443:29940563 | 29917715:29917880 | ENSG00000171094.11 | ENST00000389048.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for ALK |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_338031 | 2 | 29419635:29419726:29420407:29420542:29430036:29430138 | 29420407:29420542 | ENSG00000171094.11 | ENST00000389048.3 |
| exon_skip_338032 | 2 | 29436849:29436947:29443571:29443701:29445209:29445274 | 29443571:29443701 | ENSG00000171094.11 | ENST00000389048.3 |
| exon_skip_338034 | 2 | 29754780:29754982:29917715:29917880:29940443:29940563 | 29917715:29917880 | ENSG00000171094.11 | ENST00000389048.3 |
| 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 ALK |
| 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 |
| ENST00000389048 | 29443571 | 29443701 | Frame-shift |
| ENST00000389048 | 29420407 | 29420542 | In-frame |
| ENST00000389048 | 29917715 | 29917880 | 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 |
| ENST00000389048 | 29443571 | 29443701 | Frame-shift |
| ENST00000389048 | 29420407 | 29420542 | In-frame |
| ENST00000389048 | 29917715 | 29917880 | In-frame |
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Infer the effects of exon skipping event on protein functional features for ALK |
| 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 |
| ENST00000389048 | 6237 | 1620 | 29917715 | 29917880 | 1695 | 1859 | 262 | 317 |
| ENST00000389048 | 6237 | 1620 | 29420407 | 29420542 | 4846 | 4980 | 1313 | 1357 |
| 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 |
| ENST00000389048 | 6237 | 1620 | 29917715 | 29917880 | 1695 | 1859 | 262 | 317 |
| ENST00000389048 | 6237 | 1620 | 29420407 | 29420542 | 4846 | 4980 | 1313 | 1357 |
| 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 |
| Q9UM73 | 262 | 317 | 19 | 1620 | Chain | ID=PRO_0000016740;Note=ALK tyrosine kinase receptor |
| Q9UM73 | 262 | 317 | 264 | 427 | Domain | Note=MAM 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00128 |
| Q9UM73 | 262 | 317 | 285 | 285 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UM73 | 262 | 317 | 296 | 296 | Natural variant | ID=VAR_041479;Note=E->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=dbSNP:rs56077855,PMID:17344846 |
| Q9UM73 | 262 | 317 | 19 | 1038 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UM73 | 1313 | 1357 | 19 | 1620 | Chain | ID=PRO_0000016740;Note=ALK tyrosine kinase receptor |
| Q9UM73 | 1313 | 1357 | 1116 | 1392 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q9UM73 | 1313 | 1357 | 1308 | 1323 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z55 |
| Q9UM73 | 1313 | 1357 | 1335 | 1343 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z55 |
| Q9UM73 | 1313 | 1357 | 1356 | 1365 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z55 |
| Q9UM73 | 1313 | 1357 | 1328 | 1328 | Natural variant | ID=VAR_041488;Note=M->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=dbSNP:rs56160491,PMID:17344846 |
| Q9UM73 | 1313 | 1357 | 1060 | 1620 | Topological domain | Note=Cytoplasmic;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 |
| Q9UM73 | 262 | 317 | 19 | 1620 | Chain | ID=PRO_0000016740;Note=ALK tyrosine kinase receptor |
| Q9UM73 | 262 | 317 | 264 | 427 | Domain | Note=MAM 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00128 |
| Q9UM73 | 262 | 317 | 285 | 285 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UM73 | 262 | 317 | 296 | 296 | Natural variant | ID=VAR_041479;Note=E->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=dbSNP:rs56077855,PMID:17344846 |
| Q9UM73 | 262 | 317 | 19 | 1038 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UM73 | 1313 | 1357 | 19 | 1620 | Chain | ID=PRO_0000016740;Note=ALK tyrosine kinase receptor |
| Q9UM73 | 1313 | 1357 | 1116 | 1392 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q9UM73 | 1313 | 1357 | 1308 | 1323 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z55 |
| Q9UM73 | 1313 | 1357 | 1335 | 1343 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z55 |
| Q9UM73 | 1313 | 1357 | 1356 | 1365 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Z55 |
| Q9UM73 | 1313 | 1357 | 1328 | 1328 | Natural variant | ID=VAR_041488;Note=M->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=dbSNP:rs56160491,PMID:17344846 |
| Q9UM73 | 1313 | 1357 | 1060 | 1620 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for ALK |
| - 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-BC-A10Z-01 | exon_skip_338032 | 29443572 | 29443701 | 29443612 | 29443612 | Frame_Shift_Del | C | - | p.G1202fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_338032 | 29443572 | 29443701 | 29443664 | 29443664 | Frame_Shift_Del | C | - | p.V1185fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_338032 | 29443572 | 29443701 | 29443698 | 29443698 | Frame_Shift_Del | T | - | p.K1173fs |
| ESCA | TCGA-2H-A9GI-01 | exon_skip_338031 | 29420408 | 29420542 | 29420535 | 29420535 | Nonsense_Mutation | C | A | p.G1316* |
| READ | TCGA-AF-6136-01 | exon_skip_338032 | 29443572 | 29443701 | 29443592 | 29443592 | Nonsense_Mutation | G | A | p.R1209X |
| LUAD | TCGA-17-Z025-01 | exon_skip_338034 | 29917716 | 29917880 | 29917779 | 29917779 | Nonsense_Mutation | C | A | p.E297* |
| LUAD | TCGA-05-4432-01 | exon_skip_338034 | 29917716 | 29917880 | 29917880 | 29917881 | Splice_Site | CC | AT | p.G263_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 |
| NCIH1355_LUNG | 29420408 | 29420542 | 29420423 | 29420423 | Missense_Mutation | T | C | p.N1353S |
| HT115_LARGE_INTESTINE | 29420408 | 29420542 | 29420436 | 29420436 | Missense_Mutation | C | T | p.D1349N |
| SKUT1_SOFT_TISSUE | 29443572 | 29443701 | 29443642 | 29443642 | Missense_Mutation | C | T | p.R1192Q |
| HEC59_ENDOMETRIUM | 29443572 | 29443701 | 29443643 | 29443643 | Missense_Mutation | G | A | p.R1192W |
| KPNRTBM1_AUTONOMIC_GANGLIA | 29443572 | 29443701 | 29443695 | 29443695 | Missense_Mutation | G | T | p.F1174L |
| KELLY_AUTONOMIC_GANGLIA | 29443572 | 29443701 | 29443695 | 29443695 | Missense_Mutation | G | T | p.F1174L |
| NB14_AUTONOMIC_GANGLIA | 29443572 | 29443701 | 29443695 | 29443695 | Missense_Mutation | G | T | p.F1174L |
| SKNSH_AUTONOMIC_GANGLIA | 29443572 | 29443701 | 29443695 | 29443695 | Missense_Mutation | G | T | p.F1174L |
| CORL23_LUNG | 29917716 | 29917880 | 29917718 | 29917718 | Missense_Mutation | C | G | p.R317T |
| FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 29917716 | 29917880 | 29917754 | 29917754 | Missense_Mutation | T | C | p.D305G |
| NCIH322_LUNG | 29917716 | 29917880 | 29917802 | 29917802 | Missense_Mutation | G | T | p.S289Y |
| SNU449_LIVER | 29917716 | 29917880 | 29917825 | 29917825 | Missense_Mutation | A | T | p.H281Q |
| SKMEL30_SKIN | 29917716 | 29917880 | 29917832 | 29917832 | Missense_Mutation | G | A | p.P279L |
| CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 29443572 | 29443701 | 29443592 | 29443592 | Nonsense_Mutation | G | A | p.R1209* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ALK |
| 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 ALK |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ALK |
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RelatedDrugs for ALK |
| 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 |
| Q9UM73 | DB08865 | Crizotinib | ALK tyrosine kinase receptor | small molecule | approved | |
| Q9UM73 | DB09063 | Ceritinib | ALK tyrosine kinase receptor | small molecule | approved | |
| Q9UM73 | DB11363 | Alectinib | ALK tyrosine kinase receptor | small molecule | approved|investigational | |
| Q9UM73 | DB12010 | Fostamatinib | ALK tyrosine kinase receptor | small molecule | approved|investigational | |
| Q9UM73 | DB12130 | Lorlatinib | ALK tyrosine kinase receptor | small molecule | approved|investigational | |
| Q9UM73 | DB12267 | Brigatinib | ALK tyrosine kinase receptor | small molecule | approved|investigational |
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RelatedDiseases for ALK |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| ALK | C0007131 | Non-Small Cell Lung Carcinoma | 28 | CTD_human |
| ALK | C0027819 | Neuroblastoma | 12 | CTD_human;ORPHANET |
| ALK | C0152013 | Adenocarcinoma of lung (disorder) | 8 | CTD_human |
| ALK | C0206180 | Ki-1+ Anaplastic Large Cell Lymphoma | 6 | CTD_human |
| ALK | C2751681 | NEUROBLASTOMA, SUSCEPTIBILITY TO, 3 | 4 | UNIPROT |
| ALK | C0018199 | Granuloma, Plasma Cell | 3 | CTD_human |
| ALK | C0007621 | Neoplastic Cell Transformation | 2 | CTD_human |
| ALK | C0027627 | Neoplasm Metastasis | 2 | CTD_human |
| ALK | C0001973 | Alcoholic Intoxication, Chronic | 1 | PSYGENET |
| ALK | C0006118 | Brain Neoplasms | 1 | CTD_human |
| ALK | C0007134 | Renal Cell Carcinoma | 1 | CTD_human |
| ALK | C0011570 | Mental Depression | 1 | PSYGENET |
| ALK | C0011581 | Depressive disorder | 1 | PSYGENET |
| ALK | C0027643 | Neoplasm Recurrence, Local | 1 | CTD_human |
| ALK | C0036341 | Schizophrenia | 1 | PSYGENET |
| ALK | C0079744 | Diffuse Large B-Cell Lymphoma | 1 | CTD_human |
| ALK | C0085269 | Plasma Cell Granuloma, Pulmonary | 1 | CTD_human |
| ALK | C0278601 | Inflammatory Breast Carcinoma | 1 | CTD_human |
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