Table 2.
Domain retention annotation of ALK fusion proteins from FusionGDB
| Fusion gene | Gene | ENST | BP | Strand | BPexon | TotalExon | Protein feature loci | BPloci | TotalLen | Protein feature | Protein feature note |
|---|---|---|---|---|---|---|---|---|---|---|---|
| A. Retained protein features of in-frame ALK fusion proteins. | |||||||||||
| EML4-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1116_1392 | 1057 | 1621 | Domain | Protein kinase |
| EML4-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1197_1199 | 1057 | 1621 | Region | Note = Inhibitor binding |
| EML4-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1060_1620 | 1057 | 1621 | Topological domain | Cytoplasmic |
| NPM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1116_1392 | 1057 | 1621 | Domain | Protein kinase |
| NPM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1197_1199 | 1057 | 1621 | Region | Note = Inhibitor binding |
| NPM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1060_1620 | 1057 | 1621 | Topological domain | Cytoplasmic |
| SQSTM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1116_1392 | 1057 | 1621 | Domain | Protein kinase |
| SQSTM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1197_1199 | 1057 | 1621 | Region | Note = Inhibitor binding |
| SQSTM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1060_1620 | 1057 | 1621 | Topological domain | Cytoplasmic |
| TFG-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1116_1392 | 1057 | 1621 | Domain | Protein kinase |
| TFG-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1197_1199 | 1057 | 1621 | Region | Note = Inhibitor binding |
| TFG-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1060_1620 | 1057 | 1621 | Topological domain | Cytoplasmic |
| B. Lost protein features of in-frame ALK fusion proteins. | |||||||||||
| EML4-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 816_940 | 1057 | 1621 | Compositional bias | Note = Gly-rich |
| EML4-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 264_427 | 1057 | 1621 | Domain | MAM 1 |
| EML4-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 478_636 | 1057 | 1621 | Domain | MAM 2 |
| EML4-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 437_473 | 1057 | 1621 | Domain | Note = LDL-receptor class A |
| EML4-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 19_1038 | 1057 | 1621 | Topological domain | Extracellular |
| EML4-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1039_1059 | 1057 | 1621 | Transmembrane | Helical |
| NPM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 816_940 | 1057 | 1621 | Compositional bias | Note = Gly-rich |
| NPM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 264_427 | 1057 | 1621 | Domain | MAM 1 |
| NPM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 437_473 | 1057 | 1621 | Domain | Note = LDL-receptor class A |
| NPM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 478_636 | 1057 | 1621 | Domain | MAM 2 |
| NPM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 19_1038 | 1057 | 1621 | Topological domain | Extracellular |
| NPM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1039_1059 | 1057 | 1621 | Transmembrane | Helical |
| SQSTM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 816_940 | 1057 | 1621 | Compositional bias | Note = Gly-rich |
| SQSTM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 264_427 | 1057 | 1621 | Domain | MAM 1 |
| SQSTM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 437_473 | 1057 | 1621 | Domain | Note = LDL-receptor class A |
| SQSTM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 478_636 | 1057 | 1621 | Domain | MAM 2 |
| SQSTM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 19_1038 | 1057 | 1621 | Topological domain | Extracellular |
| SQSTM1-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1039_1059 | 1057 | 1621 | Transmembrane | Helical |
| TFG-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 816_940 | 1057 | 1621 | Compositional bias | Note = Gly-rich |
| TFG-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 264_427 | 1057 | 1621 | Domain | MAM 1 |
| TFG-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 437_473 | 1057 | 1621 | Domain | Note = LDL-receptor class A |
| TFG-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 478_636 | 1057 | 1621 | Domain | MAM 2 |
| TFG-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 19_1038 | 1057 | 1621 | Topological domain | Extracellular |
| TFG-ALK | ALK | ENST00000389048 | chr2:29446394 | - | 18 | 29 | 1039_1059 | 1057 | 1621 | Transmembrane | Helical |