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Fusion Protein:LIMK1-TYW1 |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: LIMK1-TYW1 | FusionPDB ID: 44717 | FusionGDB2.0 ID: 44717 | Hgene | Tgene | Gene symbol | LIMK1 | TYW1 | Gene ID | 3984 | 55253 |
| Gene name | LIM domain kinase 1 | tRNA-yW synthesizing protein 1 homolog | |
| Synonyms | LIMK|LIMK-1 | RSAFD1|TYW1A|YPL207W | |
| Cytomap | 7q11.23 | 7q11.21 | |
| Type of gene | protein-coding | protein-coding | |
| Description | LIM domain kinase 1LIM motif-containing protein kinase | S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthaseradical S-adenosyl methionine and flavodoxin domain-containing protein 1radical S-adenosyl methionine and flavodoxin | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | P53667 | . | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000336180, ENST00000418310, ENST00000538333, ENST00000491052, | ENST00000491969, ENST00000359626, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 7 X 6 X 4=168 | 11 X 9 X 5=495 |
| # samples | 6 | 11 | |
| ** MAII score | log2(6/168*10)=-1.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(11/495*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: LIMK1 [Title/Abstract] AND TYW1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | LIMK1(73526328)-TYW1(66489887), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | LIMK1-TYW1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. LIMK1-TYW1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. LIMK1-TYW1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. LIMK1-TYW1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. | ||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | LIMK1 | GO:0006468 | protein phosphorylation | 17512523|22328514 |
| Hgene | LIMK1 | GO:0032233 | positive regulation of actin filament bundle assembly | 17512523 |
| Hgene | LIMK1 | GO:0051444 | negative regulation of ubiquitin-protein transferase activity | 17512523 |
| Fusion gene breakpoints across LIMK1 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across TYW1 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | SARC | TCGA-DX-A1L1-01A | LIMK1 | chr7 | 73526328 | + | TYW1 | chr7 | 66489887 | + |
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Fusion ORF Analysis |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000418310 | LIMK1 | chr7 | 73526328 | + | ENST00000359626 | TYW1 | chr7 | 66489887 | + | 3925 | 1602 | 96 | 2939 | 947 |
| ENST00000336180 | LIMK1 | chr7 | 73526328 | + | ENST00000359626 | TYW1 | chr7 | 66489887 | + | 3784 | 1461 | 51 | 2798 | 915 |
| ENST00000538333 | LIMK1 | chr7 | 73526328 | + | ENST00000359626 | TYW1 | chr7 | 66489887 | + | 3802 | 1479 | 171 | 2816 | 881 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000418310 | ENST00000359626 | LIMK1 | chr7 | 73526328 | + | TYW1 | chr7 | 66489887 | + | 0.000645182 | 0.9993548 |
| ENST00000336180 | ENST00000359626 | LIMK1 | chr7 | 73526328 | + | TYW1 | chr7 | 66489887 | + | 0.000659872 | 0.9993401 |
| ENST00000538333 | ENST00000359626 | LIMK1 | chr7 | 73526328 | + | TYW1 | chr7 | 66489887 | + | 0.001030561 | 0.99896944 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >44717_44717_1_LIMK1-TYW1_LIMK1_chr7_73526328_ENST00000336180_TYW1_chr7_66489887_ENST00000359626_length(amino acids)=915AA_BP=470 MRLTLLCCTWREERMGEEGSELPVCASCGQRIYDGQYLQALNADWHADCFRCCDCSASLSHQYYEKDGQLFCKKDYWARYGESCHGCSEQ ITKGLVMVAGELKYHPECFICLTCGTFIGDGDTYTLVEHSKLYCGHCYYQTVVTPVIEQILPDSPGSHLPHTVTLVSIPASSHGKRGLSV SIDPPHGPPGCGTEHSHTVRVQGVDPGCMSPDVKNSIHVGDRILEINGTPIRNVPLDEIDLLIQETSRLLQLTLEHDPHDTLGHGLGPET SPLSSPAYTPSGEAGSSARQKPVLRSCSIDRSPGAGSLGSPASQRKDLGRSESLRVVCRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRE TGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASGMAY LHSMNIIHRDLNSHNCLVREEEEPFESSSEEEFGGEDHQSLNSIVDVEDLGKIMDHVKKEKREKEQQEEKSGLFRNMGRNEDGERRAMIT PALREALTKQGYQLIGSHSGVKLCRWTKSMLRGRGGCYKHTFYGIESHRCMETTPSLACANKCVFCWRHHTNPVGTEWRWKMDQPEMILK EAIENHQNMIKQFKGVPGVKAERFEEGMTVKHCALSLVGEPIMYPEINRFLKLLHQCKISSFLVTNAQFPAEIRNLEPVTQLYVSVDAST KDSLKKIDRPLFKDFWQRFLDSLKALAVKQQRTVYRLTLVKAWNVDELQAYAQLVSLGNPDFIEVKGVTYCGESSASSLTMAHVPWHEEV VQFVHELVDLIPEYEIACEHEHSNCLLIAHRKFKIGGEWWTWIDYNRFQELIQEYEDSGGSKTFSAKDYMARTPHWALFGASERGFDPKD -------------------------------------------------------------- >44717_44717_2_LIMK1-TYW1_LIMK1_chr7_73526328_ENST00000418310_TYW1_chr7_66489887_ENST00000359626_length(amino acids)=947AA_BP=502 MPMSSILELSTSRQGVPPSVLDWTTQFLWTLDSAQTRAPSRTLGRAAPAPGSELPVCASCGQRIYDGQYLQALNADWHADCFRCCDCSAS LSHQYYEKDGQLFCKKDYWARYGESCHGCSEQITKGLVMVAGELKYHPECFICLTCGTFIGDGDTYTLVEHSKLYCGHCYYQTVVTPVIE QILPDSPGSHLPHTVTLVSIPASSHGKRGLSVSIDPPHGPPGCGTEHSHTVRVQGVDPGCMSPDVKNSIHVGDRILEINGTPIRNVPLDE IDLLIQETSRLLQLTLEHDPHDTLGHGLGPETSPLSSPAYTPSGEAGSSARQKPVLRSCSIDRSPGAGSLGSPASQRKDLGRSESLRVVC RPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKG GTLRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRDLNSHNCLVREEEEPFESSSEEEFGGEDHQSLNSIVDVEDLGKIMDHVK KEKREKEQQEEKSGLFRNMGRNEDGERRAMITPALREALTKQGYQLIGSHSGVKLCRWTKSMLRGRGGCYKHTFYGIESHRCMETTPSLA CANKCVFCWRHHTNPVGTEWRWKMDQPEMILKEAIENHQNMIKQFKGVPGVKAERFEEGMTVKHCALSLVGEPIMYPEINRFLKLLHQCK ISSFLVTNAQFPAEIRNLEPVTQLYVSVDASTKDSLKKIDRPLFKDFWQRFLDSLKALAVKQQRTVYRLTLVKAWNVDELQAYAQLVSLG NPDFIEVKGVTYCGESSASSLTMAHVPWHEEVVQFVHELVDLIPEYEIACEHEHSNCLLIAHRKFKIGGEWWTWIDYNRFQELIQEYEDS -------------------------------------------------------------- >44717_44717_3_LIMK1-TYW1_LIMK1_chr7_73526328_ENST00000538333_TYW1_chr7_66489887_ENST00000359626_length(amino acids)=881AA_BP=436 MLLASAPRRRRFLQRAKCCDCSASLSHQYYEKDGQLFCKKDYWARYGESCHGCSEQITKGLVMVAGELKYHPECFICLTCGTFIGDGDTY TLVEHSKLYCGHCYYQTVVTPVIEQILPDSPGSHLPHTVTLVSIPASSHGKRGLSVSIDPPHGPPGCGTEHSHTVRVQGVDPGCMSPDVK NSIHVGDRILEINGTPIRNVPLDEIDLLIQETSRLLQLTLEHDPHDTLGHGLGPETSPLSSPAYTPSGEAGSSARQKPVLRSCSIDRSPG AGSLGSPASQRKDLGRSESLRVVCRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHP NVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRDLNSHNCLVREEEEPFESSSEEEFG GEDHQSLNSIVDVEDLGKIMDHVKKEKREKEQQEEKSGLFRNMGRNEDGERRAMITPALREALTKQGYQLIGSHSGVKLCRWTKSMLRGR GGCYKHTFYGIESHRCMETTPSLACANKCVFCWRHHTNPVGTEWRWKMDQPEMILKEAIENHQNMIKQFKGVPGVKAERFEEGMTVKHCA LSLVGEPIMYPEINRFLKLLHQCKISSFLVTNAQFPAEIRNLEPVTQLYVSVDASTKDSLKKIDRPLFKDFWQRFLDSLKALAVKQQRTV YRLTLVKAWNVDELQAYAQLVSLGNPDFIEVKGVTYCGESSASSLTMAHVPWHEEVVQFVHELVDLIPEYEIACEHEHSNCLLIAHRKFK -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr7:73526328/chr7:66489887) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LIMK1 | . |
| FUNCTION: Serine/threonine-protein kinase that plays an essential role in the regulation of actin filament dynamics. Acts downstream of several Rho family GTPase signal transduction pathways (PubMed:10436159, PubMed:11832213, PubMed:12807904, PubMed:15660133, PubMed:16230460, PubMed:18028908, PubMed:22328514, PubMed:23633677). Activated by upstream kinases including ROCK1, PAK1 and PAK4, which phosphorylate LIMK1 on a threonine residue located in its activation loop (PubMed:10436159). LIMK1 subsequently phosphorylates and inactivates the actin binding/depolymerizing factors cofilin-1/CFL1, cofilin-2/CFL2 and destrin/DSTN, thereby preventing the cleavage of filamentous actin (F-actin), and stabilizing the actin cytoskeleton (PubMed:11832213, PubMed:15660133, PubMed:16230460, PubMed:23633677). In this way LIMK1 regulates several actin-dependent biological processes including cell motility, cell cycle progression, and differentiation (PubMed:11832213, PubMed:15660133, PubMed:16230460, PubMed:23633677). Phosphorylates TPPP on serine residues, thereby promoting microtubule disassembly (PubMed:18028908). Stimulates axonal outgrowth and may be involved in brain development (PubMed:18028908). {ECO:0000269|PubMed:10436159, ECO:0000269|PubMed:11832213, ECO:0000269|PubMed:12807904, ECO:0000269|PubMed:15660133, ECO:0000269|PubMed:16230460, ECO:0000269|PubMed:18028908, ECO:0000269|PubMed:22328514, ECO:0000269|PubMed:23633677}.; FUNCTION: [Isoform 3]: Has a dominant negative effect on actin cytoskeletal changes. Required for atypical chemokine receptor ACKR2-induced phosphorylation of cofilin (CFL1). {ECO:0000269|PubMed:10196227}. | FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000336180 | + | 12 | 16 | 165_258 | 470.0 | 648.0 | Domain | PDZ |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000336180 | + | 12 | 16 | 25_75 | 470.0 | 648.0 | Domain | LIM zinc-binding 1 |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000336180 | + | 12 | 16 | 84_137 | 470.0 | 648.0 | Domain | LIM zinc-binding 2 |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000538333 | + | 11 | 15 | 165_258 | 436.0 | 614.0 | Domain | PDZ |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000538333 | + | 11 | 15 | 25_75 | 436.0 | 614.0 | Domain | LIM zinc-binding 1 |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000538333 | + | 11 | 15 | 84_137 | 436.0 | 614.0 | Domain | LIM zinc-binding 2 |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000336180 | + | 12 | 16 | 345_353 | 470.0 | 648.0 | Nucleotide binding | ATP |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000538333 | + | 11 | 15 | 345_353 | 436.0 | 614.0 | Nucleotide binding | ATP |
| Tgene | TYW1 | chr7:73526328 | chr7:66489887 | ENST00000359626 | 5 | 16 | 400_644 | 287.0 | 733.0 | Domain | Radical SAM core |
| - Not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000336180 | + | 12 | 16 | 339_604 | 470.0 | 648.0 | Domain | Protein kinase |
| Hgene | LIMK1 | chr7:73526328 | chr7:66489887 | ENST00000538333 | + | 11 | 15 | 339_604 | 436.0 | 614.0 | Domain | Protein kinase |
| Tgene | TYW1 | chr7:73526328 | chr7:66489887 | ENST00000359626 | 5 | 16 | 79_237 | 287.0 | 733.0 | Domain | Flavodoxin-like | |
| Tgene | TYW1 | chr7:73526328 | chr7:66489887 | ENST00000359626 | 5 | 16 | 176_208 | 287.0 | 733.0 | Nucleotide binding | FMN | |
| Tgene | TYW1 | chr7:73526328 | chr7:66489887 | ENST00000359626 | 5 | 16 | 85_89 | 287.0 | 733.0 | Nucleotide binding | FMN |
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Fusion Protein-Protein Interaction |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in |
| Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| LIMK1 | |
| TYW1 |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to LIMK1-TYW1 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to LIMK1-TYW1 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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