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Fusion Protein:LRP4-DDB2 |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: LRP4-DDB2 | FusionPDB ID: 49775 | FusionGDB2.0 ID: 49775 | Hgene | Tgene | Gene symbol | LRP4 | DDB2 | Gene ID | 4038 | 1643 |
| Gene name | LDL receptor related protein 4 | damage specific DNA binding protein 2 | |
| Synonyms | CLSS|CMS17|LRP-4|LRP10|MEGF7|SOST2 | DDBB|UV-DDB2|XPE | |
| Cytomap | 11p11.2 | 11p11.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | low-density lipoprotein receptor-related protein 4multiple epidermal growth factor-like domains 7 | DNA damage-binding protein 2DDB p48 subunitUV-DDB 2UV-damaged DNA-binding protein 2damage-specific DNA binding protein 2, 48kDaxeroderma pigmentosum group E protein | |
| Modification date | 20200313 | 20200327 | |
| UniProtAcc | O75096 Main function of 5'-partner protein: FUNCTION: Mediates SOST-dependent inhibition of bone formation. Functions as a specific facilitator of SOST-mediated inhibition of Wnt signaling. Plays a key role in the formation and the maintenance of the neuromuscular junction (NMJ), the synapse between motor neuron and skeletal muscle. Directly binds AGRIN and recruits it to the MUSK signaling complex. Mediates the AGRIN-induced phosphorylation of MUSK, the kinase of the complex. The activation of MUSK in myotubes induces the formation of NMJ by regulating different processes including the transcription of specific genes and the clustering of AChR in the postsynaptic membrane. Alternatively, may be involved in the negative regulation of the canonical Wnt signaling pathway, being able to antagonize the LRP6-mediated activation of this pathway. More generally, has been proposed to function as a cell surface endocytic receptor binding and internalizing extracellular ligands for degradation by lysosomes. May play an essential role in the process of digit differentiation (By similarity). {ECO:0000250|UniProtKB:Q8VI56, ECO:0000269|PubMed:20381006, ECO:0000269|PubMed:21471202}. | Q92466 Main function of 5'-partner protein: FUNCTION: Protein, which is both involved in DNA repair and protein ubiquitination, as part of the UV-DDB complex and DCX (DDB1-CUL4-X-box) complexes, respectively (PubMed:10882109, PubMed:11278856, PubMed:11705987, PubMed:9892649, PubMed:12732143, PubMed:15882621, PubMed:16473935, PubMed:18593899). Core component of the UV-DDB complex (UV-damaged DNA-binding protein complex), a complex that recognizes UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair (PubMed:10882109, PubMed:11278856, PubMed:11705987, PubMed:16260596, PubMed:12944386, PubMed:14751237). The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches (PubMed:10882109, PubMed:11278856, PubMed:11705987, PubMed:16260596, PubMed:12944386). Also functions as the substrate recognition module for the DCX (DDB2-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB2-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1) (PubMed:12732143, PubMed:15882621, PubMed:16473935, PubMed:18593899, PubMed:26572825). The DDB2-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage (PubMed:16678110, PubMed:16473935). The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair (PubMed:16678110, PubMed:16473935). The DDB2-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER (PubMed:15882621). The DDB2-CUL4-ROC1 complex also ubiquitinates KAT7/HBO1 in response to DNA damage, leading to its degradation: recognizes KAT7/HBO1 following phosphorylation by ATR (PubMed:26572825). {ECO:0000269|PubMed:10882109, ECO:0000269|PubMed:11278856, ECO:0000269|PubMed:11705987, ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:12944386, ECO:0000269|PubMed:14751237, ECO:0000269|PubMed:15882621, ECO:0000269|PubMed:16260596, ECO:0000269|PubMed:16473935, ECO:0000269|PubMed:16678110, ECO:0000269|PubMed:18593899, ECO:0000269|PubMed:26572825, ECO:0000269|PubMed:9892649}.; FUNCTION: [Isoform D1]: Inhibits UV-damaged DNA repair. {ECO:0000269|PubMed:14751237}.; FUNCTION: [Isoform D2]: Inhibits UV-damaged DNA repair. {ECO:0000269|PubMed:14751237}. | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000378623, | ENST00000378601, ENST00000256996, ENST00000378600, ENST00000378603, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 7 X 7 X 7=343 | 12 X 6 X 7=504 |
| # samples | 7 | 11 | |
| ** MAII score | log2(7/343*10)=-2.29278174922785 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(11/504*10)=-2.19592020997526 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Fusion gene context | PubMed: LRP4 [Title/Abstract] AND DDB2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: LRP4 [Title/Abstract] AND DDB2 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | LRP4(46914523)-DDB2(47260350), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | LRP4-DDB2 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. LRP4-DDB2 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. LRP4-DDB2 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. LRP4-DDB2 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 | LRP4 | GO:0001822 | kidney development | 20381006 |
| Hgene | LRP4 | GO:0060173 | limb development | 20381006 |
| Hgene | LRP4 | GO:0090090 | negative regulation of canonical Wnt signaling pathway | 20093106 |
| Tgene | DDB2 | GO:0000209 | protein polyubiquitination | 12732143 |
| Tgene | DDB2 | GO:0009411 | response to UV | 12732143 |
| Tgene | DDB2 | GO:0035518 | histone H2A monoubiquitination | 22334663 |
| Tgene | DDB2 | GO:0051865 | protein autoubiquitination | 12732143 |
| Tgene | DDB2 | GO:0070914 | UV-damage excision repair | 22334663 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:46914523/chr11:47260350) - 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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| Retention analysis results 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, are available here. |
| Fusion gene breakpoints across LRP4 (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 DDB2 (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 Amino Acid Sequences |
| 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) |
| ENST00000378623 | LRP4 | chr11 | 46914523 | - | ENST00000378600 | DDB2 | chr11 | 47260350 | + | 2357 | 1940 | 243 | 2159 | 638 |
| ENST00000378623 | LRP4 | chr11 | 46914523 | - | ENST00000378603 | DDB2 | chr11 | 47260350 | + | 2357 | 1940 | 243 | 2159 | 638 |
| ENST00000378623 | LRP4 | chr11 | 46914523 | - | ENST00000256996 | DDB2 | chr11 | 47260350 | + | 2357 | 1940 | 243 | 2159 | 638 |
| 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 |
| ENST00000378623 | ENST00000378600 | LRP4 | chr11 | 46914523 | - | DDB2 | chr11 | 47260350 | + | 0.006373377 | 0.9936266 |
| ENST00000378623 | ENST00000378603 | LRP4 | chr11 | 46914523 | - | DDB2 | chr11 | 47260350 | + | 0.006373377 | 0.9936266 |
| ENST00000378623 | ENST00000256996 | LRP4 | chr11 | 46914523 | - | DDB2 | chr11 | 47260350 | + | 0.006373377 | 0.9936266 |
| Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones. |
Get the fusion protein sequences from here. |
| Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for LRP4-DDB2 |
| +/-13 AA sequence from the breakpoints of the fusion protein sequences. |
| Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
| LRP4 | chr11 | 46914523 | DDB2 | chr11 | 47260350 | 1940 | 566 | EKPRAIALHPMEGLPHSHLEPGGSQD |
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Potential FusionNeoAntigen Information of LRP4-DDB2 in HLA I |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| LRP4-DDB2_46914523_47260350.msa |
| Potential FusionNeoAntigen Information * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B18:01 | MEGLPHSH | 0.997 | 0.9724 | 10 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B44:03 | MEGLPHSHL | 0.967 | 0.9709 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B47:01 | MEGLPHSHL | 0.9397 | 0.6564 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B39:13 | MEGLPHSHL | 0.7699 | 0.9804 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:01 | HPMEGLPHSH | 0.9936 | 0.8967 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:08 | HPMEGLPHSH | 0.9902 | 0.9302 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:05 | HPMEGLPHSH | 0.9851 | 0.7994 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B07:05 | HPMEGLPHSHL | 1 | 0.5792 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B07:02 | HPMEGLPHSHL | 1 | 0.5393 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B07:10 | HPMEGLPHSHL | 1 | 0.5936 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:03 | HPMEGLPHSHL | 0.9996 | 0.9485 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:05 | HPMEGLPHSHL | 0.9989 | 0.762 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:04 | HPMEGLPHSHL | 0.9983 | 0.9779 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:02 | HPMEGLPHSHL | 0.9983 | 0.9779 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B81:01 | HPMEGLPHSHL | 0.9818 | 0.5133 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B82:01 | HPMEGLPHSHL | 0.8818 | 0.519 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-C03:08 | IALHPMEGL | 0.9995 | 0.9174 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-C03:19 | IALHPMEGL | 0.9995 | 0.9932 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-C03:07 | IALHPMEGL | 0.9994 | 0.9904 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B44:09 | MEGLPHSHL | 0.9383 | 0.5878 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B39:08 | MEGLPHSHL | 0.8247 | 0.96 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B78:01 | HPMEGLPHS | 0.6523 | 0.5575 | 8 | 17 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B07:12 | HPMEGLPHSHL | 0.9999 | 0.7442 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B07:04 | HPMEGLPHSHL | 0.9994 | 0.5472 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:12 | HPMEGLPHSHL | 0.9983 | 0.9779 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B42:02 | HPMEGLPHSHL | 0.9982 | 0.9813 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B42:01 | HPMEGLPHSHL | 0.9978 | 0.9798 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B39:10 | HPMEGLPHSHL | 0.9963 | 0.982 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B78:01 | HPMEGLPHSHL | 0.9744 | 0.501 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B18:06 | MEGLPHSH | 0.9973 | 0.9756 | 10 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B18:05 | MEGLPHSH | 0.997 | 0.9724 | 10 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B18:11 | MEGLPHSH | 0.9955 | 0.9804 | 10 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-C03:03 | IALHPMEGL | 0.9995 | 0.9923 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-C03:04 | IALHPMEGL | 0.9995 | 0.9923 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B40:04 | MEGLPHSHL | 0.9994 | 0.7512 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-C03:17 | IALHPMEGL | 0.999 | 0.9792 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-C03:05 | IALHPMEGL | 0.9989 | 0.9483 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-C03:06 | IALHPMEGL | 0.9842 | 0.9936 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B44:26 | MEGLPHSHL | 0.967 | 0.9709 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B44:07 | MEGLPHSHL | 0.967 | 0.9709 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B44:13 | MEGLPHSHL | 0.967 | 0.9709 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:13 | IALHPMEGL | 0.9082 | 0.9107 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B41:03 | MEGLPHSHL | 0.7741 | 0.7929 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B39:02 | MEGLPHSHL | 0.7631 | 0.9803 | 10 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-C17:01 | IALHPMEGL | 0.6977 | 0.9794 | 5 | 14 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B78:02 | HPMEGLPHS | 0.6264 | 0.5602 | 8 | 17 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:23 | HPMEGLPHSH | 0.9937 | 0.9046 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:77 | HPMEGLPHSH | 0.9936 | 0.8967 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B07:09 | HPMEGLPHSH | 0.991 | 0.5658 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:17 | HPMEGLPHSH | 0.9908 | 0.8349 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:30 | HPMEGLPHSH | 0.9908 | 0.8349 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:11 | HPMEGLPHSH | 0.9813 | 0.906 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:24 | HPMEGLPHSH | 0.8321 | 0.8443 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B15:08 | HPMEGLPHSH | 0.7629 | 0.8975 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B15:11 | HPMEGLPHSH | 0.7601 | 0.9111 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:43 | HPMEGLPHSH | 0.7345 | 0.8985 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B18:07 | HPMEGLPHSH | 0.2577 | 0.7951 | 8 | 18 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B07:09 | HPMEGLPHSHL | 1 | 0.5812 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B07:22 | HPMEGLPHSHL | 1 | 0.5393 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:13 | HPMEGLPHSHL | 0.9996 | 0.9521 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:17 | HPMEGLPHSHL | 0.999 | 0.8646 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:30 | HPMEGLPHSHL | 0.999 | 0.8646 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B35:09 | HPMEGLPHSHL | 0.9983 | 0.9779 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B67:01 | HPMEGLPHSHL | 0.9968 | 0.8629 | 8 | 19 |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 | HLA-B82:02 | HPMEGLPHSHL | 0.8818 | 0.519 | 8 | 19 |
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Potential FusionNeoAntigen Information of LRP4-DDB2 in HLA II |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| Potential FusionNeoAntigen Information * We used NetMHCIIpan v4.1 (%rank<0.5). |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of LRP4-DDB2 |
| 3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
| File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
| 367 | ALHPMEGLPHSHLE | LRP4 | DDB2 | chr11 | 46914523 | chr11 | 47260350 | 1940 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of LRP4-DDB2 |
| Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens * We used Glide to predict the interaction between HLAs and neoantigens. |
| HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
| HLA-B14:02 | 3BVN | 367 | ALHPMEGLPHSHLE | -7.9962 | -8.1096 |
| HLA-B14:02 | 3BVN | 367 | ALHPMEGLPHSHLE | -5.70842 | -6.74372 |
| HLA-B52:01 | 3W39 | 367 | ALHPMEGLPHSHLE | -6.83737 | -6.95077 |
| HLA-B52:01 | 3W39 | 367 | ALHPMEGLPHSHLE | -4.4836 | -5.5189 |
| HLA-A11:01 | 4UQ2 | 367 | ALHPMEGLPHSHLE | -10.0067 | -10.1201 |
| HLA-A11:01 | 4UQ2 | 367 | ALHPMEGLPHSHLE | -9.03915 | -10.0745 |
| HLA-A24:02 | 5HGA | 367 | ALHPMEGLPHSHLE | -6.56204 | -6.67544 |
| HLA-A24:02 | 5HGA | 367 | ALHPMEGLPHSHLE | -5.42271 | -6.45801 |
| HLA-B44:05 | 3DX8 | 367 | ALHPMEGLPHSHLE | -7.85648 | -8.89178 |
| HLA-B44:05 | 3DX8 | 367 | ALHPMEGLPHSHLE | -5.3978 | -5.5112 |
| HLA-A02:01 | 6TDR | 367 | ALHPMEGLPHSHLE | -3.37154 | -4.40684 |
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Vaccine Design for the FusionNeoAntigens of LRP4-DDB2 |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 10 | 18 | MEGLPHSH | CATGGAGGGGTTACCACATTCTCA |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 10 | 19 | MEGLPHSHL | CATGGAGGGGTTACCACATTCTCATCT |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 5 | 14 | IALHPMEGL | CATTGCCTTGCATCCCATGGAGGGGTT |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 8 | 17 | HPMEGLPHS | GCATCCCATGGAGGGGTTACCACATTC |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 8 | 18 | HPMEGLPHSH | GCATCCCATGGAGGGGTTACCACATTCTCA |
| LRP4-DDB2 | chr11 | 46914523 | chr11 | 47260350 | 8 | 19 | HPMEGLPHSHL | GCATCCCATGGAGGGGTTACCACATTCTCATCT |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of LRP4-DDB2 |
| These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens. |
| Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
| COAD | LRP4-DDB2 | chr11 | 46914523 | ENST00000378623 | chr11 | 47260350 | ENST00000256996 | TCGA-A6-6780 |
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Potential target of CAR-T therapy development for LRP4-DDB2 |
| Predicted 3D structure. We used RoseTTAFold. |
| 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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features * Minus value of BPloci means that the break point is located before the CDS. |
| - In-frame and retained 'Transmembrane'. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Subcellular localization prediction of the transmembrane domain retained fusion proteins * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
| Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to LRP4-DDB2 |
| 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 LRP4-DDB2 |
| 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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