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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:MDK-SEC63 (FusionGDB2 ID:52375) |
Fusion Gene Summary for MDK-SEC63 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: MDK-SEC63 | Fusion gene ID: 52375 | Hgene | Tgene | Gene symbol | MDK | SEC63 | Gene ID | 4192 | 11231 |
| Gene name | midkine | SEC63 homolog, protein translocation regulator | |
| Synonyms | ARAP|MK|NEGF2 | DNAJC23|ERdj2|PCLD2|PRO2507|SEC63L | |
| Cytomap | 11p11.2 | 6q21 | |
| Type of gene | protein-coding | protein-coding | |
| Description | midkineamphiregulin-associated proteinmidgestation and kidney proteinneurite growth-promoting factor 2neurite outgrowth-promoting factor 2retinoic acid inducible factor | translocation protein SEC63 homologSEC63 protein translocation regulatorSEC63-like protein | |
| Modification date | 20200315 | 20200313 | |
| UniProtAcc | P21741 | . | |
| Ensembl transtripts involved in fusion gene | ENST00000359803, ENST00000395565, ENST00000395566, ENST00000395569, ENST00000405308, ENST00000407067, ENST00000533283, | ENST00000369002, ENST00000460009, | |
| Fusion gene scores | * DoF score | 7 X 5 X 5=175 | 38 X 14 X 15=7980 |
| # samples | 7 | 39 | |
| ** MAII score | log2(7/175*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(39/7980*10)=-4.3548427173601 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: MDK [Title/Abstract] AND SEC63 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | MDK(46405349)-SEC63(108214782), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | MDK-SEC63 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. MDK-SEC63 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted 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 | MDK | GO:0010838 | positive regulation of keratinocyte proliferation | 18469519 |
| Hgene | MDK | GO:0010976 | positive regulation of neuron projection development | 12084985 |
| Hgene | MDK | GO:0030335 | positive regulation of cell migration | 15466886 |
| Hgene | MDK | GO:0043524 | negative regulation of neuron apoptotic process | 12573468 |
| Hgene | MDK | GO:0045785 | positive regulation of cell adhesion | 12084985 |
| Hgene | MDK | GO:0048714 | positive regulation of oligodendrocyte differentiation | 27445335 |
| Hgene | MDK | GO:2000249 | regulation of actin cytoskeleton reorganization | 18469519 |
| Fusion gene breakpoints across MDK (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across SEC63 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| 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 | UCS | TCGA-N6-A4VD-01A | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
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Fusion Gene ORF analysis for MDK-SEC63 |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 3UTR-3CDS | ENST00000359803 | ENST00000369002 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| 3UTR-3CDS | ENST00000395565 | ENST00000369002 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| 3UTR-3CDS | ENST00000395566 | ENST00000369002 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| 3UTR-3CDS | ENST00000395569 | ENST00000369002 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| 3UTR-intron | ENST00000359803 | ENST00000460009 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| 3UTR-intron | ENST00000395565 | ENST00000460009 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| 3UTR-intron | ENST00000395566 | ENST00000460009 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| 3UTR-intron | ENST00000395569 | ENST00000460009 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| 5CDS-intron | ENST00000405308 | ENST00000460009 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| Frame-shift | ENST00000405308 | ENST00000369002 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| intron-3CDS | ENST00000407067 | ENST00000369002 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| intron-3CDS | ENST00000533283 | ENST00000369002 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| intron-intron | ENST00000407067 | ENST00000460009 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| intron-intron | ENST00000533283 | ENST00000460009 | MDK | chr11 | 46405349 | - | SEC63 | chr6 | 108214782 | - |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| 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) |
| 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 |
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Fusion Genomic Features for MDK-SEC63 |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for MDK-SEC63 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:46405349/:108214782) - 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 |
| MDK | . |
| FUNCTION: Secreted protein that functions as cytokine and growth factor and mediates its signal through cell-surface proteoglycan and non-proteoglycan receptors (PubMed:18469519, PubMed:12573468, PubMed:12122009, PubMed:10212223, PubMed:24458438, PubMed:15466886, PubMed:12084985, PubMed:10772929). Binds cell-surface proteoglycan receptors via their chondroitin sulfate (CS) groups (PubMed:12084985, PubMed:10212223). Thereby regulates many processes like inflammatory response, cell proliferation, cell adhesion, cell growth, cell survival, tissue regeneration, cell differentiation and cell migration (PubMed:12573468, PubMed:12122009, PubMed:10212223, PubMed:10683378, PubMed:24458438, PubMed:22323540, PubMed:12084985, PubMed:15466886, PubMed:10772929). Participates in inflammatory processes by exerting two different activities. Firstly, mediates neutrophils and macrophages recruitment to the sites of inflammation both by direct action by cooperating namely with ITGB2 via LRP1 and by inducing chemokine expression (PubMed:10683378, PubMed:24458438). This inflammation can be accompanied by epithelial cell survival and smooth muscle cell migration after renal and vessel damage, respectively (PubMed:10683378). Secondly, suppresses the development of tolerogenic dendric cells thereby inhibiting the differentiation of regulatory T cells and also promote T cell expansion through NFAT signaling and Th1 cell differentiation (PubMed:22323540). Promotes tissue regeneration after injury or trauma. After heart damage negatively regulates the recruitment of inflammatory cells and mediates cell survival through activation of anti-apoptotic signaling pathways via MAPKs and AKT pathways through the activation of angiogenesis (By similarity). Also facilitates liver regeneration as well as bone repair by recruiting macrophage at trauma site and by promoting cartilage development by facilitating chondrocyte differentiation (By similarity). Plays a role in brain by promoting neural precursor cells survival and growth through interaction with heparan sulfate proteoglycans (By similarity). Binds PTPRZ1 and promotes neuronal migration and embryonic neurons survival (PubMed:10212223). Binds SDC3 or GPC2 and mediates neurite outgrowth and cell adhesion (PubMed:12084985, PubMed:1768439). Binds chondroitin sulfate E and heparin leading to inhibition of neuronal cell adhesion induced by binding with GPC2 (PubMed:12084985). Binds CSPG5 and promotes elongation of oligodendroglial precursor-like cells (By similarity). Also binds ITGA6:ITGB1 complex; this interaction mediates MDK-induced neurite outgrowth (PubMed:15466886, PubMed:1768439). Binds LRP1; promotes neuronal survival (PubMed:10772929). Binds ITGA4:ITGB1 complex; this interaction mediates MDK-induced osteoblast cells migration through PXN phosphorylation (PubMed:15466886). Binds anaplastic lymphoma kinase (ALK) which induces ALK activation and subsequent phosphorylation of the insulin receptor substrate (IRS1), followed by the activation of mitogen-activated protein kinase (MAPK) and PI3-kinase, and the induction of cell proliferation (PubMed:12122009). Promotes epithelial to mesenchymal transition through interaction with NOTCH2 (PubMed:18469519). During arteriogenesis, plays a role in vascular endothelial cell proliferation by inducing VEGFA expression and release which in turn induces nitric oxide synthase expression. Moreover activates vasodilation through nitric oxide synthase activation (By similarity). Negatively regulates bone formation in response to mechanical load by inhibiting Wnt/beta-catenin signaling in osteoblasts (By similarity). In addition plays a role in hippocampal development, working memory, auditory response, early fetal adrenal gland development and the female reproductive system (By similarity). {ECO:0000250|UniProtKB:P12025, ECO:0000250|UniProtKB:Q9R1S9, ECO:0000269|PubMed:10212223, ECO:0000269|PubMed:10683378, ECO:0000269|PubMed:10772929, ECO:0000269|PubMed:12084985, ECO:0000269|PubMed:12122009, ECO:0000269|PubMed:12573468, ECO:0000269|PubMed:15466886, ECO:0000269|PubMed:1768439, ECO:0000269|PubMed:18469519, ECO:0000269|PubMed:22323540, ECO:0000269|PubMed:24458438}. | FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}. |
| 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. |
| - In-frame and 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 |
| - In-frame and 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 |
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Fusion Gene Sequence for MDK-SEC63 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for MDK-SEC63 |
| 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 (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs for MDK-SEC63 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for MDK-SEC63 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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