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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:KDR-RAB3IP (FusionGDB2 ID:41933) |
Fusion Gene Summary for KDR-RAB3IP |
Fusion gene summary |
Fusion gene information | Fusion gene name: KDR-RAB3IP | Fusion gene ID: 41933 | Hgene | Tgene | Gene symbol | KDR | RAB3IP | Gene ID | 3791 | 117177 |
Gene name | kinase insert domain receptor | RAB3A interacting protein | |
Synonyms | CD309|FLK1|VEGFR|VEGFR2 | RABIN3|RABIN8 | |
Cytomap | 4q12 | 12q15 | |
Type of gene | protein-coding | protein-coding | |
Description | vascular endothelial growth factor receptor 2fetal liver kinase-1kinase insert domain receptor (a type III receptor tyrosine kinase)protein-tyrosine kinase receptor Flk-1soluble VEGFR2tyrosine kinase growth factor receptor | rab-3A-interacting proteinSSX2 interacting proteinrab3A-interacting proteinrabin-3 | |
Modification date | 20200327 | 20200327 | |
UniProtAcc | P35968 | . | |
Ensembl transtripts involved in fusion gene | ENST00000263923, | ENST00000325555, ENST00000362025, ENST00000378815, ENST00000483530, ENST00000550536, ENST00000550847, ENST00000551641, ENST00000553099, ENST00000247833, | |
Fusion gene scores | * DoF score | 1 X 1 X 1=1 | 20 X 17 X 10=3400 |
# samples | 1 | 29 | |
** MAII score | log2(1/1*10)=3.32192809488736 | log2(29/3400*10)=-3.55140994101013 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Context | PubMed: KDR [Title/Abstract] AND RAB3IP [Title/Abstract] AND fusion [Title/Abstract] | ||
Most frequent breakpoint | KDR(55984771)-RAB3IP(70206744), # samples:1 | ||
Anticipated loss of major functional domain due to fusion event. | KDR-RAB3IP seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. KDR-RAB3IP seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. KDR-RAB3IP seems lost the major protein functional domain in Hgene partner, which is a kinase 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 | KDR | GO:0001934 | positive regulation of protein phosphorylation | 19033661 |
Hgene | KDR | GO:0008284 | positive regulation of cell proliferation | 7929439 |
Hgene | KDR | GO:0008360 | regulation of cell shape | 7929439 |
Hgene | KDR | GO:0010629 | negative regulation of gene expression | 26879375 |
Hgene | KDR | GO:0014068 | positive regulation of phosphatidylinositol 3-kinase signaling | 9804796 |
Hgene | KDR | GO:0018108 | peptidyl-tyrosine phosphorylation | 10037737|10102632 |
Hgene | KDR | GO:0030335 | positive regulation of cell migration | 7929439 |
Hgene | KDR | GO:0035924 | cellular response to vascular endothelial growth factor stimulus | 10102632|11387210|19033661|23529610 |
Hgene | KDR | GO:0038033 | positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway | 21885851 |
Hgene | KDR | GO:0043410 | positive regulation of MAPK cascade | 11387210 |
Hgene | KDR | GO:0046777 | protein autophosphorylation | 10037737|10102632|19033661 |
Hgene | KDR | GO:0048010 | vascular endothelial growth factor receptor signaling pathway | 10102632|11387210|15215251 |
Hgene | KDR | GO:0050927 | positive regulation of positive chemotaxis | 7929439 |
Hgene | KDR | GO:0051770 | positive regulation of nitric-oxide synthase biosynthetic process | 10600473 |
Hgene | KDR | GO:0051894 | positive regulation of focal adhesion assembly | 12820653 |
Hgene | KDR | GO:1904881 | cellular response to hydrogen sulfide | 26879375 |
Hgene | KDR | GO:2000352 | negative regulation of endothelial cell apoptotic process | 9804796 |
Tgene | RAB3IP | GO:0006612 | protein targeting to membrane | 23382462 |
Fusion gene breakpoints across KDR (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 RAB3IP (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 | GBM | TCGA-26-5135-01A | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
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Fusion Gene ORF analysis for KDR-RAB3IP |
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 |
5CDS-intron | ENST00000263923 | ENST00000325555 | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
5CDS-intron | ENST00000263923 | ENST00000362025 | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
5CDS-intron | ENST00000263923 | ENST00000378815 | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
5CDS-intron | ENST00000263923 | ENST00000483530 | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
5CDS-intron | ENST00000263923 | ENST00000550536 | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
5CDS-intron | ENST00000263923 | ENST00000550847 | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
5CDS-intron | ENST00000263923 | ENST00000551641 | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
5CDS-intron | ENST00000263923 | ENST00000553099 | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
Frame-shift | ENST00000263923 | ENST00000247833 | KDR | chr4 | 55984771 | - | RAB3IP | chr12 | 70206744 | + |
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 KDR-RAB3IP |
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) |
KDR | chr4 | 55984770 | - | RAB3IP | chr12 | 70206743 | + | 0.00027905 | 0.999721 |
KDR | chr4 | 55984770 | - | RAB3IP | chr12 | 70206743 | + | 0.00027905 | 0.999721 |
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 KDR-RAB3IP |
Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:55984771/:70206744) - 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. |
Main function of each fusion partner protein. (from UniProt) |
Hgene | Tgene |
KDR | . |
FUNCTION: Tyrosine-protein kinase that acts as a cell-surface receptor for VEGFA, VEGFC and VEGFD. Plays an essential role in the regulation of angiogenesis, vascular development, vascular permeability, and embryonic hematopoiesis. Promotes proliferation, survival, migration and differentiation of endothelial cells. Promotes reorganization of the actin cytoskeleton. Isoforms lacking a transmembrane domain, such as isoform 2 and isoform 3, may function as decoy receptors for VEGFA, VEGFC and/or VEGFD. Isoform 2 plays an important role as negative regulator of VEGFA- and VEGFC-mediated lymphangiogenesis by limiting the amount of free VEGFA and/or VEGFC and preventing their binding to FLT4. Modulates FLT1 and FLT4 signaling by forming heterodimers. Binding of vascular growth factors to isoform 1 leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate and the activation of protein kinase C. Mediates activation of MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Mediates phosphorylation of PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, reorganization of the actin cytoskeleton and activation of PTK2/FAK1. Required for VEGFA-mediated induction of NOS2 and NOS3, leading to the production of the signaling molecule nitric oxide (NO) by endothelial cells. Phosphorylates PLCG1. Promotes phosphorylation of FYN, NCK1, NOS3, PIK3R1, PTK2/FAK1 and SRC. {ECO:0000269|PubMed:10102632, ECO:0000269|PubMed:10368301, ECO:0000269|PubMed:10600473, ECO:0000269|PubMed:11387210, ECO:0000269|PubMed:12649282, ECO:0000269|PubMed:1417831, ECO:0000269|PubMed:15026417, ECO:0000269|PubMed:15215251, ECO:0000269|PubMed:15962004, ECO:0000269|PubMed:16966330, ECO:0000269|PubMed:17303569, ECO:0000269|PubMed:18529047, ECO:0000269|PubMed:19668192, ECO:0000269|PubMed:19834490, ECO:0000269|PubMed:20080685, ECO:0000269|PubMed:20224550, ECO:0000269|PubMed:20705758, ECO:0000269|PubMed:21893193, ECO:0000269|PubMed:25825981, ECO:0000269|PubMed:7929439, ECO:0000269|PubMed:9160888, ECO:0000269|PubMed:9804796, ECO:0000269|PubMed:9837777}. | 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 KDR-RAB3IP |
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 KDR-RAB3IP |
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 KDR-RAB3IP |
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 KDR-RAB3IP |
Diseases associated with fusion partners. (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |