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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:CDX2-PDCD6 (FusionGDB2 ID:15512) |
Fusion Gene Summary for CDX2-PDCD6 |
Fusion gene summary |
Fusion gene information | Fusion gene name: CDX2-PDCD6 | Fusion gene ID: 15512 | Hgene | Tgene | Gene symbol | CDX2 | PDCD6 | Gene ID | 1045 | 10016 |
Gene name | caudal type homeobox 2 | programmed cell death 6 | |
Synonyms | CDX-3|CDX2/AS|CDX3 | ALG-2|ALG2|PEF1B | |
Cytomap | 13q12.2 | 5p15.33 | |
Type of gene | protein-coding | protein-coding | |
Description | homeobox protein CDX-2caudal type homeobox transcription factor 2caudal-type homeobox protein 2homeobox protein miniCDX2 | programmed cell death protein 6apoptosis-linked gene 2 proteinapoptosis-linked gene 2 protein homologprobable calcium-binding protein ALG-2 | |
Modification date | 20200315 | 20200313 | |
UniProtAcc | Q99626 | O75340 | |
Ensembl transtripts involved in fusion gene | ENST00000381020, ENST00000548877, | ENST00000264933, ENST00000505221, ENST00000509581, ENST00000507528, ENST00000511482, | |
Fusion gene scores | * DoF score | 4 X 4 X 3=48 | 6 X 4 X 5=120 |
# samples | 4 | 7 | |
** MAII score | log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(7/120*10)=-0.777607578663552 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Context | PubMed: CDX2 [Title/Abstract] AND PDCD6 [Title/Abstract] AND fusion [Title/Abstract] | ||
Most frequent breakpoint | CDX2(28541394)-PDCD6(311408), # samples:1 | ||
Anticipated loss of major functional domain due to fusion event. |
* 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 | CDX2 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 15677472 |
Tgene | PDCD6 | GO:0001938 | positive regulation of endothelial cell proliferation | 21893193 |
Tgene | PDCD6 | GO:0006886 | intracellular protein transport | 21122810 |
Tgene | PDCD6 | GO:0010595 | positive regulation of endothelial cell migration | 21893193 |
Tgene | PDCD6 | GO:0030948 | negative regulation of vascular endothelial growth factor receptor signaling pathway | 21893193 |
Tgene | PDCD6 | GO:0032007 | negative regulation of TOR signaling | 21893193 |
Tgene | PDCD6 | GO:0034605 | cellular response to heat | 21122810 |
Tgene | PDCD6 | GO:0036324 | vascular endothelial growth factor receptor-2 signaling pathway | 21893193 |
Tgene | PDCD6 | GO:0043280 | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 16132846 |
Tgene | PDCD6 | GO:0045766 | positive regulation of angiogenesis | 21893193 |
Tgene | PDCD6 | GO:0051898 | negative regulation of protein kinase B signaling | 21893193 |
Fusion gene breakpoints across CDX2 (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 PDCD6 (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 | READ | TCGA-AG-3883 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
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Fusion Gene ORF analysis for CDX2-PDCD6 |
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 |
intron-3CDS | ENST00000381020 | ENST00000264933 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
intron-intron | ENST00000381020 | ENST00000505221 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
intron-intron | ENST00000381020 | ENST00000509581 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
intron-intron | ENST00000381020 | ENST00000507528 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
intron-3UTR | ENST00000381020 | ENST00000511482 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
5UTR-3CDS | ENST00000548877 | ENST00000264933 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
5UTR-intron | ENST00000548877 | ENST00000505221 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
5UTR-intron | ENST00000548877 | ENST00000509581 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
5UTR-intron | ENST00000548877 | ENST00000507528 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
5UTR-3UTR | ENST00000548877 | ENST00000511482 | CDX2 | chr13 | 28541394 | - | PDCD6 | chr5 | 311408 | + |
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 CDX2-PDCD6 |
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) |
CDX2 | chr13 | 28541393 | - | PDCD6 | chr5 | 311407 | + | 1.33E-08 | 1 |
CDX2 | chr13 | 28541393 | - | PDCD6 | chr5 | 311407 | + | 1.33E-08 | 1 |
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 CDX2-PDCD6 |
Go to FGviewer for the breakpoints of :-: - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. |
Main function of each fusion partner protein. (from UniProt) |
Hgene | Tgene |
CDX2 | PDCD6 |
FUNCTION: Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine. Binds preferentially to methylated DNA (PubMed:28473536). {ECO:0000269|PubMed:28473536}. | FUNCTION: Calcium sensor that plays a key role in processes such as endoplasmic reticulum (ER)-Golgi vesicular transport, endosomal biogenesis or membrane repair. Acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium: calcium-binding triggers exposure of apolar surface, promoting interaction with different sets of proteins thanks to 3 different hydrophobic pockets, leading to translocation to membranes (PubMed:20691033, PubMed:25667979). Involved in ER-Golgi transport by promoting the association between PDCD6IP and TSG101, thereby bridging together the ESCRT-III and ESCRT-I complexes (PubMed:19520058). Together with PEF1, acts as calcium-dependent adapter for the BCR(KLHL12) complex, a complex involved in ER-Golgi transport by regulating the size of COPII coats (PubMed:27716508). In response to cytosolic calcium increase, the heterodimer formed with PEF1 interacts with, and bridges together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export, which is required for neural crest specification (PubMed:27716508). Involved in the regulation of the distribution and function of MCOLN1 in the endosomal pathway (PubMed:19864416). Promotes localization and polymerization of TFG at endoplasmic reticulum exit site (PubMed:27813252). Required for T-cell receptor-, Fas-, and glucocorticoid-induced apoptosis (By similarity). May mediate Ca(2+)-regulated signals along the death pathway: interaction with DAPK1 can accelerate apoptotic cell death by increasing caspase-3 activity (PubMed:16132846). Its role in apoptosis may however be indirect, as suggested by knockout experiments (By similarity). May inhibit KDR/VEGFR2-dependent angiogenesis; the function involves inhibition of VEGF-induced phosphorylation of the Akt signaling pathway (PubMed:21893193). In case of infection by HIV-1 virus, indirectly inhibits HIV-1 production by affecting viral Gag expression and distribution (PubMed:27784779). {ECO:0000250|UniProtKB:P12815, ECO:0000269|PubMed:16132846, ECO:0000269|PubMed:19520058, ECO:0000269|PubMed:19864416, ECO:0000269|PubMed:20691033, ECO:0000269|PubMed:21893193, ECO:0000269|PubMed:25667979, ECO:0000269|PubMed:27716508, ECO:0000269|PubMed:27784779, ECO:0000269|PubMed:27813252}.; FUNCTION: [Isoform 2]: Has a lower Ca(2+) affinity than isoform 1 (By similarity). {ECO:0000250|UniProtKB:P12815}. |
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 CDX2-PDCD6 |
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 CDX2-PDCD6 |
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 CDX2-PDCD6 |
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 |
Tgene | PDCD6 | O75340 | DB11348 | Calcium Phosphate | Agonist | Small molecule | Approved |
Tgene | PDCD6 | O75340 | DB11348 | Calcium Phosphate | Agonist | Small molecule | Approved |
Tgene | PDCD6 | O75340 | DB14481 | Calcium phosphate dihydrate | Small molecule | Approved | |
Tgene | PDCD6 | O75340 | DB14481 | Calcium phosphate dihydrate | Small molecule | Approved | |
Tgene | PDCD6 | O75340 | DB01593 | Zinc | Small molecule | Approved|Investigational | |
Tgene | PDCD6 | O75340 | DB01593 | Zinc | Small molecule | Approved|Investigational | |
Tgene | PDCD6 | O75340 | DB11093 | Calcium citrate | Agonist | Small molecule | Approved|Investigational |
Tgene | PDCD6 | O75340 | DB11093 | Calcium citrate | Agonist | Small molecule | Approved|Investigational |
Tgene | PDCD6 | O75340 | DB14487 | Zinc acetate | Small molecule | Approved|Investigational | |
Tgene | PDCD6 | O75340 | DB14487 | Zinc acetate | Small molecule | Approved|Investigational |
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Related Diseases for CDX2-PDCD6 |
Diseases associated with fusion partners. (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Hgene | CDX2 | C0007102 | Malignant tumor of colon | 1 | CTD_human |
Hgene | CDX2 | C0009375 | Colonic Neoplasms | 1 | CTD_human |
Hgene | CDX2 | C0032927 | Precancerous Conditions | 1 | CTD_human |
Hgene | CDX2 | C0266225 | Persistent cloaca | 1 | GENOMICS_ENGLAND |
Hgene | CDX2 | C0282313 | Condition, Preneoplastic | 1 | CTD_human |
Tgene | PDCD6 | C0011573 | Endogenous depression | 1 | PSYGENET |