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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:CCL21-GEMIN5 (FusionGDB2 ID:14040) |
Fusion Gene Summary for CCL21-GEMIN5 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CCL21-GEMIN5 | Fusion gene ID: 14040 | Hgene | Tgene | Gene symbol | CCL21 | GEMIN5 | Gene ID | 6366 | 25929 |
| Gene name | C-C motif chemokine ligand 21 | gem nuclear organelle associated protein 5 | |
| Synonyms | 6Ckine|CKb9|ECL|SCYA21|SLC|TCA4 | GEMIN-5 | |
| Cytomap | 9p13.3 | 5q33.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | C-C motif chemokine 21Efficient Chemoattractant for Lymphocytesbeta chemokine exodus-2chemokine (C-C motif) ligand 21secondary lymphoid tissue chemokinesmall inducible cytokine subfamily A (Cys-Cys), member 21 | gem-associated protein 5 | |
| Modification date | 20200313 | 20200322 | |
| UniProtAcc | O00585 | Q8TEQ6 | |
| Ensembl transtripts involved in fusion gene | ENST00000259607, ENST00000378792, | ENST00000285873, | |
| Fusion gene scores | * DoF score | 1 X 1 X 1=1 | 1 X 1 X 1=1 |
| # samples | 1 | 1 | |
| ** MAII score | log2(1/1*10)=3.32192809488736 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: CCL21 [Title/Abstract] AND GEMIN5 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CCL21(34709139)-GEMIN5(154267910), # 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 | CCL21 | GO:0001768 | establishment of T cell polarity | 12729902 |
| Hgene | CCL21 | GO:0001954 | positive regulation of cell-matrix adhesion | 15569314|18308860 |
| Hgene | CCL21 | GO:0002407 | dendritic cell chemotaxis | 15778365 |
| Hgene | CCL21 | GO:0007186 | G protein-coupled receptor signaling pathway | 18308860 |
| Hgene | CCL21 | GO:0030838 | positive regulation of actin filament polymerization | 11242036 |
| Hgene | CCL21 | GO:0031274 | positive regulation of pseudopodium assembly | 11242036 |
| Hgene | CCL21 | GO:0031529 | ruffle organization | 15569314 |
| Hgene | CCL21 | GO:0033630 | positive regulation of cell adhesion mediated by integrin | 15569314 |
| Hgene | CCL21 | GO:0034695 | response to prostaglandin E | 14592837 |
| Hgene | CCL21 | GO:0035759 | mesangial cell-matrix adhesion | 15569314 |
| Hgene | CCL21 | GO:0043123 | positive regulation of I-kappaB kinase/NF-kappaB signaling | 15059845 |
| Hgene | CCL21 | GO:0043552 | positive regulation of phosphatidylinositol 3-kinase activity | 15059845|15778365 |
| Hgene | CCL21 | GO:0045860 | positive regulation of protein kinase activity | 15059845 |
| Hgene | CCL21 | GO:0046330 | positive regulation of JNK cascade | 15778365 |
| Hgene | CCL21 | GO:0051209 | release of sequestered calcium ion into cytosol | 14592837 |
| Hgene | CCL21 | GO:0051491 | positive regulation of filopodium assembly | 15569314 |
| Hgene | CCL21 | GO:0051897 | positive regulation of protein kinase B signaling | 15059845|15778365 |
| Hgene | CCL21 | GO:0060326 | cell chemotaxis | 18308860 |
| Hgene | CCL21 | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 12729902|15778365 |
| Hgene | CCL21 | GO:0090023 | positive regulation of neutrophil chemotaxis | 21051556 |
| Hgene | CCL21 | GO:0090630 | activation of GTPase activity | 15778365 |
| Hgene | CCL21 | GO:1903237 | negative regulation of leukocyte tethering or rolling | 18308860 |
| Hgene | CCL21 | GO:2000147 | positive regulation of cell motility | 15778365 |
| Hgene | CCL21 | GO:2000406 | positive regulation of T cell migration | 23620790 |
| Hgene | CCL21 | GO:2000529 | positive regulation of myeloid dendritic cell chemotaxis | 14592837 |
| Hgene | CCL21 | GO:2000669 | negative regulation of dendritic cell apoptotic process | 15059845 |
| Tgene | GEMIN5 | GO:0000387 | spliceosomal snRNP assembly | 18984161 |
| Fusion gene breakpoints across CCL21 (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 GEMIN5 (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 |
| ChiTaRS5.0 | N/A | AI749414 | CCL21 | chr9 | 34709139 | + | GEMIN5 | chr5 | 154267910 | - |
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Fusion Gene ORF analysis for CCL21-GEMIN5 |
| 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 | ENST00000259607 | ENST00000285873 | CCL21 | chr9 | 34709139 | + | GEMIN5 | chr5 | 154267910 | - |
| intron-3CDS | ENST00000378792 | ENST00000285873 | CCL21 | chr9 | 34709139 | + | GEMIN5 | chr5 | 154267910 | - |
| 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 CCL21-GEMIN5 |
| 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 CCL21-GEMIN5 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:34709139/:154267910) - 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 |
| CCL21 | GEMIN5 |
| FUNCTION: Inhibits hemopoiesis and stimulates chemotaxis. Chemotactic in vitro for thymocytes and activated T-cells, but not for B-cells, macrophages, or neutrophils. Shows preferential activity towards naive T-cells. May play a role in mediating homing of lymphocytes to secondary lymphoid organs. Binds to atypical chemokine receptor ACKR4 and mediates the recruitment of beta-arrestin (ARRB1/2) to ACKR4. | FUNCTION: Required for the assembly of the SMN complex that plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:16857593, PubMed:18984161, PubMed:20513430). Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP (PubMed:18984161). Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus (PubMed:18984161). GEMIN5 acts as the snRNA-binding protein of the SMN complex (PubMed:11714716, PubMed:16857593, PubMed:19377484, PubMed:19750007, PubMed:20513430, PubMed:27834343, PubMed:27881600, PubMed:27881601). Binds to the 7-methylguanosine cap of RNA molecules (PubMed:19750007, PubMed:27834343, PubMed:27881600, PubMed:27881601, Ref.25). Binds to the 3'-UTR of SMN1 mRNA and regulates its translation; does not affect mRNA stability (PubMed:25911097). May play a role in the regulation of protein synthesis via its interaction with ribosomes (PubMed:27507887). {ECO:0000269|PubMed:11714716, ECO:0000269|PubMed:16857593, ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:19377484, ECO:0000269|PubMed:19750007, ECO:0000269|PubMed:20513430, ECO:0000269|PubMed:25911097, ECO:0000269|PubMed:27507887, ECO:0000269|PubMed:27834343, ECO:0000269|PubMed:27881600, ECO:0000269|PubMed:27881601, ECO:0000269|Ref.25}. |
| 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 CCL21-GEMIN5 |
| 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 CCL21-GEMIN5 |
| 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 CCL21-GEMIN5 |
| 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 CCL21-GEMIN5 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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