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Fusion Protein:ATRX-ARHGEF9 |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: ATRX-ARHGEF9 | FusionPDB ID: 8344 | FusionGDB2.0 ID: 8344 | Hgene | Tgene | Gene symbol | ATRX | ARHGEF9 | Gene ID | 546 | 23229 |
| Gene name | ATRX chromatin remodeler | Cdc42 guanine nucleotide exchange factor 9 | |
| Synonyms | JMS|MRX52|RAD54|RAD54L|XH2|XNP|ZNF-HX | COLLYBISTIN|EIEE8|HPEM-2|PEM-2|PEM2 | |
| Cytomap | Xq21.1 | Xq11.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | transcriptional regulator ATRXATP-dependent helicase ATRXX-linked helicase IIX-linked nuclear proteinalpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae) | rho guanine nucleotide exchange factor 9Cdc42 guanine nucleotide exchange factor (GEF) 9PEM-2 homologhPEM-2 collybistinrac/Cdc42 guanine nucleotide exchange factor 9 | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | P46100 Main function of 5'-partner protein: FUNCTION: Involved in transcriptional regulation and chromatin remodeling. Facilitates DNA replication in multiple cellular environments and is required for efficient replication of a subset of genomic loci. Binds to DNA tandem repeat sequences in both telomeres and euchromatin and in vitro binds DNA quadruplex structures. May help stabilizing G-rich regions into regular chromatin structures by remodeling G4 DNA and incorporating H3.3-containing nucleosomes. Catalytic component of the chromatin remodeling complex ATRX:DAXX which has ATP-dependent DNA translocase activity and catalyzes the replication-independent deposition of histone H3.3 in pericentric DNA repeats outside S-phase and telomeres, and the in vitro remodeling of H3.3-containing nucleosomes. Its heterochromatin targeting is proposed to involve a combinatorial readout of histone H3 modifications (specifically methylation states of H3K9 and H3K4) and association with CBX5. Involved in maintaining telomere structural integrity in embryonic stem cells which probably implies recruitment of CBX5 to telomeres. Reports on the involvement in transcriptional regulation of telomeric repeat-containing RNA (TERRA) are conflicting; according to a report, it is not sufficient to decrease chromatin condensation at telomeres nor to increase expression of telomeric RNA in fibroblasts (PubMed:24500201). May be involved in telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines. Acts as negative regulator of chromatin incorporation of transcriptionally repressive histone MACROH2A1, particularily at telomeres and the alpha-globin cluster in erythroleukemic cells. Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. On the maternal allele, required for the chromatin occupancy of SMC1 and CTCTF within the H19 imprinting control region (ICR) and involved in esatblishment of histone tails modifications in the ICR. May be involved in brain development and facial morphogenesis. Binds to zinc-finger coding genes with atypical chromatin signatures and regulates its H3K9me3 levels. Forms a complex with ZNF274, TRIM28 and SETDB1 to facilitate the deposition and maintenance of H3K9me3 at the 3' exons of zinc-finger genes (PubMed:27029610). {ECO:0000269|PubMed:12953102, ECO:0000269|PubMed:14990586, ECO:0000269|PubMed:20504901, ECO:0000269|PubMed:20651253, ECO:0000269|PubMed:21029860, ECO:0000269|PubMed:22391447, ECO:0000269|PubMed:22829774, ECO:0000269|PubMed:24500201, ECO:0000269|PubMed:27029610}. | O43307 Main function of 5'-partner protein: FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for CDC42. Promotes formation of GPHN clusters (By similarity). {ECO:0000250|UniProtKB:Q9QX73, ECO:0000269|PubMed:10559246}. | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000373344, ENST00000395603, ENST00000480283, ENST00000373341, | ENST00000374872, ENST00000433323, ENST00000495564, ENST00000253401, ENST00000374870, ENST00000374878, ENST00000437457, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 17 X 13 X 9=1989 | 2 X 2 X 2=8 |
| # samples | 23 | 3 | |
| ** MAII score | log2(23/1989*10)=-3.11233750988937 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/8*10)=1.90689059560852 | |
| Fusion gene context | PubMed: ATRX [Title/Abstract] AND ARHGEF9 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: ATRX [Title/Abstract] AND ARHGEF9 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | ATRX(77041468)-ARHGEF9(62875617), # samples:3 | ||
| Anticipated loss of major functional domain due to fusion event. | ATRX-ARHGEF9 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. ATRX-ARHGEF9 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. ATRX-ARHGEF9 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. ATRX-ARHGEF9 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 | ATRX | GO:0006334 | nucleosome assembly | 20651253 |
| Hgene | ATRX | GO:0006338 | chromatin remodeling | 20651253 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chrX:77041468/chrX:62875617) - 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 ATRX (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 ARHGEF9 (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) |
| ENST00000373344 | ATRX | chrX | 77041468 | - | ENST00000253401 | ARHGEF9 | chrX | 62875617 | - | 3791 | 235 | 256 | 729 | 157 |
| ENST00000373344 | ATRX | chrX | 77041468 | - | ENST00000374878 | ARHGEF9 | chrX | 62875617 | - | 974 | 235 | 630 | 238 | 130 |
| ENST00000373344 | ATRX | chrX | 77041468 | - | ENST00000374870 | ARHGEF9 | chrX | 62875617 | - | 3782 | 235 | 256 | 729 | 157 |
| ENST00000373344 | ATRX | chrX | 77041468 | - | ENST00000437457 | ARHGEF9 | chrX | 62875617 | - | 3782 | 235 | 256 | 729 | 157 |
| ENST00000395603 | ATRX | chrX | 77041468 | - | ENST00000253401 | ARHGEF9 | chrX | 62875617 | - | 3791 | 235 | 256 | 729 | 157 |
| ENST00000395603 | ATRX | chrX | 77041468 | - | ENST00000374878 | ARHGEF9 | chrX | 62875617 | - | 974 | 235 | 630 | 238 | 130 |
| ENST00000395603 | ATRX | chrX | 77041468 | - | ENST00000374870 | ARHGEF9 | chrX | 62875617 | - | 3782 | 235 | 256 | 729 | 157 |
| ENST00000395603 | ATRX | chrX | 77041468 | - | ENST00000437457 | ARHGEF9 | chrX | 62875617 | - | 3782 | 235 | 256 | 729 | 157 |
| ENST00000373344 | ATRX | chrX | 77041467 | - | ENST00000253401 | ARHGEF9 | chrX | 62875617 | - | 3791 | 235 | 256 | 729 | 157 |
| ENST00000373344 | ATRX | chrX | 77041467 | - | ENST00000374878 | ARHGEF9 | chrX | 62875617 | - | 974 | 235 | 630 | 238 | 130 |
| ENST00000373344 | ATRX | chrX | 77041467 | - | ENST00000374870 | ARHGEF9 | chrX | 62875617 | - | 3782 | 235 | 256 | 729 | 157 |
| ENST00000373344 | ATRX | chrX | 77041467 | - | ENST00000437457 | ARHGEF9 | chrX | 62875617 | - | 3782 | 235 | 256 | 729 | 157 |
| ENST00000395603 | ATRX | chrX | 77041467 | - | ENST00000253401 | ARHGEF9 | chrX | 62875617 | - | 3791 | 235 | 256 | 729 | 157 |
| ENST00000395603 | ATRX | chrX | 77041467 | - | ENST00000374878 | ARHGEF9 | chrX | 62875617 | - | 974 | 235 | 630 | 238 | 130 |
| ENST00000395603 | ATRX | chrX | 77041467 | - | ENST00000374870 | ARHGEF9 | chrX | 62875617 | - | 3782 | 235 | 256 | 729 | 157 |
| ENST00000395603 | ATRX | chrX | 77041467 | - | ENST00000437457 | ARHGEF9 | chrX | 62875617 | - | 3782 | 235 | 256 | 729 | 157 |
| 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 |
| ENST00000373344 | ENST00000253401 | ATRX | chrX | 77041468 | - | ARHGEF9 | chrX | 62875617 | - | 0.00406581 | 0.9959341 |
| ENST00000373344 | ENST00000374878 | ATRX | chrX | 77041468 | - | ARHGEF9 | chrX | 62875617 | - | 0.014187951 | 0.98581207 |
| ENST00000373344 | ENST00000374870 | ATRX | chrX | 77041468 | - | ARHGEF9 | chrX | 62875617 | - | 0.0033853 | 0.99661475 |
| ENST00000373344 | ENST00000437457 | ATRX | chrX | 77041468 | - | ARHGEF9 | chrX | 62875617 | - | 0.0033853 | 0.99661475 |
| ENST00000395603 | ENST00000253401 | ATRX | chrX | 77041468 | - | ARHGEF9 | chrX | 62875617 | - | 0.00406581 | 0.9959341 |
| ENST00000395603 | ENST00000374878 | ATRX | chrX | 77041468 | - | ARHGEF9 | chrX | 62875617 | - | 0.014187951 | 0.98581207 |
| ENST00000395603 | ENST00000374870 | ATRX | chrX | 77041468 | - | ARHGEF9 | chrX | 62875617 | - | 0.0033853 | 0.99661475 |
| ENST00000395603 | ENST00000437457 | ATRX | chrX | 77041468 | - | ARHGEF9 | chrX | 62875617 | - | 0.0033853 | 0.99661475 |
| ENST00000373344 | ENST00000253401 | ATRX | chrX | 77041467 | - | ARHGEF9 | chrX | 62875617 | - | 0.00406581 | 0.9959341 |
| ENST00000373344 | ENST00000374878 | ATRX | chrX | 77041467 | - | ARHGEF9 | chrX | 62875617 | - | 0.014187951 | 0.98581207 |
| ENST00000373344 | ENST00000374870 | ATRX | chrX | 77041467 | - | ARHGEF9 | chrX | 62875617 | - | 0.0033853 | 0.99661475 |
| ENST00000373344 | ENST00000437457 | ATRX | chrX | 77041467 | - | ARHGEF9 | chrX | 62875617 | - | 0.0033853 | 0.99661475 |
| ENST00000395603 | ENST00000253401 | ATRX | chrX | 77041467 | - | ARHGEF9 | chrX | 62875617 | - | 0.00406581 | 0.9959341 |
| ENST00000395603 | ENST00000374878 | ATRX | chrX | 77041467 | - | ARHGEF9 | chrX | 62875617 | - | 0.014187951 | 0.98581207 |
| ENST00000395603 | ENST00000374870 | ATRX | chrX | 77041467 | - | ARHGEF9 | chrX | 62875617 | - | 0.0033853 | 0.99661475 |
| ENST00000395603 | ENST00000437457 | ATRX | chrX | 77041467 | - | ARHGEF9 | chrX | 62875617 | - | 0.0033853 | 0.99661475 |
| 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 ATRX-ARHGEF9 |
| +/-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 |
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Potential FusionNeoAntigen Information of ATRX-ARHGEF9 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. |
| 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) |
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Potential FusionNeoAntigen Information of ATRX-ARHGEF9 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 ATRX-ARHGEF9 |
| 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. |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ATRX-ARHGEF9 |
| 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 |
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Vaccine Design for the FusionNeoAntigens of ATRX-ARHGEF9 |
| 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 |
| 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 ATRX-ARHGEF9 |
| 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 |
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Potential target of CAR-T therapy development for ATRX-ARHGEF9 |
| 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 ATRX-ARHGEF9 |
| 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 ATRX-ARHGEF9 |
| 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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