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Fusion gene ID: 6962 |
FusionGeneSummary for CHD1_RGMB |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CHD1_RGMB | Fusion gene ID: 6962 | Hgene | Tgene | Gene symbol | CHD1 | RGMB | Gene ID | 1105 | 285704 |
| Gene name | chromodomain helicase DNA binding protein 1 | repulsive guidance molecule BMP co-receptor b | |
| Synonyms | PILBOS | DRAGON | |
| Cytomap | 5q15-q21.1 | 5q15 | |
| Type of gene | protein-coding | protein-coding | |
| Description | chromodomain-helicase-DNA-binding protein 1ATP-dependent helicase CHD1CHD-1 | RGM domain family member BDRG11-responsive axonal guidance and outgrowth of neuriteRGM domain family, member Brepulsive guidance molecule Brepulsive guidance molecule family member b | |
| Modification date | 20180522 | 20180523 | |
| UniProtAcc | O14646 | Q6NW40 | |
| Ensembl transtripts involved in fusion gene | ENST00000284049, ENST00000511067, | ENST00000504776, ENST00000308234, ENST00000513185, | |
| Fusion gene scores | * DoF score | 6 X 7 X 5=210 | 1 X 1 X 1=1 |
| # samples | 7 | 2 | |
| ** MAII score | log2(7/210*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(2/1*10)=4.32192809488736 | |
| Context | PubMed: CHD1 [Title/Abstract] AND RGMB [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * 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 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | RV | COAD | TCGA-DM-A288-01A | CHD1 | chr5 | 98215256 | - | RGMB | chr5 | 98128789 | + |
| TCGA | LD | COAD | TCGA-A6-6648-01A | CHD1 | chr5 | 98204199 | - | RGMB | chr5 | 98128789 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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 | ENST00000284049 | ENST00000504776 | CHD1 | chr5 | 98215256 | - | RGMB | chr5 | 98128789 | + |
| 5CDS-intron | ENST00000284049 | ENST00000308234 | CHD1 | chr5 | 98215256 | - | RGMB | chr5 | 98128789 | + |
| 5CDS-intron | ENST00000284049 | ENST00000513185 | CHD1 | chr5 | 98215256 | - | RGMB | chr5 | 98128789 | + |
| intron-intron | ENST00000511067 | ENST00000504776 | CHD1 | chr5 | 98215256 | - | RGMB | chr5 | 98128789 | + |
| intron-intron | ENST00000511067 | ENST00000308234 | CHD1 | chr5 | 98215256 | - | RGMB | chr5 | 98128789 | + |
| intron-intron | ENST00000511067 | ENST00000513185 | CHD1 | chr5 | 98215256 | - | RGMB | chr5 | 98128789 | + |
| 5CDS-intron | ENST00000284049 | ENST00000504776 | CHD1 | chr5 | 98204199 | - | RGMB | chr5 | 98128789 | + |
| 5CDS-intron | ENST00000284049 | ENST00000308234 | CHD1 | chr5 | 98204199 | - | RGMB | chr5 | 98128789 | + |
| 5CDS-intron | ENST00000284049 | ENST00000513185 | CHD1 | chr5 | 98204199 | - | RGMB | chr5 | 98128789 | + |
| 5UTR-intron | ENST00000511067 | ENST00000504776 | CHD1 | chr5 | 98204199 | - | RGMB | chr5 | 98128789 | + |
| 5UTR-intron | ENST00000511067 | ENST00000308234 | CHD1 | chr5 | 98204199 | - | RGMB | chr5 | 98128789 | + |
| 5UTR-intron | ENST00000511067 | ENST00000513185 | CHD1 | chr5 | 98204199 | - | RGMB | chr5 | 98128789 | + |
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FusionProtFeatures for CHD1_RGMB |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CHD1 | RGMB |
| ATP-dependent chromatin-remodeling factor whichfunctions as substrate recognition component of the transcriptionregulatory histone acetylation (HAT) complex SAGA. Regulatespolymerase II transcription. Also required for efficienttranscription by RNA polymerase I, and more specifically thepolymerase I transcription termination step. Regulates negativelyDNA replication. Not only involved in transcription-relatedchromatin-remodeling, but also required to maintain a specificchromatin configuration across the genome. Is also associated withhistone deacetylase (HDAC) activity (By similarity). Required forthe bridging of SNF2, the FACT complex, the PAF complex as well asthe U2 snRNP complex to H3K4me3. Functions to modulate theefficiency of pre-mRNA splicing in part through physical bridgingof spliceosomal components to H3K4me3 (PubMed:18042460,PubMed:28866611). Required for maintaining open chromatin andpluripotency in embryonic stem cells (By similarity).{ECO:0000250|UniProtKB:P40201, ECO:0000269|PubMed:18042460,ECO:0000269|PubMed:28866611}. | Member of the repulsive guidance molecule (RGM) familythat contributes to the patterning of the developing nervoussystem (By similarity). Acts as a bone morphogenetic protein (BMP)coreceptor that potentiates BMP signaling (By similarity).Promotes neuronal adhesion (By similarity). May inhibit neuriteoutgrowth. {ECO:0000250, ECO:0000269|PubMed:19324014}. |
| 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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FusionGeneSequence for CHD1_RGMB |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for CHD1_RGMB |
| 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 |
| CHD1 | ARRB1, HDAC1, BCLAF1, SRSF3, NCOR1, SAFB, SSRP1, CEBPA, HMGA1, HIST1H3A, MLLT1, PAF1, ELAVL1, SIRT7, ISG15, SPP1, FBXW11, HIST3H3, CUL7, OBSL1, NTRK1, CTR9, RTF1, HNRNPU, NPM1, RPL10, TMPO, BTRC, INO80B, RNF157 | RGMB |
| - 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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RelatedDrugs for CHD1_RGMB |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Hgene | CHD1 | O14646 | DB00445 | Epirubicin | Chromodomain-helicase-DNA-binding protein 1 | small molecule | approved |
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RelatedDiseases for CHD1_RGMB |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | RGMB | C0003873 | Rheumatoid Arthritis | 1 | CTD_human |
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