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Fusion gene ID: 30491 |
FusionGeneSummary for RARB_PRDM8 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RARB_PRDM8 | Fusion gene ID: 30491 | Hgene | Tgene | Gene symbol | RARB | PRDM8 | Gene ID | 5915 | 56978 |
| Gene name | retinoic acid receptor beta | PR/SET domain 8 | |
| Synonyms | HAP|MCOPS12|NR1B2|RARbeta1|RRB2 | EPM10|KMT8D|PFM5 | |
| Cytomap | 3p24.2 | 4q21.21 | |
| Type of gene | protein-coding | protein-coding | |
| Description | retinoic acid receptor betaHBV-activated proteinRAR-betaRAR-epsilonhepatitis B virus activated proteinnuclear receptor subfamily 1 group B member 2retinoic acid receptor, beta polypeptide | PR domain zinc finger protein 8PR domain 8PR-domain containing protein 8 | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | P10826 | Q9NQV8 | |
| Ensembl transtripts involved in fusion gene | ENST00000404969, ENST00000437042, ENST00000330688, ENST00000462272, ENST00000458646, | ENST00000504452, ENST00000508061, ENST00000339711, ENST00000415738, | |
| Fusion gene scores | * DoF score | 3 X 2 X 3=18 | 1 X 1 X 1=1 |
| # samples | 3 | 1 | |
| ** MAII score | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: RARB [Title/Abstract] AND PRDM8 [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 | SARC | TCGA-DX-A1KY-01A | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| * 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 | ENST00000404969 | ENST00000504452 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| 5CDS-3UTR | ENST00000404969 | ENST00000508061 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| 5CDS-5UTR | ENST00000404969 | ENST00000339711 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| 5CDS-intron | ENST00000404969 | ENST00000415738 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-intron | ENST00000437042 | ENST00000504452 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-3UTR | ENST00000437042 | ENST00000508061 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-5UTR | ENST00000437042 | ENST00000339711 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-intron | ENST00000437042 | ENST00000415738 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-intron | ENST00000330688 | ENST00000504452 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-3UTR | ENST00000330688 | ENST00000508061 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-5UTR | ENST00000330688 | ENST00000339711 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-intron | ENST00000330688 | ENST00000415738 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-intron | ENST00000462272 | ENST00000504452 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-3UTR | ENST00000462272 | ENST00000508061 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-5UTR | ENST00000462272 | ENST00000339711 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-intron | ENST00000462272 | ENST00000415738 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-intron | ENST00000458646 | ENST00000504452 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-3UTR | ENST00000458646 | ENST00000508061 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-5UTR | ENST00000458646 | ENST00000339711 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
| intron-intron | ENST00000458646 | ENST00000415738 | RARB | chr3 | 25216066 | + | PRDM8 | chr4 | 81112626 | + |
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FusionProtFeatures for RARB_PRDM8 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RARB | PRDM8 |
| Receptor for retinoic acid. Retinoic acid receptors bindas heterodimers to their target response elements in response totheir ligands, all-trans or 9-cis retinoic acid, and regulate geneexpression in various biological processes. The RXR/RARheterodimers bind to the retinoic acid response elements (RARE)composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In theabsence or presence of hormone ligand, acts mainly as an activatorof gene expression due to weak binding to corepressors. In concertwith RARG, required for skeletal growth, matrix homeostasis andgrowth plate function. {ECO:0000269|PubMed:12554770}. | Probable histone methyltransferase, preferentiallyacting on 'Lys-9' of histone H3 (By similarity). Involved in thecontrol of steroidogenesis through transcriptional repression ofsteroidogenesis marker genes such as CYP17A1 and LHCGR (Bysimilarity). Forms with BHLHE22 a transcriptional repressorcomplex controlling genes involved in neural development andneuronal differentiation (By similarity). In the retina, it isrequired for rod bipolar and type 2 OFF-cone bipolar cell survival(By similarity). {ECO:0000250|UniProtKB:Q8BZ97}. |
| 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 RARB_PRDM8 |
| 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 RARB_PRDM8 |
| 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 |
| RARB | NCOA1, CEBPA, CEBPB, GATA3, RXRG, HR, RXRA, NCOR2, RXRB, PNRC1, MAP6, HACE1, SMAD2, PRKD2, CCNH, ITGB1BP2, MEOX2, ARID1A, SMARCE1, SMARCD3, PSMC5, RARA | PRDM8 | NHLRC1, MCM2 |
| - 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 RARB_PRDM8 |
| 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 | RARB | P10826 | DB00210 | Adapalene | Retinoic acid receptor beta | small molecule | approved |
| Hgene | RARB | P10826 | DB00459 | Acitretin | Retinoic acid receptor beta | small molecule | approved |
| Hgene | RARB | P10826 | DB00523 | Alitretinoin | Retinoic acid receptor beta | small molecule | approved|investigational |
| Hgene | RARB | P10826 | DB00799 | Tazarotene | Retinoic acid receptor beta | small molecule | approved|investigational |
| Hgene | RARB | P10826 | DB00755 | Tretinoin | Retinoic acid receptor beta | small molecule | approved|investigational|nutraceutical |
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RelatedDiseases for RARB_PRDM8 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | RARB | C0001418 | Adenocarcinoma | 1 | CTD_human |
| Hgene | RARB | C0007137 | Squamous cell carcinoma | 1 | CTD_human |
| Hgene | RARB | C0007873 | Uterine Cervical Neoplasm | 1 | CTD_human |
| Hgene | RARB | C0014175 | Endometriosis | 1 | CTD_human |
| Hgene | RARB | C0018671 | Head and Neck Neoplasms | 1 | CTD_human |
| Hgene | RARB | C0024121 | Lung Neoplasms | 1 | CTD_human |
| Hgene | RARB | C0038356 | Stomach Neoplasms | 1 | CTD_human |
| Hgene | RARB | C0149940 | Sciatic Neuropathy | 1 | CTD_human |
| Hgene | RARB | C1458155 | Mammary Neoplasms | 1 | CTD_human |
| Hgene | RARB | C3809803 | MICROPHTHALMIA, SYNDROMIC 12 | 1 | UNIPROT |
| Tgene | PRDM8 | C4225258 | EPILEPSY, PROGRESSIVE MYOCLONIC, 10 | 1 | ORPHANET;UNIPROT |
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