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Fusion gene ID: 30470 |
FusionGeneSummary for RARA_MSL1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RARA_MSL1 | Fusion gene ID: 30470 | Hgene | Tgene | Gene symbol | RARA | MSL1 | Gene ID | 5914 | 339287 |
| Gene name | retinoic acid receptor alpha | male specific lethal 1 homolog | |
| Synonyms | NR1B1|RAR | MSL-1|hMSL1 | |
| Cytomap | 17q21.2 | 17q21.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | retinoic acid receptor alphaRAR-alphanuclear receptor subfamily 1 group B member 1nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long formretinoic acid nuclear receptor alpha variant 1retinoic acid nuclear receptor alpha variant 2 | male-specific lethal 1 homologMSL1-like 1male-specific lethal 1-like 1male-specific lethal-1 homolog 1 | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | P10276 | Q68DK7 | |
| Ensembl transtripts involved in fusion gene | ENST00000254066, ENST00000394089, ENST00000425707, ENST00000394086, ENST00000394081, ENST00000420042, | ENST00000398532, ENST00000577454, ENST00000578648, ENST00000579565, | |
| Fusion gene scores | * DoF score | 29 X 12 X 7=2436 | 7 X 4 X 4=112 |
| # samples | 42 | 7 | |
| ** MAII score | log2(42/2436*10)=-2.53605290024021 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(7/112*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: RARA [Title/Abstract] AND MSL1 [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 |
| Hgene | RARA | GO:0007165 | signal transduction | 2825025 |
| Hgene | RARA | GO:0030853 | negative regulation of granulocyte differentiation | 19917671 |
| Hgene | RARA | GO:0032689 | negative regulation of interferon-gamma production | 18416830 |
| Hgene | RARA | GO:0032720 | negative regulation of tumor necrosis factor production | 18416830 |
| Hgene | RARA | GO:0032736 | positive regulation of interleukin-13 production | 18416830 |
| Hgene | RARA | GO:0032753 | positive regulation of interleukin-4 production | 18416830 |
| Hgene | RARA | GO:0032754 | positive regulation of interleukin-5 production | 18416830 |
| Hgene | RARA | GO:0045630 | positive regulation of T-helper 2 cell differentiation | 18416830 |
| Hgene | RARA | GO:0045892 | negative regulation of transcription, DNA-templated | 20080953 |
| Hgene | RARA | GO:0045893 | positive regulation of transcription, DNA-templated | 18845237|19850744|20080953 |
| Hgene | RARA | GO:0045944 | positive regulation of transcription by RNA polymerase II | 19850744 |
| Hgene | RARA | GO:0071300 | cellular response to retinoic acid | 19917671 |
| Hgene | RARA | GO:0071391 | cellular response to estrogen stimulus | 20080953 |
| Tgene | MSL1 | GO:0043984 | histone H4-K16 acetylation | 20018852 |
| 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 | BRCA | TCGA-AR-A254-01A | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| * 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 |
| Frame-shift | ENST00000254066 | ENST00000398532 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| Frame-shift | ENST00000254066 | ENST00000577454 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| Frame-shift | ENST00000254066 | ENST00000578648 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| 5CDS-5UTR | ENST00000254066 | ENST00000579565 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| Frame-shift | ENST00000394089 | ENST00000398532 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| Frame-shift | ENST00000394089 | ENST00000577454 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| Frame-shift | ENST00000394089 | ENST00000578648 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| 5CDS-5UTR | ENST00000394089 | ENST00000579565 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| Frame-shift | ENST00000425707 | ENST00000398532 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| Frame-shift | ENST00000425707 | ENST00000577454 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| Frame-shift | ENST00000425707 | ENST00000578648 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| 5CDS-5UTR | ENST00000425707 | ENST00000579565 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-3CDS | ENST00000394086 | ENST00000398532 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-3CDS | ENST00000394086 | ENST00000577454 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-3CDS | ENST00000394086 | ENST00000578648 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-5UTR | ENST00000394086 | ENST00000579565 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-3CDS | ENST00000394081 | ENST00000398532 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-3CDS | ENST00000394081 | ENST00000577454 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-3CDS | ENST00000394081 | ENST00000578648 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-5UTR | ENST00000394081 | ENST00000579565 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-3CDS | ENST00000420042 | ENST00000398532 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-3CDS | ENST00000420042 | ENST00000577454 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-3CDS | ENST00000420042 | ENST00000578648 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
| intron-5UTR | ENST00000420042 | ENST00000579565 | RARA | chr17 | 38487648 | + | MSL1 | chr17 | 38282436 | + |
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FusionProtFeatures for RARA_MSL1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RARA | MSL1 |
| 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 of ligand, the RXR-RAR heterodimers associate with amultiprotein complex containing transcription corepressors thatinduce histone acetylation, chromatin condensation andtranscriptional suppression. On ligand binding, the corepressorsdissociate from the receptors and associate with the coactivatorsleading to transcriptional activation. RARA plays an essentialrole in the regulation of retinoic acid-induced germ celldevelopment during spermatogenesis. Has a role in the survival ofearly spermatocytes at the beginning prophase of meiosis. InSertoli cells, may promote the survival and development of earlymeiotic prophase spermatocytes. In concert with RARG, required forskeletal growth, matrix homeostasis and growth plate function (Bysimilarity). {ECO:0000250|UniProtKB:P11416,ECO:0000269|PubMed:16417524, ECO:0000269|PubMed:19850744,ECO:0000269|PubMed:20215566}. | Component of histone acetyltransferase complexresponsible for the majority of histone H4 acetylation at 'Lys-16'(H4K16ac) which is implicated in the formation of higher-orderchromatin structure. Greatly enhances MSL2 E3 ubiquitin ligaseactivity, promoting monoubiquitination of histone H2B at 'Lys-34'(H2BK34Ub). This modification in turn stimulates histone H3methylation at 'Lys-4' (H3K4me) and 'Lys-79' (H3K79me) and leadsto gene activation, including that of HOXA9 and MEIS1. In the MSLcomplex, acts as a scaffold to tether MSL3 and KAT8 together forenzymatic activity regulation. {ECO:0000269|PubMed:16227571,ECO:0000269|PubMed:21726816, ECO:0000269|PubMed:22547026}. |
| 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 RARA_MSL1 |
| 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 RARA_MSL1 |
| 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 |
| RARA | NRBF2, ZBTB16, MECR, RXRG, RXRB, NCOA6, GADD45G, GADD45A, NRIP1, KAT2B, HDAC3, HDAC4, TDG, PML, TRIP4, KDM5A, RXRA, POU2F1, NCOR2, NR0B2, BAG1, TADA3, NCOR1, NKX2-1, TRIM24, IRX4, SP1, NPAS2, CLOCK, ARNTL, NR2E3, CCND3, NCOA2, SRC, AJUBA, LIMD1, WTIP, SKI, HR, PIN1, SUV39H1, PSMC5, EP300, PARP1, MED6, TOP2B, SAP130, HNRNPU, RFC4, NPM1, MRTO4, SNRNP40, MED1, NCOA1, HMGA1, RUVBL1, RUNX1, SIAH1, RARA, HDAC2, NCOA3, CREBBP, LRIF1, KLF5, SMARCD3, ARID1A, SPI1, PRDX6, NR1H2, ITGB1BP2, MED25, MAPK6, FOXO1, MAPK1, TRIM32, PHF8, TNIP1, HACE1, SQSTM1, UBQLN1, ARID5A, UBE3A, PRAM1, FAS, PRAME, TBL1XR1, SUZ12, EZH2, USP7, TMEM54, MMS19, AKT1, FN1, WWOX, E2F1, MBD3, MTA2, CBX5, CEBPA, HDAC1, NSD1, TEKT4, SNW1, SIRT1, ACTN4, SRF, MDM2, ZNF131, RARG, RARB, TRIM25 | MSL1 | KAT8, MSL2, MSL3, CRKL, FCHSD2, MMS19, SOX2, HIST2H2BE, UBE2D3, RNF40, RNF20, PAF1, CDK9, FAM96B, MOV10, NXF1, NUPR1, TP53BP1, MORF4L1, RAN, KPNB1, SNW1, MRGBP, PPM1G, HORMAD1, SMARCC1, MSL3P1, PBK, AHCYL2, HSPB1, HIST1H2BG, HIST1H3A, SLC33A1, IBTK, CNTROB, GMNN |
| - 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 RARA_MSL1 |
| 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 | RARA | P10276 | DB00210 | Adapalene | Retinoic acid receptor alpha | small molecule | approved |
| Hgene | RARA | P10276 | DB00459 | Acitretin | Retinoic acid receptor alpha | small molecule | approved |
| Hgene | RARA | P10276 | DB00982 | Isotretinoin | Retinoic acid receptor alpha | small molecule | approved |
| Hgene | RARA | P10276 | DB00523 | Alitretinoin | Retinoic acid receptor alpha | small molecule | approved|investigational |
| Hgene | RARA | P10276 | DB00799 | Tazarotene | Retinoic acid receptor alpha | small molecule | approved|investigational |
| Hgene | RARA | P10276 | DB00755 | Tretinoin | Retinoic acid receptor alpha | small molecule | approved|investigational|nutraceutical |
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RelatedDiseases for RARA_MSL1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | RARA | C0023487 | Acute Promyelocytic Leukemia | 22 | CTD_human;HPO;ORPHANET |
| Hgene | RARA | C0036341 | Schizophrenia | 3 | PSYGENET |
| Hgene | RARA | C0005586 | Bipolar Disorder | 1 | PSYGENET |
| Hgene | RARA | C0010701 | Phyllodes Tumor | 1 | CTD_human |
| Hgene | RARA | C0085183 | Neoplasms, Second Primary | 1 | CTD_human |
| Hgene | RARA | C0149940 | Sciatic Neuropathy | 1 | CTD_human |
| Hgene | RARA | C0206650 | Fibroadenoma | 1 | CTD_human |
| Hgene | RARA | C0525045 | Mood Disorders | 1 | PSYGENET |
| Hgene | RARA | C1458155 | Mammary Neoplasms | 1 | CTD_human |
| Hgene | RARA | C2239176 | Liver carcinoma | 1 | CTD_human |
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