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Fusion gene ID: 30264 |
FusionGeneSummary for RALGAPA1_FOXA1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RALGAPA1_FOXA1 | Fusion gene ID: 30264 | Hgene | Tgene | Gene symbol | RALGAPA1 | FOXA1 | Gene ID | 253959 | 3169 |
| Gene name | Ral GTPase activating protein catalytic alpha subunit 1 | forkhead box A1 | |
| Synonyms | GARNL1|GRIPE|RalGAPalpha1|TULIP1|p240 | HNF3A|TCF3A | |
| Cytomap | 14q13.2 | 14q21.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | ral GTPase-activating protein subunit alpha-1GAP-related interacting protein to E12GTPase activating Rap/RanGAP domain-like 1Ral GTPase activating protein, alpha subunit 1 (catalytic)tuberin-like protein 1 | hepatocyte nuclear factor 3-alphaHNF-3-alphaHNF-3ATCF-3Aforkhead box protein A1transcription factor 3A | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q6GYQ0 | P55317 | |
| Ensembl transtripts involved in fusion gene | ENST00000389698, ENST00000307138, ENST00000258840, ENST00000382366, ENST00000554704, | ENST00000250448, ENST00000540786, ENST00000545425, | |
| Fusion gene scores | * DoF score | 3 X 3 X 2=18 | 5 X 4 X 3=60 |
| # samples | 4 | 5 | |
| ** MAII score | log2(4/18*10)=1.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(5/60*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: RALGAPA1 [Title/Abstract] AND FOXA1 [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 |
| Tgene | FOXA1 | GO:0032355 | response to estradiol | 16087863 |
| Tgene | FOXA1 | GO:0043065 | positive regulation of apoptotic process | 19127412 |
| Tgene | FOXA1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 16331276|19127412|20160041 |
| 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 | LD | PRAD | TCGA-V1-A8MF-01A | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| * 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 | ENST00000389698 | ENST00000250448 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| 5CDS-5UTR | ENST00000389698 | ENST00000540786 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| 5CDS-5UTR | ENST00000389698 | ENST00000545425 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| Frame-shift | ENST00000307138 | ENST00000250448 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| 5CDS-5UTR | ENST00000307138 | ENST00000540786 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| 5CDS-5UTR | ENST00000307138 | ENST00000545425 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| Frame-shift | ENST00000258840 | ENST00000250448 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| 5CDS-5UTR | ENST00000258840 | ENST00000540786 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| 5CDS-5UTR | ENST00000258840 | ENST00000545425 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| Frame-shift | ENST00000382366 | ENST00000250448 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| 5CDS-5UTR | ENST00000382366 | ENST00000540786 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| 5CDS-5UTR | ENST00000382366 | ENST00000545425 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| intron-3CDS | ENST00000554704 | ENST00000250448 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| intron-5UTR | ENST00000554704 | ENST00000540786 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
| intron-5UTR | ENST00000554704 | ENST00000545425 | RALGAPA1 | chr14 | 36277936 | - | FOXA1 | chr14 | 38061916 | - |
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FusionProtFeatures for RALGAPA1_FOXA1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RALGAPA1 | FOXA1 |
| Transcription factor that is involved in embryonicdevelopment, establishment of tissue-specific gene expression andregulation of gene expression in differentiated tissues. Isthought to act as a 'pioneer' factor opening the compactedchromatin for other proteins through interactions with nucleosomalcore histones and thereby replacing linker histones at targetenhancer and/or promoter sites. Binds DNA with the consensussequence 5'-[AC]A[AT]T[AG]TT[GT][AG][CT]T[CT]-3' (By similarity).Proposed to play a role in translating the epigenetic signaturesinto cell type-specific enhancer-driven transcriptional programs.Its differential recruitment to chromatin is dependent ondistribution of histone H3 methylated at 'Lys-5' (H3K4me2) inestrogen-regulated genes. Involved in the development of multipleendoderm-derived organ systems such as liver, pancreas, lung andprostate; FOXA1 and FOXA2 seem to have at least in part redundantroles (By similarity). Modulates the transcriptional activity ofnuclear hormone receptors. Is involved in ESR1-mediatedtranscription; required for ESR1 binding to the NKX2-1 promoter inbreast cancer cells; binds to the RPRM promoter and is requiredfor the estrogen-induced repression of RPRM. Involved inregulation of apoptosis by inhibiting the expression of BCL2.Involved in cell cycle regulation by activating expression ofCDKN1B, alone or in conjunction with BRCA1. Originally describedas a transcription activator for a number of liver genes such asAFP, albumin, tyrosine aminotransferase, PEPCK, etc. Interactswith the cis-acting regulatory regions of these genes. Involved inglucose homeostasis. {ECO:0000250, ECO:0000269|PubMed:16087863,ECO:0000269|PubMed:16331276, ECO:0000269|PubMed:18358809,ECO:0000269|PubMed:19127412, ECO:0000269|PubMed:19917725}. |
| 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 RALGAPA1_FOXA1 |
| 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 RALGAPA1_FOXA1 |
| 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 |
| RALGAPA1 | TERF1, TERF2, SLMAP, GFOD1, AP2M1, CEP63, DUSP23, PTPRH, NKIRAS2 | FOXA1 | AR, ONECUT1, HDAC7, TLE1, ELAVL1, AHR, SEZ6L2, EED, PIAS1, SATB1, SATB2, NAA40, RECQL, CREB1, HOXB9, NACC1, NFIX, DLX1, DLX5, HOXD13, LDB1, NFIC, NKX2-5, PBX1, UBA7, UBP1, VARS, H2AFY, RCC1, MGME1, RPA2, ALX4, FOXA3, MSH3, PLOD2, HMGA1, KBTBD7, LDB2, TFAP4, PLOD1, KMT2C, NUP153, KRT13, DDX24, UTP20, UBTF, NOL6, RBM19, DDX47, ADAR, UTP18, WDR75, HNRNPH2, UTP14A, DDX56, DDX52, MPHOSPH10, NOL10, TBL3, DDX31, SKIV2L2, GLTSCR2, ESF1, RACGAP1, SSRP1, DDX50, H2AFX, NOP16, GPATCH4, LOC102724159, NSUN2, NOL8, RPL5, ALYREF, KIF23, XRN2, URB2, NOL11, DDX51, EXOSC10, KDM6A, DNTTIP2, POP1, NIP7, RBM34, TARDBP, RRP15, KRI1, REXO4, NOM1, NKRF, SDAD1, IGLC7, NOC4L, PAK1IP1, WDR12, AATF, DEK, CCDC137, RRP9, RCOR3, ODF2, EIF5A, PWP1, LUC7L2, PARN, C9orf114, DSG2, LOC113230, TOP2A, PHF2, CCDC59, YWHAB, DIMT1, UTP11L, DHX37, RRP36, WDR46, PPP1CC, LUC7L, HIST1H3A, DNAJC9, RPLP0, ISG20L2, DDX49, C11orf98, NR2F2, TMPO, RNH1, GAR1, NOL7, RPL13A, NGDN, USP36, GATA3, NSUN5, C14orf169, C3orf17, RALY, IGHG2, MCM7, PNO1, SRSF6, CIRBP, MCM3, PAXIP1, FUBP3, RPL28, WDR5, GRHL2, RPS27, UHRF1, RSL24D1, RPS17, ESR1, DNMT1, EXOSC2, ABT1, RPL10, NME1, ARL6IP4, SF1, GTF2I, DIEXF, CD3EAP, TSR1, RPS19BP1, DHX33, RAB10, PRSS1, HDGF, NOP10, TRIM33, SRSF9, PRDX2, HNRNPUL2, TUBGCP6, YLPM1, EIF1AY, SNRPGP15, DAZAP1, IGKV3-20, C12orf43, MAGOH, ARF3, CPSF7, ASH2L, DSTN, CMSS1, NOSIP, EZR, RBM4, ALKBH5, SEC14L5, SUMO1, L1RE1, PARP2, RPF1, POLR1E, TPT1, C6orf211, TRPS1, RPS5, EXOSC6, EXOSC9, DPY30, SRSF12, EXOSC4, RPL32, SAFB, FIP1L1, CSNK1A1, TXNDC17, GPI, TRA2A, NCOA3, ACTR3C, PINX1, FAM207A, RPL30, DDX42, ARF6, PRPF3, FCF1, SNRPA1, MCTS1, LAS1L, PHF6, DDX55, WBSCR22, POLR1C, STAU1, NCOA6, XPO1, SF3B4, HBD, TSPYL1, EXOSC3, CDK1, CORO7, TLE3, VPS35, AGR2, CCT6A, VRK1, HBA1, CBX5, PSIP1, CHD4, RBMX2, APRT, EXOSC1, MROH8, PRPF6, DNAJB1, LGALS3, CCDC67, ZFP42, RBM25, CHD3, ARPC2, XPO5, DNAH7, TEX10, DNAJA1, GMPS, SEPT11, OSTF1, FAM50A, CSE1L, RRP7A, MARS, GSTM3, PRMT6, PSMD2, ZYX, VWA8, RBM17, ZFP91, RBBP4, KPNA4, AGBL1, B4GAT1, KAT7, HNRNPUL1, MPHOSPH6, COPG1 |
| - 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 RALGAPA1_FOXA1 |
| 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 |
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RelatedDiseases for RALGAPA1_FOXA1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | FOXA1 | C0033578 | Prostatic Neoplasms | 2 | CTD_human |
| Tgene | FOXA1 | C0015695 | Fatty Liver | 1 | CTD_human |
| Tgene | FOXA1 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
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