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Fusion gene ID: 20123 |
FusionGeneSummary for LRP1_ATF1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LRP1_ATF1 | Fusion gene ID: 20123 | Hgene | Tgene | Gene symbol | LRP1 | ATF1 | Gene ID | 10438 | 2668 |
| Gene name | C1D nuclear receptor corepressor | glial cell derived neurotrophic factor | |
| Synonyms | LRP1|Rrp47|SUN-CoR|SUNCOR|hC1D | ATF|ATF1|ATF2|HFB1-GDNF|HSCR3 | |
| Cytomap | 2p14 | 5p13.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nuclear nucleic acid-binding protein C1DC1D DNA-binding proteinC1D nuclear receptor co-repressornuclear DNA-binding proteinsmall unique nuclear receptor co-repressorsmall unique nuclear receptor corepressor | glial cell line-derived neurotrophic factorastrocyte-derived trophic factor | |
| Modification date | 20180519 | 20180519 | |
| UniProtAcc | Q07954 | P18846 | |
| Ensembl transtripts involved in fusion gene | ENST00000553277, ENST00000243077, ENST00000338962, ENST00000554174, ENST00000553446, | ENST00000262053, ENST00000539132, | |
| Fusion gene scores | * DoF score | 16 X 14 X 7=1568 | 5 X 7 X 3=105 |
| # samples | 17 | 10 | |
| ** MAII score | log2(17/1568*10)=-3.20531890797751 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(10/105*10)=-0.070389327891398 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: LRP1 [Title/Abstract] AND ATF1 [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 | ATF1 | GO:0001755 | neural crest cell migration | 15242795 |
| Tgene | ATF1 | GO:0008284 | positive regulation of cell proliferation | 22897442 |
| Tgene | ATF1 | GO:0031175 | neuron projection development | 15242795 |
| Tgene | ATF1 | GO:0032770 | positive regulation of monooxygenase activity | 12358785 |
| Tgene | ATF1 | GO:0043524 | negative regulation of neuron apoptotic process | 8493557 |
| Tgene | ATF1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 12358785 |
| Tgene | ATF1 | GO:0048255 | mRNA stabilization | 12358785 |
| Tgene | ATF1 | GO:0051584 | regulation of dopamine uptake involved in synaptic transmission | 8493557 |
| Tgene | ATF1 | GO:0072107 | positive regulation of ureteric bud formation | 8657307 |
| Tgene | ATF1 | GO:0090190 | positive regulation of branching involved in ureteric bud morphogenesis | 8657307|17229286 |
| Tgene | ATF1 | GO:2001240 | negative regulation of extrinsic apoptotic signaling pathway in absence of ligand | 10921886 |
| 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-AB2G-01A | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| * 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 | ENST00000553277 | ENST00000262053 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| 5CDS-intron | ENST00000553277 | ENST00000539132 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| Frame-shift | ENST00000243077 | ENST00000262053 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| 5CDS-intron | ENST00000243077 | ENST00000539132 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| Frame-shift | ENST00000338962 | ENST00000262053 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| 5CDS-intron | ENST00000338962 | ENST00000539132 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| Frame-shift | ENST00000554174 | ENST00000262053 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| 5CDS-intron | ENST00000554174 | ENST00000539132 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| intron-3CDS | ENST00000553446 | ENST00000262053 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
| intron-intron | ENST00000553446 | ENST00000539132 | LRP1 | chr12 | 57539273 | + | ATF1 | chr12 | 51189692 | + |
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FusionProtFeatures for LRP1_ATF1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LRP1 | ATF1 |
| Endocytic receptor involved in endocytosis and inphagocytosis of apoptotic cells. Required for early embryonicdevelopment. Involved in cellular lipid homeostasis. Involved inthe plasma clearance of chylomicron remnants and activated LRPAP1(alpha 2-macroglobulin), as well as the local metabolism ofcomplexes between plasminogen activators and their endogenousinhibitors. May modulate cellular events, such as APP metabolism,kinase-dependent intracellular signaling, neuronal calciumsignaling as well as neurotransmission (PubMed:11907044,PubMed:12888553, PubMed:12713657). Acts as an alpha-2-macroglobulin receptor (PubMed:26142438).{ECO:0000269|PubMed:11907044, ECO:0000269|PubMed:12713657,ECO:0000269|PubMed:12888553, ECO:0000269|PubMed:26142438}. (Microbial infection) Functions as a receptor forPseudomonas aeruginosa exotoxin A. {ECO:0000269|PubMed:1618748}. | This protein binds the cAMP response element (CRE)(consensus: 5'-GTGACGT[AC][AG]-3'), a sequence present in manyviral and cellular promoters. Binds to the Tax-responsive element(TRE) of HTLV-I. Mediates PKA-induced stimulation of CRE-reportergenes. Represses the expression of FTH1 and other antioxidantdetoxification genes. Triggers cell proliferation andtransformation. {ECO:0000269|PubMed:18794154,ECO:0000269|PubMed:20980392}. |
| 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 LRP1_ATF1 |
| 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 LRP1_ATF1 |
| 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 |
| LRP1 | SERPINE1, CANX, CALR, PDIA2, MMP14, KAT5, CALCR, SHC1, THBS1, GIPC1, MAPK8IP1, DLG4, MAPK8IP2, SYNJ2BP, NOS1AP, SCN3A, APBA2, DAB1, ITGB1BP1, ANAPC10, A2M, PDGFB, SRC, DAB2, MDK, F8, GULP1, PLAUR, PLAT, F9, LRPAP1, LPL, LIPC, SNX17, APBB1, USP3, CACNA1A, APOE, RIC8B, CC2D1A, SNRNP70, ANKS1B, PID1, HNRNPDL, MAPRE1, FBXO6, CUBN, CHFR, SKIL, RANBP9, APP, COPS5, EGFR, ZFP41, DIAPH1, FOXB1, KCTD18, INTS6, TNKS2, TNKS, FOXF2, BCKDHB, TUBB8, SAMD1, TUBA4A, TUBB3, LOXL2, MTG2, SLC25A6, SLC25A30, GATB, SMOC1, C17orf80, GSG2, NME4, HARS2, TUBA1A, TUBB4A, SLC25A23, LCOR, CCRN4L, FAM115A, SLC25A25, MTO1, C1orf85, PC, PTGES2, SLC26A6, GFPT2, GFPT1, HSPA5, RPL23, TUBB2A, NPC2, MTPAP, TUBB4B, RPUSD3, GNB2, NPRL3, FAM132B, ERAL1, GCNT1, TUBB2B, PTCD2, SENP1, MAP2K7, RTEL1, LGALS9 | ATF1 | BRCA1, CSNK2A1, CSNK2B, CAMK2A, CREBBP, SPI1, HNF1B, GABPA, FOSL2, SRA1, CACNG2, TRPV5, TUFT1, ATF2, JUNB, CREB1, NFATC1, DNMT3L, MAPKAPK2, MAPKAPK3, RPS6KA5, CTAGE5, ARHGAP22, CCDC97, IDO2, CREBRF, CSGALNACT2, ARIH1, TFAP4, HSPA8, NFIL3, SSH1 |
| - 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 LRP1_ATF1 |
| 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 | LRP1 | Q07954 | DB00031 | Tenecteplase | Prolow-density lipoprotein receptor-related protein 1 | biotech | approved |
| Hgene | LRP1 | Q07954 | DB00025 | Antihemophilic factor, human recombinant | Prolow-density lipoprotein receptor-related protein 1 | biotech | approved|investigational |
| Hgene | LRP1 | Q07954 | DB00100 | Coagulation Factor IX (Recombinant) | Prolow-density lipoprotein receptor-related protein 1 | biotech | approved|investigational |
| Tgene | ATF1 | P18846 | DB00852 | Pseudoephedrine | Cyclic AMP-dependent transcription factor ATF-1 | small molecule | approved |
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RelatedDiseases for LRP1_ATF1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | LRP1 | C0036341 | Schizophrenia | 1 | CTD_human |
| Hgene | LRP1 | C0041696 | Unipolar Depression | 1 | PSYGENET |
| Hgene | LRP1 | C0149931 | Migraine Disorders | 1 | CTD_human |
| Hgene | LRP1 | C0338480 | Common Migraine | 1 | CTD_human |
| Hgene | LRP1 | C1269683 | Major Depressive Disorder | 1 | PSYGENET |
| Tgene | ATF1 | C0032460 | Polycystic Ovary Syndrome | 1 | CTD_human |
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