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Fusion gene ID: 1578 |
FusionGeneSummary for ALX4_LMX1A |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: ALX4_LMX1A | Fusion gene ID: 1578 | Hgene | Tgene | Gene symbol | ALX4 | LMX1A | Gene ID | 60529 | 4009 |
| Gene name | ALX homeobox 4 | LIM homeobox transcription factor 1 alpha | |
| Synonyms | CRS5|FND2 | LMX1|LMX1.1 | |
| Cytomap | 11p11.2 | 1q23.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | homeobox protein aristaless-like 4aristaless-like homeobox 4homeodomain transcription factor ALX4 | LIM homeobox transcription factor 1-alphaLIM/homeobox protein 1.1 | |
| Modification date | 20180519 | 20180519 | |
| UniProtAcc | Q9H161 | Q8TE12 | |
| Ensembl transtripts involved in fusion gene | ENST00000329255, | ENST00000342310, ENST00000294816, ENST00000367893, ENST00000489443, | |
| Fusion gene scores | * DoF score | 2 X 2 X 2=8 | 3 X 2 X 2=12 |
| # samples | 2 | 3 | |
| ** MAII score | log2(2/8*10)=1.32192809488736 | log2(3/12*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: ALX4 [Title/Abstract] AND LMX1A [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-HB-A3YV-01A | ALX4 | chr11 | 44331147 | - | LMX1A | chr1 | 165183050 | - |
| * 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 | ENST00000329255 | ENST00000342310 | ALX4 | chr11 | 44331147 | - | LMX1A | chr1 | 165183050 | - |
| Frame-shift | ENST00000329255 | ENST00000294816 | ALX4 | chr11 | 44331147 | - | LMX1A | chr1 | 165183050 | - |
| Frame-shift | ENST00000329255 | ENST00000367893 | ALX4 | chr11 | 44331147 | - | LMX1A | chr1 | 165183050 | - |
| 5CDS-intron | ENST00000329255 | ENST00000489443 | ALX4 | chr11 | 44331147 | - | LMX1A | chr1 | 165183050 | - |
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FusionProtFeatures for ALX4_LMX1A |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| ALX4 | LMX1A |
| Transcription factor involved in skull and limbdevelopment. Plays an essential role in craniofacial development,skin and hair follicle development. {ECO:0000269|PubMed:19692347}. | Acts as a transcriptional activator by binding to anA/T-rich sequence, the FLAT element, in the insulin gene promoter.Required for development of the roof plate and, in turn, forspecification of dorsal cell fates in the CNS and developingvertebrae (By similarity). {ECO:0000250}. |
| 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 ALX4_LMX1A |
| 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 ALX4_LMX1A |
| 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 |
| ALX4 | CEBPE, EMX1, GATA4, FOXA3, HOXA3, HOXB6, HOXD3, SOX2, HOXB13, ALX4, RBPJ, FOXA1, FOXE1 | LMX1A | TCF3, LMX1A, ISL1, LHX3, GRB2 |
| - 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 ALX4_LMX1A |
| 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 ALX4_LMX1A |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | ALX4 | C1865044 | PARIETAL FORAMINA 2 | 2 | CTD_human;UNIPROT |
| Hgene | ALX4 | C0024121 | Lung Neoplasms | 1 | CTD_human |
| Hgene | ALX4 | C0152427 | Polydactyly | 1 | CTD_human |
| Hgene | ALX4 | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
| Hgene | ALX4 | C3809819 | CRANIOSYNOSTOSIS 5, SUSCEPTIBILITY TO | 1 | UNIPROT |
| Tgene | LMX1A | C0036341 | Schizophrenia | 1 | PSYGENET |
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