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Fusion gene ID: 20439 |
FusionGeneSummary for LYAR_COL6A3 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LYAR_COL6A3 | Fusion gene ID: 20439 | Hgene | Tgene | Gene symbol | LYAR | COL6A3 | Gene ID | 55646 | 1293 |
| Gene name | Ly1 antibody reactive | collagen type VI alpha 3 chain | |
| Synonyms | ZC2HC2|ZLYAR | BTHLM1|DYT27|UCMD1 | |
| Cytomap | 4p16.3 | 2q37.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cell growth-regulating nucleolar proteinLy1 antibody reactive homolog | collagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3 | |
| Modification date | 20180519 | 20180523 | |
| UniProtAcc | Q9NX58 | P12111 | |
| Ensembl transtripts involved in fusion gene | ENST00000343470, ENST00000452476, | ENST00000347401, ENST00000353578, ENST00000295550, ENST00000472056, ENST00000409809, ENST00000346358, ENST00000392004, ENST00000392003, ENST00000473258, | |
| Fusion gene scores | * DoF score | 4 X 4 X 2=32 | 8 X 8 X 2=128 |
| # samples | 4 | 8 | |
| ** MAII score | log2(4/32*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(8/128*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: LYAR [Title/Abstract] AND COL6A3 [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 |
| ChiTaRS3.1 | BU616556 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| * 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 |
| intron-3CDS | ENST00000343470 | ENST00000347401 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000343470 | ENST00000353578 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000343470 | ENST00000295550 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000343470 | ENST00000472056 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000343470 | ENST00000409809 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000343470 | ENST00000346358 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-intron | ENST00000343470 | ENST00000392004 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-intron | ENST00000343470 | ENST00000392003 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-intron | ENST00000343470 | ENST00000473258 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000452476 | ENST00000347401 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000452476 | ENST00000353578 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000452476 | ENST00000295550 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000452476 | ENST00000472056 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000452476 | ENST00000409809 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-3CDS | ENST00000452476 | ENST00000346358 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-intron | ENST00000452476 | ENST00000392004 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-intron | ENST00000452476 | ENST00000392003 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
| intron-intron | ENST00000452476 | ENST00000473258 | LYAR | chr4 | 4283622 | + | COL6A3 | chr2 | 238275370 | + |
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FusionProtFeatures for LYAR_COL6A3 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LYAR | COL6A3 |
| Plays a role in the maintenance of the appropriateprocessing of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and theirsubsequent processing to produce 18S and 28S rRNAs(PubMed:24495227). Also acts at the level of transcriptionregulation. Along with PRMT5, binds the gamma-globin (HBG1/HBG2)promoter and represses its expression (PubMed:25092918). Inneuroblastoma cells, may also repress the expression of oxidativestress genes, including CHAC1, HMOX1, SLC7A11, ULBP1 and SNORD41that encodes a small nucleolar RNA (PubMed:28686580).Preferentially binds to a DNA motif containing 5'-GGTTAT-3'(PubMed:25092918). Stimulates phagocytosis of photoreceptor outersegments by retinal pigment epithelial cells (By similarity).Prevents nucleolin/NCL self-cleavage, maintaining a normal steady-state level of NCL protein in undifferentiated embryonic stemcells (ESCs), which in turn is essential for ESC self-renewal (Bysimilarity). {ECO:0000250|UniProtKB:Q08288,ECO:0000269|PubMed:24495227, ECO:0000269|PubMed:25092918,ECO:0000269|PubMed:28686580}. |
| 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 LYAR_COL6A3 |
| 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 LYAR_COL6A3 |
| 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 |
| - 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 LYAR_COL6A3 |
| 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 LYAR_COL6A3 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | COL6A3 | C1834674 | Bethlem myopathy | 4 | CTD_human;ORPHANET;UNIPROT |
| Tgene | COL6A3 | C0000786 | Spontaneous abortion | 1 | CTD_human |
| Tgene | COL6A3 | C0410179 | Scleroatonic muscular dystrophy | 1 | CTD_human;ORPHANET;UNIPROT |
| Tgene | COL6A3 | C4225336 | DYSTONIA 27 | 1 | ORPHANET;UNIPROT |
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