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Fusion gene ID: 32734 |
FusionGeneSummary for SCAF11_MALAT1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SCAF11_MALAT1 | Fusion gene ID: 32734 | Hgene | Tgene | Gene symbol | SCAF11 | MALAT1 | Gene ID | 9169 | 378938 |
| Gene name | SR-related CTD associated factor 11 | metastasis associated lung adenocarcinoma transcript 1 | |
| Synonyms | CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP | HCN|LINC00047|NCRNA00047|NEAT2|PRO2853 | |
| Cytomap | 12q12 | 11q13.1 | |
| Type of gene | protein-coding | ncRNA | |
| Description | protein SCAF11CTD-associated SR protein 11SC35-interacting protein 1SFRS2-interacting proteinSR-related and CTD-associated factor 11SRSF2-interacting proteinrenal carcinoma antigen NY-REN-40serine/arginine-rich splicing factor 2-interacting protein | hepcarcinlong intergenic non-protein coding RNA 47metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)nuclear enriched abundant transcript 2nuclear paraspeckle assembly transcript 2 (non-protein coding) | |
| Modification date | 20180519 | 20180527 | |
| UniProtAcc | Q99590 | ||
| Ensembl transtripts involved in fusion gene | ENST00000550629, ENST00000465950, ENST00000369367, ENST00000549162, ENST00000419565, ENST00000395454, ENST00000395453, | ENST00000534336, | |
| Fusion gene scores | * DoF score | 4 X 4 X 1=16 | 71 X 110 X 1=7810 |
| # samples | 4 | 126 | |
| ** MAII score | log2(4/16*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(126/7810*10)=-2.63189881464206 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: SCAF11 [Title/Abstract] AND MALAT1 [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 | SCAF11 | GO:0000245 | spliceosomal complex assembly | 9447963 |
| Hgene | SCAF11 | GO:0000375 | RNA splicing, via transesterification reactions | 9447963 |
| Hgene | SCAF11 | GO:0008380 | RNA splicing | 9447963 |
| 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 | BI060233 | SCAF11 | chr12 | 46332533 | - | MALAT1 | chr11 | 65272342 | - |
| * 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-3UTR | ENST00000550629 | ENST00000534336 | SCAF11 | chr12 | 46332533 | - | MALAT1 | chr11 | 65272342 | - |
| intron-3UTR | ENST00000465950 | ENST00000534336 | SCAF11 | chr12 | 46332533 | - | MALAT1 | chr11 | 65272342 | - |
| intron-3UTR | ENST00000369367 | ENST00000534336 | SCAF11 | chr12 | 46332533 | - | MALAT1 | chr11 | 65272342 | - |
| intron-3UTR | ENST00000549162 | ENST00000534336 | SCAF11 | chr12 | 46332533 | - | MALAT1 | chr11 | 65272342 | - |
| intron-3UTR | ENST00000419565 | ENST00000534336 | SCAF11 | chr12 | 46332533 | - | MALAT1 | chr11 | 65272342 | - |
| intron-3UTR | ENST00000395454 | ENST00000534336 | SCAF11 | chr12 | 46332533 | - | MALAT1 | chr11 | 65272342 | - |
| intron-3UTR | ENST00000395453 | ENST00000534336 | SCAF11 | chr12 | 46332533 | - | MALAT1 | chr11 | 65272342 | - |
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FusionProtFeatures for SCAF11_MALAT1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SCAF11 | MALAT1 |
| Plays a role in pre-mRNA alternative splicing byregulating spliceosome assembly. {ECO:0000269|PubMed:9447963}. | Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}. |
| 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 SCAF11_MALAT1 |
| 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 SCAF11_MALAT1 |
| 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 SCAF11_MALAT1 |
| 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 SCAF11_MALAT1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | MALAT1 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Tgene | MALAT1 | C0023903 | Liver neoplasms | 1 | CTD_human |
| Tgene | MALAT1 | C0027626 | Neoplasm Invasiveness | 1 | CTD_human |
| Tgene | MALAT1 | C0027627 | Neoplasm Metastasis | 1 | CTD_human |
| Tgene | MALAT1 | C0032460 | Polycystic Ovary Syndrome | 1 | CTD_human |
| Tgene | MALAT1 | C0236663 | Alcohol withdrawal syndrome | 1 | PSYGENET |
| Tgene | MALAT1 | C0279626 | Squamous cell carcinoma of esophagus | 1 | CTD_human |
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