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Fusion gene ID: 23915 |
FusionGeneSummary for NEAT1_IGKC |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: NEAT1_IGKC | Fusion gene ID: 23915 | Hgene | Tgene | Gene symbol | NEAT1 | IGKC | Gene ID | 283131 | 3514 |
| Gene name | nuclear paraspeckle assembly transcript 1 | immunoglobulin kappa constant | |
| Synonyms | LINC00084|NCRNA00084|TncRNA|VINC | HCAK1|IGKCD|Km | |
| Cytomap | 11q13.1 | 2p11.2 | |
| Type of gene | ncRNA | other | |
| Description | MENepsilon/betalong intergenic non-protein coding RNA 84nuclear enriched abundant transcript 1nuclear paraspeckle assembly transcript 1 (non-protein coding)trophoblast MHC class II suppressortrophoblast-derived noncoding RNAvirus inducible non-codin | immunoglobulin kappa (invariant region)immunoglobulin kappa constant regionimmunoglobulin kappa light chain (VJ) | |
| Modification date | 20180520 | 20180523 | |
| UniProtAcc | P01834 | ||
| Ensembl transtripts involved in fusion gene | ENST00000384994, | ENST00000390237, | |
| Fusion gene scores | * DoF score | 24 X 30 X 3=2160 | 21 X 29 X 2=1218 |
| # samples | 31 | 35 | |
| ** MAII score | log2(31/2160*10)=-2.80069119177659 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(35/1218*10)=-1.799087306074 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: NEAT1 [Title/Abstract] AND IGKC [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 | AK026198 | NEAT1 | chr11 | 65191274 | + | IGKC | chr2 | 89156872 | - |
| * 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 | ENST00000384994 | ENST00000390237 | NEAT1 | chr11 | 65191274 | + | IGKC | chr2 | 89156872 | - |
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FusionProtFeatures for NEAT1_IGKC |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| NEAT1 | IGKC |
| 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}. | Constant region of immunoglobulin heavy chains.Immunoglobulins, also known as antibodies, are membrane-bound orsecreted glycoproteins produced by B lymphocytes. In therecognition phase of humoral immunity, the membrane-boundimmunoglobulins serve as receptors which, upon binding of aspecific antigen, trigger the clonal expansion and differentiationof B lymphocytes into immunoglobulins-secreting plasma cells.Secreted immunoglobulins mediate the effector phase of humoralimmunity, which results in the elimination of bound antigens(PubMed:22158414, PubMed:20176268). The antigen binding site isformed by the variable domain of one heavy chain, together withthat of its associated light chain. Thus, each immunoglobulin hastwo antigen binding sites with remarkable affinity for aparticular antigen. The variable domains are assembled by aprocess called V-(D)-J rearrangement and can then be subjected tosomatic hypermutations which, after exposure to antigen andselection, allow affinity maturation for a particular antigen(PubMed:17576170, PubMed:20176268). {ECO:0000303|PubMed:17576170,ECO:0000303|PubMed:20176268, ECO:0000303|PubMed:22158414}. |
| 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 NEAT1_IGKC |
| 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 NEAT1_IGKC |
| 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 NEAT1_IGKC |
| 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 NEAT1_IGKC |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | NEAT1 | C0023903 | Liver neoplasms | 1 | CTD_human |
| Hgene | NEAT1 | C3495559 | Juvenile arthritis | 1 | CTD_human |
| Tgene | IGKC | C0013374 | Dysgammaglobulinemia | 1 | CTD_human |
| Tgene | IGKC | C0027121 | Myositis | 1 | CTD_human |
| Tgene | IGKC | C3279824 | Kappa-Chain Deficiency | 1 | ORPHANET;UNIPROT |
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