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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:NLRP12-LIN28B (FusionGDB2 ID:59379) |
Fusion Gene Summary for NLRP12-LIN28B |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: NLRP12-LIN28B | Fusion gene ID: 59379 | Hgene | Tgene | Gene symbol | NLRP12 | LIN28B | Gene ID | 91662 | 389421 |
| Gene name | NLR family pyrin domain containing 12 | lin-28 homolog B | |
| Synonyms | CLR19.3|FCAS2|NALP12|PAN6|PYPAF7|RNO|RNO2 | CSDD2 | |
| Cytomap | 19q13.42 | 6q16.3-q21 | |
| Type of gene | protein-coding | protein-coding | |
| Description | NACHT, LRR and PYD domains-containing protein 12PYRIN-containing APAF1-like protein 7monarch 1nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12regulated by nitric oxide | protein lin-28 homolog BLin-28.2lin-28B | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | P59046 | Q6ZN17 | |
| Ensembl transtripts involved in fusion gene | ENST00000324134, ENST00000345770, ENST00000351894, ENST00000354278, ENST00000391772, ENST00000391773, ENST00000391775, ENST00000535162, | ENST00000345080, | |
| Fusion gene scores | * DoF score | 3 X 3 X 1=9 | 3 X 2 X 1=6 |
| # samples | 3 | 3 | |
| ** MAII score | log2(3/9*10)=1.73696559416621 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(3/6*10)=2.32192809488736 | |
| Context | PubMed: NLRP12 [Title/Abstract] AND LIN28B [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | NLRP12(54309935)-LIN28B(105531207), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 | NLRP12 | GO:0009968 | negative regulation of signal transduction | 16203735 |
| Hgene | NLRP12 | GO:0031953 | negative regulation of protein autophosphorylation | 16203735 |
| Hgene | NLRP12 | GO:0032088 | negative regulation of NF-kappaB transcription factor activity | 18230725 |
| Hgene | NLRP12 | GO:0043122 | regulation of I-kappaB kinase/NF-kappaB signaling | 12019269 |
| Hgene | NLRP12 | GO:0043124 | negative regulation of I-kappaB kinase/NF-kappaB signaling | 16203735 |
| Hgene | NLRP12 | GO:0043281 | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 12019269 |
| Hgene | NLRP12 | GO:0045345 | positive regulation of MHC class I biosynthetic process | 12759408 |
| Hgene | NLRP12 | GO:0045409 | negative regulation of interleukin-6 biosynthetic process | 16203735 |
| Hgene | NLRP12 | GO:0045751 | negative regulation of Toll signaling pathway | 16203735 |
| Hgene | NLRP12 | GO:0050710 | negative regulation of cytokine secretion | 16203735 |
| Hgene | NLRP12 | GO:0050711 | negative regulation of interleukin-1 secretion | 16203735 |
| Hgene | NLRP12 | GO:1901223 | negative regulation of NIK/NF-kappaB signaling | 17237370 |
| Hgene | NLRP12 | GO:1901224 | positive regulation of NIK/NF-kappaB signaling | 12019269 |
| Tgene | LIN28B | GO:0050779 | RNA destabilization | 18951094 |
| Tgene | LIN28B | GO:2000632 | negative regulation of pre-miRNA processing | 18951094 |
| Tgene | LIN28B | GO:2000635 | negative regulation of primary miRNA processing | 18951094 |
| Fusion gene breakpoints across NLRP12 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across LIN28B (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS5.0 | N/A | BI492067 | NLRP12 | chr19 | 54309935 | - | LIN28B | chr6 | 105531207 | - |
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Fusion Gene ORF analysis for NLRP12-LIN28B |
| 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-intron | ENST00000324134 | ENST00000345080 | NLRP12 | chr19 | 54309935 | - | LIN28B | chr6 | 105531207 | - |
| intron-intron | ENST00000345770 | ENST00000345080 | NLRP12 | chr19 | 54309935 | - | LIN28B | chr6 | 105531207 | - |
| intron-intron | ENST00000351894 | ENST00000345080 | NLRP12 | chr19 | 54309935 | - | LIN28B | chr6 | 105531207 | - |
| intron-intron | ENST00000354278 | ENST00000345080 | NLRP12 | chr19 | 54309935 | - | LIN28B | chr6 | 105531207 | - |
| intron-intron | ENST00000391772 | ENST00000345080 | NLRP12 | chr19 | 54309935 | - | LIN28B | chr6 | 105531207 | - |
| intron-intron | ENST00000391773 | ENST00000345080 | NLRP12 | chr19 | 54309935 | - | LIN28B | chr6 | 105531207 | - |
| intron-intron | ENST00000391775 | ENST00000345080 | NLRP12 | chr19 | 54309935 | - | LIN28B | chr6 | 105531207 | - |
| intron-intron | ENST00000535162 | ENST00000345080 | NLRP12 | chr19 | 54309935 | - | LIN28B | chr6 | 105531207 | - |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
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Fusion Genomic Features for NLRP12-LIN28B |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for NLRP12-LIN28B |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:54309935/:105531207) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| NLRP12 | LIN28B |
| FUNCTION: Plays an essential role as an potent mitigator of inflammation (PubMed:30559449). Primarily expressed in dendritic cells and macrophages, inhibits both canonical and non-canonical NF-kappa-B and ERK activation pathways (PubMed:15489334, PubMed:17947705). Functions as a negative regulator of NOD2 by targeting it to degradation via the proteasome pathway (PubMed:30559449). In turn, promotes bacterial tolerance (PubMed:30559449). Inhibits also the DDX58-mediated immune signaling against RNA viruses by reducing the E3 ubiquitin ligase TRIM25-mediated 'Lys-63'-linked DDX58 activation but enhancing the E3 ubiquitin ligase RNF125-mediated 'Lys-48'-linked DDX58 degradation (PubMed:30902577). Acts also as a negative regulator of inflammatory response to mitigate obesity and obesity-associated diseases in adipose tissue (By similarity). {ECO:0000250|UniProtKB:E9Q5R7, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17947705, ECO:0000269|PubMed:30559449, ECO:0000269|PubMed:30902577}. | FUNCTION: Suppressor of microRNA (miRNA) biogenesis, including that of let-7 and possibly of miR107, miR-143 and miR-200c. Binds primary let-7 transcripts (pri-let-7), including pri-let-7g and pri-let-7a-1, and sequester them in the nucleolus, away from the microprocessor complex, hence preventing their processing into mature miRNA (PubMed:22118463). Does not act on pri-miR21 (PubMed:22118463). The repression of let-7 expression is required for normal development and contributes to maintain the pluripotent state of embryonic stem cells by preventing let-7-mediated differentiation. When overexpressed, recruits ZCCHC11/TUT4 uridylyltransferase to pre-let-7 transcripts, leading to their terminal uridylation and degradation (PubMed:19703396). This activity might not be relevant in vivo, as LIN28B-mediated inhibition of let-7 miRNA maturation appears to be ZCCHC11-independent (PubMed:22118463). Interaction with target pre-miRNAs occurs via an 5'-GGAG-3' motif in the pre-miRNA terminal loop. Mediates MYC-induced let-7 repression (By similarity). When overexpressed, isoform 1 stimulates growth of the breast adenocarcinoma cell line MCF-7. Isoform 2 has no effect on cell growth. {ECO:0000250|UniProtKB:Q45KJ6, ECO:0000269|PubMed:16971064, ECO:0000269|PubMed:18951094, ECO:0000269|PubMed:19703396, ECO:0000269|PubMed:22118463}. |
| 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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Fusion Gene Sequence for NLRP12-LIN28B |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for NLRP12-LIN28B |
| 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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Related Drugs for NLRP12-LIN28B |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for NLRP12-LIN28B |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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