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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:NFKB1-RPRD1A (FusionGDB2 ID:HG4790TG55197) |
Fusion Gene Summary for NFKB1-RPRD1A |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: NFKB1-RPRD1A | Fusion gene ID: hg4790tg55197 | Hgene | Tgene | Gene symbol | NFKB1 | RPRD1A | Gene ID | 4790 | 55197 |
| Gene name | nuclear factor kappa B subunit 1 | regulation of nuclear pre-mRNA domain containing 1A | |
| Synonyms | CVID12|EBP-1|KBF1|NF-kB|NF-kB1|NF-kappa-B1|NF-kappaB|NFKB-p105|NFKB-p50|NFkappaB|p105|p50 | HsT3101|P15RS | |
| Cytomap | ('NFKB1')('RPRD1A') 4q24 | 18q12.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nuclear factor NF-kappa-B p105 subunitDNA-binding factor KBF1NF-kappabetanuclear factor NF-kappa-B p50 subunitnuclear factor kappa-B DNA binding subunitnuclear factor of kappa light polypeptide gene enhancer in B-cells 1 | regulation of nuclear pre-mRNA domain-containing protein 1ACDKN2B-related proteinCyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)cyclin-dependent kinase 2B-inhibitor-related proteinp15INK4B-related protein | |
| Modification date | 20200329 | 20200313 | |
| UniProtAcc | P19838 | . | |
| Ensembl transtripts involved in fusion gene | ENST00000226574, ENST00000505458, ENST00000600343, ENST00000394820, ENST00000510638, | ||
| Fusion gene scores | * DoF score | 12 X 10 X 8=960 | 10 X 9 X 5=450 |
| # samples | 12 | 12 | |
| ** MAII score | log2(12/960*10)=-3 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(12/450*10)=-1.90689059560852 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: NFKB1 [Title/Abstract] AND RPRD1A [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | NFKB1(103538248)-RPRD1A(33570301), # 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 | NFKB1 | GO:0010629 | negative regulation of gene expression | 26687115 |
| Hgene | NFKB1 | GO:0010956 | negative regulation of calcidiol 1-monooxygenase activity | 15243130 |
| Hgene | NFKB1 | GO:0045893 | positive regulation of transcription, DNA-templated | 17426251 |
| Hgene | NFKB1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 1406630 |
| Hgene | NFKB1 | GO:1900127 | positive regulation of hyaluronan biosynthetic process | 17324121 |
| Fusion gene information * 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 |
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Fusion Gene ORF analysis for NFKB1-RPRD1A |
| 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 |
| 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 NFKB1-RPRD1A |
| 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) |
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Fusion Protein Features for NFKB1-RPRD1A |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:103538248/:33570301) - 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 |
| NFKB1 | . |
| FUNCTION: NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and RelB-p50 complexes are transcriptional activators. The NF-kappa-B p50-p50 homodimer is a transcriptional repressor, but can act as a transcriptional activator when associated with BCL3. NFKB1 appears to have dual functions such as cytoplasmic retention of attached NF-kappa-B proteins by p105 and generation of p50 by a cotranslational processing. The proteasome-mediated process ensures the production of both p50 and p105 and preserves their independent function, although processing of NFKB1/p105 also appears to occur post-translationally. p50 binds to the kappa-B consensus sequence 5'-GGRNNYYCC-3', located in the enhancer region of genes involved in immune response and acute phase reactions. In a complex with MAP3K8, NFKB1/p105 represses MAP3K8-induced MAPK signaling; active MAP3K8 is released by proteasome-dependent degradation of NFKB1/p105. {ECO:0000269|PubMed:15485931}. | FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (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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Fusion Gene Sequence for NFKB1-RPRD1A |
| 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 NFKB1-RPRD1A |
| 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 NFKB1-RPRD1A |
| 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 |
| Hgene | NFKB1 | P19838 | DB00852 | Pseudoephedrine | Inhibitor | Small molecule | Approved |
| Hgene | NFKB1 | P19838 | DB08814 | Triflusal | Antagonist | Small molecule | Approved|Investigational |
| Hgene | NFKB1 | P19838 | DB01041 | Thalidomide | Antagonist | Small molecule | Approved|Investigational|Withdrawn |
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Related Diseases for NFKB1-RPRD1A |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | NFKB1 | C0001973 | Alcoholic Intoxication, Chronic | 4 | PSYGENET |
| Hgene | NFKB1 | C0007102 | Malignant tumor of colon | 2 | CTD_human |
| Hgene | NFKB1 | C0007621 | Neoplastic Cell Transformation | 2 | CTD_human |
| Hgene | NFKB1 | C0009375 | Colonic Neoplasms | 2 | CTD_human |
| Hgene | NFKB1 | C4225277 | IMMUNODEFICIENCY, COMMON VARIABLE, 12 | 2 | GENOMICS_ENGLAND |
| Hgene | NFKB1 | C0001418 | Adenocarcinoma | 1 | CTD_human |
| Hgene | NFKB1 | C0007786 | Brain Ischemia | 1 | CTD_human |
| Hgene | NFKB1 | C0008312 | Primary biliary cirrhosis | 1 | CTD_human |
| Hgene | NFKB1 | C0009447 | Common Variable Immunodeficiency | 1 | CTD_human;ORPHANET |
| Hgene | NFKB1 | C0010093 | Corpus Luteum Cyst | 1 | CTD_human |
| Hgene | NFKB1 | C0011860 | Diabetes Mellitus, Non-Insulin-Dependent | 1 | CTD_human |
| Hgene | NFKB1 | C0020500 | Hyperoxaluria | 1 | CTD_human |
| Hgene | NFKB1 | C0022660 | Kidney Failure, Acute | 1 | CTD_human |
| Hgene | NFKB1 | C0022661 | Kidney Failure, Chronic | 1 | CTD_human |
| Hgene | NFKB1 | C0023892 | Biliary cirrhosis | 1 | CTD_human |
| Hgene | NFKB1 | C0023895 | Liver diseases | 1 | CTD_human |
| Hgene | NFKB1 | C0029927 | Ovarian Cysts | 1 | CTD_human |
| Hgene | NFKB1 | C0086565 | Liver Dysfunction | 1 | CTD_human |
| Hgene | NFKB1 | C0205641 | Adenocarcinoma, Basal Cell | 1 | CTD_human |
| Hgene | NFKB1 | C0205642 | Adenocarcinoma, Oxyphilic | 1 | CTD_human |
| Hgene | NFKB1 | C0205643 | Carcinoma, Cribriform | 1 | CTD_human |
| Hgene | NFKB1 | C0205644 | Carcinoma, Granular Cell | 1 | CTD_human |
| Hgene | NFKB1 | C0205645 | Adenocarcinoma, Tubular | 1 | CTD_human |
| Hgene | NFKB1 | C0238065 | Secondary Biliary Cholangitis | 1 | CTD_human |
| Hgene | NFKB1 | C0525045 | Mood Disorders | 1 | PSYGENET |
| Hgene | NFKB1 | C0917798 | Cerebral Ischemia | 1 | CTD_human |
| Hgene | NFKB1 | C1298681 | Oxalosis | 1 | CTD_human |
| Hgene | NFKB1 | C1565662 | Acute Kidney Insufficiency | 1 | CTD_human |
| Hgene | NFKB1 | C1846546 | Recurrent sinopulmonary infections | 1 | GENOMICS_ENGLAND |
| Hgene | NFKB1 | C2609414 | Acute kidney injury | 1 | CTD_human |
| Hgene | NFKB1 | C4551595 | Biliary Cirrhosis, Primary, 1 | 1 | CTD_human |
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