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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:CD74-CD40 (FusionGDB2 ID:HG972TG958) |
Fusion Gene Summary for CD74-CD40 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CD74-CD40 | Fusion gene ID: hg972tg958 | Hgene | Tgene | Gene symbol | CD74 | CD40 | Gene ID | 972 | 958 |
| Gene name | CD74 molecule | CD40 molecule | |
| Synonyms | DHLAG|HLADG|II|Ia-GAMMA|p33 | Bp50|CDW40|TNFRSF5|p50 | |
| Cytomap | ('CD74')('CD40') 5q33.1 | 20q13.12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | HLA class II histocompatibility antigen gamma chainCD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)CD74 molecule, major histocompatibility complex, class II invariant chainHLA-DR antigens-associated | tumor necrosis factor receptor superfamily member 5B cell surface antigen CD40B cell-associated moleculeCD40 molecule, TNF receptor superfamily member 5CD40L receptor | |
| Modification date | 20200313 | 20200327 | |
| UniProtAcc | P04233 | . | |
| Ensembl transtripts involved in fusion gene | ENST00000377795, ENST00000009530, ENST00000353334, ENST00000524315, | ||
| Fusion gene scores | * DoF score | 43 X 51 X 20=43860 | 6 X 4 X 4=96 |
| # samples | 59 | 6 | |
| ** MAII score | log2(59/43860*10)=-6.21604704731175 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(6/96*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: CD74 [Title/Abstract] AND CD40 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CD74(149781200)-CD40(44754189), # 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 | CD74 | GO:0001516 | prostaglandin biosynthetic process | 12782713 |
| Hgene | CD74 | GO:0001934 | positive regulation of protein phosphorylation | 24942581 |
| Hgene | CD74 | GO:0002792 | negative regulation of peptide secretion | 19849849 |
| Hgene | CD74 | GO:0033674 | positive regulation of kinase activity | 24942581 |
| Hgene | CD74 | GO:0043066 | negative regulation of apoptotic process | 12782713 |
| Hgene | CD74 | GO:0043123 | positive regulation of I-kappaB kinase/NF-kappaB signaling | 24942581 |
| Hgene | CD74 | GO:0043410 | positive regulation of MAPK cascade | 24942581 |
| Hgene | CD74 | GO:0043518 | negative regulation of DNA damage response, signal transduction by p53 class mediator | 17045821 |
| Hgene | CD74 | GO:0045657 | positive regulation of monocyte differentiation | 24942581 |
| Hgene | CD74 | GO:0045893 | positive regulation of transcription, DNA-templated | 24942581 |
| Hgene | CD74 | GO:0046598 | positive regulation of viral entry into host cell | 24942581 |
| Hgene | CD74 | GO:0050731 | positive regulation of peptidyl-tyrosine phosphorylation | 17045821 |
| Hgene | CD74 | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 17045821|24942581 |
| Tgene | CD40 | GO:0023035 | CD40 signaling pathway | 31331973 |
| Tgene | CD40 | GO:2000353 | positive regulation of endothelial cell apoptotic process | 12885753 |
| 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 |
| ChimerDB4 | BLCA | TCGA-XF-A9T5-01A | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
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Fusion Gene ORF analysis for CD74-CD40 |
| 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 |
| 5CDS-intron | ENST00000377795 | ENST00000372276 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| 5CDS-intron | ENST00000377795 | ENST00000372285 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| 5CDS-intron | ENST00000377795 | ENST00000489304 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| intron-intron | ENST00000009530 | ENST00000372276 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| intron-intron | ENST00000009530 | ENST00000372285 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| intron-intron | ENST00000009530 | ENST00000489304 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| intron-intron | ENST00000353334 | ENST00000372276 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| intron-intron | ENST00000353334 | ENST00000372285 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| intron-intron | ENST00000353334 | ENST00000489304 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| intron-intron | ENST00000524315 | ENST00000372276 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| intron-intron | ENST00000524315 | ENST00000372285 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| intron-intron | ENST00000524315 | ENST00000489304 | CD74 | chr5 | 149781200 | - | CD40 | chr20 | 44754189 | + |
| 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 CD74-CD40 |
| 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 CD74-CD40 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:149781200/:44754189) - 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 |
| CD74 | . |
| FUNCTION: Plays a critical role in MHC class II antigen processing by stabilizing peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to the endosomal/lysosomal system where the antigen processing and binding of antigenic peptides to MHC class II takes place. Serves as cell surface receptor for the cytokine MIF.; FUNCTION: [Class-II-associated invariant chain peptide]: Binds to the peptide-binding site of MHC class II alpha/beta heterodimers forming an alpha-beta-CLIP complex, thereby preventing the loading of antigenic peptides to the MHC class II complex until its release by HLA-DM in the endosome. {ECO:0000269|PubMed:1448172}.; FUNCTION: [Isoform p41]: Stabilizes the conformation of mature CTSL by binding to its active site and serving as a chaperone to help maintain a pool of mature enzyme in endocytic compartments and extracellular space of antigen-presenting cells (APCs). Has antiviral activity by stymieing the endosomal entry of Ebola virus and coronaviruses, including SARS-CoV-2 (PubMed:32855215). Disrupts cathepsin-mediated Ebola virus glycoprotein processing, which prevents viral fusion and entry. This antiviral activity is specific to p41 isoform (PubMed:32855215). {ECO:0000250|UniProtKB:P04441, ECO:0000269|PubMed:32855215}. | 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 CD74-CD40 |
| 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 CD74-CD40 |
| 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 CD74-CD40 |
| 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 CD74-CD40 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | CD74 | C0006142 | Malignant neoplasm of breast | 1 | CTD_human |
| Hgene | CD74 | C0007131 | Non-Small Cell Lung Carcinoma | 1 | CTD_human |
| Hgene | CD74 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Hgene | CD74 | C0162557 | Liver Failure, Acute | 1 | CTD_human |
| Hgene | CD74 | C0678222 | Breast Carcinoma | 1 | CTD_human |
| Hgene | CD74 | C1257931 | Mammary Neoplasms, Human | 1 | CTD_human |
| Hgene | CD74 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
| Hgene | CD74 | C4704874 | Mammary Carcinoma, Human | 1 | CTD_human |
| Tgene | C0003873 | Rheumatoid Arthritis | 3 | CTD_human | |
| Tgene | C1720957 | Hyper-IgM Immunodeficiency Syndrome, Type 3 | 3 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT | |
| Tgene | C0026691 | Mucocutaneous Lymph Node Syndrome | 2 | CTD_human | |
| Tgene | C0006142 | Malignant neoplasm of breast | 1 | CTD_human | |
| Tgene | C0020456 | Hyperglycemia | 1 | CTD_human | |
| Tgene | C0020459 | Hyperinsulinism | 1 | CTD_human | |
| Tgene | C0021655 | Insulin Resistance | 1 | CTD_human | |
| Tgene | C0026769 | Multiple Sclerosis | 1 | CTD_human | |
| Tgene | C0028754 | Obesity | 1 | CTD_human | |
| Tgene | C0038220 | Status Epilepticus | 1 | CTD_human | |
| Tgene | C0270823 | Petit mal status | 1 | CTD_human | |
| Tgene | C0311335 | Grand Mal Status Epilepticus | 1 | CTD_human | |
| Tgene | C0393734 | Complex Partial Status Epilepticus | 1 | CTD_human | |
| Tgene | C0678222 | Breast Carcinoma | 1 | CTD_human | |
| Tgene | C0751324 | Multiple Sclerosis, Acute Fulminating | 1 | CTD_human | |
| Tgene | C0751522 | Status Epilepticus, Subclinical | 1 | CTD_human | |
| Tgene | C0751523 | Non-Convulsive Status Epilepticus | 1 | CTD_human | |
| Tgene | C0751524 | Simple Partial Status Epilepticus | 1 | CTD_human | |
| Tgene | C0920563 | Insulin Sensitivity | 1 | CTD_human | |
| Tgene | C1257931 | Mammary Neoplasms, Human | 1 | CTD_human | |
| Tgene | C1257963 | Endogenous Hyperinsulinism | 1 | CTD_human | |
| Tgene | C1257964 | Exogenous Hyperinsulinism | 1 | CTD_human | |
| Tgene | C1257965 | Compensatory Hyperinsulinemia | 1 | CTD_human | |
| Tgene | C1458155 | Mammary Neoplasms | 1 | CTD_human | |
| Tgene | C1855520 | Hyperglycemia, Postprandial | 1 | CTD_human | |
| Tgene | C4704874 | Mammary Carcinoma, Human | 1 | CTD_human |
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