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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:HMG20B-CNOT3 (FusionGDB2 ID:36795) |
Fusion Gene Summary for HMG20B-CNOT3 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: HMG20B-CNOT3 | Fusion gene ID: 36795 | Hgene | Tgene | Gene symbol | HMG20B | CNOT3 | Gene ID | 10362 | 4849 |
| Gene name | high mobility group 20B | CCR4-NOT transcription complex subunit 3 | |
| Synonyms | BRAF25|BRAF35|HMGX2|HMGXB2|PP7706|SMARCE1r|SOXL|pp8857 | IDDSADF|LENG2|NOT3|NOT3H | |
| Cytomap | 19p13.3 | 19q13.42 | |
| Type of gene | protein-coding | protein-coding | |
| Description | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-relatedBRCA2-associated factor 35HMG box domain containing 2HMG box-containing protein 20BHMG domain-containing protein 2HMG domain-containing protein HMGX2 | CCR4-NOT transcription complex subunit 3CCR4-associated factor 3NOT3 (negative regulator of transcription 3, yeast) homologleukocyte receptor cluster member 2 | |
| Modification date | 20200327 | 20200313 | |
| UniProtAcc | Q9P0W2 | O75175 | |
| Ensembl transtripts involved in fusion gene | ENST00000585741, ENST00000333651, | ENST00000221232, ENST00000496327, ENST00000358389, ENST00000406403, | |
| Fusion gene scores | * DoF score | 4 X 3 X 4=48 | 5 X 5 X 4=100 |
| # samples | 4 | 5 | |
| ** MAII score | log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: HMG20B [Title/Abstract] AND CNOT3 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | HMG20B(3573798)-CNOT3(54657451), # 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 |
| Fusion gene breakpoints across HMG20B (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across CNOT3 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| 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-FD-A3B6 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + |
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Fusion Gene ORF analysis for HMG20B-CNOT3 |
| 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 |
| 3UTR-3CDS | ENST00000585741 | ENST00000221232 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + |
| 3UTR-3UTR | ENST00000585741 | ENST00000496327 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + |
| 3UTR-intron | ENST00000585741 | ENST00000358389 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + |
| 3UTR-intron | ENST00000585741 | ENST00000406403 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + |
| 5CDS-3UTR | ENST00000333651 | ENST00000496327 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + |
| 5CDS-intron | ENST00000333651 | ENST00000358389 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + |
| 5CDS-intron | ENST00000333651 | ENST00000406403 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + |
| In-frame | ENST00000333651 | ENST00000221232 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + |
| 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) |
| ENST00000333651 | HMG20B | chr19 | 3573798 | + | ENST00000221232 | CNOT3 | chr19 | 54657451 | + | 721 | 222 | 12 | 446 | 144 |
| 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 |
| ENST00000333651 | ENST00000221232 | HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + | 0.02125981 | 0.9787402 |
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Fusion Genomic Features for HMG20B-CNOT3 |
| 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) |
| HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + | 0.228736 | 0.77126396 |
| HMG20B | chr19 | 3573798 | + | CNOT3 | chr19 | 54657451 | + | 0.228736 | 0.77126396 |
| 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. |
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| 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 HMG20B-CNOT3 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:3573798/chr19:54657451) - 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 |
| HMG20B | CNOT3 |
| FUNCTION: Required for correct progression through G2 phase of the cell cycle and entry into mitosis. Required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. | FUNCTION: Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. May be involved in metabolic regulation; may be involved in recruitment of the CCR4-NOT complex to deadenylation target mRNAs involved in energy metabolism. Involved in mitotic progression and regulation of the spindle assembly checkpoint by regulating the stability of MAD1L1 mRNA. Can repress transcription and may link the CCR4-NOT complex to transcriptional regulation; the repressive function may involve histone deacetylases. Involved in the maintenance of embryonic stem (ES) cell identity. {ECO:0000269|PubMed:14707134, ECO:0000269|PubMed:22342980, ECO:0000269|PubMed:22367759}. |
| 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 |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000358389 | 0 | 18 | 314_395 | 0 | 572.0 | Compositional bias | Note=Pro-rich | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000358389 | 0 | 18 | 397_425 | 0 | 572.0 | Compositional bias | Note=Gly/Ser-rich | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000358389 | 0 | 18 | 457_655 | 0 | 572.0 | Compositional bias | Note=Pro-rich | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000358389 | 0 | 18 | 661_753 | 0 | 572.0 | Region | Note=Repressor domain |
| - 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 |
| Hgene | HMG20B | chr19:3573798 | chr19:54657451 | ENST00000333651 | + | 3 | 10 | 190_257 | 49 | 318.0 | Coiled coil | Ontology_term=ECO:0000255 |
| Hgene | HMG20B | chr19:3573798 | chr19:54657451 | ENST00000333651 | + | 3 | 10 | 70_138 | 49 | 318.0 | DNA binding | HMG box |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000221232 | 15 | 18 | 314_395 | 679 | 754.0 | Compositional bias | Note=Pro-rich | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000221232 | 15 | 18 | 397_425 | 679 | 754.0 | Compositional bias | Note=Gly/Ser-rich | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000221232 | 15 | 18 | 457_655 | 679 | 754.0 | Compositional bias | Note=Pro-rich | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000406403 | 14 | 17 | 314_395 | 679 | 754.0 | Compositional bias | Note=Pro-rich | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000406403 | 14 | 17 | 397_425 | 679 | 754.0 | Compositional bias | Note=Gly/Ser-rich | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000406403 | 14 | 17 | 457_655 | 679 | 754.0 | Compositional bias | Note=Pro-rich | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000221232 | 15 | 18 | 661_753 | 679 | 754.0 | Region | Note=Repressor domain | |
| Tgene | CNOT3 | chr19:3573798 | chr19:54657451 | ENST00000406403 | 14 | 17 | 661_753 | 679 | 754.0 | Region | Note=Repressor domain |
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Fusion Gene Sequence for HMG20B-CNOT3 |
| 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. |
| >36795_36795_1_HMG20B-CNOT3_HMG20B_chr19_3573798_ENST00000333651_CNOT3_chr19_54657451_ENST00000221232_length(transcript)=721nt_BP=222nt GCGGGCGGTTGGTTGGAGCGTCGCGCAGTCGGGAGGTCCGGGAAAGTTTCTTTGGAGGTCCGGCCCGGAGCGGCCATGTCCCACGGCCCC AAGCAGCCCGGCGCGGCCGCCGCGCCGGCGGGCGGCAAGGCTCCGGGCCAGCATGGGGGCTTCGTGGTGACTGTCAAGCAAGAGCGCGGC GAGGGTCCACGCGCGGGCGAGAAGGGGTCCCACGAGGAGGAGGGCACTAAGGCACAGTATCTGGCAGCCAAGGCCCTAAAGAAGCAGTCA TGGCGATTCCACACCAAGTACATGATGTGGTTCCAGAGGCACGAGGAGCCCAAGACCATCACTGACGAGTTTGAGCAGGGCACCTACATC TACTTTGACTACGAGAAGTGGGGCCAGCGGAAGAAGGAAGGCTTCACCTTTGAGTACCGCTACCTGGAGGACCGGGACCTCCAGTGACAC CGGCCCCTCCCTCTACCCACCCCCTTCCCCCGCATGCTGATCCCCCTGCCCAGGTGAGGGCCCTGCCCTGGAAGACTGGAGGGAGGCCCC AAGCCACGGGGCATCCCCCTCTCCCAGGAAGCAGGGAGGGGGCCGGGAGGTTTTCCTCTCAGCCCCACCCTGGGGGCCCGGGGGCGAGGG CTGCCCCCTCCTCCCCTCCCCAGTGAGGGACATTTTTTGGTAAACCTATTTTCATTTTGGAAAATATTTATGAATAAATAGTTTTATATG >36795_36795_1_HMG20B-CNOT3_HMG20B_chr19_3573798_ENST00000333651_CNOT3_chr19_54657451_ENST00000221232_length(amino acids)=144AA_BP=53 MERRAVGRSGKVSLEVRPGAAMSHGPKQPGAAAAPAGGKAPGQHGGFVVTVKQERGEGPRAGEKGSHEEEGTKAQYLAAKALKKQSWRFH -------------------------------------------------------------- |
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Fusion Gene PPI Analysis for HMG20B-CNOT3 |
| 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 HMG20B-CNOT3 |
| 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 HMG20B-CNOT3 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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