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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:CCT3-KDM1A (FusionGDB2 ID:14301) |
Fusion Gene Summary for CCT3-KDM1A |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CCT3-KDM1A | Fusion gene ID: 14301 | Hgene | Tgene | Gene symbol | CCT3 | KDM1A | Gene ID | 7203 | 23028 |
| Gene name | chaperonin containing TCP1 subunit 3 | lysine demethylase 1A | |
| Synonyms | CCT-gamma|CCTG|PIG48|TCP-1-gamma|TRIC5 | AOF2|BHC110|CPRF|KDM1|LSD1 | |
| Cytomap | 1q22 | 1p36.12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | T-complex protein 1 subunit gammaT-complex protein 1, gamma subunitTCP1 (t-complex-1) ring complex, polypeptide 5chaperonin containing TCP1, subunit 3 (gamma)hTRiC5 | lysine-specific histone demethylase 1ABRAF35-HDAC complex protein BHC110FAD-binding protein BRAF35-HDAC complex, 110 kDa subunitamine oxidase (flavin containing) domain 2flavin-containing amine oxidase domain-containing protein 2lysine (K)-specific d | |
| Modification date | 20200327 | 20200329 | |
| UniProtAcc | P49368 | O60341 | |
| Ensembl transtripts involved in fusion gene | ENST00000295688, ENST00000368259, ENST00000368261, ENST00000472765, ENST00000368256, | ENST00000356634, ENST00000400181, ENST00000542151, | |
| Fusion gene scores | * DoF score | 24 X 18 X 12=5184 | 3 X 5 X 3=45 |
| # samples | 28 | 5 | |
| ** MAII score | log2(28/5184*10)=-4.21056698593966 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/45*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: CCT3 [Title/Abstract] AND KDM1A [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CCT3(156303338)-KDM1A(23370920), # 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 |
| Tgene | KDM1A | GO:0033169 | histone H3-K9 demethylation | 16079795|20228790 |
| Tgene | KDM1A | GO:0034644 | cellular response to UV | 24217620 |
| Tgene | KDM1A | GO:0034720 | histone H3-K4 demethylation | 15620353|20228790|24217620 |
| Tgene | KDM1A | GO:0043433 | negative regulation of DNA-binding transcription factor activity | 19497860 |
| Tgene | KDM1A | GO:0045892 | negative regulation of transcription, DNA-templated | 19497860 |
| Tgene | KDM1A | GO:0045944 | positive regulation of transcription by RNA polymerase II | 20833138 |
| Tgene | KDM1A | GO:0051091 | positive regulation of DNA-binding transcription factor activity | 20833138 |
| Fusion gene breakpoints across CCT3 (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 KDM1A (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 |
| ChimerDB4 | LGG | TCGA-TM-A84J-01A | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
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Fusion Gene ORF analysis for CCT3-KDM1A |
| 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 | ENST00000295688 | ENST00000356634 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000295688 | ENST00000400181 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000295688 | ENST00000542151 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000368259 | ENST00000356634 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000368259 | ENST00000400181 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000368259 | ENST00000542151 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000368261 | ENST00000356634 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000368261 | ENST00000400181 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000368261 | ENST00000542151 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000472765 | ENST00000356634 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000472765 | ENST00000400181 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5CDS-intron | ENST00000472765 | ENST00000542151 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5UTR-intron | ENST00000368256 | ENST00000356634 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5UTR-intron | ENST00000368256 | ENST00000400181 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 5UTR-intron | ENST00000368256 | ENST00000542151 | CCT3 | chr1 | 156303338 | - | KDM1A | chr1 | 23370920 | + |
| 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 CCT3-KDM1A |
| 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) |
| CCT3 | chr1 | 156303337 | - | KDM1A | chr1 | 23370919 | + | 9.55E-12 | 1 |
| CCT3 | chr1 | 156303337 | - | KDM1A | chr1 | 23370919 | + | 9.55E-12 | 1 |
| 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 CCT3-KDM1A |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:156303338/:23370920) - 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 |
| CCT3 | KDM1A |
| FUNCTION: Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis (PubMed:25467444). The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance (PubMed:25467444). As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia (PubMed:20080638). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {ECO:0000269|PubMed:20080638, ECO:0000269|PubMed:25467444, ECO:0000305}. | FUNCTION: Histone demethylase that can demethylate both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context (PubMed:15620353, PubMed:15811342, PubMed:16140033, PubMed:16079794, PubMed:16079795, PubMed:16223729). Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed (PubMed:15620353, PubMed:15811342, PubMed:16079794, PubMed:21300290). Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me (PubMed:15620353, PubMed:20389281, PubMed:21300290, PubMed:23721412). May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity (PubMed:16140033, PubMed:16079794, PubMed:16885027, PubMed:21300290, PubMed:23721412). Also acts as a coactivator of androgen receptor (AR)-dependent transcription, by being recruited to AR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in AR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A (PubMed:16079795). Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7 (PubMed:20389281). {ECO:0000269|PubMed:12032298, ECO:0000269|PubMed:15620353, ECO:0000269|PubMed:15811342, ECO:0000269|PubMed:16079794, ECO:0000269|PubMed:16079795, ECO:0000269|PubMed:16140033, ECO:0000269|PubMed:16223729, ECO:0000269|PubMed:16885027, ECO:0000269|PubMed:16956976, ECO:0000269|PubMed:17805299, ECO:0000269|PubMed:20228790, ECO:0000269|PubMed:20389281, ECO:0000269|PubMed:20562920, ECO:0000269|PubMed:21300290, ECO:0000269|PubMed:23721412}. |
| 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 CCT3-KDM1A |
| 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 CCT3-KDM1A |
| 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 CCT3-KDM1A |
| 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 CCT3-KDM1A |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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