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Fusion Protein:KDM4B-CHAF1A |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: KDM4B-CHAF1A | FusionPDB ID: 41799 | FusionGDB2.0 ID: 41799 | Hgene | Tgene | Gene symbol | KDM4B | CHAF1A | Gene ID | 23030 | 10036 |
| Gene name | lysine demethylase 4B | chromatin assembly factor 1 subunit A | |
| Synonyms | JMJD2B|TDRD14B | CAF-1|CAF1|CAF1B|CAF1P150|P150 | |
| Cytomap | 19p13.3 | 19p13.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | lysine-specific demethylase 4BjmjC domain-containing histone demethylation protein 3Bjumonji domain containing 2Bjumonji domain-containing protein 2Blysine (K)-specific demethylase 4Btudor domain containing 14B | chromatin assembly factor 1 subunit ACAF-1 subunit ACAF-I 150 kDa subunitCAF-I p150CTB-50L17.7chromatin assembly factor I (150 kDa)chromatin assembly factor I p150 subunithp150 | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | O94953 | Q13111 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000159111, ENST00000381759, ENST00000536461, ENST00000592175, | ENST00000587368, ENST00000301280, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 30 X 16 X 14=6720 | 5 X 6 X 6=180 |
| # samples | 38 | 7 | |
| ** MAII score | log2(38/6720*10)=-4.14438990933518 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(7/180*10)=-1.36257007938471 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: KDM4B [Title/Abstract] AND CHAF1A [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | KDM4B(5082515)-CHAF1A(4418017), # samples:2 | ||
| Anticipated loss of major functional domain due to fusion event. | KDM4B-CHAF1A seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. KDM4B-CHAF1A seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. KDM4B-CHAF1A seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. KDM4B-CHAF1A seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. | ||
| * 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 | KDM4B | GO:0033169 | histone H3-K9 demethylation | 21914792 |
| Hgene | KDM4B | GO:0070544 | histone H3-K36 demethylation | 21914792 |
| Tgene | CHAF1A | GO:0006335 | DNA replication-dependent nucleosome assembly | 14718166 |
| Tgene | CHAF1A | GO:0031497 | chromatin assembly | 8858152 |
| Fusion gene breakpoints across KDM4B (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 CHAF1A (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 Sample Information |
| Fusion gene information from FusionGDB2.0. |
| 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-DU-8163-01A | KDM4B | chr19 | 5082515 | - | CHAF1A | chr19 | 4418017 | + |
| ChimerDB4 | LGG | TCGA-DU-8163-01A | KDM4B | chr19 | 5082515 | + | CHAF1A | chr19 | 4418017 | + |
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Fusion ORF Analysis |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| 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) |
| ENST00000159111 | KDM4B | chr19 | 5082515 | + | ENST00000301280 | CHAF1A | chr19 | 4418017 | + | 3414 | 1136 | 218 | 3046 | 942 |
| ENST00000381759 | KDM4B | chr19 | 5082515 | + | ENST00000301280 | CHAF1A | chr19 | 4418017 | + | 3403 | 1125 | 207 | 3035 | 942 |
| ENST00000536461 | KDM4B | chr19 | 5082515 | + | ENST00000301280 | CHAF1A | chr19 | 4418017 | + | 3236 | 958 | 40 | 2868 | 942 |
| 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 |
| ENST00000159111 | ENST00000301280 | KDM4B | chr19 | 5082515 | + | CHAF1A | chr19 | 4418017 | + | 0.001380299 | 0.9986197 |
| ENST00000381759 | ENST00000301280 | KDM4B | chr19 | 5082515 | + | CHAF1A | chr19 | 4418017 | + | 0.001337451 | 0.9986626 |
| ENST00000536461 | ENST00000301280 | KDM4B | chr19 | 5082515 | + | CHAF1A | chr19 | 4418017 | + | 0.00129263 | 0.9987074 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >41799_41799_1_KDM4B-CHAF1A_KDM4B_chr19_5082515_ENST00000159111_CHAF1A_chr19_4418017_ENST00000301280_length(amino acids)=942AA_BP=305 MGSEDHGAQNPSCKIMTFRPTMEEFKDFNKYVAYIESQGAHRAGLAKIIPPKEWKPRQTYDDIDDVVIPAPIQQVVTGQSGLFTQYNIQK KAMTVGEYRRLANSEKYCTPRHQDFDDLERKYWKNLTFVSPIYGADISGSLYDDDVAQWNIGSLRTILDMVERECGTIIEGVNTPYLYFG MWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFPGSSQGCDAFLRHKMTLISPIILKKYGIPFSRITQEAGEFMI TFPYGYHAGFNHGFNCAESTNFATLRWIDYGKVATQITKKFVKGSTEKNKLRLQRDQERLGKQLKLRAEREEKEKLKEEAKRAKEEAKKK KEEEKELKEKERREKREKDEKEKAEKQRLKEERRKERQEALEAKLEEKRKKEEEKRLREEEKRIKAEKAEITRFFQKPKTPQAPKTLAGS CGKFAPFEIKEHMVLAPRRRTAFHPDLCSQLDQLLQQQSGEFSFLKDLKGRQPLRSGPTHVSTRNADIFNSDVVIVERGKGDGVPERRKF GRMKLLQFCENHRPAYWGTWNKKTALIRARDPWAQDTKLLDYEVDSDEEWEEEEPGESLSHSEGDDDDDMGEDEDEDDGFFVPHGYLSED EGVTEECADPENHKVRQKLKAKEWDEFLAKGKRFRVLQPVKIGCVWAADRDCAGDDLKVLQQFAACFLETLPAQEEQTPKASKRERRDEQ ILAQLLPLLHGNVNGSKVIIREFQEHCRRGLLSNHTGSPRSPSTTYLHTPTPSEDAAIPSKSRLKRLISENSVYEKRPDFRMCWYVHPQV LQSFQQEHLPVPCQWSYVTSVPSAPKEDSGSVPSTGPSQGTPISLKRKSAGSMCITQFMKKRRHDGQIGAEDMDGFQADTEEEEEEEGDC -------------------------------------------------------------- >41799_41799_2_KDM4B-CHAF1A_KDM4B_chr19_5082515_ENST00000381759_CHAF1A_chr19_4418017_ENST00000301280_length(amino acids)=942AA_BP=305 MGSEDHGAQNPSCKIMTFRPTMEEFKDFNKYVAYIESQGAHRAGLAKIIPPKEWKPRQTYDDIDDVVIPAPIQQVVTGQSGLFTQYNIQK KAMTVGEYRRLANSEKYCTPRHQDFDDLERKYWKNLTFVSPIYGADISGSLYDDDVAQWNIGSLRTILDMVERECGTIIEGVNTPYLYFG MWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFPGSSQGCDAFLRHKMTLISPIILKKYGIPFSRITQEAGEFMI TFPYGYHAGFNHGFNCAESTNFATLRWIDYGKVATQITKKFVKGSTEKNKLRLQRDQERLGKQLKLRAEREEKEKLKEEAKRAKEEAKKK KEEEKELKEKERREKREKDEKEKAEKQRLKEERRKERQEALEAKLEEKRKKEEEKRLREEEKRIKAEKAEITRFFQKPKTPQAPKTLAGS CGKFAPFEIKEHMVLAPRRRTAFHPDLCSQLDQLLQQQSGEFSFLKDLKGRQPLRSGPTHVSTRNADIFNSDVVIVERGKGDGVPERRKF GRMKLLQFCENHRPAYWGTWNKKTALIRARDPWAQDTKLLDYEVDSDEEWEEEEPGESLSHSEGDDDDDMGEDEDEDDGFFVPHGYLSED EGVTEECADPENHKVRQKLKAKEWDEFLAKGKRFRVLQPVKIGCVWAADRDCAGDDLKVLQQFAACFLETLPAQEEQTPKASKRERRDEQ ILAQLLPLLHGNVNGSKVIIREFQEHCRRGLLSNHTGSPRSPSTTYLHTPTPSEDAAIPSKSRLKRLISENSVYEKRPDFRMCWYVHPQV LQSFQQEHLPVPCQWSYVTSVPSAPKEDSGSVPSTGPSQGTPISLKRKSAGSMCITQFMKKRRHDGQIGAEDMDGFQADTEEEEEEEGDC -------------------------------------------------------------- >41799_41799_3_KDM4B-CHAF1A_KDM4B_chr19_5082515_ENST00000536461_CHAF1A_chr19_4418017_ENST00000301280_length(amino acids)=942AA_BP=305 MGSEDHGAQNPSCKIMTFRPTMEEFKDFNKYVAYIESQGAHRAGLAKIIPPKEWKPRQTYDDIDDVVIPAPIQQVVTGQSGLFTQYNIQK KAMTVGEYRRLANSEKYCTPRHQDFDDLERKYWKNLTFVSPIYGADISGSLYDDDVAQWNIGSLRTILDMVERECGTIIEGVNTPYLYFG MWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFPGSSQGCDAFLRHKMTLISPIILKKYGIPFSRITQEAGEFMI TFPYGYHAGFNHGFNCAESTNFATLRWIDYGKVATQITKKFVKGSTEKNKLRLQRDQERLGKQLKLRAEREEKEKLKEEAKRAKEEAKKK KEEEKELKEKERREKREKDEKEKAEKQRLKEERRKERQEALEAKLEEKRKKEEEKRLREEEKRIKAEKAEITRFFQKPKTPQAPKTLAGS CGKFAPFEIKEHMVLAPRRRTAFHPDLCSQLDQLLQQQSGEFSFLKDLKGRQPLRSGPTHVSTRNADIFNSDVVIVERGKGDGVPERRKF GRMKLLQFCENHRPAYWGTWNKKTALIRARDPWAQDTKLLDYEVDSDEEWEEEEPGESLSHSEGDDDDDMGEDEDEDDGFFVPHGYLSED EGVTEECADPENHKVRQKLKAKEWDEFLAKGKRFRVLQPVKIGCVWAADRDCAGDDLKVLQQFAACFLETLPAQEEQTPKASKRERRDEQ ILAQLLPLLHGNVNGSKVIIREFQEHCRRGLLSNHTGSPRSPSTTYLHTPTPSEDAAIPSKSRLKRLISENSVYEKRPDFRMCWYVHPQV LQSFQQEHLPVPCQWSYVTSVPSAPKEDSGSVPSTGPSQGTPISLKRKSAGSMCITQFMKKRRHDGQIGAEDMDGFQADTEEEEEEEGDC -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:5082515/chr19:4418017) - 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 |
| KDM4B | CHAF1A |
| FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate. {ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:28262558}. | FUNCTION: Core component of the CAF-1 complex, a complex that is thought to mediate chromatin assembly in DNA replication and DNA repair. Assembles histone octamers onto replicating DNA in vitro. CAF-1 performs the first step of the nucleosome assembly process, bringing newly synthesized histones H3 and H4 to replicating DNA; histones H2A/H2B can bind to this chromatin precursor subsequent to DNA replication to complete the histone octamer. It may play a role in heterochromatin maintenance in proliferating cells by bringing newly synthesized cbx proteins to heterochromatic DNA replication foci. {ECO:0000250|UniProtKB:Q5R1T0}. |
| 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. |
| - 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 | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000159111 | + | 9 | 23 | 146_309 | 306.0 | 1097.0 | Domain | JmjC |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000159111 | + | 9 | 23 | 15_57 | 306.0 | 1097.0 | Domain | JmjN |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000381759 | + | 9 | 12 | 146_309 | 306.0 | 449.0 | Domain | JmjC |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000381759 | + | 9 | 12 | 15_57 | 306.0 | 449.0 | Domain | JmjN |
| Tgene | CHAF1A | chr19:5082515 | chr19:4418017 | ENST00000301280 | 2 | 15 | 323_453 | 320.0 | 957.0 | Compositional bias | Note=Arg/Glu/Lys-rich | |
| Tgene | CHAF1A | chr19:5082515 | chr19:4418017 | ENST00000301280 | 2 | 15 | 602_608 | 320.0 | 957.0 | Compositional bias | Note=Poly-Glu | |
| Tgene | CHAF1A | chr19:5082515 | chr19:4418017 | ENST00000301280 | 2 | 15 | 619_623 | 320.0 | 957.0 | Compositional bias | Note=Poly-Asp | |
| Tgene | CHAF1A | chr19:5082515 | chr19:4418017 | ENST00000301280 | 2 | 15 | 905_911 | 320.0 | 957.0 | Compositional bias | Note=Poly-Glu | |
| Tgene | CHAF1A | chr19:5082515 | chr19:4418017 | ENST00000301280 | 2 | 15 | 642_678 | 320.0 | 957.0 | Region | Note=Necessary for homodimerization and competence for chromatin assembly | |
| Tgene | CHAF1A | chr19:5082515 | chr19:4418017 | ENST00000301280 | 2 | 15 | 660_956 | 320.0 | 957.0 | Region | Note=Binds to p60 |
| - 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 | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000159111 | + | 9 | 23 | 463_535 | 306.0 | 1097.0 | Compositional bias | Note=Pro-rich |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000381759 | + | 9 | 12 | 463_535 | 306.0 | 449.0 | Compositional bias | Note=Pro-rich |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000159111 | + | 9 | 23 | 917_974 | 306.0 | 1097.0 | Domain | Note=Tudor 1 |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000159111 | + | 9 | 23 | 975_1031 | 306.0 | 1097.0 | Domain | Note=Tudor 2 |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000381759 | + | 9 | 12 | 917_974 | 306.0 | 449.0 | Domain | Note=Tudor 1 |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000381759 | + | 9 | 12 | 975_1031 | 306.0 | 449.0 | Domain | Note=Tudor 2 |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000159111 | + | 9 | 23 | 731_789 | 306.0 | 1097.0 | Zinc finger | Note=PHD-type 1 |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000159111 | + | 9 | 23 | 794_827 | 306.0 | 1097.0 | Zinc finger | C2HC pre-PHD-type |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000159111 | + | 9 | 23 | 850_907 | 306.0 | 1097.0 | Zinc finger | PHD-type 2 |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000381759 | + | 9 | 12 | 731_789 | 306.0 | 449.0 | Zinc finger | Note=PHD-type 1 |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000381759 | + | 9 | 12 | 794_827 | 306.0 | 449.0 | Zinc finger | C2HC pre-PHD-type |
| Hgene | KDM4B | chr19:5082515 | chr19:4418017 | ENST00000381759 | + | 9 | 12 | 850_907 | 306.0 | 449.0 | Zinc finger | PHD-type 2 |
| Tgene | CHAF1A | chr19:5082515 | chr19:4418017 | ENST00000301280 | 2 | 15 | 233_246 | 320.0 | 957.0 | Motif | Note=PxVxL motif | |
| Tgene | CHAF1A | chr19:5082515 | chr19:4418017 | ENST00000301280 | 2 | 15 | 1_314 | 320.0 | 957.0 | Region | Note=Binds to CBX1 chromo shadow domain | |
| Tgene | CHAF1A | chr19:5082515 | chr19:4418017 | ENST00000301280 | 2 | 15 | 1_49 | 320.0 | 957.0 | Region | Note=Binds to PCNA |
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Fusion Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| KDM4B | |
| CHAF1A |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to KDM4B-CHAF1A |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to KDM4B-CHAF1A |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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