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Fusion Protein:CUX1-YEATS2 |
Fusion Gene and Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: CUX1-YEATS2 | FusionPDB ID: 20746 | FusionGDB2.0 ID: 20746 | Hgene | Tgene | Gene symbol | CUX1 | YEATS2 | Gene ID | 1523 | 55689 |
Gene name | cut like homeobox 1 | YEATS domain containing 2 | |
Synonyms | CASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75 | FAME4 | |
Cytomap | 7q22.1 | 3q27.1 | |
Type of gene | protein-coding | protein-coding | |
Description | protein CASPHomeobox protein cut-like 1CCAAT displacement proteinCUX1 gene Alternatively Spliced Productcut homologgolgi integral membrane protein 6homeobox protein cux-1putative protein product of Nbla10317 | YEATS domain-containing protein 2 | |
Modification date | 20200320 | 20200313 | |
UniProtAcc | P39880 Main function of 5'-partner protein: FUNCTION: Transcription factor involved in the control of neuronal differentiation in the brain. Regulates dendrite development and branching, and dendritic spine formation in cortical layers II-III. Also involved in the control of synaptogenesis. In addition, it has probably a broad role in mammalian development as a repressor of developmentally regulated gene expression. May act by preventing binding of positively-activing CCAAT factors to promoters. Component of nf-munr repressor; binds to the matrix attachment regions (MARs) (5' and 3') of the immunoglobulin heavy chain enhancer. Represses T-cell receptor (TCR) beta enhancer function by binding to MARbeta, an ATC-rich DNA sequence located upstream of the TCR beta enhancer. Binds to the TH enhancer; may require the basic helix-loop-helix protein TCF4 as a coactivator. {ECO:0000250|UniProtKB:P53564}.; FUNCTION: [CDP/Cux p110]: Plays a role in cell cycle progression, in particular at the G1/S transition. As cells progress into S phase, a fraction of CUX1 molecules is proteolytically processed into N-terminally truncated proteins of 110 kDa. While CUX1 only transiently binds to DNA and carries the CCAAT-displacement activity, CDP/Cux p110 makes a stable interaction with DNA and stimulates expression of genes such as POLA1. {ECO:0000269|PubMed:15099520}. | . | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000292538, ENST00000360264, ENST00000393824, ENST00000425244, ENST00000437600, ENST00000547394, ENST00000292535, ENST00000546411, ENST00000549414, ENST00000550008, ENST00000556210, ENST00000560541, | ENST00000305135, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 32 X 26 X 13=10816 | 9 X 8 X 5=360 |
# samples | 37 | 9 | |
** MAII score | log2(37/10816*10)=-4.86949797576587 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(9/360*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Fusion gene context | PubMed: CUX1 [Title/Abstract] AND YEATS2 [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: CUX1 [Title/Abstract] AND YEATS2 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CUX1(101459373)-YEATS2(183490093), # samples:2 | ||
Anticipated loss of major functional domain due to fusion event. | CUX1-YEATS2 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. CUX1-YEATS2 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. CUX1-YEATS2 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. CUX1-YEATS2 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) |
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Partner | Gene | GO ID | GO term | PubMed ID |
Tgene | YEATS2 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 18838386 |
Tgene | YEATS2 | GO:0043966 | histone H3 acetylation | 18838386 |
Tgene | YEATS2 | GO:0045892 | negative regulation of transcription, DNA-templated | 18838386 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr7:101459373/chr3:183490093) - 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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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * 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 Amino Acid Sequences |
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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) |
ENST00000437600 | CUX1 | chr7 | 101459373 | + | ENST00000305135 | YEATS2 | chr3 | 183490093 | + | 4779 | 415 | 352 | 2736 | 794 |
ENST00000292538 | CUX1 | chr7 | 101459373 | + | ENST00000305135 | YEATS2 | chr3 | 183490093 | + | 4453 | 89 | 26 | 2410 | 794 |
ENST00000393824 | CUX1 | chr7 | 101459373 | + | ENST00000305135 | YEATS2 | chr3 | 183490093 | + | 4450 | 86 | 23 | 2407 | 794 |
ENST00000547394 | CUX1 | chr7 | 101459373 | + | ENST00000305135 | YEATS2 | chr3 | 183490093 | + | 4449 | 85 | 22 | 2406 | 794 |
ENST00000360264 | CUX1 | chr7 | 101459373 | + | ENST00000305135 | YEATS2 | chr3 | 183490093 | + | 4447 | 83 | 20 | 2404 | 794 |
ENST00000425244 | CUX1 | chr7 | 101459373 | + | ENST00000305135 | YEATS2 | chr3 | 183490093 | + | 4437 | 73 | 10 | 2394 | 794 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000437600 | ENST00000305135 | CUX1 | chr7 | 101459373 | + | YEATS2 | chr3 | 183490093 | + | 0.005676038 | 0.99432397 |
ENST00000292538 | ENST00000305135 | CUX1 | chr7 | 101459373 | + | YEATS2 | chr3 | 183490093 | + | 0.004709894 | 0.99529016 |
ENST00000393824 | ENST00000305135 | CUX1 | chr7 | 101459373 | + | YEATS2 | chr3 | 183490093 | + | 0.004712359 | 0.99528766 |
ENST00000547394 | ENST00000305135 | CUX1 | chr7 | 101459373 | + | YEATS2 | chr3 | 183490093 | + | 0.004700045 | 0.99529994 |
ENST00000360264 | ENST00000305135 | CUX1 | chr7 | 101459373 | + | YEATS2 | chr3 | 183490093 | + | 0.004676187 | 0.99532384 |
ENST00000425244 | ENST00000305135 | CUX1 | chr7 | 101459373 | + | YEATS2 | chr3 | 183490093 | + | 0.004726671 | 0.9952734 |
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Get the fusion protein sequences from here. |
Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for CUX1-YEATS2 |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 415 | 111 | PQKSGSQGSVMATLQLPATNLANLAN |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 415 | 20 | MFQYWKRFDLQQLQVVGVPVGSALPS |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 73 | 111 | PQKSGSQGSVMATLQLPATNLANLAN |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 73 | 20 | MFQYWKRFDLQQLQVVGVPVGSALPS |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 83 | 111 | PQKSGSQGSVMATLQLPATNLANLAN |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 83 | 20 | MFQYWKRFDLQQLQVVGVPVGSALPS |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 85 | 111 | PQKSGSQGSVMATLQLPATNLANLAN |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 85 | 20 | MFQYWKRFDLQQLQVVGVPVGSALPS |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 86 | 111 | PQKSGSQGSVMATLQLPATNLANLAN |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 86 | 20 | MFQYWKRFDLQQLQVVGVPVGSALPS |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 89 | 111 | PQKSGSQGSVMATLQLPATNLANLAN |
CUX1 | chr7 | 101459373 | YEATS2 | chr3 | 183490093 | 89 | 20 | MFQYWKRFDLQQLQVVGVPVGSALPS |
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Potential FusionNeoAntigen Information of CUX1-YEATS2 in HLA I |
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CUX1-YEATS2_101459373_183490093.msa |
![]() * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B48:01 | SQGSVMATL | 0.9749 | 0.6897 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B39:01 | SQGSVMATL | 0.9439 | 0.8717 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B39:13 | SQGSVMATL | 0.9195 | 0.9159 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-A02:38 | TLQLPATNL | 0.7562 | 0.8672 | 12 | 21 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-A02:21 | SQGSVMATL | 0.7085 | 0.5397 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B13:02 | SQGSVMATL | 0.6539 | 0.7383 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B13:01 | SQGSVMATL | 0.5322 | 0.9778 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-A02:17 | TLQLPATNL | 0.5178 | 0.8167 | 12 | 21 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B39:09 | SQGSVMATL | 0.9427 | 0.7549 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B39:08 | SQGSVMATL | 0.9042 | 0.8072 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B39:05 | SQGSVMATL | 0.8887 | 0.8605 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B15:04 | SQGSVMATL | 0.7752 | 0.8815 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-C15:02 | GSVMATLQL | 0.999 | 0.8539 | 7 | 16 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-C15:05 | GSVMATLQL | 0.9988 | 0.8869 | 7 | 16 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B39:02 | SQGSVMATL | 0.9566 | 0.9143 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-C01:03 | TLQLPATNL | 0.8697 | 0.9756 | 12 | 21 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B15:73 | SQGSVMATL | 0.8637 | 0.8797 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B39:11 | SQGSVMATL | 0.8469 | 0.7266 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B15:73 | TLQLPATNL | 0.7957 | 0.9921 | 12 | 21 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B15:30 | SQGSVMATL | 0.7645 | 0.8129 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-A02:06 | SQGSVMATL | 0.7085 | 0.5397 | 5 | 14 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B15:30 | TLQLPATNL | 0.6851 | 0.9908 | 12 | 21 |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 | HLA-B40:21 | TLQLPATNL | 0.0471 | 0.8709 | 12 | 21 |
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Potential FusionNeoAntigen Information of CUX1-YEATS2 in HLA II |
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![]() * We used NetMHCIIpan v4.1 (%rank<0.5). |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of CUX1-YEATS2 |
![]() * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
7289 | QGSVMATLQLPATN | CUX1 | YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 89 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CUX1-YEATS2 |
![]() * We used Glide to predict the interaction between HLAs and neoantigens. |
HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
HLA-B14:02 | 3BVN | 7289 | QGSVMATLQLPATN | -5.6364 | -5.6364 |
HLA-A24:02 | 5HGA | 7289 | QGSVMATLQLPATN | -9.18993 | -9.18993 |
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Vaccine Design for the FusionNeoAntigens of CUX1-YEATS2 |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 12 | 21 | TLQLPATNL | CAGGTTGTCGGGGTACCAGTTGGGTCT |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 5 | 14 | SQGSVMATL | CGCTTTGATTTACAGCAGCTGCAGGTT |
CUX1-YEATS2 | chr7 | 101459373 | chr3 | 183490093 | 7 | 16 | GSVMATLQL | GATTTACAGCAGCTGCAGGTTGTCGGG |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of CUX1-YEATS2 |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
PRAD | CUX1-YEATS2 | chr7 | 101459373 | ENST00000292538 | chr3 | 183490093 | ENST00000305135 | TCGA-ZG-A9L1-01A |
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Potential target of CAR-T therapy development for CUX1-YEATS2 |
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![]() * Minus value of BPloci means that the break point is located before the CDS. |
- In-frame and retained 'Transmembrane'. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
![]() * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to CUX1-YEATS2 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to CUX1-YEATS2 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |