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Fusion Protein:CDKAL1-E2F3 |
Fusion Gene and Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: CDKAL1-E2F3 | FusionPDB ID: 15329 | FusionGDB2.0 ID: 15329 | Hgene | Tgene | Gene symbol | CDKAL1 | E2F3 | Gene ID | 54901 | 1871 |
Gene name | CDK5 regulatory subunit associated protein 1 like 1 | E2F transcription factor 3 | |
Synonyms | - | E2F-3 | |
Cytomap | 6p22.3 | 6p22.3 | |
Type of gene | protein-coding | protein-coding | |
Description | threonylcarbamoyladenosine tRNA methylthiotransferasetRNA-t(6)A37 methylthiotransferase | transcription factor E2F3 | |
Modification date | 20200322 | 20200322 | |
UniProtAcc | Q5VV42 Main function of 5'-partner protein: FUNCTION: Catalyzes the methylthiolation of N6-threonylcarbamoyladenosine (t(6)A), leading to the formation of 2-methylthio-N6-threonylcarbamoyladenosine (ms(2)t(6)A) at position 37 in tRNAs that read codons beginning with adenine. {ECO:0000250|UniProtKB:Q91WE6}. | O00716 Main function of 5'-partner protein: FUNCTION: Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F3 binds specifically to RB1 in a cell-cycle dependent manner. Inhibits adipogenesis, probably through the repression of CEBPA binding to its target gene promoters (By similarity). {ECO:0000250|UniProtKB:O35261}. | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000274695, ENST00000378610, ENST00000378624, ENST00000476517, | ENST00000346618, ENST00000535432, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 37 X 20 X 14=10360 | 4 X 5 X 5=100 |
# samples | 39 | 6 | |
** MAII score | log2(39/10360*10)=-4.73140606882431 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(6/100*10)=-0.736965594166206 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Fusion gene context | PubMed: CDKAL1 [Title/Abstract] AND E2F3 [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: CDKAL1 [Title/Abstract] AND E2F3 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CDKAL1(20548936)-E2F3(20480077), # samples:2 E2F3(20404063)-CDKAL1(20846306), # samples:1 E2F3(20404063)-CDKAL1(20546577), # samples:1 E2F3(20404063)-CDKAL1(20955650), # samples:1 | ||
Anticipated loss of major functional domain due to fusion event. | CDKAL1-E2F3 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. CDKAL1-E2F3 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. CDKAL1-E2F3 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. CDKAL1-E2F3 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. CDKAL1-E2F3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. CDKAL1-E2F3 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF. CDKAL1-E2F3 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF. E2F3-CDKAL1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. E2F3-CDKAL1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. E2F3-CDKAL1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted 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 | E2F3 | GO:0000082 | G1/S transition of mitotic cell cycle | 17062573 |
Tgene | E2F3 | GO:0006606 | protein import into nucleus | 17062573 |
Tgene | E2F3 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 7739537 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr6:20548936/chr6:20480077) - 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) |
ENST00000274695 | CDKAL1 | chr6 | 20739846 | + | ENST00000346618 | E2F3 | chr6 | 20488343 | + | 4314 | 635 | 167 | 1033 | 288 |
ENST00000274695 | CDKAL1 | chr6 | 20739846 | + | ENST00000535432 | E2F3 | chr6 | 20488343 | + | 4162 | 635 | 167 | 1033 | 288 |
ENST00000378624 | CDKAL1 | chr6 | 20739846 | + | ENST00000346618 | E2F3 | chr6 | 20488343 | + | 4201 | 522 | 264 | 920 | 218 |
ENST00000378624 | CDKAL1 | chr6 | 20739846 | + | ENST00000535432 | E2F3 | chr6 | 20488343 | + | 4049 | 522 | 264 | 920 | 218 |
ENST00000378610 | CDKAL1 | chr6 | 20739846 | + | ENST00000346618 | E2F3 | chr6 | 20488343 | + | 4157 | 478 | 10 | 876 | 288 |
ENST00000378610 | CDKAL1 | chr6 | 20739846 | + | ENST00000535432 | E2F3 | chr6 | 20488343 | + | 4005 | 478 | 10 | 876 | 288 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000274695 | ENST00000346618 | CDKAL1 | chr6 | 20739846 | + | E2F3 | chr6 | 20488343 | + | 0.000462702 | 0.99953735 |
ENST00000274695 | ENST00000535432 | CDKAL1 | chr6 | 20739846 | + | E2F3 | chr6 | 20488343 | + | 0.000466189 | 0.9995338 |
ENST00000378624 | ENST00000346618 | CDKAL1 | chr6 | 20739846 | + | E2F3 | chr6 | 20488343 | + | 0.000597881 | 0.99940217 |
ENST00000378624 | ENST00000535432 | CDKAL1 | chr6 | 20739846 | + | E2F3 | chr6 | 20488343 | + | 0.000511025 | 0.99948895 |
ENST00000378610 | ENST00000346618 | CDKAL1 | chr6 | 20739846 | + | E2F3 | chr6 | 20488343 | + | 0.000457641 | 0.99954236 |
ENST00000378610 | ENST00000535432 | CDKAL1 | chr6 | 20739846 | + | E2F3 | chr6 | 20488343 | + | 0.000462426 | 0.9995376 |
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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 CDKAL1-E2F3 |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
CDKAL1 | chr6 | 20739846 | E2F3 | chr6 | 20488343 | 478 | 156 | PRQDYLKGLSIIGSLQIHLASTQGPI |
CDKAL1 | chr6 | 20739846 | E2F3 | chr6 | 20488343 | 522 | 86 | PRQDYLKGLSIIGSLQIHLASTQGPI |
CDKAL1 | chr6 | 20739846 | E2F3 | chr6 | 20488343 | 635 | 156 | PRQDYLKGLSIIGSLQIHLASTQGPI |
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Potential FusionNeoAntigen Information of CDKAL1-E2F3 in HLA I |
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CDKAL1-E2F3_20739846_20488343.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) |
CDKAL1-E2F3 | chr6 | 20739846 | chr6 | 20488343 | 635 | HLA-C15:06 | LSIIGSLQI | 0.9982 | 0.5519 | 8 | 17 |
CDKAL1-E2F3 | chr6 | 20739846 | chr6 | 20488343 | 635 | HLA-C15:05 | LSIIGSLQI | 0.9981 | 0.5674 | 8 | 17 |
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Potential FusionNeoAntigen Information of CDKAL1-E2F3 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 CDKAL1-E2F3 |
![]() * 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 |
4259 | KGLSIIGSLQIHLA | CDKAL1 | E2F3 | chr6 | 20739846 | chr6 | 20488343 | 635 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDKAL1-E2F3 |
![]() * 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 | 4259 | KGLSIIGSLQIHLA | -5.6364 | -5.6364 |
HLA-A24:02 | 5HGA | 4259 | KGLSIIGSLQIHLA | -9.18993 | -9.18993 |
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Vaccine Design for the FusionNeoAntigens of CDKAL1-E2F3 |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
CDKAL1-E2F3 | chr6 | 20739846 | chr6 | 20488343 | 8 | 17 | LSIIGSLQI | CTGAGTATCATTGGGAGCCTACAAATA |
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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 CDKAL1-E2F3 |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
ESCA | CDKAL1-E2F3 | chr6 | 20739846 | ENST00000274695 | chr6 | 20488343 | ENST00000346618 | TCGA-JY-A6FH |
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Potential target of CAR-T therapy development for CDKAL1-E2F3 |
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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 CDKAL1-E2F3 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to CDKAL1-E2F3 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |