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Fusion Protein:LDB1-PCGF6 |
Fusion Gene and Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: LDB1-PCGF6 | FusionPDB ID: 44303 | FusionGDB2.0 ID: 44303 | Hgene | Tgene | Gene symbol | LDB1 | PCGF6 | Gene ID | 9079 | 84108 |
Gene name | LIM domain binding 2 | polycomb group ring finger 6 | |
Synonyms | CLIM1|LDB-2|LDB1 | MBLR|RNF134 | |
Cytomap | 4p15.32 | 10q24.33 | |
Type of gene | protein-coding | protein-coding | |
Description | LIM domain-binding protein 2LIM binding domain 2LIM domain-binding factor CLIM1LIM domain-binding factor-2carboxyl-terminal LIM domain-binding protein 1 | polycomb group RING finger protein 6Mel18 and Bmi1-like RING finger proteinring finger protein 134 | |
Modification date | 20200313 | 20200320 | |
UniProtAcc | Q86U70 Main function of 5'-partner protein: FUNCTION: Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. Plays a role in the development of interneurons and motor neurons in cooperation with LHX3 and ISL1. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression. Acts with LMO2 in the regulation of red blood cell development, maintaining erythroid precursors in an immature state (By similarity). {ECO:0000250|UniProtKB:P70662}. | . | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000425280, ENST00000490751, ENST00000361198, | ENST00000490296, ENST00000337211, ENST00000369847, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 2 X 2 X 2=8 | 3 X 3 X 2=18 |
# samples | 2 | 3 | |
** MAII score | log2(2/8*10)=1.32192809488736 | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
Fusion gene context | PubMed: LDB1 [Title/Abstract] AND PCGF6 [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: LDB1 [Title/Abstract] AND PCGF6 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | LDB1(103879843)-PCGF6(105086389), # samples:1 | ||
Anticipated loss of major functional domain due to fusion event. | LDB1-PCGF6 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. LDB1-PCGF6 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 | PCGF6 | GO:0045892 | negative regulation of transcription, DNA-templated | 8521824 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr10:103879843/chr10:105086389) - 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) |
ENST00000425280 | LDB1 | chr10 | 103879843 | - | ENST00000337211 | PCGF6 | chr10 | 105086389 | - | 1720 | 368 | 139 | 453 | 104 |
ENST00000425280 | LDB1 | chr10 | 103879843 | - | ENST00000369847 | PCGF6 | chr10 | 105086389 | - | 1720 | 368 | 139 | 453 | 104 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000425280 | ENST00000337211 | LDB1 | chr10 | 103879843 | - | PCGF6 | chr10 | 105086389 | - | 0.40133005 | 0.59866995 |
ENST00000425280 | ENST00000369847 | LDB1 | chr10 | 103879843 | - | PCGF6 | chr10 | 105086389 | - | 0.40133005 | 0.59866995 |
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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 LDB1-PCGF6 |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
LDB1 | chr10 | 103879843 | PCGF6 | chr10 | 105086389 | 368 | 76 | AGDVKMSVGCACPAIGKEVCSSFRRS |
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Potential FusionNeoAntigen Information of LDB1-PCGF6 in HLA I |
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![]() * 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) |
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Potential FusionNeoAntigen Information of LDB1-PCGF6 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 LDB1-PCGF6 |
![]() * 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. |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of LDB1-PCGF6 |
![]() * We used Glide to predict the interaction between HLAs and neoantigens. |
HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
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Vaccine Design for the FusionNeoAntigens of LDB1-PCGF6 |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
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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 LDB1-PCGF6 |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
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Potential target of CAR-T therapy development for LDB1-PCGF6 |
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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 LDB1-PCGF6 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to LDB1-PCGF6 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |