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Fusion Protein:AP3B1-DCTN4 |
Fusion Gene and Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: AP3B1-DCTN4 | FusionPDB ID: 5266 | FusionGDB2.0 ID: 5266 | Hgene | Tgene | Gene symbol | AP3B1 | DCTN4 | Gene ID | 8546 | 51164 |
Gene name | adaptor related protein complex 3 subunit beta 1 | dynactin subunit 4 | |
Synonyms | ADTB3|ADTB3A|HPS|HPS2|PE | DYN4|P62 | |
Cytomap | 5q14.1 | 5q33.1 | |
Type of gene | protein-coding | protein-coding | |
Description | AP-3 complex subunit beta-1AP-3 complex beta-3A subunitadaptor protein complex AP-3 subunit beta-1adaptor related protein complex 3 beta 1 subunitbeta-3A-adaptinclathrin assembly protein complex 3 beta-1 large chain | dynactin subunit 4dynactin 4 (p62)dynactin p62 subunitdynactin subunit p62 | |
Modification date | 20200313 | 20200313 | |
UniProtAcc | O00203 Main function of 5'-partner protein: FUNCTION: Subunit of non-clathrin- and clathrin-associated adaptor protein complex 3 (AP-3) that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. AP-3 appears to be involved in the sorting of a subset of transmembrane proteins targeted to lysosomes and lysosome-related organelles. In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals. {ECO:0000305|PubMed:9151686}. | Q9UJW0 Main function of 5'-partner protein: FUNCTION: Could have a dual role in dynein targeting and in ACTR1A/Arp1 subunit of dynactin pointed-end capping. Could be involved in ACTR1A pointed-end binding and in additional roles in linking dynein and dynactin to the cortical cytoskeleton. | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000255194, ENST00000519295, ENST00000523204, | ENST00000424236, ENST00000446090, ENST00000521093, ENST00000447998, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 10 X 12 X 6=720 | 5 X 7 X 4=140 |
# samples | 12 | 7 | |
** MAII score | log2(12/720*10)=-2.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(7/140*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Fusion gene context | PubMed: AP3B1 [Title/Abstract] AND DCTN4 [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: AP3B1 [Title/Abstract] AND DCTN4 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | AP3B1(77423854)-DCTN4(150136049), # samples:2 | ||
Anticipated loss of major functional domain due to fusion event. | AP3B1-DCTN4 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. AP3B1-DCTN4 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 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:77423854/chr5:150136049) - 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) |
ENST00000255194 | AP3B1 | chr5 | 77423854 | - | ENST00000447998 | DCTN4 | chr5 | 150136049 | - | 6101 | 2144 | 65 | 3391 | 1108 |
ENST00000519295 | AP3B1 | chr5 | 77423854 | - | ENST00000447998 | DCTN4 | chr5 | 150136049 | - | 6050 | 2093 | 272 | 3340 | 1022 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000255194 | ENST00000447998 | AP3B1 | chr5 | 77423854 | - | DCTN4 | chr5 | 150136049 | - | 0.00019585 | 0.9998042 |
ENST00000519295 | ENST00000447998 | AP3B1 | chr5 | 77423854 | - | DCTN4 | chr5 | 150136049 | - | 0.000208563 | 0.99979144 |
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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 AP3B1-DCTN4 |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
AP3B1 | chr5 | 77423854 | DCTN4 | chr5 | 150136049 | 2093 | 607 | PDPSVRNVEVIELVDSHYCPSCLENM |
AP3B1 | chr5 | 77423854 | DCTN4 | chr5 | 150136049 | 2144 | 693 | PDPSVRNVEVIELVDSHYCPSCLENM |
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Potential FusionNeoAntigen Information of AP3B1-DCTN4 in HLA I |
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AP3B1-DCTN4_77423854_150136049.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) |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B18:01 | IELVDSHY | 0.9978 | 0.7813 | 10 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B13:02 | RNVEVIELV | 0.8237 | 0.5571 | 5 | 14 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B15:02 | EVIELVDSHY | 0.9928 | 0.7177 | 8 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B15:31 | VIELVDSHY | 0.8602 | 0.685 | 9 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B15:31 | EVIELVDSHY | 0.9896 | 0.654 | 8 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B18:06 | IELVDSHY | 0.9979 | 0.7853 | 10 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B18:05 | IELVDSHY | 0.9978 | 0.7813 | 10 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B18:11 | IELVDSHY | 0.9863 | 0.7172 | 10 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-A25:01 | EVIELVDSH | 0.9895 | 0.7222 | 8 | 17 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-A25:01 | EVIELVDSHY | 0.9988 | 0.6261 | 8 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B35:20 | EVIELVDSHY | 0.9872 | 0.7202 | 8 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B15:08 | EVIELVDSHY | 0.976 | 0.5977 | 8 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B15:11 | EVIELVDSHY | 0.9724 | 0.5977 | 8 | 18 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | HLA-B35:43 | EVIELVDSHY | 0.9686 | 0.6033 | 8 | 18 |
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Potential FusionNeoAntigen Information of AP3B1-DCTN4 in HLA II |
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AP3B1-DCTN4_77423854_150136049.msa |
![]() * 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) |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | DRB1-1410 | DPSVRNVEVIELVDS | 1 | 16 |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 | DRB1-1410 | PDPSVRNVEVIELVD | 0 | 15 |
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Fusion breakpoint peptide structures of AP3B1-DCTN4 |
![]() * 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 |
6434 | NVEVIELVDSHYCP | AP3B1 | DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 2144 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of AP3B1-DCTN4 |
![]() * 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 | 6434 | NVEVIELVDSHYCP | -6.69561 | -6.80901 |
HLA-B14:02 | 3BVN | 6434 | NVEVIELVDSHYCP | -4.57314 | -5.60844 |
HLA-B52:01 | 3W39 | 6434 | NVEVIELVDSHYCP | -8.26982 | -8.38322 |
HLA-B52:01 | 3W39 | 6434 | NVEVIELVDSHYCP | -4.20619 | -5.24149 |
HLA-A11:01 | 4UQ2 | 6434 | NVEVIELVDSHYCP | -6.38936 | -6.50276 |
HLA-A11:01 | 4UQ2 | 6434 | NVEVIELVDSHYCP | -5.4102 | -6.4455 |
HLA-A24:02 | 5HGA | 6434 | NVEVIELVDSHYCP | -7.10684 | -7.22024 |
HLA-A24:02 | 5HGA | 6434 | NVEVIELVDSHYCP | -5.37582 | -6.41112 |
HLA-B44:05 | 3DX8 | 6434 | NVEVIELVDSHYCP | -5.61918 | -5.73258 |
HLA-B44:05 | 3DX8 | 6434 | NVEVIELVDSHYCP | -4.56468 | -5.59998 |
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Vaccine Design for the FusionNeoAntigens of AP3B1-DCTN4 |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 10 | 18 | IELVDSHY | ATAGAGTTGGTGGACTCCCATTAT |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 5 | 14 | RNVEVIELV | CGAAATGTAGAAGTAATAGAGTTGGTG |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 8 | 17 | EVIELVDSH | GAAGTAATAGAGTTGGTGGACTCCCAT |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 8 | 18 | EVIELVDSHY | GAAGTAATAGAGTTGGTGGACTCCCATTAT |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 9 | 18 | VIELVDSHY | GTAATAGAGTTGGTGGACTCCCATTAT |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 0 | 15 | PDPSVRNVEVIELVD | CCCGACCCATCAGTTCGAAATGTAGAAGTAATAGAGTTGGTGGAC |
AP3B1-DCTN4 | chr5 | 77423854 | chr5 | 150136049 | 1 | 16 | DPSVRNVEVIELVDS | GACCCATCAGTTCGAAATGTAGAAGTAATAGAGTTGGTGGACTCC |
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Information of the samples that have these potential fusion neoantigens of AP3B1-DCTN4 |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
KIRC | AP3B1-DCTN4 | chr5 | 77423854 | ENST00000255194 | chr5 | 150136049 | ENST00000447998 | TCGA-BP-4986-01A |
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Potential target of CAR-T therapy development for AP3B1-DCTN4 |
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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 AP3B1-DCTN4 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to AP3B1-DCTN4 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |