|
Fusion gene ID: 10466 |
FusionGeneSummary for DPF3_TDP1 |
Fusion gene summary |
Fusion gene information | Fusion gene name: DPF3_TDP1 | Fusion gene ID: 10466 | Hgene | Tgene | Gene symbol | DPF3 | TDP1 | Gene ID | 8110 | 55775 |
Gene name | double PHD fingers 3 | tyrosyl-DNA phosphodiesterase 1 | |
Synonyms | BAF45C|CERD4 | - | |
Cytomap | 14q24.2 | 14q32.11 | |
Type of gene | protein-coding | protein-coding | |
Description | zinc finger protein DPF3BRG1-associated factor 45CD4, zinc and double PHD fingers, family 3zinc finger protein cer-d4 | tyrosyl-DNA phosphodiesterase 1tyr-DNA phosphodiesterase 1 | |
Modification date | 20180523 | 20180523 | |
UniProtAcc | Q92784 | Q9NUW8 | |
Ensembl transtripts involved in fusion gene | ENST00000556509, ENST00000557704, ENST00000541685, ENST00000546183, | ENST00000393452, ENST00000393454, ENST00000335725, ENST00000555565, ENST00000357382, ENST00000555880, | |
Fusion gene scores | * DoF score | 1 X 1 X 1=1 | 3 X 3 X 2=18 |
# samples | 1 | 3 | |
** MAII score | log2(1/1*10)=3.32192809488736 | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
Context | PubMed: DPF3 [Title/Abstract] AND TDP1 [Title/Abstract] AND fusion [Title/Abstract] | ||
Functional or gene categories assigned by FusionGDB annotation | DDR (DNA damage repair) gene involved fusion gene, retained protein feature but frameshift. |
* 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 |
Tgene | TDP1 | GO:0000012 | single strand break repair | 15811850 |
Tgene | TDP1 | GO:0006281 | DNA repair | 17948061 |
Tgene | TDP1 | GO:0006302 | double-strand break repair | 12023295 |
Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
TCGA | RV | LGG | TCGA-P5-A77W-01A | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
* LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
Frame-shift | ENST00000556509 | ENST00000393452 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
Frame-shift | ENST00000556509 | ENST00000393454 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
Frame-shift | ENST00000556509 | ENST00000335725 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
5CDS-3UTR | ENST00000556509 | ENST00000555565 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
5CDS-5UTR | ENST00000556509 | ENST00000357382 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
5CDS-5UTR | ENST00000556509 | ENST00000555880 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
intron-3CDS | ENST00000557704 | ENST00000393452 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
intron-3CDS | ENST00000557704 | ENST00000393454 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
intron-3CDS | ENST00000557704 | ENST00000335725 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
intron-3UTR | ENST00000557704 | ENST00000555565 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
intron-5UTR | ENST00000557704 | ENST00000357382 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
intron-5UTR | ENST00000557704 | ENST00000555880 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
Frame-shift | ENST00000541685 | ENST00000393452 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
Frame-shift | ENST00000541685 | ENST00000393454 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
Frame-shift | ENST00000541685 | ENST00000335725 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
5CDS-3UTR | ENST00000541685 | ENST00000555565 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
5CDS-5UTR | ENST00000541685 | ENST00000357382 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
5CDS-5UTR | ENST00000541685 | ENST00000555880 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
Frame-shift | ENST00000546183 | ENST00000393452 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
Frame-shift | ENST00000546183 | ENST00000393454 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
Frame-shift | ENST00000546183 | ENST00000335725 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
5CDS-3UTR | ENST00000546183 | ENST00000555565 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
5CDS-5UTR | ENST00000546183 | ENST00000357382 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
5CDS-5UTR | ENST00000546183 | ENST00000555880 | DPF3 | chr14 | 73219972 | - | TDP1 | chr14 | 90437519 | + |
Top |
FusionProtFeatures for DPF3_TDP1 |
Main function of each fusion partner protein. (from UniProt) |
Hgene | Tgene |
DPF3 | TDP1 |
Belongs to the neuron-specific chromatin remodelingcomplex (nBAF complex). During neural development a switch from astem/progenitor to a post-mitotic chromatin remodeling mechanismoccurs as neurons exit the cell cycle and become committed totheir adult state. The transition from proliferating neuralstem/progenitor cells to post-mitotic neurons requires a switch insubunit composition of the npBAF and nBAF complexes. As neuralprogenitors exit mitosis and differentiate into neurons, npBAFcomplexes which contain ACTL6A/BAF53A and PHF10/BAF45A, areexchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45Bor DPF3/BAF45C subunits in neuron-specific complexes (nBAF). ThenpBAF complex is essential for the self-renewal/proliferativecapacity of the multipotent neural stem cells. The nBAF complexalong with CREST plays a role regulating the activity of genesessential for dendrite growth (By similarity). Muscle-specificcomponent of the BAF complex, a multiprotein complex involved intranscriptional activation and repression of select genes bychromatin remodeling (alteration of DNA-nucleosome topology).Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac,H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it actsas a tissue-specific anchor between histone acetylations andmethylations and chromatin remodeling. It thereby probably playsan essential role in heart and skeletal muscle development.{ECO:0000250, ECO:0000269|PubMed:18765789}. | DNA repair enzyme that can remove a variety of covalentadducts from DNA through hydrolysis of a 3'-phosphodiester bond,giving rise to DNA with a free 3' phosphate. Catalyzes thehydrolysis of dead-end complexes between DNA and the topoisomeraseI active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates onprotruding 3' ends on DNA double-strand breaks due to DNA damageby radiation and free radicals. Acts on blunt-ended double-strandDNA breaks and on single-stranded DNA. Has low 3'exonucleaseactivity and can remove a single nucleoside from the 3'end of DNAand RNA molecules with 3'hydroxyl groups. Has no exonucleaseactivity towards DNA or RNA with a 3'phosphate.{ECO:0000269|PubMed:12023295, ECO:0000269|PubMed:15111055,ECO:0000269|PubMed:15811850, ECO:0000269|PubMed:16141202,ECO:0000269|PubMed:22822062}. |
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. |
- In-frame and 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 |
- In-frame and 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 |
Top |
FusionGeneSequence for DPF3_TDP1 |
For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
* Fusion amino acid sequences. |
* Fusion transcript sequences (only coding sequence (CDS) region). |
* Fusion transcript sequences (Full-length transcript). |
Top |
FusionGenePPI for DPF3_TDP1 |
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 (BIOGRID-3.4.160) |
Hgene | Hgene's interactors | Tgene | Tgene's interactors |
DPF3 | RELA, NFKB1, SMARCA4, SMARCA2, SMARCC1, SMARCD1, SMARCB1, ARID1A, ARID1B, SMARCC2, SMARCD3, SMARCD2, ARID2, PBRM1, BRD7, SMARCE1, BCL7A, BCL7C, BCL7B, ACTL6A, ACTL6B, SS18, SS18L1, AGMAT, NEUROD1, CSNK2A1, CSNK2A2, CSNK2B, SNRNP200, UBR5, UBR4, HDGFRP3, HSPA1L, IGKC, AIFM1, TECR, TUBA8, TUBA3E, XPOT, EEF1A2, TIMM50, AHSA1, HEY1, DCX | TDP1 | ATM, VAMP2, MOV10, NUP153, POLB, APLF, GOLGA1, VCP, CETN1, CSNK1D |
- Retained PPIs in in-frame fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
- Lost PPIs in in-frame fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
- Retained PPIs, but lost function due to frame-shift fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
Top |
RelatedDrugs for DPF3_TDP1 |
Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for DPF3_TDP1 |
Diseases associated with fusion partners. (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Tgene | TDP1 | C1846574 | SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE, WITH AXONAL NEUROPATHY | 1 | CTD_human;ORPHANET;UNIPROT |