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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 10466

FusionGeneSummary for DPF3_TDP1

check button Fusion gene summary
Fusion gene informationFusion gene name: DPF3_TDP1
Fusion gene ID: 10466
HgeneTgene
Gene symbol

DPF3

TDP1

Gene ID

8110

55775

Gene namedouble PHD fingers 3tyrosyl-DNA phosphodiesterase 1
SynonymsBAF45C|CERD4-
Cytomap

14q24.2

14q32.11

Type of geneprotein-codingprotein-coding
Descriptionzinc finger protein DPF3BRG1-associated factor 45CD4, zinc and double PHD fingers, family 3zinc finger protein cer-d4tyrosyl-DNA phosphodiesterase 1tyr-DNA phosphodiesterase 1
Modification date2018052320180523
UniProtAcc

Q92784

Q9NUW8

Ensembl transtripts involved in fusion geneENST00000556509, ENST00000557704, 
ENST00000541685, ENST00000546183, 
ENST00000393452, ENST00000393454, 
ENST00000335725, ENST00000555565, 
ENST00000357382, ENST00000555880, 
Fusion gene scores* DoF score1 X 1 X 1=13 X 3 X 2=18
# samples 13
** MAII scorelog2(1/1*10)=3.32192809488736log2(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 annotationDDR (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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneTDP1

GO:0000012

single strand break repair

15811850

TgeneTDP1

GO:0006281

DNA repair

17948061

TgeneTDP1

GO:0006302

double-strand break repair

12023295


check button 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 typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLGGTCGA-P5-A77W-01ADPF3chr14

73219972

-TDP1chr14

90437519

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000556509ENST00000393452DPF3chr14

73219972

-TDP1chr14

90437519

+
Frame-shiftENST00000556509ENST00000393454DPF3chr14

73219972

-TDP1chr14

90437519

+
Frame-shiftENST00000556509ENST00000335725DPF3chr14

73219972

-TDP1chr14

90437519

+
5CDS-3UTRENST00000556509ENST00000555565DPF3chr14

73219972

-TDP1chr14

90437519

+
5CDS-5UTRENST00000556509ENST00000357382DPF3chr14

73219972

-TDP1chr14

90437519

+
5CDS-5UTRENST00000556509ENST00000555880DPF3chr14

73219972

-TDP1chr14

90437519

+
intron-3CDSENST00000557704ENST00000393452DPF3chr14

73219972

-TDP1chr14

90437519

+
intron-3CDSENST00000557704ENST00000393454DPF3chr14

73219972

-TDP1chr14

90437519

+
intron-3CDSENST00000557704ENST00000335725DPF3chr14

73219972

-TDP1chr14

90437519

+
intron-3UTRENST00000557704ENST00000555565DPF3chr14

73219972

-TDP1chr14

90437519

+
intron-5UTRENST00000557704ENST00000357382DPF3chr14

73219972

-TDP1chr14

90437519

+
intron-5UTRENST00000557704ENST00000555880DPF3chr14

73219972

-TDP1chr14

90437519

+
Frame-shiftENST00000541685ENST00000393452DPF3chr14

73219972

-TDP1chr14

90437519

+
Frame-shiftENST00000541685ENST00000393454DPF3chr14

73219972

-TDP1chr14

90437519

+
Frame-shiftENST00000541685ENST00000335725DPF3chr14

73219972

-TDP1chr14

90437519

+
5CDS-3UTRENST00000541685ENST00000555565DPF3chr14

73219972

-TDP1chr14

90437519

+
5CDS-5UTRENST00000541685ENST00000357382DPF3chr14

73219972

-TDP1chr14

90437519

+
5CDS-5UTRENST00000541685ENST00000555880DPF3chr14

73219972

-TDP1chr14

90437519

+
Frame-shiftENST00000546183ENST00000393452DPF3chr14

73219972

-TDP1chr14

90437519

+
Frame-shiftENST00000546183ENST00000393454DPF3chr14

73219972

-TDP1chr14

90437519

+
Frame-shiftENST00000546183ENST00000335725DPF3chr14

73219972

-TDP1chr14

90437519

+
5CDS-3UTRENST00000546183ENST00000555565DPF3chr14

73219972

-TDP1chr14

90437519

+
5CDS-5UTRENST00000546183ENST00000357382DPF3chr14

73219972

-TDP1chr14

90437519

+
5CDS-5UTRENST00000546183ENST00000555880DPF3chr14

73219972

-TDP1chr14

90437519

+

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FusionProtFeatures for DPF3_TDP1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
DPF3

Q92784

TDP1

Q9NUW8

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}.

check buttonRetention 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

download page

.

* 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for DPF3_TDP1


check button 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).

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FusionGenePPI for DPF3_TDP1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
DPF3RELA, 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, DCXTDP1ATM, VAMP2, MOV10, NUP153, POLB, APLF, GOLGA1, VCP, CETN1, CSNK1D


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for DPF3_TDP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for DPF3_TDP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneTDP1C1846574SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE, WITH AXONAL NEUROPATHY1CTD_human;ORPHANET;UNIPROT