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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: 13307

FusionGeneSummary for FEN1_GDPD4

check button Fusion gene summary
Fusion gene informationFusion gene name: FEN1_GDPD4
Fusion gene ID: 13307
HgeneTgene
Gene symbol

FEN1

GDPD4

Gene ID

2237

220032

Gene nameflap structure-specific endonuclease 1glycerophosphodiester phosphodiesterase domain containing 4
SynonymsFEN-1|MF1|RAD2GDE6
Cytomap

11q12.2

11q13.5

Type of geneprotein-codingprotein-coding
Descriptionflap endonuclease 1DNase IVmaturation factor-1glycerophosphodiester phosphodiesterase domain-containing protein 4GDPD domain containing proteinglycerophosphodiester phosphodiesterase 6ugpQ
Modification date2018052320180329
UniProtAcc

P39748

Q6W3E5

Ensembl transtripts involved in fusion geneENST00000305885, ENST00000376217, 
ENST00000315938, ENST00000527489, 
Fusion gene scores* DoF score2 X 2 X 2=89 X 4 X 2=72
# samples 28
** MAII scorelog2(2/8*10)=1.32192809488736log2(8/72*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: FEN1 [Title/Abstract] AND GDPD4 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneFEN1

GO:0043137

DNA replication, removal of RNA primer

18995831

HgeneFEN1

GO:0090305

nucleic acid phosphodiester bond hydrolysis

18499658


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
TCGARVSKCMTCGA-EB-A82B-01AFEN1chr11

61560500

+GDPD4chr11

76940277

-
* 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
5UTR-3CDSENST00000305885ENST00000376217FEN1chr11

61560500

+GDPD4chr11

76940277

-
5UTR-3CDSENST00000305885ENST00000315938FEN1chr11

61560500

+GDPD4chr11

76940277

-
5UTR-intronENST00000305885ENST00000527489FEN1chr11

61560500

+GDPD4chr11

76940277

-

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FusionProtFeatures for FEN1_GDPD4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
FEN1

P39748

GDPD4

Q6W3E5

Structure-specific nuclease with 5'-flap endonucleaseand 5'-3' exonuclease activities involved in DNA replication andrepair. During DNA replication, cleaves the 5'-overhanging flapstructure that is generated by displacement synthesis when DNApolymerase encounters the 5'-end of a downstream Okazaki fragment.It enters the flap from the 5'-end and then tracks to cleave theflap base, leaving a nick for ligation. Also involved in the longpatch base excision repair (LP-BER) pathway, by cleaving withinthe apurinic/apyrimidinic (AP) site-terminated flap. Acts as agenome stabilization factor that prevents flaps from equilibratinginto structurs that lead to duplications and deletions. Alsopossesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved inreplication and repair of rDNA and in repairing mitochondrial DNA.{ECO:0000255|HAMAP-Rule:MF_03140, ECO:0000269|PubMed:10744741,ECO:0000269|PubMed:11986308, ECO:0000269|PubMed:18443037,ECO:0000269|PubMed:20729856, ECO:0000269|PubMed:7961795,ECO:0000269|PubMed:8621570}.

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 FEN1_GDPD4


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 FEN1_GDPD4


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
FEN1HNRNPA1, BLM, WRN, CDK2, CCNA2, CDK1, PCNA, EP300, ARHGDIA, EEF1G, APEX1, HUS1, RAD9A, RAD1, NCAPG, DDX11, ENDOG, GSK3B, RAD21, TERF1, APP, RAP1A, VRK1, PAXIP1, FN1, AICDA, ELAC2, HARS, PFDN1, TNPO3, LPP, PPP2R5D, SHFM1, SHMT2, MOV10, NXF1, DNA2, WDR76, DUSP19, DRG1, LIG1, MRE11A, MSH2, MSH6, RECQL, WBSCR22, TFG, NTRK1, LRPPRC, LTN1, PPP1R21, TRA2A, CHPF2, FOXA3, FOXL1, FOXO4, FOXP3, SNW1, CDC5L, EGFR, WDR4, SNRNP27, GTF2E2, FGB, USP47, ACTL6A, PTCRA, ATM, UBE2N, HLTF, PARP1, PARP2, DLD, HSD17B10, SOD1, HEY1GDPD4


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 FEN1_GDPD4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneFEN1P39748DB01592IronFlap endonuclease 1 {ECO:0000255|HAMAP-Rule:MF_03140}small moleculeapproved

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RelatedDiseases for FEN1_GDPD4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneFEN1C0009404Colorectal Neoplasms1CTD_human