	FusionGeneSummary
	FusionProtFeature
	FusionGeneSequence
	FusionGenePPI
	RelatedDrugs
	RelatedDiseases

Fusion gene ID: 11070

FusionGeneSummary for EFNA4_FLAD1

Fusion gene summary

Fusion gene information	Fusion gene name: EFNA4_FLAD1
	Fusion gene ID: 11070
		Hgene	Tgene
	Gene symbol	EFNA4	FLAD1
	Gene ID	1945	80308
	Gene name	ephrin A4	flavin adenine dinucleotide synthetase 1
	Synonyms	EFL4\|EPLG4\|LERK4	FAD1\|FADS\|LSMFLAD\|PP591
	Cytomap	1q21.3	1q21.3
	Type of gene	protein-coding	protein-coding
	Description	ephrin-A4LERK-4eph-related receptor tyrosine kinase ligand 4ligand of eph-related kinase 4	FAD synthaseFAD pyrophosphorylaseFAD-synthetaseFMN adenylyltransferaseFad1, flavin adenine dinucleotide synthetase, homolog
	Modification date	20180523	20180523
	UniProtAcc	P52798	Q8NFF5
	Ensembl transtripts involved in fusion gene	ENST00000368409, ENST00000359751, ENST00000427683,	ENST00000368433, ENST00000315144, ENST00000368432, ENST00000368431, ENST00000292180, ENST00000487371, ENST00000405236, ENST00000295530, ENST00000368428,
Fusion gene scores	* DoF score	2 X 1 X 2=4	5 X 3 X 5=75
	# samples	3	5
	** MAII score	log2(3/4*10)=2.90689059560852	log2(5/75*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: EFNA4 [Title/Abstract] AND FLAD1 [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)

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

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	BRCA	TCGA-E2-A1LE-01A	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
TCGA	RV	LUSC	TCGA-66-2771-01A	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+

* 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	ENST00000368409	ENST00000368433	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000368409	ENST00000315144	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000368409	ENST00000368432	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
In-frame	ENST00000368409	ENST00000368431	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000368409	ENST00000292180	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-3UTR	ENST00000368409	ENST00000487371	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-3UTR	ENST00000368409	ENST00000405236	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-5UTR	ENST00000368409	ENST00000295530	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-intron	ENST00000368409	ENST00000368428	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000359751	ENST00000368433	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000359751	ENST00000315144	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000359751	ENST00000368432	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
In-frame	ENST00000359751	ENST00000368431	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000359751	ENST00000292180	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-3UTR	ENST00000359751	ENST00000487371	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-3UTR	ENST00000359751	ENST00000405236	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-5UTR	ENST00000359751	ENST00000295530	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-intron	ENST00000359751	ENST00000368428	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000427683	ENST00000368433	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000427683	ENST00000315144	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000427683	ENST00000368432	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
In-frame	ENST00000427683	ENST00000368431	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
Frame-shift	ENST00000427683	ENST00000292180	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-3UTR	ENST00000427683	ENST00000487371	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-3UTR	ENST00000427683	ENST00000405236	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-5UTR	ENST00000427683	ENST00000295530	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-intron	ENST00000427683	ENST00000368428	EFNA4	chr1	155039916	+	FLAD1	chr1	154960581	+
5CDS-intron	ENST00000368409	ENST00000368433	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000368409	ENST00000315144	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000368409	ENST00000368432	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000368409	ENST00000368431	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000368409	ENST00000292180	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000368409	ENST00000487371	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000368409	ENST00000405236	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000368409	ENST00000295530	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000368409	ENST00000368428	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000359751	ENST00000368433	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000359751	ENST00000315144	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000359751	ENST00000368432	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000359751	ENST00000368431	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000359751	ENST00000292180	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000359751	ENST00000487371	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000359751	ENST00000405236	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000359751	ENST00000295530	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000359751	ENST00000368428	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000427683	ENST00000368433	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000427683	ENST00000315144	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000427683	ENST00000368432	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000427683	ENST00000368431	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000427683	ENST00000292180	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000427683	ENST00000487371	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000427683	ENST00000405236	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000427683	ENST00000295530	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+
5CDS-intron	ENST00000427683	ENST00000368428	EFNA4	chr1	155039916	+	FLAD1	chr1	154965189	+

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FusionProtFeatures for EFNA4_FLAD1

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
EFNA4 P52798	FLAD1 Q8NFF5
Cell surface GPI-bound ligand for Eph receptors, afamily of receptor tyrosine kinases which are crucial formigration, repulsion and adhesion during neuronal, vascular andepithelial development. Binds promiscuously Eph receptors residingon adjacent cells, leading to contact-dependent bidirectionalsignaling into neighboring cells. May play a role in theinteraction between activated B-lymphocytes and dendritic cells intonsils.	Catalyzes the adenylation of flavin mononucleotide (FMN)to form flavin adenine dinucleotide (FAD) coenzyme.{ECO:0000269\|PubMed:16643857, ECO:0000269\|PubMed:27259049}.

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
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.

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

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FusionGeneSequence for EFNA4_FLAD1

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 EFNA4_FLAD1

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page
.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene	Hgene's interactors	Tgene	Tgene's interactors
EFNA4	EPHA3, MOV10, NXF1	FLAD1	TRIM23, PRTFDC1, FLAD1, ICT1, NUDT21, GRB7, TK1, CDKN1A, SMN1, RCC1, ANXA7, DAK, SORD, GEMIN4, TNRC6B, REL, SDCBP, TCF4, MOV10, NXF1, KLHL14, PSG1, PLEKHO2, PSPH, SH3GLB1, PFAS, FAM19A3, FSCN3, PTPN1

- 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

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RelatedDrugs for EFNA4_FLAD1

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

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RelatedDiseases for EFNA4_FLAD1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Tgene	FLAD1	C0410214	Myopathy with Abnormal Lipid Metabolism	1	UNIPROT

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Fusion gene ID: 11070

FusionGeneSummary for EFNA4_FLAD1

FusionProtFeatures for EFNA4_FLAD1

FusionGeneSequence for EFNA4_FLAD1

FusionGenePPI for EFNA4_FLAD1

RelatedDrugs for EFNA4_FLAD1

RelatedDiseases for EFNA4_FLAD1