Home

Download

Statistics

Examples

Help

Contact

	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:PLXNB2-NDUFA4L2 (FusionGDB2 ID:66564)

Fusion Gene Summary for PLXNB2-NDUFA4L2

Fusion gene summary

Fusion gene information	Fusion gene name: PLXNB2-NDUFA4L2
	Fusion gene ID: 66564
		Hgene	Tgene
	Gene symbol	PLXNB2	NDUFA4L2
	Gene ID	23654	56901
	Gene name	plexin B2	NDUFA4 mitochondrial complex associated like 2
	Synonyms	MM1\|Nbla00445\|PLEXB2\|dJ402G11.3	COXFA4L2\|NUOMS
	Cytomap	22q13.33	12q13.3
	Type of gene	protein-coding	protein-coding
	Description	plexin-B2	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4-like 2NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2NADH:ubiquinone oxidoreductase MLRQ subunit homologcytochrome c oxidase subunit FA4 like 2
	Modification date	20200313	20200329
	UniProtAcc	.	Q9NRX3
	Ensembl transtripts involved in fusion gene	ENST00000359337, ENST00000449103, ENST00000496720,	ENST00000393825, ENST00000556732, ENST00000557276, ENST00000554503,
Fusion gene scores	* DoF score	19 X 16 X 11=3344	2 X 3 X 2=12
	# samples	22	3
	** MAII score	log2(22/3344*10)=-3.92599941855622 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/12*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: PLXNB2 [Title/Abstract] AND NDUFA4L2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	PLXNB2(50724229)-NDUFA4L2(57631118), # samples:1
Anticipated loss of major functional domain due to fusion event.	PLXNB2-NDUFA4L2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.

* 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
Hgene	PLXNB2	GO:0007156	homophilic cell adhesion via plasma membrane adhesion molecules	16122393
Hgene	PLXNB2	GO:0010976	positive regulation of neuron projection development	16122393

Fusion gene breakpoints across PLXNB2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across NDUFA4L2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	KIRC	TCGA-CZ-5460-01A	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-

Top

Fusion Gene ORF analysis for PLXNB2-NDUFA4L2

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
5CDS-5UTR	ENST00000359337	ENST00000393825	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
5CDS-5UTR	ENST00000449103	ENST00000393825	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
5CDS-intron	ENST00000359337	ENST00000556732	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
5CDS-intron	ENST00000359337	ENST00000557276	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
5CDS-intron	ENST00000449103	ENST00000556732	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
5CDS-intron	ENST00000449103	ENST00000557276	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
5UTR-3CDS	ENST00000496720	ENST00000554503	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
5UTR-5UTR	ENST00000496720	ENST00000393825	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
5UTR-intron	ENST00000496720	ENST00000556732	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
5UTR-intron	ENST00000496720	ENST00000557276	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
Frame-shift	ENST00000359337	ENST00000554503	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-
In-frame	ENST00000449103	ENST00000554503	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

ENST00000449103

PLXNB2

chr22

50724229

ENST00000554503

NDUFA4L2

chr12

57631118

3406

2229

117

2333

738

DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000449103	ENST00000554503	PLXNB2	chr22	50724229	-	NDUFA4L2	chr12	57631118	-	0.009333206	0.9906668

Top

Fusion Genomic Features for PLXNB2-NDUFA4L2

FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

Top

Fusion Protein Features for PLXNB2-NDUFA4L2

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr22:50724229/chr12:57631118)
- 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.

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

Hgene	Tgene
.	NDUFA4L2 Q9NRX3
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000359337

20_466

696

1839.0

Domain

Sema

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000449103

20_466

696

1839.0

Domain

Sema

- 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

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000359337

803_893

696

1839.0

Domain

Note=IPT/TIG 1

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000359337

895_980

696

1839.0

Domain

Note=IPT/TIG 2

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000359337

983_1092

696

1839.0

Domain

Note=IPT/TIG 3

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000449103

803_893

696

1839.0

Domain

Note=IPT/TIG 1

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000449103

895_980

696

1839.0

Domain

Note=IPT/TIG 2

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000449103

983_1092

696

1839.0

Domain

Note=IPT/TIG 3

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000359337

1219_1838

696

1839.0

Topological domain

Cytoplasmic

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000359337

20_1197

696

1839.0

Topological domain

Extracellular

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000449103

1219_1838

696

1839.0

Topological domain

Cytoplasmic

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000449103

20_1197

696

1839.0

Topological domain

Extracellular

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000359337

1198_1218

696

1839.0

Transmembrane

Helical

Hgene

PLXNB2

chr22:50724229

chr12:57631118

ENST00000449103

1198_1218

696

1839.0

Transmembrane

Helical

Top

Fusion Gene Sequence for PLXNB2-NDUFA4L2

For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>66564_66564_1_PLXNB2-NDUFA4L2_PLXNB2_chr22_50724229_ENST00000449103_NDUFA4L2_chr12_57631118_ENST00000554503_length(transcript)=3406nt_BP=2229nt
ATGGCAGCAGCGCGGGCCAGAGCGCAGCGCCGAGCGCGGCCCGGGCGCCATCGAGCCTTGGCGGCGGACGTGCAGAGAATCTCGATGCTG
GCCTGGAGCAGAAACTGAGCTGGACCACTGGAGCCTCGGGTGCGGGGGGCAATGGCACTGCAGCTCTGGGCCCTGACCCTGCTGGGCCTG
CTGGGCGCAGGTGCCAGCCTGAGGCCCCGCAAGCTGGACTTCTTCCGCAGCGAGAAAGAGCTGAACCACCTGGCTGTGGATGAGGCCTCA
GGCGTGGTGTACCTGGGGGCGGTGAATGCCCTCTACCAGCTGGATGCGAAGCTGCAGCTGGAGCAGCAGGTGGCCACGGGCCCGGCCCTG
GACAACAAGAAGTGCACGCCGCCCATCGAGGCCAGCCAGTGCCATGAGGCTGAGATGACTGACAATGTCAACCAGCTGCTGCTGCTCGAC
CCTCCCAGGAAGCGCCTGGTGGAGTGCGGCAGCCTCTTCAAGGGCATCTGCGCTCTGCGCGCCCTGAGCAACATCTCCCTCCGCCTGTTC
TACGAGGACGGCAGCGGGGAGAAGTCTTTCGTGGCCAGCAATGATGAGGGCGTGGCCACAGTGGGGCTGGTGAGCTCCACGGGTCCTGGT
GGTGACCGCGTGCTGTTTGTGGGCAAAGGCAATGGGCCACACGACAACGGCATCATCGTGAGCACTCGGCTGTTGGACCGGACTGACAGC
AGGGAGGCCTTTGAAGCCTACACGGACCACGCCACCTACAAGGCCGGCTACCTGTCCACCAACACACAGCAGTTCGTGGCGGCCTTCGAG
GACGGCCCCTACGTCTTCTTTGTCTTCAACCAGCAGGACAAGCACCCGGCCCGGAACCGCACGCTGCTGGCACGCATGTGCAGAGAAGAC
CCCAACTACTACTCCTACCTGGAGATGGACCTGCAGTGCCGGGACCCCGACATCCACGCCGCTGCCTTTGGCACCTGCCTGGCCGCCTCC
GTGGCTGCGCCTGGCTCTGGCAGGGTGCTATATGCTGTCTTCAGCAGAGACAGCCGGAGCAGTGGGGGGCCCGGTGCGGGCCTCTGCCTG
TTCCCGCTGGACAAGGTGCACGCCAAGATGGAGGCCAACCGCAACGCCTGTTACACAGGCACCCGGGAGGCCCGTGACATCTTCTACAAG
CCCTTCCACGGCGATATCCAGTGCGGCGGCCACGCGCCGGGCTCCAGCAAGAGCTTCCCATGTGGCTCGGAGCACCTGCCCTACCCGCTG
GGCAGCCGCGACGGGCTCAGAGGCACAGCCGTGCTGCAGCGTGGAGGCCTGAACCTCACGGCCGTGACGGTCGCCGCCGAGAACAACCAC
ACTGTTGCTTTTCTGGGCACCTCTGATGGCCGGATCCTCAAGGTGTACCTCACCCCAGATGGCACCTCCTCAGAGTACGACTCTATCCTT
GTGGAGATAAACAAGAGAGTCAAGCGCGACCTGGTACTGTCTGGAGACCTGGGCAGCCTGTACGCCATGACCCAGGACAAGGTGTTCCGG
CTGCCGGTGCAGGAGTGCCTGAGCTACCCGACCTGCACCCAGTGCCGCGACTCCCAGGACCCCTACTGCGGCTGGTGCGTCGTCGAGGGA
CGATGCACCCGGAAGGCCGAGTGTCCGCGGGCCGAGGAGGCCAGCCACTGGCTGTGGAGCCGAAGCAAGTCCTGCGTGGCCGTCACCAGC
GCCCAGCCACAGAACATGAGCCGGCGGGCCCAGGGGGAGGTGCAGCTGACCGTCAGCCCCCTCCCTGCCCTGAGCGAGGAGGACGAGTTG
CTGTGCCTTTTTGGGGAGTCGCCGCCACACCCCGCCCGCGTGGAGGGCGAGGCCGTCATCTGCAACTCCCCAAGCAGCATCCCCGTCACA
CCGCCAGGCCAGGACCACGTGGCCGTGACCATCCAGCTCCTCCTTAGACGAGGCAACATCTTCCTCACGTCCTACCAGTACCCCTTCTAC
GACTGCCGCCAGGCCATGAGCCTGGAGGAGAACCTGCCGTGCATCTCCTGCGTGAGCAACCGCTGGACCTGCCAGTGGGACCTGCGCTAC
CACGAGTGCCGGGAGGCTTCGCCCAACCCTGAGGACGGCATCGTCCGTGCCCACATGGAGGACAGCTGTCCCCAGTTCCTGGGACCCAGC
CCCCTGGTGATCCCCATGAACCACGAGACAGATGTGAACTTCCAGGGCAAGAACCTGGACACCGTGAAGCAGGTGCAGACATCTGGAGGA
GAGAGTCGGAGAGCAGAAACCACTTGGCTCCCAGACAATTCCCCTACAGGCTTTGGGCCTGGAATTGAGGAGAAAGTGAGCTAAGTTGGG
GTGGGGTGAGTCCAAAGAAGCACGGGCTGGGCCAAGCTAAGCTGCTCTGGGCTGGGCTGATCCCTCCCCACTCAGGGGCGGGACCCCAGG
AGGAGGGAGAGGACAGAGCCACTGCAGAGGACCAGACTGGGAAAACAACGATATGGCAGGAGCCAGTCTTGGGGCCCGCTTCTACCGGCA
GATCAAAAGACATCCGGGGATCATCCCGATGATCGGCTTAATCTGCCTGGGCATGGGCAGCGCTGCGCTTTACTTGCTGCGACTCGCCCT
TCGCAGCCCCGACGTCTGCTGGGACAGAAAGAACAACCCGGAGCCCTGGAACCGCCTGAGCCCCAATGACCAATACAAGTTCCTTGCAGT
TTCCACTGACTATAAGAAGCTGAAGAAGGACCGGCCAGACTTCTAAGCCAGGCTGGGCTGCCAGTGCCATGCAAGCCACAGCCAGCCAGC
CCATCCACTTCTTCCACTCCTCCCCGCAGGCCCCAAGGCATCACTCCGGCCACCCTGTCCCGCTACTGCTTACACAGGCCGGGTTCCCAC
GCAGAGGGGAGGCTGCTCCACCCCTACTCTCCTCCCTTGCTCCCAGCAGCGGAAGCGCCTCTGACCCTTGGCTTGAGTCCCACGTGGGGG
AGGAGGAGGCAGGCAGCACCAGCAGGGGTCCACCAAGAGCCCAGACCAGCCCCTCTGCCCTCCTACCCGGGCCTCGAAGGGTGTGGCACA
GGCTACGTGTTGAGCGTGGCCTACGTGAGCCAACAAGAAGCAGGGGCCTCTGAGTGCCAAGCGACGTGGCGGGCTCCACGTTAGCCCAGG
CTCTGAGAGCCAGCCCAGGGGCGGCGCTGCTCAGCTTGGGCTGGTCCAGGGCCTGCCCAGGCTGGGGCACCTTTGCCTCCTGAGGCGCAG
CGCACTCCTCCCCTGCCCAAGCCTACTGCCTCCCGCTGCCGCCAGTACCCCCTCCAGCCCCACACCTGGGCCTCCCCCTGCCACTCCCCT

>66564_66564_1_PLXNB2-NDUFA4L2_PLXNB2_chr22_50724229_ENST00000449103_NDUFA4L2_chr12_57631118_ENST00000554503_length(amino acids)=738AA_BP=704
MEPRVRGAMALQLWALTLLGLLGAGASLRPRKLDFFRSEKELNHLAVDEASGVVYLGAVNALYQLDAKLQLEQQVATGPALDNKKCTPPI
EASQCHEAEMTDNVNQLLLLDPPRKRLVECGSLFKGICALRALSNISLRLFYEDGSGEKSFVASNDEGVATVGLVSSTGPGGDRVLFVGK
GNGPHDNGIIVSTRLLDRTDSREAFEAYTDHATYKAGYLSTNTQQFVAAFEDGPYVFFVFNQQDKHPARNRTLLARMCREDPNYYSYLEM
DLQCRDPDIHAAAFGTCLAASVAAPGSGRVLYAVFSRDSRSSGGPGAGLCLFPLDKVHAKMEANRNACYTGTREARDIFYKPFHGDIQCG
GHAPGSSKSFPCGSEHLPYPLGSRDGLRGTAVLQRGGLNLTAVTVAAENNHTVAFLGTSDGRILKVYLTPDGTSSEYDSILVEINKRVKR
DLVLSGDLGSLYAMTQDKVFRLPVQECLSYPTCTQCRDSQDPYCGWCVVEGRCTRKAECPRAEEASHWLWSRSKSCVAVTSAQPQNMSRR
AQGEVQLTVSPLPALSEEDELLCLFGESPPHPARVEGEAVICNSPSSIPVTPPGQDHVAVTIQLLLRRGNIFLTSYQYPFYDCRQAMSLE
ENLPCISCVSNRWTCQWDLRYHECREASPNPEDGIVRAHMEDSCPQFLGPSPLVIPMNHETDVNFQGKNLDTVKQVQTSGGESRRAETTW

--------------------------------------------------------------

Top

Fusion Gene PPI Analysis for PLXNB2-NDUFA4L2

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

- 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

Related Drugs for PLXNB2-NDUFA4L2

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

Top

Related Diseases for PLXNB2-NDUFA4L2

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source