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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:MAGED2-IFT43 (FusionGDB2 ID:50762)

Fusion Gene Summary for MAGED2-IFT43

check button Fusion gene summary
Fusion gene informationFusion gene name: MAGED2-IFT43
Fusion gene ID: 50762
HgeneTgene
Gene symbol

MAGED2

IFT43

Gene ID

10916

112752

Gene nameMAGE family member D2intraflagellar transport 43
Synonyms11B6|BARTS5|BCG-1|BCG1|HCA10|MAGE-D2C14orf179|CED3|RP81|SRTD18
Cytomap

Xp11.21

14q24.3

Type of geneprotein-codingprotein-coding
Descriptionmelanoma-associated antigen D2MAGE-D2 antigenbreast cancer-associated gene 1 proteinhepatocellular carcinoma-associated protein JCL-1melanoma antigen family D, 2melanoma antigen family D2intraflagellar transport protein 43 homologIFT complex A subunitintraflagellar transport 43 homolog
Modification date2020031320200319
UniProtAcc

Q9UNF1

Q96FT9

Ensembl transtripts involved in fusion geneENST00000497484, ENST00000218439, 
ENST00000347546, ENST00000375053, 
ENST00000375058, ENST00000375060, 
ENST00000375062, ENST00000375068, 
ENST00000396224, 		ENST00000238628, 
ENST00000314067, ENST00000553338, 
ENST00000556742, 
Fusion gene scores* DoF score13 X 9 X 4=4685 X 6 X 7=210
# samples 1310
** MAII scorelog2(13/468*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/210*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MAGED2 [Title/Abstract] AND IFT43 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMAGED2(54837490)-IFT43(76450444), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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

check buttonFusion gene breakpoints across MAGED2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across IFT43 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/ACD644593MAGED2chrX

54837490

+IFT43chr14

76450444

+


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Fusion Gene ORF analysis for MAGED2-IFT43

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
3UTR-intronENST00000497484ENST00000238628MAGED2chrX

54837490

+IFT43chr14

76450444

+
3UTR-intronENST00000497484ENST00000314067MAGED2chrX

54837490

+IFT43chr14

76450444

+
3UTR-intronENST00000497484ENST00000553338MAGED2chrX

54837490

+IFT43chr14

76450444

+
3UTR-intronENST00000497484ENST00000556742MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000218439ENST00000238628MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000218439ENST00000314067MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000218439ENST00000553338MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000218439ENST00000556742MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000347546ENST00000238628MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000347546ENST00000314067MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000347546ENST00000553338MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000347546ENST00000556742MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375053ENST00000238628MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375053ENST00000314067MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375053ENST00000553338MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375053ENST00000556742MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375058ENST00000238628MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375058ENST00000314067MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375058ENST00000553338MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375058ENST00000556742MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375060ENST00000238628MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375060ENST00000314067MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375060ENST00000553338MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375060ENST00000556742MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375062ENST00000238628MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375062ENST00000314067MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375062ENST00000553338MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375062ENST00000556742MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375068ENST00000238628MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375068ENST00000314067MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375068ENST00000553338MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000375068ENST00000556742MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000396224ENST00000238628MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000396224ENST00000314067MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000396224ENST00000553338MAGED2chrX

54837490

+IFT43chr14

76450444

+
5CDS-intronENST00000396224ENST00000556742MAGED2chrX

54837490

+IFT43chr14

76450444

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for MAGED2-IFT43


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution 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.

check buttonDistribution 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.

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Fusion Protein Features for MAGED2-IFT43


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:54837490/:76450444)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MAGED2

Q9UNF1

IFT43

Q96FT9

FUNCTION: Regulates the expression, localization to the plasma membrane and function of the sodium chloride cotransporters SLC12A1 and SLC12A3, two key components of salt reabsorption in the distal renal tubule. {ECO:0000269|PubMed:27120771}.FUNCTION: As a component of IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), it is involved in ciliogenesis (PubMed:28400947, PubMed:28973684). Involved in retrograde ciliary transport along microtubules from the ciliary tip to the base (PubMed:21378380). {ECO:0000269|PubMed:21378380, ECO:0000269|PubMed:28400947, ECO:0000269|PubMed:28973684}.

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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Fusion Gene Sequence for MAGED2-IFT43


check button 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.

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Fusion Gene PPI Analysis for MAGED2-IFT43


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


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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Related Drugs for MAGED2-IFT43


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for MAGED2-IFT43


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