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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:APLP2-MAD1L1 (FusionGDB2 ID:5457)

Fusion Gene Summary for APLP2-MAD1L1

check button Fusion gene summary
Fusion gene informationFusion gene name: APLP2-MAD1L1
Fusion gene ID: 5457
HgeneTgene
Gene symbol

APLP2

MAD1L1

Gene ID

334

8379

Gene nameamyloid beta precursor like protein 2mitotic arrest deficient 1 like 1
SynonymsAPLP-2|APPH|APPL2|CDEBPMAD1|PIG9|TP53I9|TXBP181
Cytomap

11q24.3

7p22.3

Type of geneprotein-codingprotein-coding
Descriptionamyloid-like protein 2CDEI box-binding proteinamyloid beta (A4) precursor-like protein 2amyloid precursor protein homolog HSD-2testicular tissue protein Li 23mitotic spindle assembly checkpoint protein MAD1MAD1 mitotic arrest deficient like 1MAD1-like protein 1mitotic arrest deficient 1-like protein 1mitotic checkpoint MAD1 protein homologmitotic-arrest deficient 1, yeast, homolog-like 1tax-binding prote
Modification date2020031320200313
UniProtAcc

Q06481

Q9Y6D9

Ensembl transtripts involved in fusion geneENST00000532456, ENST00000263574, 
ENST00000278756, ENST00000338167, 
ENST00000345598, ENST00000528499, 
ENST00000543137, ENST00000539648, 
ENST00000265854, ENST00000399654, 
ENST00000402746, ENST00000406869, 
ENST00000486340, 
Fusion gene scores* DoF score32 X 25 X 10=800023 X 16 X 12=4416
# samples 3637
** MAII scorelog2(36/8000*10)=-4.47393118833241
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(37/4416*10)=-3.57714299626186
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: APLP2 [Title/Abstract] AND MAD1L1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAPLP2(129980509)-MAD1L1(2272554), # 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
TgeneMAD1L1

GO:0007094

mitotic spindle assembly checkpoint

18981471

TgeneMAD1L1

GO:0090235

regulation of metaphase plate congression

20133940


check buttonFusion gene breakpoints across APLP2 (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 MAD1L1 (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/ABP359675APLP2chr11

129980509

+MAD1L1chr7

2272554

-


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Fusion Gene ORF analysis for APLP2-MAD1L1

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-5UTRENST00000532456ENST00000265854APLP2chr11

129980509

+MAD1L1chr7

2272554

-
3UTR-5UTRENST00000532456ENST00000399654APLP2chr11

129980509

+MAD1L1chr7

2272554

-
3UTR-5UTRENST00000532456ENST00000402746APLP2chr11

129980509

+MAD1L1chr7

2272554

-
3UTR-5UTRENST00000532456ENST00000406869APLP2chr11

129980509

+MAD1L1chr7

2272554

-
3UTR-intronENST00000532456ENST00000486340APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000263574ENST00000265854APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000263574ENST00000399654APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000263574ENST00000402746APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000263574ENST00000406869APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000278756ENST00000265854APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000278756ENST00000399654APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000278756ENST00000402746APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000278756ENST00000406869APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000338167ENST00000265854APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000338167ENST00000399654APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000338167ENST00000402746APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000338167ENST00000406869APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000345598ENST00000265854APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000345598ENST00000399654APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000345598ENST00000402746APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000345598ENST00000406869APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000528499ENST00000265854APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000528499ENST00000399654APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000528499ENST00000402746APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000528499ENST00000406869APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000543137ENST00000265854APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000543137ENST00000399654APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000543137ENST00000402746APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-5UTRENST00000543137ENST00000406869APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-intronENST00000263574ENST00000486340APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-intronENST00000278756ENST00000486340APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-intronENST00000338167ENST00000486340APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-intronENST00000345598ENST00000486340APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-intronENST00000528499ENST00000486340APLP2chr11

129980509

+MAD1L1chr7

2272554

-
5CDS-intronENST00000543137ENST00000486340APLP2chr11

129980509

+MAD1L1chr7

2272554

-
intron-5UTRENST00000539648ENST00000265854APLP2chr11

129980509

+MAD1L1chr7

2272554

-
intron-5UTRENST00000539648ENST00000399654APLP2chr11

129980509

+MAD1L1chr7

2272554

-
intron-5UTRENST00000539648ENST00000402746APLP2chr11

129980509

+MAD1L1chr7

2272554

-
intron-5UTRENST00000539648ENST00000406869APLP2chr11

129980509

+MAD1L1chr7

2272554

-
intron-intronENST00000539648ENST00000486340APLP2chr11

129980509

+MAD1L1chr7

2272554

-

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 APLP2-MAD1L1


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 APLP2-MAD1L1


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/:129980509/:2272554)
- 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
APLP2

Q06481

MAD1L1

Q9Y6D9

FUNCTION: May play a role in the regulation of hemostasis. The soluble form may have inhibitory properties towards coagulation factors. May interact with cellular G-protein signaling pathways. May bind to the DNA 5'-GTCACATG-3'(CDEI box). Inhibits trypsin, chymotrypsin, plasmin, factor XIA and plasma and glandular kallikrein. Modulates the Cu/Zn nitric oxide-catalyzed autodegradation of GPC1 heparan sulfate side chains in fibroblasts (By similarity). {ECO:0000250, ECO:0000269|PubMed:8307156}.FUNCTION: Component of the spindle-assembly checkpoint that prevents the onset of anaphase until all chromosomes are properly aligned at the metaphase plate (PubMed:10049595, PubMed:20133940, PubMed:29162720). Forms a heterotetrameric complex with the closed conformation form of MAD2L1 (C-MAD2) at unattached kinetochores during prometaphase, recruits an open conformation of MAD2L1 (O-MAD2) and promotes the conversion of O-MAD2 to C-MAD2, which ensures mitotic checkpoint signaling (PubMed:29162720). {ECO:0000269|PubMed:10049595, ECO:0000269|PubMed:20133940, ECO:0000269|PubMed:29162720}.

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 APLP2-MAD1L1


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 APLP2-MAD1L1


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 APLP2-MAD1L1


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 APLP2-MAD1L1


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