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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:MATR3-AMACR (FusionGDB2 ID:51577)

Fusion Gene Summary for MATR3-AMACR

check button Fusion gene summary
Fusion gene informationFusion gene name: MATR3-AMACR
Fusion gene ID: 51577
HgeneTgene
Gene symbol

MATR3

AMACR

Gene ID

9782

23600

Gene namematrin 3alpha-methylacyl-CoA racemase
SynonymsALS21|MPD2|VCPDMAMACRD|CBAS4|P504S|RACE|RM
Cytomap

5q31.2

5p13.2

Type of geneprotein-codingprotein-coding
Descriptionmatrin-3vocal cord and pharyngeal weakness with distal myopathyalpha-methylacyl-CoA racemase2-methylacyl-CoA racemase
Modification date2020031520200313
UniProtAcc

P43243

Q9UHK6

Ensembl transtripts involved in fusion geneENST00000509990, ENST00000361059, 
ENST00000504203, ENST00000502929, 
ENST00000394800, ENST00000507197, 
ENST00000394805, ENST00000502499, 
ENST00000510056, ENST00000503811, 
ENST00000335606, ENST00000382072, 
ENST00000514195, ENST00000382085, 
ENST00000502637, ENST00000441713, 
ENST00000426255, ENST00000512079, 
ENST00000382068, 
Fusion gene scores* DoF score39 X 15 X 12=702028 X 3 X 4=336
# samples 4123
** MAII scorelog2(41/7020*10)=-4.09777521568648
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(23/336*10)=-0.546827371834385
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MATR3 [Title/Abstract] AND AMACR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMATR3(138629494)-AMACR(34006004), # samples:2
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
HgeneMATR3

GO:0002218

activation of innate immune response

28712728

HgeneMATR3

GO:0010608

posttranscriptional regulation of gene expression

21771347

TgeneAMACR

GO:0008206

bile acid metabolic process

10655068


check buttonFusion gene breakpoints across MATR3 (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 AMACR (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
ChimerDB4PRADTCGA-YL-A8SCMATR3chr5

138629494

+AMACRchr5

34006004

-
ChimerDB4PRADTCGA-YL-A8SCMATR3chr5

138629494

+AMACRchr5

34006004

-


Top

Fusion Gene ORF analysis for MATR3-AMACR

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
intron-3CDSENST00000509990ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000509990ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000509990ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000509990ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000509990ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000509990ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000509990ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000509990ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000509990ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000361059ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000361059ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000361059ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000361059ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000361059ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000361059ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000361059ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000361059ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000361059ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000504203ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000504203ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000504203ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000504203ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000504203ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000504203ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000504203ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000504203ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000504203ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000502929ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000502929ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000502929ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000502929ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000502929ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000502929ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000502929ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000502929ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000502929ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000394800ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000394800ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000394800ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000394800ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000394800ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000394800ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000394800ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000394800ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000394800ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000507197ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-3CDSENST00000507197ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000507197ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000507197ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000507197ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000507197ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000507197ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000507197ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
intron-5UTRENST00000507197ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-3CDSENST00000394805ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-3CDSENST00000394805ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000394805ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000394805ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000394805ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000394805ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000394805ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000394805ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000394805ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-3CDSENST00000502499ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-3CDSENST00000502499ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000502499ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000502499ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000502499ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000502499ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000502499ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000502499ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000502499ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-3CDSENST00000510056ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-3CDSENST00000510056ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000510056ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000510056ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000510056ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000510056ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000510056ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000510056ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000510056ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-3CDSENST00000503811ENST00000335606MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-3CDSENST00000503811ENST00000382072MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000503811ENST00000514195MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000503811ENST00000382085MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000503811ENST00000502637MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000503811ENST00000441713MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000503811ENST00000426255MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000503811ENST00000512079MATR3chr5

138629494

+AMACRchr5

34006004

-
5UTR-5UTRENST00000503811ENST00000382068MATR3chr5

138629494

+AMACRchr5

34006004

-

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 MATR3-AMACR


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 MATR3-AMACR


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MATR3

P43243

AMACR

Q9UHK6

FUNCTION: May play a role in transcription or may interact with other nuclear matrix proteins to form the internal fibrogranular network. In association with the SFPQ-NONO heteromer may play a role in nuclear retention of defective RNAs. Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway (PubMed:28712728). May bind to specific miRNA hairpins (PubMed:28431233). {ECO:0000269|PubMed:11525732, ECO:0000269|PubMed:28431233, ECO:0000269|PubMed:28712728}.FUNCTION: Catalyzes the interconversion of (R)- and (S)-stereoisomers of alpha-methyl-branched-chain fatty acyl-CoA esters (PubMed:7649182, PubMed:10655068, PubMed:11060359). Acts only on coenzyme A thioesters, not on free fatty acids, and accepts as substrates a wide range of alpha-methylacyl-CoAs, including pristanoyl-CoA, trihydroxycoprostanoyl-CoA (an intermediate in bile acid synthesis), and arylpropionic acids like the anti-inflammatory drug ibuprofen (2-(4-isobutylphenyl)propionic acid) but neither 3-methyl-branched nor linear-chain acyl-CoAs (PubMed:7649182, PubMed:10655068, PubMed:11060359). {ECO:0000269|PubMed:10655068, ECO:0000269|PubMed:11060359, ECO:0000269|PubMed:7649182}.

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 MATR3-AMACR


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 MATR3-AMACR


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 MATR3-AMACR


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 MATR3-AMACR


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMATR3C3807521AMYOTROPHIC LATERAL SCLEROSIS 215GENOMICS_ENGLAND;UNIPROT
HgeneMATR3C0002736Amyotrophic Lateral Sclerosis2GENOMICS_ENGLAND;ORPHANET
HgeneMATR3C2678065Myofibrillar Myopathy1GENOMICS_ENGLAND
TgeneAMACRC0033578Prostatic Neoplasms3CTD_human
TgeneAMACRC0376358Malignant neoplasm of prostate3CTD_human
TgeneAMACRC1858328Bile acid synthesis defect, congenital, 43CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneAMACRC3280428Alpha-Methylacyl-CoA Racemase Deficiency3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneAMACRC0023893Liver Cirrhosis, Experimental2CTD_human
TgeneAMACRC0001430Adenoma1CTD_human
TgeneAMACRC0009402Colorectal Carcinoma1CTD_human
TgeneAMACRC0009404Colorectal Neoplasms1CTD_human
TgeneAMACRC0011195Dejerine-Sottas Disease (disorder)1CTD_human
TgeneAMACRC0019816Hereditary, Type VII, Motor and Sensory Neuropathy1CTD_human
TgeneAMACRC0023895Liver diseases1CTD_human
TgeneAMACRC0027888Hereditary Motor and Sensory Neuropathies1CTD_human
TgeneAMACRC0036341Schizophrenia1PSYGENET
TgeneAMACRC0086565Liver Dysfunction1CTD_human
TgeneAMACRC0205646Adenoma, Basal Cell1CTD_human
TgeneAMACRC0205647Follicular adenoma1CTD_human
TgeneAMACRC0205648Adenoma, Microcystic1CTD_human
TgeneAMACRC0205649Adenoma, Monomorphic1CTD_human
TgeneAMACRC0205650Papillary adenoma1CTD_human
TgeneAMACRC0205651Adenoma, Trabecular1CTD_human