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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:CRK-MATR3 (FusionGDB2 ID:HG1398TG9782)

Fusion Gene Summary for CRK-MATR3

check button Fusion gene summary
Fusion gene informationFusion gene name: CRK-MATR3
Fusion gene ID: hg1398tg9782
HgeneTgene
Gene symbol

CRK

MATR3

Gene ID

1398

9782

Gene nameCRK proto-oncogene, adaptor proteinmatrin 3
SynonymsCRKII|p38ALS21|MPD2|VCPDM
Cytomap('CRK')('MATR3')

17p13.3

5q31.2

Type of geneprotein-codingprotein-coding
Descriptionadapter molecule crkproto-oncogene c-Crkv-crk avian sarcoma virus CT10 oncogene homologv-crk sarcoma virus CT10 oncogene-like proteinmatrin-3vocal cord and pharyngeal weakness with distal myopathy
Modification date2020032720200315
UniProtAcc

P46108

.
Ensembl transtripts involved in fusion geneENST00000300574, ENST00000398970, 
ENST00000574295, ENST00000572145, 
Fusion gene scores* DoF score15 X 11 X 7=115510 X 10 X 6=600
# samples 1813
** MAII scorelog2(18/1155*10)=-2.68182403997375
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/600*10)=-2.20645087746743
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointCRK(1359171)-MATR3(138642928), # 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
HgeneCRK

GO:0009966

regulation of signal transduction

17515907

HgeneCRK

GO:0032956

regulation of actin cytoskeleton organization

11870224

HgeneCRK

GO:0043087

regulation of GTPase activity

11870224

HgeneCRK

GO:0048013

ephrin receptor signaling pathway

11870224

HgeneCRK

GO:0061045

negative regulation of wound healing

17515907

HgeneCRK

GO:2000146

negative regulation of cell motility

17515907

TgeneMATR3

GO:0002218

activation of innate immune response

28712728

TgeneMATR3

GO:0010608

posttranscriptional regulation of gene expression

21771347



check button Fusion gene information
* 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
ChimerDB4STADTCGA-BR-8078-01ACRKchr17

1359171

-MATR3chr5

138642928

+


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Fusion Gene ORF analysis for CRK-MATR3

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
5CDS-5UTRENST00000300574ENST00000361059CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000300574ENST00000394800CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000300574ENST00000394805CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000300574ENST00000502929CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000300574ENST00000509990CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000300574ENST00000510056CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000398970ENST00000361059CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000398970ENST00000394800CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000398970ENST00000394805CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000398970ENST00000502929CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000398970ENST00000509990CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000398970ENST00000510056CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000574295ENST00000361059CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000574295ENST00000394800CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000574295ENST00000394805CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000574295ENST00000502929CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000574295ENST00000509990CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-5UTRENST00000574295ENST00000510056CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000300574ENST00000502499CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000300574ENST00000503811CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000300574ENST00000504203CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000300574ENST00000507197CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000398970ENST00000502499CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000398970ENST00000503811CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000398970ENST00000504203CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000398970ENST00000507197CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000574295ENST00000502499CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000574295ENST00000503811CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000574295ENST00000504203CRKchr17

1359171

-MATR3chr5

138642928

+
5CDS-intronENST00000574295ENST00000507197CRKchr17

1359171

-MATR3chr5

138642928

+
intron-5UTRENST00000572145ENST00000361059CRKchr17

1359171

-MATR3chr5

138642928

+
intron-5UTRENST00000572145ENST00000394800CRKchr17

1359171

-MATR3chr5

138642928

+
intron-5UTRENST00000572145ENST00000394805CRKchr17

1359171

-MATR3chr5

138642928

+
intron-5UTRENST00000572145ENST00000502929CRKchr17

1359171

-MATR3chr5

138642928

+
intron-5UTRENST00000572145ENST00000509990CRKchr17

1359171

-MATR3chr5

138642928

+
intron-5UTRENST00000572145ENST00000510056CRKchr17

1359171

-MATR3chr5

138642928

+
intron-intronENST00000572145ENST00000502499CRKchr17

1359171

-MATR3chr5

138642928

+
intron-intronENST00000572145ENST00000503811CRKchr17

1359171

-MATR3chr5

138642928

+
intron-intronENST00000572145ENST00000504203CRKchr17

1359171

-MATR3chr5

138642928

+
intron-intronENST00000572145ENST00000507197CRKchr17

1359171

-MATR3chr5

138642928

+

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 CRK-MATR3


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)
CRKchr171359170-MATR3chr5138642927+3.66E-081
CRKchr171359170-MATR3chr5138642927+3.66E-081


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.
genomic feature of top 1%

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Fusion Protein Features for CRK-MATR3


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/:1359171/:138642928)
- 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
CRK

P46108

.
FUNCTION: Involved in cell branching and adhesion mediated by BCAR1-CRK-RAPGEF1 signaling and activation of RAP1. {ECO:0000269|PubMed:12432078}.; FUNCTION: [Isoform Crk-II]: Regulates cell adhesion, spreading and migration (PubMed:31311869). Mediates attachment-induced MAPK8 activation, membrane ruffling and cell motility in a Rac-dependent manner. Involved in phagocytosis of apoptotic cells and cell motility via its interaction with DOCK1 and DOCK4 (PubMed:19004829). May regulate the EFNA5-EPHA3 signaling (By similarity). {ECO:0000250|UniProtKB:Q64010, ECO:0000269|PubMed:11870224, ECO:0000269|PubMed:1630456, ECO:0000269|PubMed:17515907, ECO:0000269|PubMed:19004829, ECO:0000269|PubMed:31311869}.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}.

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 CRK-MATR3


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 CRK-MATR3


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 CRK-MATR3


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 CRK-MATR3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCRKC0151744Myocardial Ischemia1CTD_human
TgeneC3807521AMYOTROPHIC LATERAL SCLEROSIS 215GENOMICS_ENGLAND;UNIPROT
TgeneC0002736Amyotrophic Lateral Sclerosis2GENOMICS_ENGLAND;ORPHANET
TgeneC2678065Myofibrillar Myopathy1GENOMICS_ENGLAND