FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CPSF3L-MXRA8 (FusionGDB2 ID:19133)

Fusion Gene Summary for CPSF3L-MXRA8

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF3L-MXRA8
Fusion gene ID: 19133
HgeneTgene
Gene symbol

CPSF3L

MXRA8

Gene ID

54973

54587

Gene nameintegrator complex subunit 11matrix remodeling associated 8
SynonymsCPSF3L|CPSF73L|INT11|RC-68|RC68ASP3
Cytomap

1p36.33

1p36.33

Type of geneprotein-codingprotein-coding
Descriptionintegrator complex subunit 11CPSF3-like proteincleavage and polyadenylation specific factor 3-likecleavage and polyadenylation-specific factor 3-like proteinprotein related to CPSF subunits of 68 kDarelated to CPSF subunits 68 kDamatrix remodeling-associated protein 8limitrinmatrix-remodeling-associated protein 8matrix-remodelling associated 8
Modification date2020031320200315
UniProtAcc.

Q9BRK3

Ensembl transtripts involved in fusion geneENST00000435064, ENST00000411962, 
ENST00000462432, ENST00000540437, 
ENST00000421495, ENST00000419704, 
ENST00000450926, ENST00000545578, 
ENST00000309212, ENST00000342753, 
ENST00000445648, ENST00000477278, 
Fusion gene scores* DoF score8 X 8 X 6=3844 X 4 X 5=80
# samples 106
** MAII scorelog2(10/384*10)=-1.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/80*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CPSF3L [Title/Abstract] AND MXRA8 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCPSF3L(1255835)-MXRA8(1289612), # samples:1
CPSF3L(1255836)-MXRA8(1289612), # samples:1
Anticipated loss of major functional domain due to fusion event.CPSF3L-MXRA8 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCPSF3L

GO:0016180

snRNA processing

16239144


check buttonFusion gene breakpoints across CPSF3L (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 MXRA8 (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
ChimerDB4BRCATCGA-A8-A07GCPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
ChimerDB4BRCATCGA-A8-A07G-01ACPSF3Lchr1

1255836

-MXRA8chr1

1289612

-


Top

Fusion Gene ORF analysis for CPSF3L-MXRA8

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
Frame-shiftENST00000435064ENST00000309212CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000435064ENST00000342753CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000435064ENST00000445648CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000435064ENST00000477278CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000411962ENST00000309212CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000411962ENST00000342753CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000411962ENST00000445648CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000411962ENST00000477278CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000462432ENST00000309212CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000462432ENST00000342753CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000462432ENST00000445648CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000462432ENST00000477278CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
In-frameENST00000540437ENST00000309212CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
In-frameENST00000540437ENST00000342753CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
In-frameENST00000540437ENST00000445648CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
In-frameENST00000540437ENST00000477278CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000421495ENST00000309212CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000421495ENST00000342753CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000421495ENST00000445648CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000421495ENST00000477278CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000419704ENST00000309212CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000419704ENST00000342753CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000419704ENST00000445648CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
intron-3CDSENST00000419704ENST00000477278CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000450926ENST00000309212CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000450926ENST00000342753CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000450926ENST00000445648CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000450926ENST00000477278CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000545578ENST00000309212CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000545578ENST00000342753CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000545578ENST00000445648CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000545578ENST00000477278CPSF3Lchr1

1255835

-MXRA8chr1

1289612

-
Frame-shiftENST00000435064ENST00000309212CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000435064ENST00000342753CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000435064ENST00000445648CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000435064ENST00000477278CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000411962ENST00000309212CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000411962ENST00000342753CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000411962ENST00000445648CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000411962ENST00000477278CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000462432ENST00000309212CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000462432ENST00000342753CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000462432ENST00000445648CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000462432ENST00000477278CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
In-frameENST00000540437ENST00000309212CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
In-frameENST00000540437ENST00000342753CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
In-frameENST00000540437ENST00000445648CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
In-frameENST00000540437ENST00000477278CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000421495ENST00000309212CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000421495ENST00000342753CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000421495ENST00000445648CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000421495ENST00000477278CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000419704ENST00000309212CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000419704ENST00000342753CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000419704ENST00000445648CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
intron-3CDSENST00000419704ENST00000477278CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000450926ENST00000309212CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000450926ENST00000342753CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000450926ENST00000445648CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000450926ENST00000477278CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000545578ENST00000309212CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000545578ENST00000342753CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000545578ENST00000445648CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-
Frame-shiftENST00000545578ENST00000477278CPSF3Lchr1

1255836

-MXRA8chr1

1289612

-

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

Top

Fusion Genomic Features for CPSF3L-MXRA8


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.

Top

Fusion Protein Features for CPSF3L-MXRA8


check button Go to

FGviewer for the breakpoints of chr1:1255835-chr1:1289612

.
- 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
.MXRA8

Q9BRK3

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Transmembrane protein which can modulate activity of various signaling pathways, probably via binding to integrin ITGAV:ITGB3 (PubMed:22492581, PubMed:23386276). Mediates heterophilic cell-cell interactions in vitro (By similarity). Inhibits osteoclastogenesis downstream of TNFSF11/RANKL and CSF1, where it may function by attenuating signaling via integrin ITGB3 and MAP kinase p38 (By similarity). Plays a role in cartilage formation where it promotes proliferation and maturation of growth plate chondrocytes (By similarity). Stimulates formation of primary cilia in chondrocytes (By similarity). Enhances expression of genes involved in the hedgehog signaling pathway in chondrocytes, including the hedgehog signaling molecule IHH; may also promote signaling via the PTHLH/PTHrP pathway (By similarity). Plays a role in angiogenesis where it suppresses migration of endothelial cells and also promotes their apoptosis (PubMed:23386276). Inhibits VEGF-induced activation of AKT and p38 MAP kinase in endothelial cells (PubMed:23386276). Also inhibits VTN (vitronectin)-mediated integrin ITGAV:ITGB3 signaling and activation of PTK2/FAK (PubMed:23386276). May play a role in the maturation and maintenance of the blood-brain barrier (By similarity). {ECO:0000250|UniProtKB:Q9DBV4, ECO:0000269|PubMed:22492581, ECO:0000269|PubMed:23386276}.; FUNCTION: (Microbial infection) Contributes to arthritogenic alphavirus pathogenesis and acts as a receptor for these viruses. {ECO:0000269|PubMed:29769725}.

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
HgeneCPSF3Lchr1:1255835chr1:1289612ENST00000540437-51968_7372.66666666666667607.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1255836chr1:1289612ENST00000540437-51968_7372.66666666666667607.0MotifNote=HXHXDH motif

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCPSF3Lchr1:1255835chr1:1289612ENST00000419704-11568_730500.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1255835chr1:1289612ENST00000435064-31768_7366.66666666666667601.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1255835chr1:1289612ENST00000450926-31768_7366.66666666666667579.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1255835chr1:1289612ENST00000545578-41868_7337.666666666666664572.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1255836chr1:1289612ENST00000419704-11568_730500.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1255836chr1:1289612ENST00000435064-31768_7366.66666666666667601.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1255836chr1:1289612ENST00000450926-31768_7366.66666666666667579.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1255836chr1:1289612ENST00000545578-41868_7337.666666666666664572.0MotifNote=HXHXDH motif
TgeneMXRA8chr1:1255835chr1:1289612ENST00000309212510364_367368.3333333333333443.0Compositional biasNote=Poly-Arg
TgeneMXRA8chr1:1255835chr1:1289612ENST00000445648510364_367368.3333333333333451.0Compositional biasNote=Poly-Arg
TgeneMXRA8chr1:1255836chr1:1289612ENST00000309212510364_367368.3333333333333443.0Compositional biasNote=Poly-Arg
TgeneMXRA8chr1:1255836chr1:1289612ENST00000445648510364_367368.3333333333333451.0Compositional biasNote=Poly-Arg
TgeneMXRA8chr1:1255835chr1:1289612ENST00000309212510160_288368.3333333333333443.0DomainNote=Ig-like V-type 2
TgeneMXRA8chr1:1255835chr1:1289612ENST0000030921251029_157368.3333333333333443.0DomainNote=Ig-like V-type 1
TgeneMXRA8chr1:1255835chr1:1289612ENST00000445648510160_288368.3333333333333451.0DomainNote=Ig-like V-type 2
TgeneMXRA8chr1:1255835chr1:1289612ENST0000044564851029_157368.3333333333333451.0DomainNote=Ig-like V-type 1
TgeneMXRA8chr1:1255836chr1:1289612ENST00000309212510160_288368.3333333333333443.0DomainNote=Ig-like V-type 2
TgeneMXRA8chr1:1255836chr1:1289612ENST0000030921251029_157368.3333333333333443.0DomainNote=Ig-like V-type 1
TgeneMXRA8chr1:1255836chr1:1289612ENST00000445648510160_288368.3333333333333451.0DomainNote=Ig-like V-type 2
TgeneMXRA8chr1:1255836chr1:1289612ENST0000044564851029_157368.3333333333333451.0DomainNote=Ig-like V-type 1
TgeneMXRA8chr1:1255835chr1:1289612ENST00000309212510252_254368.3333333333333443.0MotifRGD
TgeneMXRA8chr1:1255835chr1:1289612ENST00000445648510252_254368.3333333333333451.0MotifRGD
TgeneMXRA8chr1:1255836chr1:1289612ENST00000309212510252_254368.3333333333333443.0MotifRGD
TgeneMXRA8chr1:1255836chr1:1289612ENST00000445648510252_254368.3333333333333451.0MotifRGD
TgeneMXRA8chr1:1255835chr1:1289612ENST0000030921251020_341368.3333333333333443.0Topological domainExtracellular
TgeneMXRA8chr1:1255835chr1:1289612ENST00000309212510363_442368.3333333333333443.0Topological domainCytoplasmic
TgeneMXRA8chr1:1255835chr1:1289612ENST0000044564851020_341368.3333333333333451.0Topological domainExtracellular
TgeneMXRA8chr1:1255835chr1:1289612ENST00000445648510363_442368.3333333333333451.0Topological domainCytoplasmic
TgeneMXRA8chr1:1255836chr1:1289612ENST0000030921251020_341368.3333333333333443.0Topological domainExtracellular
TgeneMXRA8chr1:1255836chr1:1289612ENST00000309212510363_442368.3333333333333443.0Topological domainCytoplasmic
TgeneMXRA8chr1:1255836chr1:1289612ENST0000044564851020_341368.3333333333333451.0Topological domainExtracellular
TgeneMXRA8chr1:1255836chr1:1289612ENST00000445648510363_442368.3333333333333451.0Topological domainCytoplasmic
TgeneMXRA8chr1:1255835chr1:1289612ENST00000309212510342_362368.3333333333333443.0TransmembraneHelical
TgeneMXRA8chr1:1255835chr1:1289612ENST00000445648510342_362368.3333333333333451.0TransmembraneHelical
TgeneMXRA8chr1:1255836chr1:1289612ENST00000309212510342_362368.3333333333333443.0TransmembraneHelical
TgeneMXRA8chr1:1255836chr1:1289612ENST00000445648510342_362368.3333333333333451.0TransmembraneHelical


Top

Fusion Gene Sequence for CPSF3L-MXRA8


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.

Top

Fusion Gene PPI Analysis for CPSF3L-MXRA8


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


Top

Related Drugs for CPSF3L-MXRA8


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

Top

Related Diseases for CPSF3L-MXRA8


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