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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:MCF2L-RGCC (FusionGDB2 ID:51869)

Fusion Gene Summary for MCF2L-RGCC

check button Fusion gene summary
Fusion gene informationFusion gene name: MCF2L-RGCC
Fusion gene ID: 51869
HgeneTgene
Gene symbol

MCF2L

RGCC

Gene ID

23263

28984

Gene nameMCF.2 cell line derived transforming sequence likeregulator of cell cycle
SynonymsARHGEF14|DBS|OSTC13orf15|RGC-32|RGC32|bA157L14.2
Cytomap

13q34

13q14.11

Type of geneprotein-codingprotein-coding
Descriptionguanine nucleotide exchange factor DBSDBL's big sisterMCF2 transforming sequence-like proteinregulator of cell cycle RGCCresponse gene to complement 32 protein
Modification date2020031320200313
UniProtAcc

O15068

.
Ensembl transtripts involved in fusion geneENST00000375608, ENST00000442652, 
ENST00000375604, ENST00000397030, 
ENST00000535094, ENST00000421756, 
ENST00000375601, ENST00000397036, 
ENST00000434480, ENST00000423482, 
ENST00000375597, ENST00000397024, 
ENST00000480321, ENST00000397021, 
ENST00000379359, ENST00000487837, 
Fusion gene scores* DoF score11 X 7 X 8=6162 X 1 X 2=4
# samples 102
** MAII scorelog2(10/616*10)=-2.62293035092018
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/4*10)=2.32192809488736
Context

PubMed: MCF2L [Title/Abstract] AND RGCC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMCF2L(113699675)-RGCC(42040959), # 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
TgeneRGCC

GO:0001100

negative regulation of exit from mitosis

17146433

TgeneRGCC

GO:0001937

negative regulation of endothelial cell proliferation

19652095

TgeneRGCC

GO:0003331

positive regulation of extracellular matrix constituent secretion

19158077

TgeneRGCC

GO:0010628

positive regulation of gene expression

21307346

TgeneRGCC

GO:0010718

positive regulation of epithelial to mesenchymal transition

21307346

TgeneRGCC

GO:0016525

negative regulation of angiogenesis

19652095

TgeneRGCC

GO:0032967

positive regulation of collagen biosynthetic process

19158077

TgeneRGCC

GO:0043537

negative regulation of blood vessel endothelial cell migration

19652095

TgeneRGCC

GO:0045737

positive regulation of cyclin-dependent protein serine/threonine kinase activity

11687586

TgeneRGCC

GO:0051496

positive regulation of stress fiber assembly

19158077

TgeneRGCC

GO:0071158

positive regulation of cell cycle arrest

17146433

TgeneRGCC

GO:0071850

mitotic cell cycle arrest

17146433

TgeneRGCC

GO:0090272

negative regulation of fibroblast growth factor production

19652095

TgeneRGCC

GO:1901203

positive regulation of extracellular matrix assembly

21307346

TgeneRGCC

GO:1901991

negative regulation of mitotic cell cycle phase transition

17146433

TgeneRGCC

GO:2000048

negative regulation of cell-cell adhesion mediated by cadherin

19158077|21307346

TgeneRGCC

GO:2000353

positive regulation of endothelial cell apoptotic process

19652095


check buttonFusion gene breakpoints across MCF2L (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 RGCC (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
ChimerDB4THCATCGA-KS-A41J-01AMCF2Lchr13

113699675

+RGCCchr13

42040959

+


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Fusion Gene ORF analysis for MCF2L-RGCC

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-shiftENST00000375608ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000375608ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000442652ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000442652ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000375604ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000375604ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000397030ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000397030ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000535094ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000535094ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000421756ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000421756ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000375601ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000375601ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
intron-3CDSENST00000397036ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
intron-3UTRENST00000397036ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000434480ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000434480ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000423482ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000423482ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000375597ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000375597ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
intron-3CDSENST00000397024ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
intron-3UTRENST00000397024ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
3UTR-3CDSENST00000480321ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
3UTR-3UTRENST00000480321ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+
Frame-shiftENST00000397021ENST00000379359MCF2Lchr13

113699675

+RGCCchr13

42040959

+
5CDS-3UTRENST00000397021ENST00000487837MCF2Lchr13

113699675

+RGCCchr13

42040959

+

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 MCF2L-RGCC


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 MCF2L-RGCC


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
MCF2L

O15068

.
FUNCTION: Guanine nucleotide exchange factor that catalyzes guanine nucleotide exchange on RHOA and CDC42, and thereby contributes to the regulation of RHOA and CDC42 signaling pathways (By similarity). Seems to lack activity with RAC1. Becomes activated and highly tumorigenic by truncation of the N-terminus (By similarity). Isoform 5 activates CDC42 (PubMed:15157669). {ECO:0000250|UniProtKB:Q63406, ECO:0000269|PubMed:15157669}.; FUNCTION: [Isoform 3]: Does not catalyze guanine nucleotide exchange on CDC42 (PubMed:15157669). {ECO:0000269|PubMed:15157669}.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.

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 MCF2L-RGCC


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 MCF2L-RGCC


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 MCF2L-RGCC


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 MCF2L-RGCC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneRGCCC0151744Myocardial Ischemia1CTD_human