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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:CFL1-SF1 (FusionGDB2 ID:16169)

Fusion Gene Summary for CFL1-SF1

check button Fusion gene summary
Fusion gene informationFusion gene name: CFL1-SF1
Fusion gene ID: 16169
HgeneTgene
Gene symbol

CFL1

SF1

Gene ID

6944

7536

Gene namevacuolar protein sorting 72 homologsplicing factor 1
SynonymsCFL1|Swc2|TCFL1|YL-1|YL1BBP|D11S636|MBBP|ZCCHC25|ZFM1|ZNF162
Cytomap

1q21.3

11q13.1

Type of geneprotein-codingprotein-coding
Descriptionvacuolar protein sorting-associated protein 72 homologtranscription factor-like 1transformation suppressor gene YL-1splicing factor 1mammalian branch point-binding proteintranscription factor ZFM1zinc finger gene in MEN1 locuszinc finger protein 162
Modification date2020031320200318
UniProtAcc

P23528

.
Ensembl transtripts involved in fusion geneENST00000530157, ENST00000525451, 
ENST00000308162, ENST00000527344, 
ENST00000531407, ENST00000524553, 
ENST00000534769, ENST00000531413, 
ENST00000377387, ENST00000377390, 
ENST00000377394, ENST00000227503, 
ENST00000334944, ENST00000422298, 
ENST00000433274, ENST00000489544, 
Fusion gene scores* DoF score17 X 15 X 5=127510 X 8 X 5=400
# samples 189
** MAII scorelog2(18/1275*10)=-2.82442843541655
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/400*10)=-2.15200309344505
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CFL1 [Title/Abstract] AND SF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCFL1(65625568)-SF1(64544098), # samples:1
Anticipated loss of major functional domain due to fusion event.CFL1-SF1 seems lost the major protein functional domain in Tgene 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

check buttonFusion gene breakpoints across CFL1 (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 SF1 (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
ChimerDB4Non-CancerERR315404CFL1chr11

65625568

-SF1chr11

64544098

-


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Fusion Gene ORF analysis for CFL1-SF1

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-3CDSENST00000530157ENST00000377387CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000530157ENST00000377390CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000530157ENST00000377394CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000530157ENST00000227503CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000530157ENST00000334944CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000530157ENST00000422298CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000530157ENST00000433274CFL1chr11

65625568

-SF1chr11

64544098

-
intron-intronENST00000530157ENST00000489544CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000525451ENST00000377387CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000525451ENST00000377390CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000525451ENST00000377394CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000525451ENST00000227503CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000525451ENST00000334944CFL1chr11

65625568

-SF1chr11

64544098

-
5CDS-5UTRENST00000525451ENST00000422298CFL1chr11

65625568

-SF1chr11

64544098

-
5CDS-5UTRENST00000525451ENST00000433274CFL1chr11

65625568

-SF1chr11

64544098

-
5CDS-intronENST00000525451ENST00000489544CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000308162ENST00000377387CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000308162ENST00000377390CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000308162ENST00000377394CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000308162ENST00000227503CFL1chr11

65625568

-SF1chr11

64544098

-
Frame-shiftENST00000308162ENST00000334944CFL1chr11

65625568

-SF1chr11

64544098

-
5CDS-5UTRENST00000308162ENST00000422298CFL1chr11

65625568

-SF1chr11

64544098

-
5CDS-5UTRENST00000308162ENST00000433274CFL1chr11

65625568

-SF1chr11

64544098

-
5CDS-intronENST00000308162ENST00000489544CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000527344ENST00000377387CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000527344ENST00000377390CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000527344ENST00000377394CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000527344ENST00000227503CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000527344ENST00000334944CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000527344ENST00000422298CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000527344ENST00000433274CFL1chr11

65625568

-SF1chr11

64544098

-
intron-intronENST00000527344ENST00000489544CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531407ENST00000377387CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531407ENST00000377390CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531407ENST00000377394CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531407ENST00000227503CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531407ENST00000334944CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000531407ENST00000422298CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000531407ENST00000433274CFL1chr11

65625568

-SF1chr11

64544098

-
intron-intronENST00000531407ENST00000489544CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000524553ENST00000377387CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000524553ENST00000377390CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000524553ENST00000377394CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000524553ENST00000227503CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000524553ENST00000334944CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000524553ENST00000422298CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000524553ENST00000433274CFL1chr11

65625568

-SF1chr11

64544098

-
intron-intronENST00000524553ENST00000489544CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000534769ENST00000377387CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000534769ENST00000377390CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000534769ENST00000377394CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000534769ENST00000227503CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000534769ENST00000334944CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000534769ENST00000422298CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000534769ENST00000433274CFL1chr11

65625568

-SF1chr11

64544098

-
intron-intronENST00000534769ENST00000489544CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531413ENST00000377387CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531413ENST00000377390CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531413ENST00000377394CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531413ENST00000227503CFL1chr11

65625568

-SF1chr11

64544098

-
intron-3CDSENST00000531413ENST00000334944CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000531413ENST00000422298CFL1chr11

65625568

-SF1chr11

64544098

-
intron-5UTRENST00000531413ENST00000433274CFL1chr11

65625568

-SF1chr11

64544098

-
intron-intronENST00000531413ENST00000489544CFL1chr11

65625568

-SF1chr11

64544098

-

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 CFL1-SF1


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 CFL1-SF1


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
CFL1

P23528

.
FUNCTION: Binds to F-actin and exhibits pH-sensitive F-actin depolymerizing activity (PubMed:11812157). In conjunction with the subcortical maternal complex (SCMC), plays an essential role for zygotes to progress beyond the first embryonic cell divisions via regulation of actin dynamics (PubMed:15580268). Required for the centralization of the mitotic spindle and symmetric division of zygotes (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization in epithelial cells (PubMed:21834987). Required for the up-regulation of atypical chemokine receptor ACKR2 from endosomal compartment to cell membrane, increasing its efficiency in chemokine uptake and degradation (PubMed:23633677). Required for neural tube morphogenesis and neural crest cell migration (By similarity). {ECO:0000250|UniProtKB:P18760, ECO:0000269|PubMed:11812157, ECO:0000269|PubMed:15580268, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:23633677}.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 CFL1-SF1


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 CFL1-SF1


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 CFL1-SF1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCFL1P23528DB09130CopperSmall moleculeApproved|Investigational
HgeneCFL1P23528DB09130CopperSmall moleculeApproved|Investigational

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Related Diseases for CFL1-SF1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCFL1C0006142Malignant neoplasm of breast1CTD_human
HgeneCFL1C0027626Neoplasm Invasiveness1CTD_human
HgeneCFL1C0027627Neoplasm Metastasis1CTD_human
HgeneCFL1C0032927Precancerous Conditions1CTD_human
HgeneCFL1C0038219Status Dysraphicus1CTD_human
HgeneCFL1C0080178Spina Bifida1CTD_human
HgeneCFL1C0266508Rachischisis1CTD_human
HgeneCFL1C0279626Squamous cell carcinoma of esophagus1CTD_human
HgeneCFL1C0282313Condition, Preneoplastic1CTD_human
HgeneCFL1C0678222Breast Carcinoma1CTD_human
HgeneCFL1C1257931Mammary Neoplasms, Human1CTD_human
HgeneCFL1C1458155Mammary Neoplasms1CTD_human
HgeneCFL1C4704874Mammary Carcinoma, Human1CTD_human
TgeneSF1C0025202melanoma1CTD_human