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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:PFKFB4-COL7A1 (FusionGDB2 ID:64036)

Fusion Gene Summary for PFKFB4-COL7A1

check button Fusion gene summary
Fusion gene informationFusion gene name: PFKFB4-COL7A1
Fusion gene ID: 64036
HgeneTgene
Gene symbol

PFKFB4

COL7A1

Gene ID

5210

1294

Gene name6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4collagen type VII alpha 1 chain
Synonyms-EBD1|EBDCT|EBR1|NDNC8
Cytomap

3p21.31

3p21.31

Type of geneprotein-codingprotein-coding
Description6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 46PF-2-K/Fru-2,6-P2ase 46PF-2-K/Fru-2,6-P2ase testis-type isozymePFK/FBPase 4bifunctional enzyme with kinase and biphosphatase activitiescollagen alpha-1(VII) chainLC collagencollagen VII, alpha-1 polypeptidecollagen, type VII, alpha 1long-chain collagen
Modification date2020031320200329
UniProtAcc.

Q02388

Ensembl transtripts involved in fusion geneENST00000232375, ENST00000536104, 
ENST00000416568, ENST00000541519, 
ENST00000383734, ENST00000490115, 
ENST00000545984, 		ENST00000454817, 
ENST00000328333, ENST00000470076, 
Fusion gene scores* DoF score6 X 5 X 4=1205 X 8 X 4=160
# samples 66
** MAII scorelog2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/160*10)=-1.41503749927884
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PFKFB4 [Title/Abstract] AND COL7A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPFKFB4(48559419)-COL7A1(48608711), # samples:1
Anticipated loss of major functional domain due to fusion event.PFKFB4-COL7A1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism 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 PFKFB4 (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 COL7A1 (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
ChimerDB4HNSCTCGA-CV-5432-01APFKFB4chr3

48559419

-COL7A1chr3

48608711

-


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Fusion Gene ORF analysis for PFKFB4-COL7A1

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
In-frameENST00000232375ENST00000454817PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
In-frameENST00000232375ENST00000328333PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
5CDS-intronENST00000232375ENST00000470076PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
In-frameENST00000536104ENST00000454817PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
In-frameENST00000536104ENST00000328333PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
5CDS-intronENST00000536104ENST00000470076PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
In-frameENST00000416568ENST00000454817PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
In-frameENST00000416568ENST00000328333PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
5CDS-intronENST00000416568ENST00000470076PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
Frame-shiftENST00000541519ENST00000454817PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
Frame-shiftENST00000541519ENST00000328333PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
5CDS-intronENST00000541519ENST00000470076PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
In-frameENST00000383734ENST00000454817PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
In-frameENST00000383734ENST00000328333PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
5CDS-intronENST00000383734ENST00000470076PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
5UTR-3CDSENST00000490115ENST00000454817PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
5UTR-3CDSENST00000490115ENST00000328333PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
5UTR-intronENST00000490115ENST00000470076PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
intron-3CDSENST00000545984ENST00000454817PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
intron-3CDSENST00000545984ENST00000328333PFKFB4chr3

48559419

-COL7A1chr3

48608711

-
intron-intronENST00000545984ENST00000470076PFKFB4chr3

48559419

-COL7A1chr3

48608711

-

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 PFKFB4-COL7A1


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 PFKFB4-COL7A1


check button Go to

FGviewer for the breakpoints of chr3:48559419-chr3:48608711

.
- 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
.COL7A1

Q02388

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: Stratified squamous epithelial basement membrane protein that forms anchoring fibrils which may contribute to epithelial basement membrane organization and adherence by interacting with extracellular matrix (ECM) proteins such as type IV collagen.

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
HgenePFKFB4chr3:48559419chr3:48608711ENST00000232375-1314168_173450.0470.0Nucleotide bindingATP
HgenePFKFB4chr3:48559419chr3:48608711ENST00000232375-1314348_351450.0470.0Nucleotide bindingATP
HgenePFKFB4chr3:48559419chr3:48608711ENST00000232375-1314392_396450.0470.0Nucleotide bindingATP
HgenePFKFB4chr3:48559419chr3:48608711ENST00000232375-131446_54450.0470.0Nucleotide bindingATP
HgenePFKFB4chr3:48559419chr3:48608711ENST00000232375-13141_249450.0470.0RegionNote=6-phosphofructo-2-kinase
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000328333901182872_29442356.02945.0DomainBPTI/Kunitz inhibitor
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000454817891172872_29442324.02913.0DomainBPTI/Kunitz inhibitor
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000328333901182553_25552356.02945.0MotifCell attachment site
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000454817891172553_25552324.02913.0MotifCell attachment site
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000328333901182785_29442356.02945.0RegionNote=Nonhelical region (NC2)
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000454817891172785_29442324.02913.0RegionNote=Nonhelical region (NC2)

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePFKFB4chr3:48559419chr3:48608711ENST00000232375-1314250_469450.0470.0RegionNote=Fructose-2%2C6-bisphosphatase
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000328333901181054_12292356.02945.0DomainVWFA 2
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000032833390118234_3292356.02945.0DomainFibronectin type-III 1
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000032833390118330_4162356.02945.0DomainFibronectin type-III 2
TgeneCOL7A1chr3:48559419chr3:48608711ENST000003283339011838_2112356.02945.0DomainVWFA 1
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000032833390118417_5072356.02945.0DomainFibronectin type-III 3
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000032833390118510_5972356.02945.0DomainFibronectin type-III 4
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000032833390118600_6872356.02945.0DomainFibronectin type-III 5
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000032833390118688_7752356.02945.0DomainFibronectin type-III 6
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000032833390118778_8662356.02945.0DomainFibronectin type-III 7
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000032833390118869_9572356.02945.0DomainFibronectin type-III 8
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000032833390118958_10512356.02945.0DomainFibronectin type-III 9
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000454817891171054_12292324.02913.0DomainVWFA 2
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000045481789117234_3292324.02913.0DomainFibronectin type-III 1
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000045481789117330_4162324.02913.0DomainFibronectin type-III 2
TgeneCOL7A1chr3:48559419chr3:48608711ENST000004548178911738_2112324.02913.0DomainVWFA 1
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000045481789117417_5072324.02913.0DomainFibronectin type-III 3
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000045481789117510_5972324.02913.0DomainFibronectin type-III 4
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000045481789117600_6872324.02913.0DomainFibronectin type-III 5
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000045481789117688_7752324.02913.0DomainFibronectin type-III 6
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000045481789117778_8662324.02913.0DomainFibronectin type-III 7
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000045481789117869_9572324.02913.0DomainFibronectin type-III 8
TgeneCOL7A1chr3:48559419chr3:48608711ENST0000045481789117958_10512324.02913.0DomainFibronectin type-III 9
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000328333901181170_11722356.02945.0MotifCell attachment site
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000328333901181334_13362356.02945.0MotifCell attachment site
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000328333901182008_20102356.02945.0MotifCell attachment site
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000454817891171170_11722324.02913.0MotifCell attachment site
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000454817891171334_13362324.02913.0MotifCell attachment site
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000454817891172008_20102324.02913.0MotifCell attachment site
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000328333901181254_14772356.02945.0RegionNote=Interrupted collagenous region
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000328333901181254_27842356.02945.0RegionNote=Triple-helical region
TgeneCOL7A1chr3:48559419chr3:48608711ENST000003283339011817_12532356.02945.0RegionNote=Nonhelical region (NC1)
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000454817891171254_14772324.02913.0RegionNote=Interrupted collagenous region
TgeneCOL7A1chr3:48559419chr3:48608711ENST00000454817891171254_27842324.02913.0RegionNote=Triple-helical region
TgeneCOL7A1chr3:48559419chr3:48608711ENST000004548178911717_12532324.02913.0RegionNote=Nonhelical region (NC1)


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Fusion Gene Sequence for PFKFB4-COL7A1


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 PFKFB4-COL7A1


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 PFKFB4-COL7A1


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 PFKFB4-COL7A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCOL7A1C0432322Dominant dystrophic epidermolysis bullosa, albopapular type (disorder)18CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL7A1C0079474Hallopeau-Siemens Disease16CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL7A1C0432321Epidermolysis bullosa, pretibial3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL7A1C1851573Transient bullous dermolysis of the newborn3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL7A1C0079294Epidermolysis Bullosa Dystrophica2CTD_human;GENOMICS_ENGLAND
TgeneCOL7A1C0268371Epidermolysis Bullosa With Congenital Localized Absence Of Skin And Deformity Of Nails2CTD_human;GENOMICS_ENGLAND
TgeneCOL7A1C1275114Epidermolysis Bullosa Pruriginosa2CTD_human;ORPHANET;UNIPROT
TgeneCOL7A1C0006142Malignant neoplasm of breast1CTD_human;UNIPROT
TgeneCOL7A1C0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneCOL7A1C0009402Colorectal Carcinoma1CTD_human
TgeneCOL7A1C0009404Colorectal Neoplasms1CTD_human
TgeneCOL7A1C0235874Disease Exacerbation1CTD_human
TgeneCOL7A1C0678222Breast Carcinoma1CTD_human
TgeneCOL7A1C1257931Mammary Neoplasms, Human1CTD_human
TgeneCOL7A1C1458155Mammary Neoplasms1CTD_human
TgeneCOL7A1C1843477Epidermolysis Bullosa Simplex Superficialis1ORPHANET
TgeneCOL7A1C1843761TOENAIL DYSTROPHY, ISOLATED1CTD_human;UNIPROT
TgeneCOL7A1C4704874Mammary Carcinoma, Human1CTD_human