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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:COL4A5-XRCC4 (FusionGDB2 ID:18380)

Fusion Gene Summary for COL4A5-XRCC4

check button Fusion gene summary
Fusion gene informationFusion gene name: COL4A5-XRCC4
Fusion gene ID: 18380
HgeneTgene
Gene symbol

COL4A5

XRCC4

Gene ID

1287

7518

Gene namecollagen type IV alpha 5 chainX-ray repair cross complementing 4
SynonymsASLN|ATS|ATS1|CA54SSMED
Cytomap

Xq22.3

5q14.2

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-5(IV) chaincollagen IV, alpha-5 polypeptidecollagen of basement membrane, alpha-5 chaincollagen, type IV, alpha 5dA149D17.3dA24A23.1DNA repair protein XRCC4X-ray repair complementing defective repair in Chinese hamster cells 4
Modification date2020031320200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000477429, ENST00000328300, 
ENST00000361603, 		ENST00000282268, 
ENST00000338635, ENST00000396027, 
ENST00000511817, ENST00000509268, 
Fusion gene scores* DoF score12 X 9 X 6=6489 X 8 X 4=288
# samples 129
** MAII scorelog2(12/648*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/288*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL4A5 [Title/Abstract] AND XRCC4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL4A5(107683436)-XRCC4(82648944), # 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
TgeneXRCC4

GO:0006302

double-strand break repair

9242410

TgeneXRCC4

GO:0006303

double-strand break repair via nonhomologous end joining

12517771

TgeneXRCC4

GO:0010165

response to X-ray

9242410

TgeneXRCC4

GO:0051103

DNA ligation involved in DNA repair

12517771

TgeneXRCC4

GO:0051351

positive regulation of ligase activity

9242410


check buttonFusion gene breakpoints across COL4A5 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across XRCC4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4LUSCTCGA-43-3920-01ACOL4A5chrX

107683436

-XRCC4chr5

82648944

+


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Fusion Gene ORF analysis for COL4A5-XRCC4

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
3UTR-3CDSENST00000477429ENST00000282268COL4A5chrX

107683436

-XRCC4chr5

82648944

+
3UTR-3CDSENST00000477429ENST00000338635COL4A5chrX

107683436

-XRCC4chr5

82648944

+
3UTR-3CDSENST00000477429ENST00000396027COL4A5chrX

107683436

-XRCC4chr5

82648944

+
3UTR-3CDSENST00000477429ENST00000511817COL4A5chrX

107683436

-XRCC4chr5

82648944

+
3UTR-intronENST00000477429ENST00000509268COL4A5chrX

107683436

-XRCC4chr5

82648944

+
5CDS-intronENST00000328300ENST00000509268COL4A5chrX

107683436

-XRCC4chr5

82648944

+
5CDS-intronENST00000361603ENST00000509268COL4A5chrX

107683436

-XRCC4chr5

82648944

+
Frame-shiftENST00000328300ENST00000338635COL4A5chrX

107683436

-XRCC4chr5

82648944

+
Frame-shiftENST00000328300ENST00000396027COL4A5chrX

107683436

-XRCC4chr5

82648944

+
Frame-shiftENST00000328300ENST00000511817COL4A5chrX

107683436

-XRCC4chr5

82648944

+
Frame-shiftENST00000361603ENST00000338635COL4A5chrX

107683436

-XRCC4chr5

82648944

+
Frame-shiftENST00000361603ENST00000396027COL4A5chrX

107683436

-XRCC4chr5

82648944

+
Frame-shiftENST00000361603ENST00000511817COL4A5chrX

107683436

-XRCC4chr5

82648944

+
In-frameENST00000328300ENST00000282268COL4A5chrX

107683436

-XRCC4chr5

82648944

+
In-frameENST00000361603ENST00000282268COL4A5chrX

107683436

-XRCC4chr5

82648944

+

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)
ENST00000328300COL4A5chrX107683436-ENST00000282268XRCC4chr582648944+95332512938986
ENST00000361603COL4A5chrX107683436-ENST00000282268XRCC4chr582648944+95332512938986

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
ENST00000328300ENST00000282268COL4A5chrX107683436-XRCC4chr582648944+0.864626350.13537364
ENST00000361603ENST00000282268COL4A5chrX107683436-XRCC4chr582648944+0.864626350.13537364

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Fusion Genomic Features for COL4A5-XRCC4


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.
genomic feature

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 COL4A5-XRCC4


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/chrX:107683436/chr5:82648944)
- 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
..
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}.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
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000328300-1531461_1685271692.0DomainCollagen IV NC1
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000361603-1511461_1685271686.0DomainCollagen IV NC1
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000328300-15327_41271692.0RegionNote=Nonhelical region (NC2)
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000328300-15342_1456271692.0RegionNote=Triple-helical region
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000361603-15127_41271686.0RegionNote=Nonhelical region (NC2)
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000361603-15142_1456271686.0RegionNote=Triple-helical region
TgeneXRCC4chrX:107683436chr5:82648944ENST0000028226868131_165297335.0Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST0000028226868184_212297335.0Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST0000033863568131_165297337.0Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST0000033863568184_212297337.0Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST0000039602768131_165297335.0Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST0000039602768184_212297335.0Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST0000051181768131_165297337.0Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST0000051181768184_212297337.0Coiled coilOntology_term=ECO:0000255


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Fusion Gene Sequence for COL4A5-XRCC4


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.
>18380_18380_1_COL4A5-XRCC4_COL4A5_chrX_107683436_ENST00000328300_XRCC4_chr5_82648944_ENST00000282268_length(transcript)=953nt_BP=325nt
AGAAGGGAAAAGTTCTCCTGAGAGACCGGCTTTGGGGAGGGGAGGGGGGAAGGAAGAGTAGCTCCTTCTTCTTCTTCTTTTTTTTTTCTT
CCACTCTTAAAAAGCTTCTTTCTCTTCACCCAAGCCTCACTGTCCCTCTCCGGCTCTAGCTCTCTCCATATAAACCCTCAAGATTATGTC
AATTGGTTAGAGCCAGCCGGGAATTTCGTGCGGGTGCTGAAGGAGCTGCGGGAGCCGGAGAAGAATGAAACTGCGTGGAGTCAGCCTGGC
TGCCGGCTTGTTCTTACTGGCCCTGAGTCTTTGGGGGCAGCCTGCAGAGGCTGCGGCCTGATTCTTCACTACCTGAGACGTCTAAAAAGG
AGCACATCTCAGCTGAAAACATGTCTTTAGAAACTCTGAGAAACAGCAGCCCAGAAGACCTCTTTGATGAGATTTAACAGTCTCAAAAAA
TACTTTGATGTTCACTAGACTATGTTTTCTATTCATTTCTTTAAAATGAAAAAGGAGAATTTCAAGTCAGCAGCCGCTATTACCGTATCT
TACAATTTAATTACATACACAGTGAATTGAAACCATTGTGCAAAATGGATTACACATGTATACAAAGATACGATTTGATGATGACACTGG
CACATTATTCTAAACTATTCATTCAGCATGCCTATAATTACATAAATTGTATGAGACTTTTTGTTGCAAAGGACACATTTATCATATTCA
TTCACACATATTATATGTGATAGCTGTCCAACATCCTGTCTGGGAAGATTTTGAAAACAGGACAAAGAAAACATCATTTTAAAATGTCTT
CAGCTTTTTTTGAATAGACGTATTCAAACATATTCTGAACATTGATGTTTGAACATTTTAATTTGTGTGATGATGTAGAAAATATAATTT

>18380_18380_1_COL4A5-XRCC4_COL4A5_chrX_107683436_ENST00000328300_XRCC4_chr5_82648944_ENST00000282268_length(amino acids)=86AA_BP=65

--------------------------------------------------------------
>18380_18380_2_COL4A5-XRCC4_COL4A5_chrX_107683436_ENST00000361603_XRCC4_chr5_82648944_ENST00000282268_length(transcript)=953nt_BP=325nt
AGAAGGGAAAAGTTCTCCTGAGAGACCGGCTTTGGGGAGGGGAGGGGGGAAGGAAGAGTAGCTCCTTCTTCTTCTTCTTTTTTTTTTCTT
CCACTCTTAAAAAGCTTCTTTCTCTTCACCCAAGCCTCACTGTCCCTCTCCGGCTCTAGCTCTCTCCATATAAACCCTCAAGATTATGTC
AATTGGTTAGAGCCAGCCGGGAATTTCGTGCGGGTGCTGAAGGAGCTGCGGGAGCCGGAGAAGAATGAAACTGCGTGGAGTCAGCCTGGC
TGCCGGCTTGTTCTTACTGGCCCTGAGTCTTTGGGGGCAGCCTGCAGAGGCTGCGGCCTGATTCTTCACTACCTGAGACGTCTAAAAAGG
AGCACATCTCAGCTGAAAACATGTCTTTAGAAACTCTGAGAAACAGCAGCCCAGAAGACCTCTTTGATGAGATTTAACAGTCTCAAAAAA
TACTTTGATGTTCACTAGACTATGTTTTCTATTCATTTCTTTAAAATGAAAAAGGAGAATTTCAAGTCAGCAGCCGCTATTACCGTATCT
TACAATTTAATTACATACACAGTGAATTGAAACCATTGTGCAAAATGGATTACACATGTATACAAAGATACGATTTGATGATGACACTGG
CACATTATTCTAAACTATTCATTCAGCATGCCTATAATTACATAAATTGTATGAGACTTTTTGTTGCAAAGGACACATTTATCATATTCA
TTCACACATATTATATGTGATAGCTGTCCAACATCCTGTCTGGGAAGATTTTGAAAACAGGACAAAGAAAACATCATTTTAAAATGTCTT
CAGCTTTTTTTGAATAGACGTATTCAAACATATTCTGAACATTGATGTTTGAACATTTTAATTTGTGTGATGATGTAGAAAATATAATTT

>18380_18380_2_COL4A5-XRCC4_COL4A5_chrX_107683436_ENST00000361603_XRCC4_chr5_82648944_ENST00000282268_length(amino acids)=86AA_BP=65

--------------------------------------------------------------

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Fusion Gene PPI Analysis for COL4A5-XRCC4


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
TgeneXRCC4chrX:107683436chr5:82648944ENST00000282268681_213297.6666666666667335.0IFFO1
TgeneXRCC4chrX:107683436chr5:82648944ENST00000338635681_213297.6666666666667337.0IFFO1
TgeneXRCC4chrX:107683436chr5:82648944ENST00000396027681_213297.6666666666667335.0IFFO1
TgeneXRCC4chrX:107683436chr5:82648944ENST00000511817681_213297.6666666666667337.0IFFO1
TgeneXRCC4chrX:107683436chr5:82648944ENST0000028226868180_213297.6666666666667335.0LIG4
TgeneXRCC4chrX:107683436chr5:82648944ENST0000033863568180_213297.6666666666667337.0LIG4
TgeneXRCC4chrX:107683436chr5:82648944ENST0000039602768180_213297.6666666666667335.0LIG4
TgeneXRCC4chrX:107683436chr5:82648944ENST0000051181768180_213297.6666666666667337.0LIG4


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 COL4A5-XRCC4


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 COL4A5-XRCC4


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