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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 7968

FusionGeneSummary for COL4A5_XRCC4

check button Fusion gene summary
Fusion gene informationFusion gene name: COL4A5_XRCC4
Fusion gene ID: 7968
HgeneTgene
Gene symbol

COL4A5

XRCC4

Gene ID

1287

7518

Gene namecollagen type IV alpha 5 chainX-ray repair cross complementing 4
SynonymsASLN|ATS|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 date2018052320180523
UniProtAcc

P29400

Q13426

Ensembl transtripts involved in fusion geneENST00000328300, ENST00000361603, 
ENST00000477429, 		ENST00000282268, 
ENST00000338635, ENST00000396027, 
ENST00000511817, ENST00000509268, 
Fusion gene scores* DoF score3 X 2 X 2=124 X 3 X 4=48
# samples 34
** MAII scorelog2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(4/48*10)=-0.263034405833794
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]

Functional or gene categories assigned by FusionGDB annotation
* 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 button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLUSCTCGA-43-3920-01ACOL4A5chrX

107683436

+XRCC4chr5

82648944

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-frameENST00000328300ENST00000282268COL4A5chrX

107683436

+XRCC4chr5

82648944

+
Frame-shiftENST00000328300ENST00000338635COL4A5chrX

107683436

+XRCC4chr5

82648944

+
Frame-shiftENST00000328300ENST00000396027COL4A5chrX

107683436

+XRCC4chr5

82648944

+
Frame-shiftENST00000328300ENST00000511817COL4A5chrX

107683436

+XRCC4chr5

82648944

+
5CDS-intronENST00000328300ENST00000509268COL4A5chrX

107683436

+XRCC4chr5

82648944

+
In-frameENST00000361603ENST00000282268COL4A5chrX

107683436

+XRCC4chr5

82648944

+
Frame-shiftENST00000361603ENST00000338635COL4A5chrX

107683436

+XRCC4chr5

82648944

+
Frame-shiftENST00000361603ENST00000396027COL4A5chrX

107683436

+XRCC4chr5

82648944

+
Frame-shiftENST00000361603ENST00000511817COL4A5chrX

107683436

+XRCC4chr5

82648944

+
5CDS-intronENST00000361603ENST00000509268COL4A5chrX

107683436

+XRCC4chr5

82648944

+
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

+

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FusionProtFeatures for COL4A5_XRCC4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COL4A5

P29400

XRCC4

Q13426

Type IV collagen is the major structural component ofglomerular basement membranes (GBM), forming a 'chicken-wire'meshwork together with laminins, proteoglycans andentactin/nidogen. Involved in DNA non-homologous end joining (NHEJ)required for double-strand break repair and V(D)J recombination.Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complexis responsible for the NHEJ ligation step, and XRCC4 enhances thejoining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNAends is dependent on the assembly of the DNA-dependent proteinkinase complex DNA-PK to these DNA ends.{ECO:0000269|PubMed:10757784, ECO:0000269|PubMed:10854421,ECO:0000269|PubMed:16412978, ECO:0000269|PubMed:8548796}.

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_1685271692DomainCollagen IV NC1
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000361603+1511461_1685271686DomainCollagen IV NC1
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000328300+15327_41271692RegionNote=Nonhelical region (NC2)
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000328300+15342_1456271692RegionNote=Triple-helical region
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000361603+15127_41271686RegionNote=Nonhelical region (NC2)
HgeneCOL4A5chrX:107683436chr5:82648944ENST00000361603+15142_1456271686RegionNote=Triple-helical region
TgeneXRCC4chrX:107683436chr5:82648944ENST00000282268+68131_165297335Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST00000282268+68184_212297335Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST00000338635+68131_165297337Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST00000338635+68184_212297337Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST00000396027+68131_165297335Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST00000396027+68184_212297335Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST00000511817+68131_165297337Coiled coilOntology_term=ECO:0000255
TgeneXRCC4chrX:107683436chr5:82648944ENST00000511817+68184_212297337Coiled coilOntology_term=ECO:0000255


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FusionGeneSequence for COL4A5_XRCC4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_COL4A5_ENST00000328300_chrX_107683436_+_XRCC4_ENST00000282268_chr5_82648944_+_64aa

>In-frame_COL4A5_ENST00000361603_chrX_107683436_+_XRCC4_ENST00000282268_chr5_82648944_+_64aa


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_COL4A5_ENST00000328300_chrX_107683436_+_XRCC4_ENST00000282268_chr5_82648944_+_193nt
ATGAAACTGCGTGGAGTCAGCCTGGCTGCCGGCTTGTTCTTACTGGCCCTGAGTCTTTGGGGGCAGCCTGCAGAGGCTGCGGCCTGATTC
TTCACTACCTGAGACGTCTAAAAAGGAGCACATCTCAGCTGAAAACATGTCTTTAGAAACTCTGAGAAACAGCAGCCCAGAAGACCTCTT

>In-frame_COL4A5_ENST00000361603_chrX_107683436_+_XRCC4_ENST00000282268_chr5_82648944_+_193nt
ATGAAACTGCGTGGAGTCAGCCTGGCTGCCGGCTTGTTCTTACTGGCCCTGAGTCTTTGGGGGCAGCCTGCAGAGGCTGCGGCCTGATTC
TTCACTACCTGAGACGTCTAAAAAGGAGCACATCTCAGCTGAAAACATGTCTTTAGAAACTCTGAGAAACAGCAGCCCAGAAGACCTCTT


* Fusion transcript sequences (Full-length transcript).
>In-frame_COL4A5_ENST00000328300_chrX_107683436_+_XRCC4_ENST00000282268_chr5_82648944_+_953nt
AGAAGGGAAAAGTTCTCCTGAGAGACCGGCTTTGGGGAGGGGAGGGGGGAAGGAAGAGTAGCTCCTTCTTCTTCTTCTTTTTTTTTTCTT
CCACTCTTAAAAAGCTTCTTTCTCTTCACCCAAGCCTCACTGTCCCTCTCCGGCTCTAGCTCTCTCCATATAAACCCTCAAGATTATGTC
AATTGGTTAGAGCCAGCCGGGAATTTCGTGCGGGTGCTGAAGGAGCTGCGGGAGCCGGAGAAGAATGAAACTGCGTGGAGTCAGCCTGGC
TGCCGGCTTGTTCTTACTGGCCCTGAGTCTTTGGGGGCAGCCTGCAGAGGCTGCGGCCTGATTCTTCACTACCTGAGACGTCTAAAAAGG
AGCACATCTCAGCTGAAAACATGTCTTTAGAAACTCTGAGAAACAGCAGCCCAGAAGACCTCTTTGATGAGATTTAACAGTCTCAAAAAA
TACTTTGATGTTCACTAGACTATGTTTTCTATTCATTTCTTTAAAATGAAAAAGGAGAATTTCAAGTCAGCAGCCGCTATTACCGTATCT
TACAATTTAATTACATACACAGTGAATTGAAACCATTGTGCAAAATGGATTACACATGTATACAAAGATACGATTTGATGATGACACTGG
CACATTATTCTAAACTATTCATTCAGCATGCCTATAATTACATAAATTGTATGAGACTTTTTGTTGCAAAGGACACATTTATCATATTCA
TTCACACATATTATATGTGATAGCTGTCCAACATCCTGTCTGGGAAGATTTTGAAAACAGGACAAAGAAAACATCATTTTAAAATGTCTT
CAGCTTTTTTTGAATAGACGTATTCAAACATATTCTGAACATTGATGTTTGAACATTTTAATTTGTGTGATGATGTAGAAAATATAATTT

>In-frame_COL4A5_ENST00000361603_chrX_107683436_+_XRCC4_ENST00000282268_chr5_82648944_+_953nt
AGAAGGGAAAAGTTCTCCTGAGAGACCGGCTTTGGGGAGGGGAGGGGGGAAGGAAGAGTAGCTCCTTCTTCTTCTTCTTTTTTTTTTCTT
CCACTCTTAAAAAGCTTCTTTCTCTTCACCCAAGCCTCACTGTCCCTCTCCGGCTCTAGCTCTCTCCATATAAACCCTCAAGATTATGTC
AATTGGTTAGAGCCAGCCGGGAATTTCGTGCGGGTGCTGAAGGAGCTGCGGGAGCCGGAGAAGAATGAAACTGCGTGGAGTCAGCCTGGC
TGCCGGCTTGTTCTTACTGGCCCTGAGTCTTTGGGGGCAGCCTGCAGAGGCTGCGGCCTGATTCTTCACTACCTGAGACGTCTAAAAAGG
AGCACATCTCAGCTGAAAACATGTCTTTAGAAACTCTGAGAAACAGCAGCCCAGAAGACCTCTTTGATGAGATTTAACAGTCTCAAAAAA
TACTTTGATGTTCACTAGACTATGTTTTCTATTCATTTCTTTAAAATGAAAAAGGAGAATTTCAAGTCAGCAGCCGCTATTACCGTATCT
TACAATTTAATTACATACACAGTGAATTGAAACCATTGTGCAAAATGGATTACACATGTATACAAAGATACGATTTGATGATGACACTGG
CACATTATTCTAAACTATTCATTCAGCATGCCTATAATTACATAAATTGTATGAGACTTTTTGTTGCAAAGGACACATTTATCATATTCA
TTCACACATATTATATGTGATAGCTGTCCAACATCCTGTCTGGGAAGATTTTGAAAACAGGACAAAGAAAACATCATTTTAAAATGTCTT
CAGCTTTTTTTGAATAGACGTATTCAAACATATTCTGAACATTGATGTTTGAACATTTTAATTTGTGTGATGATGTAGAAAATATAATTT


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FusionGenePPI 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
COL4A5DAZAP2, TK1, CDKN1A, SMN1, NR1H2, ANXA7, VHL, ELAVL1, ANTXR2, STRN3, PDK1, DAP3, KIF21B, CASC5, VPS26B, CEP170P1, PLOD1, COL8A2, COLGALT2XRCC4IFFO1, ACTN1, NHEJ1, XRCC4, LIG4, PNKP, CAAP1, CHD3, VIM, NBN, SETMAR, PRKDC, XRCC6, XRCC5, CALM1, ERG, APTX, SRP54, NUDT21, USP7, CWC27, DENR, DDX5, VPS41, CSNK2A1, BIN1, ASTE1, FAM9B, ALDH7A1, IFFO2, NFKB1, APPBP2, LONRF2, APLF, MED4, NF2, MTMR7, FAM60A, RNF135, FYTTD1, DNAJC9, HSDL2, DNPEP, KIF3A


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:107683436chr5:82648944ENST00000282268+68180_213297335LIG4
TgeneXRCC4chrX:107683436chr5:82648944ENST00000338635+68180_213297337LIG4
TgeneXRCC4chrX:107683436chr5:82648944ENST00000396027+68180_213297335LIG4
TgeneXRCC4chrX:107683436chr5:82648944ENST00000511817+68180_213297337LIG4


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for COL4A5_XRCC4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for COL4A5_XRCC4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL4A5C1567742Alport Syndrome, X-Linked17CTD_human;ORPHANET;UNIPROT
HgeneCOL4A5C0086533Leiomyoma, Epithelioid1CTD_human
TgeneXRCC4C4225288SHORT STATURE, MICROCEPHALY, AND ENDOCRINE DYSFUNCTION2UNIPROT
TgeneXRCC4C0008625Chromosome Aberrations1CTD_human
TgeneXRCC4C0036341Schizophrenia1PSYGENET