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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: 30650

FusionGeneSummary for RBFA_XRCC5

check button Fusion gene summary
Fusion gene informationFusion gene name: RBFA_XRCC5
Fusion gene ID: 30650
HgeneTgene
Gene symbol

RBFA

XRCC5

Gene ID

79863

7520

Gene nameribosome binding factor AX-ray repair cross complementing 5
SynonymsC18orf22|HsT169KARP-1|KARP1|KU80|KUB2|Ku86|NFIV
Cytomap

18q23

2q35

Type of geneprotein-codingprotein-coding
Descriptionputative ribosome-binding factor A, mitochondrialribosome binding factor A (putative)X-ray repair cross-complementing protein 586 kDa subunit of Ku antigenATP-dependent DNA helicase 2 subunit 2ATP-dependent DNA helicase II 80 kDa subunitCTC box-binding factor 85 kDa subunitCTC85CTCBFDNA repair protein XRCC5Ku autoantigen, 80kDaKu
Modification date2018051920180523
UniProtAcc

Q8N0V3

P13010

Ensembl transtripts involved in fusion geneENST00000306735, ENST00000586847, 
ENST00000262197, 
ENST00000392133, 
ENST00000392132, ENST00000471649, 
Fusion gene scores* DoF score4 X 5 X 5=1006 X 5 X 3=90
# samples 77
** MAII scorelog2(7/100*10)=-0.514573172829758
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/90*10)=-0.362570079384708
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RBFA [Title/Abstract] AND XRCC5 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationDDR (DNA damage repair) gene involved fusion gene, retained protein feature but frameshift.
* 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
TgeneXRCC5

GO:0002218

activation of innate immune response

28712728

TgeneXRCC5

GO:0006303

double-strand break repair via nonhomologous end joining

26359349

TgeneXRCC5

GO:0045860

positive regulation of protein kinase activity

22504299

TgeneXRCC5

GO:0071480

cellular response to gamma radiation

26359349


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
TCGALDLGGTCGA-FG-A711-01ARBFAchr18

77802219

+XRCC5chr2

217054948

+
* 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
Frame-shitENST00000306735ENST00000392133RBFAchr18

77802219

+XRCC5chr2

217054948

+
Frame-shitENST00000306735ENST00000392132RBFAchr18

77802219

+XRCC5chr2

217054948

+
5CDS-intronENST00000306735ENST00000471649RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-3CDSENST00000586847ENST00000392133RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-3CDSENST00000586847ENST00000392132RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-intronENST00000586847ENST00000471649RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-3CDSENST00000262197ENST00000392133RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-3CDSENST00000262197ENST00000392132RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-intronENST00000262197ENST00000471649RBFAchr18

77802219

+XRCC5chr2

217054948

+

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FusionProtFeatures for RBFA_XRCC5


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

Q8N0V3

XRCC5

P13010

Single-stranded DNA-dependent ATP-dependent helicase.Has a role in chromosome translocation. The DNA helicase IIcomplex binds preferentially to fork-like ends of double-strandedDNA in a cell cycle-dependent manner. It works in the 3'-5'direction. Binding to DNA may be mediated by XRCC6. Involved inDNA non-homologous end joining (NHEJ) required for double-strandbreak repair and V(D)J recombination. The XRCC5/6 dimer acts asregulatory subunit of the DNA-dependent protein kinase complexDNA-PK by increasing the affinity of the catalytic subunit PRKDCto DNA by 100-fold. The XRCC5/6 dimer is probably involved instabilizing broken DNA ends and bringing them together(PubMed:12145306, PubMed:20383123, PubMed:7957065,PubMed:8621488). The assembly of the DNA-PK complex to DNA ends isrequired for the NHEJ ligation step. In association with NAA15,the XRCC5/6 dimer binds to the osteocalcin promoter and activatesosteocalcin expression (PubMed:20383123). The XRCC5/6 dimerprobably also acts as a 5'-deoxyribose-5-phosphate lyase (5'-dRPlyase), by catalyzing the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site near double-strand breaks. XRCC5probably acts as the catalytic subunit of 5'-dRP activity, andallows to 'clean' the termini of abasic sites, a class ofnucleotide damage commonly associated with strand breaks, beforesuch broken ends can be joined. The XRCC5/6 dimer together withAPEX1 acts as a negative regulator of transcription(PubMed:8621488). Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNPcomplex, a complex that serves as a platform for IRF3phosphorylation and subsequent innate immune response activationthrough the cGAS-STING pathway. {ECO:0000269|PubMed:12145306,ECO:0000269|PubMed:20383123, ECO:0000269|PubMed:28712728,ECO:0000269|PubMed:7957065, ECO:0000269|PubMed:8621488}.

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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FusionGeneSequence for RBFA_XRCC5


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.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for RBFA_XRCC5


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
RBFAKBTBD7, CMTM5, SCN2B, EPB41L3, METTL15, CDH5, ZZEF1, TRIM69, EXT2, SIRT1, HECTD3, KBTBD6, ZNF638, CD70XRCC5XRCC6, AR, TERF2, TERF2IP, CHEK1, RBM14, NCOA6, KAT2A, VAV1, TYK2, TERT, PRKDC, POU2F1, WRN, POLA1, PCNA, TOP2A, PRIM1, POLR2E, POLR2D, ORC2, ORC1, RFC1, BIN1, APEX1, CD40, HSF1, HDLBP, DHX9, H2AFY, SIRT6, NR1H4, CHD1L, BRCA1, BARD1, ESR1, PARP1, PDX1, MSX2, RUNX2, NAA15, H2AFX, PHF1, XRCC4, LIG4, ILF2, THRA, THRB, BMI1, CHAF1A, HIST1H3E, H3F3A, TERF1, BAZ1A, SMARCA5, CHRAC1, POLE3, MYC, MME, USF1, HDAC5, RBM39, APLF, PSMA3, COIL, POLR2A, LIG3, HOXB7, YY1, VHL, RNF146, SMARCAD1, ATM, ATR, NBN, ORC3, ORC6, ORC4, TCF7L2, HDGF, CENPA, MSH6, HOXC4, MDC1, CEBPA, ARRB1, ARRB2, RAD23A, SIRT7, HNRNPA1, RNF8, HNRNPC, SUPT16H, SSRP1, TMPO, TOP1, DDX17, ERG, ISG15, TONSL, CUL3, CDK2, BAX, KCND3, GRK5, DYNC1H1, TFAP4, PAF1, PTER, YARS, PGR, XRCC5, ECT2, TP53BP1, CSNK2A1, SMURF1, FMNL1, PNKP, FN1, VCAM1, GZMA, CDH1, GZMB, NOS2, ITGA4, DCLRE1C, IGSF8, ICAM1, SOX2, HDAC6, CDC16, TARDBP, C1QBP, CUL2, CSDE1, DNMBP, EIF3J, EIF4B, GANAB, HSPA4, JUP, MSH2, NARS, NCL, PLCB3, PRMT3, RPL24, SAMHD1, SF1, TRMT1, HYOU1, RPA1, RPA2, RPA3, ATRX, ELF3, EHF, HUWE1, PPARG, CUL7, OBSL1, CCDC8, SUZ12, EED, RNF2, EGFR, UBE2I, SUMO2, MAST3, WDR76, RPS6KB2, HSPB1, PHRF1, NTRK1, SCARNA22, EWSR1, SRPK2, CBL, COX6B1, DYNC1I2, ERF, NDST1, IGF2R, LIMS1, MSH5, NFIB, PCDH7, PPM1A, ABCE1, ROCK1, BRPF1, NCOA3, MPDZ, MAP3K6, GOLGA5, SNUPN, SMYD5, WWP1, ZZEF1, RTEL1, LAMTOR1, ASAP3, PEAK1, C17orf49, MITD1, MIB2, CEP128, CRY1, MACROD1, MCM2, NF2, SENP3, TFAP2A, NANOG, UHRF2, NFATC1, NFATC2, AHSA1, RNF126, USP11, DERL1, ZNF746, CDK5RAP1, SPTA1, DLD, DNM1L, HSD17B10, SOD1, VDAC1, TRIM25, EP300, UBE2S, YAP1, MTF1, DDB2, DDB1


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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RelatedDrugs for RBFA_XRCC5


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 RBFA_XRCC5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneXRCC5C0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneXRCC5C0678306alcohol sensitivity1PSYGENET