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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: 14944

FusionGeneSummary for GNE_RPA3

check button Fusion gene summary
Fusion gene informationFusion gene name: GNE_RPA3
Fusion gene ID: 14944
HgeneTgene
Gene symbol

GNE

RPA3

Gene ID

10020

6119

Gene nameglucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinasereplication protein A3
SynonymsDMRV|GLCNE|IBM2|NM|Uae1REPA3|RP-A p14
Cytomap

9p13.3

7p21.3

Type of geneprotein-codingprotein-coding
Descriptionbifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinaseN-acylmannosamine kinaseUDP-GlcNAc-2-epimerase/ManAc kinaseUDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinasereplication protein A 14 kDa subunitRF-A protein 3replication factor A protein 3replication protein A3, 14kDa
Modification date2018051920180523
UniProtAcc

Q9Y223

P35244

Ensembl transtripts involved in fusion geneENST00000396594, ENST00000539815, 
ENST00000543356, ENST00000539208, 
ENST00000447283, ENST00000377902, 
ENST00000223129, ENST00000406109, 
ENST00000396682, ENST00000401447, 
Fusion gene scores* DoF score6 X 6 X 4=1443 X 2 X 3=18
# samples 63
** MAII scorelog2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: GNE [Title/Abstract] AND RPA3 [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
TgeneRPA3

GO:0006284

base-excision repair

9765279


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
ChiTaRS3.1AW753960GNEchr9

36237296

-RPA3chr7

7722774

+
* 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
intron-intronENST00000396594ENST00000223129GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000396594ENST00000406109GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000396594ENST00000396682GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000396594ENST00000401447GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000539815ENST00000223129GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000539815ENST00000406109GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000539815ENST00000396682GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000539815ENST00000401447GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000543356ENST00000223129GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000543356ENST00000406109GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000543356ENST00000396682GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000543356ENST00000401447GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000539208ENST00000223129GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000539208ENST00000406109GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000539208ENST00000396682GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000539208ENST00000401447GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000447283ENST00000223129GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000447283ENST00000406109GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000447283ENST00000396682GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000447283ENST00000401447GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000377902ENST00000223129GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000377902ENST00000406109GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000377902ENST00000396682GNEchr9

36237296

-RPA3chr7

7722774

+
intron-intronENST00000377902ENST00000401447GNEchr9

36237296

-RPA3chr7

7722774

+

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FusionProtFeatures for GNE_RPA3


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

Q9Y223

RPA3

P35244

As part of the heterotrimeric replication protein Acomplex (RPA/RP-A), binds and stabilizes single-stranded DNAintermediates that form during DNA replication or upon DNA stress.It prevents their reannealing and in parallel, recruits andactivates different proteins and complexes involved in DNAmetabolism. Thereby, it plays an essential role both in DNAreplication and the cellular response to DNA damage(PubMed:9430682). In the cellular response to DNA damage, the RPAcomplex controls DNA repair and DNA damage checkpoint activation.Through recruitment of ATRIP activates the ATR kinase a masterregulator of the DNA damage response (PubMed:24332808). It isrequired for the recruitment of the DNA double-strand break repairfactors RAD51 and RAD52 to chromatin, in response to DNA damage.Also recruits to sites of DNA damage proteins like XPA and XPGthat are involved in nucleotide excision repair and is requiredfor this mechanism of DNA repair (PubMed:7697716). Plays also arole in base excision repair (BER), probably through interactionwith UNG (PubMed:9765279). Also recruits SMARCAL1/HARP, which isinvolved in replication fork restart, to sites of DNA damage. Mayalso play a role in telomere maintenance. RPA3 has its own single-stranded DNA-binding activity and may be responsible for polarityof the binding of the complex to DNA (PubMed:19010961). As part ofthe alternative replication protein A complex, aRPA, binds single-stranded DNA and probably plays a role in DNA repair. Compared tothe RPA2-containing, canonical RPA complex, may not supportchromosomal DNA replication and cell cycle progression through S-phase. The aRPA may not promote efficient priming by DNApolymerase alpha but could support DNA synthesis by polymerasedelta in presence of PCNA and replication factor C (RFC), the dualincision/excision reaction of nucleotide excision repair andRAD51-dependent strand exchange (PubMed:19996105).{ECO:0000269|PubMed:19010961, ECO:0000269|PubMed:19116208,ECO:0000269|PubMed:19996105, ECO:0000269|PubMed:7697716,ECO:0000269|PubMed:9430682, ECO:0000269|PubMed:9765279,ECO:0000303|PubMed:24332808}.

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 GNE_RPA3


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 GNE_RPA3


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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RelatedDrugs for GNE_RPA3


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 GNE_RPA3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGNEC1853926NONAKA MYOPATHY12CTD_human;ORPHANET;UNIPROT
HgeneGNEC0342853Sialuria3CTD_human;UNIPROT
HgeneGNEC0238190Inclusion Body Myositis (disorder)1CTD_human
HgeneGNEC1833373Inclusion Body Myopathy, Autosomal Recessive1CTD_human