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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:RNF168-PHC3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RNF168-PHC3
FusionPDB ID: 74873
FusionGDB2.0 ID: 74873
HgeneTgene
Gene symbol

RNF168

PHC3

Gene ID

165918

80012

Gene namering finger protein 168polyhomeotic homolog 3
SynonymsRIDL|hRNF168EDR3|HPH3
Cytomap

3q29

3q26.2

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase RNF168RING-type E3 ubiquitin transferase RNF168ring finger protein 168, E3 ubiquitin protein ligasepolyhomeotic-like protein 3early development regulator 3early development regulatory protein 3homolog of polyhomeotic 3polyhomeotic like 3
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000318037, ENST00000474275, 
ENST00000481639, ENST00000497658, 
ENST00000467570, ENST00000494943, 
ENST00000495893, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 5 X 5=1508 X 7 X 6=336
# samples 610
** MAII scorelog2(6/150*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/336*10)=-1.74846123300404
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: RNF168 [Title/Abstract] AND PHC3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RNF168(196229743)-PHC3(169840532), # samples:1
Anticipated loss of major functional domain due to fusion event.RNF168-PHC3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
RNF168-PHC3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
RNF168-PHC3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
RNF168-PHC3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
HgeneRNF168

GO:0006302

double-strand break repair

19203578|19203579|22980979

HgeneRNF168

GO:0006511

ubiquitin-dependent protein catabolic process

22373579

HgeneRNF168

GO:0006974

cellular response to DNA damage stimulus

19500350|20550933|22373579|22508508|22980979

HgeneRNF168

GO:0010212

response to ionizing radiation

19203578|19203579

HgeneRNF168

GO:0016567

protein ubiquitination

22373579

HgeneRNF168

GO:0035518

histone H2A monoubiquitination

22980979

HgeneRNF168

GO:0036351

histone H2A-K13 ubiquitination

22980979

HgeneRNF168

GO:0036352

histone H2A-K15 ubiquitination

22980979

HgeneRNF168

GO:0045739

positive regulation of DNA repair

19203578|19203579

HgeneRNF168

GO:0070534

protein K63-linked ubiquitination

22266820

HgeneRNF168

GO:0070535

histone H2A K63-linked ubiquitination

19203578|19203579|19500350


check buttonFusion gene breakpoints across RNF168 (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 PHC3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4Non-Cancer203NRNF168chr3

196229743

-PHC3chr3

169840532

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000318037RNF168chr3196229743-ENST00000495893PHC3chr3169840532-117428968722095407
ENST00000318037RNF168chr3196229743-ENST00000494943PHC3chr3169840532-41058968722095407
ENST00000318037RNF168chr3196229743-ENST00000467570PHC3chr3169840532-18288968721753293

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
ENST00000318037ENST00000495893RNF168chr3196229743-PHC3chr3169840532-0.0004773160.9995227
ENST00000318037ENST00000494943RNF168chr3196229743-PHC3chr3169840532-0.0006794540.9993205
ENST00000318037ENST00000467570RNF168chr3196229743-PHC3chr3169840532-0.0262306030.9737694

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>74873_74873_1_RNF168-PHC3_RNF168_chr3_196229743_ENST00000318037_PHC3_chr3_169840532_ENST00000467570_length(amino acids)=293AA_BP=8
MAKNQRKWVYQVEDVCEEEMPEESDECVRMDRTPPPPTLSPAAITVGRGEDLTSEHPLLEQVELPAVASVSASVIKSPSDPSHVSVPPPP
LLLPAATTRSNSTSMHSSIPSIENKPPQAIVKPQILTHVIEGFVIQEGLEPFPVSRSSLLIEQPVKKRPLLDNQVINSVCVQPELQNNTK
HADNSSDTEMEDMIAEETLEEMDSELLKCEFCGKMGYANEFLRSKRFCTMSCAKRYNVSCSKKFALSRWNRKPDNQSLGHRGRRPSGPDG

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

>74873_74873_2_RNF168-PHC3_RNF168_chr3_196229743_ENST00000318037_PHC3_chr3_169840532_ENST00000494943_length(amino acids)=407AA_BP=8
MAKNQRKWVYQVEDVCEEEMPEESDECVRMDRTPPPPTLSPAAITVGRGEDLTSEHPLLEQVELPAVASVSASVIKSPSDPSHVSVPPPP
LLLPAATTRSNSTSMHSSIPSIENKPPQAIVKPQILTHVIEGFVIQEGLEPFPVSRSSLLIEQPVKKRPLLDNQVINSVCVQPELQNNTK
HADNSSDTEMEDMIAEETLEEMDSELLKCEFCGKMGYANEFLRSKRFCTMSCAKRYNVSCSKKFALSRWNRKPDNQSLGHRGRRPSGPDG
AAREHILRQLPITYPSAEEDLASHEDSVPSAMTTRLRRQSERERERELRDVRIRKMPENSDLLPVAQTEPSIWTVDDVWAFIHSLPGCQD

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

>74873_74873_3_RNF168-PHC3_RNF168_chr3_196229743_ENST00000318037_PHC3_chr3_169840532_ENST00000495893_length(amino acids)=407AA_BP=8
MAKNQRKWVYQVEDVCEEEMPEESDECVRMDRTPPPPTLSPAAITVGRGEDLTSEHPLLEQVELPAVASVSASVIKSPSDPSHVSVPPPP
LLLPAATTRSNSTSMHSSIPSIENKPPQAIVKPQILTHVIEGFVIQEGLEPFPVSRSSLLIEQPVKKRPLLDNQVINSVCVQPELQNNTK
HADNSSDTEMEDMIAEETLEEMDSELLKCEFCGKMGYANEFLRSKRFCTMSCAKRYNVSCSKKFALSRWNRKPDNQSLGHRGRRPSGPDG
AAREHILRQLPITYPSAEEDLASHEDSVPSAMTTRLRRQSERERERELRDVRIRKMPENSDLLPVAQTEPSIWTVDDVWAFIHSLPGCQD

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Fusion Protein Functional Features


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/chr3:196229743/chr3:169840532)
- 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: 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: 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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRNF168chr3:196229743chr3:169840532ENST00000318037-1616_55100.33333333333333572.0Zinc fingerRING-type
TgenePHC3chr3:196229743chr3:169840532ENST000004742750519_260187.0Compositional biasNote=Poly-Thr
TgenePHC3chr3:196229743chr3:169840532ENST0000047427505324_5390187.0Compositional biasNote=Gln-rich
TgenePHC3chr3:196229743chr3:169840532ENST0000047427505346_6700187.0Compositional biasNote=Pro-rich
TgenePHC3chr3:196229743chr3:169840532ENST000004742750589_2870187.0Compositional biasNote=Ser-rich
TgenePHC3chr3:196229743chr3:169840532ENST000004976580419_260152.0Compositional biasNote=Poly-Thr
TgenePHC3chr3:196229743chr3:169840532ENST0000049765804324_5390152.0Compositional biasNote=Gln-rich
TgenePHC3chr3:196229743chr3:169840532ENST0000049765804346_6700152.0Compositional biasNote=Pro-rich
TgenePHC3chr3:196229743chr3:169840532ENST000004976580489_2870152.0Compositional biasNote=Ser-rich
TgenePHC3chr3:196229743chr3:169840532ENST0000047427505919_9830187.0DomainSAM
TgenePHC3chr3:196229743chr3:169840532ENST00000494943715919_983584.0984.0DomainSAM
TgenePHC3chr3:196229743chr3:169840532ENST00000495893715919_983596.0996.0DomainSAM
TgenePHC3chr3:196229743chr3:169840532ENST0000049765804919_9830152.0DomainSAM
TgenePHC3chr3:196229743chr3:169840532ENST0000047427505691_7200187.0MotifNote=HD1
TgenePHC3chr3:196229743chr3:169840532ENST00000494943715691_720584.0984.0MotifNote=HD1
TgenePHC3chr3:196229743chr3:169840532ENST00000495893715691_720596.0996.0MotifNote=HD1
TgenePHC3chr3:196229743chr3:169840532ENST0000049765804691_7200152.0MotifNote=HD1
TgenePHC3chr3:196229743chr3:169840532ENST0000047427505776_8100187.0Zinc fingerFCS-type
TgenePHC3chr3:196229743chr3:169840532ENST00000494943715776_810584.0984.0Zinc fingerFCS-type
TgenePHC3chr3:196229743chr3:169840532ENST00000495893715776_810596.0996.0Zinc fingerFCS-type
TgenePHC3chr3:196229743chr3:169840532ENST0000049765804776_8100152.0Zinc fingerFCS-type

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRNF168chr3:196229743chr3:169840532ENST00000318037-16115_177100.33333333333333572.0Compositional biasGlu-rich
HgeneRNF168chr3:196229743chr3:169840532ENST00000318037-16110_128100.33333333333333572.0MotifLR motif 1
HgeneRNF168chr3:196229743chr3:169840532ENST00000318037-16143_151100.33333333333333572.0MotifUMI motif
HgeneRNF168chr3:196229743chr3:169840532ENST00000318037-16168_191100.33333333333333572.0MotifMIU motif 1
HgeneRNF168chr3:196229743chr3:169840532ENST00000318037-16439_462100.33333333333333572.0MotifMIU motif 2
HgeneRNF168chr3:196229743chr3:169840532ENST00000318037-16466_477100.33333333333333572.0MotifLR motif 2
TgenePHC3chr3:196229743chr3:169840532ENST0000049494371519_26584.0984.0Compositional biasNote=Poly-Thr
TgenePHC3chr3:196229743chr3:169840532ENST00000494943715324_539584.0984.0Compositional biasNote=Gln-rich
TgenePHC3chr3:196229743chr3:169840532ENST00000494943715346_670584.0984.0Compositional biasNote=Pro-rich
TgenePHC3chr3:196229743chr3:169840532ENST0000049494371589_287584.0984.0Compositional biasNote=Ser-rich
TgenePHC3chr3:196229743chr3:169840532ENST0000049589371519_26596.0996.0Compositional biasNote=Poly-Thr
TgenePHC3chr3:196229743chr3:169840532ENST00000495893715324_539596.0996.0Compositional biasNote=Gln-rich
TgenePHC3chr3:196229743chr3:169840532ENST00000495893715346_670596.0996.0Compositional biasNote=Pro-rich
TgenePHC3chr3:196229743chr3:169840532ENST0000049589371589_287596.0996.0Compositional biasNote=Ser-rich


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
RNF168
PHC3


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to RNF168-PHC3


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to RNF168-PHC3


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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