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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: 31604

FusionGeneSummary for RNF4_ZFYVE28

check button Fusion gene summary
Fusion gene informationFusion gene name: RNF4_ZFYVE28
Fusion gene ID: 31604
HgeneTgene
Gene symbol

RNF4

ZFYVE28

Gene ID

6047

57732

Gene namering finger protein 4zinc finger FYVE-type containing 28
SynonymsRES4-26|SLX5|SNURFLST2|LYST2
Cytomap

4p16.3

4p16.3

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase RNF4E3 ubiquitin ligase RNF4RING-type E3 ubiquitin transferase RNF4small nuclear RING finger proteinlateral signaling target protein 2 homologhLst2zinc finger FYVE domain-containing protein 28zinc finger, FYVE domain containing 28
Modification date2018052320180523
UniProtAcc

P78317

Q9HCC9

Ensembl transtripts involved in fusion geneENST00000314289, ENST00000541204, 
ENST00000509258, ENST00000511843, 
ENST00000511859, ENST00000506706, 
ENST00000511600, 
ENST00000290974, 
ENST00000511071, ENST00000515312, 
ENST00000515169, ENST00000509171, 
ENST00000503000, ENST00000508471, 
ENST00000505421, 
Fusion gene scores* DoF score4 X 4 X 3=488 X 6 X 7=336
# samples 48
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/336*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RNF4 [Title/Abstract] AND ZFYVE28 [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
HgeneRNF4

GO:0045944

positive regulation of transcription by RNA polymerase II

12885770

HgeneRNF4

GO:0046685

response to arsenic-containing substance

20943951


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
TCGALDBLCATCGA-CF-A47V-01ARNF4chr4

2598056

+ZFYVE28chr4

2321998

-
* 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-3CDSENST00000314289ENST00000290974RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000314289ENST00000511071RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000314289ENST00000515312RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000314289ENST00000515169RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000314289ENST00000509171RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000314289ENST00000503000RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000314289ENST00000508471RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000314289ENST00000505421RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000541204ENST00000290974RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000541204ENST00000511071RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000541204ENST00000515312RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000541204ENST00000515169RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000541204ENST00000509171RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000541204ENST00000503000RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000541204ENST00000508471RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000541204ENST00000505421RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000509258ENST00000290974RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000509258ENST00000511071RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000509258ENST00000515312RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000509258ENST00000515169RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000509258ENST00000509171RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000509258ENST00000503000RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000509258ENST00000508471RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000509258ENST00000505421RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000511843ENST00000290974RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000511843ENST00000511071RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000511843ENST00000515312RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511843ENST00000515169RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511843ENST00000509171RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511843ENST00000503000RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511843ENST00000508471RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511843ENST00000505421RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000511859ENST00000290974RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000511859ENST00000511071RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000511859ENST00000515312RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511859ENST00000515169RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511859ENST00000509171RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511859ENST00000503000RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511859ENST00000508471RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511859ENST00000505421RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000506706ENST00000290974RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000506706ENST00000511071RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000506706ENST00000515312RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000506706ENST00000515169RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000506706ENST00000509171RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000506706ENST00000503000RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000506706ENST00000508471RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000506706ENST00000505421RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000511600ENST00000290974RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000511600ENST00000511071RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-3CDSENST00000511600ENST00000515312RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511600ENST00000515169RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511600ENST00000509171RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511600ENST00000503000RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511600ENST00000508471RNF4chr4

2598056

+ZFYVE28chr4

2321998

-
intron-intronENST00000511600ENST00000505421RNF4chr4

2598056

+ZFYVE28chr4

2321998

-

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FusionProtFeatures for RNF4_ZFYVE28


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RNF4

P78317

ZFYVE28

Q9HCC9

E3 ubiquitin-protein ligase which binds polysumoylatedchains covalently attached to proteins and mediates 'Lys-6'-,'Lys-11'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination ofthose substrates and their subsequent targeting to the proteasomefor degradation. Regulates the degradation of several proteinsincluding PML and the transcriptional activator PEA3. Involved inchromosome alignment and spindle assembly, it regulates thekinetochore CENPH-CENPI-CENPK complex by targeting polysumoylatedCENPI to proteasomal degradation. Regulates the cellular responsesto hypoxia and heat shock through degradation of respectivelyEPAS1 and PARP1. Alternatively, it may also bind DNA/nucleosomesand have a more direct role in the regulation of transcription forinstance enhancing basal transcription and steroid receptor-mediated transcriptional activation. {ECO:0000269|PubMed:12885770,ECO:0000269|PubMed:18408734, ECO:0000269|PubMed:19307308,ECO:0000269|PubMed:20026589, ECO:0000269|PubMed:20212317,ECO:0000269|PubMed:20943951}.

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 RNF4_ZFYVE28


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 RNF4_ZFYVE28


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
RNF4AR, PATZ1, TCF20, ESR1, PGR, TBP, SP1, UBE2D1, UBE2D2, UBE2D3, UBE2D4, UBE2L6, UBE2T, UBE2W, UEVLD, UBE2E1, UBE2E3, UBE2H, UBE2I, UBE2K, UBE2E2, IKBKG, RNF4, SUMO2, TRIM28, PML, SART1, UHRF1, MDC1, RPA1, SUMO1, TDG, APEX1, TRPS1, SKIL, NFE2L2, TRAIP, HNF4A, SRPK2, UBC, HIST2H3C, ATXN1, TARDBP, MECP2, NCOA1, TERF2, FANCA, UBE2N, MAP3K7, TAB2, TAB3, USP11, MYC, CTNNB1, TRIM25, MIS18BP1, UBE2A, UBE2BZFYVE28EGF, RAB5A, RAB4A, RAB7A, EGFR, PRNP


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 RNF4_ZFYVE28


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 RNF4_ZFYVE28


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