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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:TRIM27-PFDN4 (FusionGDB2 ID:93392)

Fusion Gene Summary for TRIM27-PFDN4

check button Fusion gene summary
Fusion gene informationFusion gene name: TRIM27-PFDN4
Fusion gene ID: 93392
HgeneTgene
Gene symbol

TRIM27

PFDN4

Gene ID

5987

5203

Gene nametripartite motif containing 27prefoldin subunit 4
SynonymsRFP|RNF76C1|PFD4
Cytomap

6p22.1

20q13.2

Type of geneprotein-codingprotein-coding
Descriptionzinc finger protein RFPRFP transforming proteinRING finger protein 76RING-type E3 ubiquitin transferase TRIM27ret finger proteintripartite motif protein TRIM27tripartite motif-containing protein 27prefoldin subunit 4prefoldin 4protein C-1
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000377194, ENST00000377199, 
ENST00000498117, ENST00000459807, 
ENST00000412687, ENST00000437160, 
ENST00000427689, ENST00000435528, 
ENST00000485666, ENST00000468364, 
ENST00000455861, ENST00000417660, 
ENST00000400720, ENST00000495323, 
ENST00000491158, ENST00000437415, 
ENST00000468047, ENST00000431123, 
ENST00000452265, 		ENST00000371419, 
ENST00000487129, 
Fusion gene scores* DoF score5 X 9 X 7=3157 X 6 X 5=210
# samples 99
** MAII scorelog2(9/315*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/210*10)=-1.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TRIM27 [Title/Abstract] AND PFDN4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTRIM27(28889668)-PFDN4(52835557), # samples:1
Anticipated loss of major functional domain due to fusion event.TRIM27-PFDN4 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
TRIM27-PFDN4 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
TRIM27-PFDN4 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
TRIM27-PFDN4 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted 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
HgeneTRIM27

GO:0000122

negative regulation of transcription by RNA polymerase II

10976108

HgeneTRIM27

GO:0006469

negative regulation of protein kinase activity

22128329

HgeneTRIM27

GO:0032897

negative regulation of viral transcription

18248090

HgeneTRIM27

GO:0034314

Arp2/3 complex-mediated actin nucleation

23452853

HgeneTRIM27

GO:0042147

retrograde transport, endosome to Golgi

23452853

HgeneTRIM27

GO:0045087

innate immune response

18248090

HgeneTRIM27

GO:0045814

negative regulation of gene expression, epigenetic

10976108

HgeneTRIM27

GO:0051091

positive regulation of DNA-binding transcription factor activity

23077300


check buttonFusion gene breakpoints across TRIM27 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across PFDN4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4OVTCGA-13-0890TRIM27chr6

28889668

-PFDN4chr20

52835557

+


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Fusion Gene ORF analysis for TRIM27-PFDN4

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-shiftENST00000377194ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
5CDS-3UTRENST00000377194ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
Frame-shiftENST00000377199ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
5CDS-3UTRENST00000377199ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
5UTR-3CDSENST00000498117ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
5UTR-3UTRENST00000498117ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000459807ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000459807ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000412687ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000412687ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000437160ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000437160ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000427689ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000427689ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000435528ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000435528ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000485666ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000485666ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000468364ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000468364ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000455861ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000455861ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000417660ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000417660ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000400720ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000400720ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000495323ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000495323ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000491158ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000491158ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000437415ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000437415ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000468047ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000468047ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000431123ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000431123ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3CDSENST00000452265ENST00000371419TRIM27chr6

28889668

-PFDN4chr20

52835557

+
intron-3UTRENST00000452265ENST00000487129TRIM27chr6

28889668

-PFDN4chr20

52835557

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for TRIM27-PFDN4


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
TRIM27chr628889668-PFDN4chr2052835557+0.0002787380.9997212
TRIM27chr628889668-PFDN4chr2052835557+0.0002787380.9997212

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for TRIM27-PFDN4


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
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.
- 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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Fusion Gene Sequence for TRIM27-PFDN4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for TRIM27-PFDN4


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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Related Drugs for TRIM27-PFDN4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for TRIM27-PFDN4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTRIM27C0238463Papillary thyroid carcinoma2ORPHANET