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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:SMG5-PMF1 (FusionGDB2 ID:83530)

Fusion Gene Summary for SMG5-PMF1

check button Fusion gene summary
Fusion gene informationFusion gene name: SMG5-PMF1
Fusion gene ID: 83530
HgeneTgene
Gene symbol

SMG5

PMF1

Gene ID

23381

100527963

Gene nameSMG5 nonsense mediated mRNA decay factorPMF1-BGLAP readthrough
SynonymsEST1B|LPTS-RP1|LPTSRP1|SMG-5PMF-1|PMF1
Cytomap

1q22

1q22

Type of geneprotein-codingprotein-coding
Descriptionprotein SMG5EST1 telomerase component homolog BEST1-like protein BEst1p-like protein BLPTS interacting proteinever shorter telomeres 1Bsmg-5 homolog, nonsense mediated mRNA decay factorPMF1-BGLAP proteinpolyamine-modulated factor 1
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000361813, ENST00000368267, 
ENST00000489907, 		ENST00000368279, 
ENST00000368273, ENST00000368277, 
ENST00000565805, ENST00000567140, 
Fusion gene scores* DoF score11 X 13 X 4=5723 X 6 X 3=54
# samples 135
** MAII scorelog2(13/572*10)=-2.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/54*10)=-0.111031312388744
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMG5 [Title/Abstract] AND PMF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMG5(156235572)-PMF1(156206079), # samples:3
Anticipated loss of major functional domain due to fusion event.SMG5-PMF1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
SMG5-PMF1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SMG5-PMF1 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

check buttonFusion gene breakpoints across SMG5 (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 PMF1 (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
ChimerDB4STADTCGA-BR-8373-01ASMG5chr1

156235572

-PMF1chr1

156206079

+
ChimerDB4STADTCGA-BR-8373SMG5chr1

156235571

-PMF1chr1

156206078

+
ChimerDB4STADTCGA-BR-8373-01ASMG5chr1

156235572

-PMF1chr1

156206079

+
ChimerDB4STADTCGA-BR-8373-01ASMG5chr1

156235572

-PMF1chr1

156206140

+
ChimerDB4STADTCGA-BR-8373-01ASMG5chr1

156235572

-PMF1chr1

156206079

+


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Fusion Gene ORF analysis for SMG5-PMF1

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
5CDS-intronENST00000361813ENST00000368279SMG5chr1

156235572

-PMF1chr1

156206079

+
5CDS-intronENST00000361813ENST00000368273SMG5chr1

156235572

-PMF1chr1

156206079

+
5CDS-intronENST00000361813ENST00000368277SMG5chr1

156235572

-PMF1chr1

156206079

+
5CDS-intronENST00000361813ENST00000565805SMG5chr1

156235572

-PMF1chr1

156206079

+
5CDS-intronENST00000361813ENST00000567140SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000368267ENST00000368279SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000368267ENST00000368273SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000368267ENST00000368277SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000368267ENST00000565805SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000368267ENST00000567140SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000489907ENST00000368279SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000489907ENST00000368273SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000489907ENST00000368277SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000489907ENST00000565805SMG5chr1

156235572

-PMF1chr1

156206079

+
intron-intronENST00000489907ENST00000567140SMG5chr1

156235572

-PMF1chr1

156206079

+
5CDS-intronENST00000361813ENST00000368279SMG5chr1

156235571

-PMF1chr1

156206078

+
5CDS-intronENST00000361813ENST00000368273SMG5chr1

156235571

-PMF1chr1

156206078

+
5CDS-intronENST00000361813ENST00000368277SMG5chr1

156235571

-PMF1chr1

156206078

+
5CDS-intronENST00000361813ENST00000565805SMG5chr1

156235571

-PMF1chr1

156206078

+
5CDS-intronENST00000361813ENST00000567140SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000368267ENST00000368279SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000368267ENST00000368273SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000368267ENST00000368277SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000368267ENST00000565805SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000368267ENST00000567140SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000489907ENST00000368279SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000489907ENST00000368273SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000489907ENST00000368277SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000489907ENST00000565805SMG5chr1

156235571

-PMF1chr1

156206078

+
intron-intronENST00000489907ENST00000567140SMG5chr1

156235571

-PMF1chr1

156206078

+
Frame-shiftENST00000361813ENST00000368279SMG5chr1

156235572

-PMF1chr1

156206140

+
Frame-shiftENST00000361813ENST00000368273SMG5chr1

156235572

-PMF1chr1

156206140

+
Frame-shiftENST00000361813ENST00000368277SMG5chr1

156235572

-PMF1chr1

156206140

+
5CDS-intronENST00000361813ENST00000565805SMG5chr1

156235572

-PMF1chr1

156206140

+
5CDS-intronENST00000361813ENST00000567140SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-3CDSENST00000368267ENST00000368279SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-3CDSENST00000368267ENST00000368273SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-3CDSENST00000368267ENST00000368277SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-intronENST00000368267ENST00000565805SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-intronENST00000368267ENST00000567140SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-3CDSENST00000489907ENST00000368279SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-3CDSENST00000489907ENST00000368273SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-3CDSENST00000489907ENST00000368277SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-intronENST00000489907ENST00000565805SMG5chr1

156235572

-PMF1chr1

156206140

+
intron-intronENST00000489907ENST00000567140SMG5chr1

156235572

-PMF1chr1

156206140

+

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 SMG5-PMF1


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)
SMG5chr1156235571-PMF1chr1156206078+7.44E-091
SMG5chr1156235571-PMF1chr1156206078+7.44E-091
SMG5chr1156235571-PMF1chr1156206139+7.51E-091
SMG5chr1156235571-PMF1chr1156206078+7.44E-091
SMG5chr1156235571-PMF1chr1156206078+7.44E-091
SMG5chr1156235571-PMF1chr1156206139+7.51E-091

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 SMG5-PMF1


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 SMG5-PMF1


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 SMG5-PMF1


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 SMG5-PMF1


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 SMG5-PMF1


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