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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:PHF23-RRM1 (FusionGDB2 ID:64465)

Fusion Gene Summary for PHF23-RRM1

check button Fusion gene summary
Fusion gene informationFusion gene name: PHF23-RRM1
Fusion gene ID: 64465
HgeneTgene
Gene symbol

PHF23

RRM1

Gene ID

79142

6240

Gene namePHD finger protein 23ribonucleotide reductase catalytic subunit M1
SynonymshJUNE-1bR1|RIR1|RR1
Cytomap

17p13.1

11p15.4

Type of geneprotein-codingprotein-coding
DescriptionPHD finger protein 23PDH-containing protein JUNE-1PHD finger protein 23aribonucleoside-diphosphate reductase large subunitribonucleoside-diphosphate reductase subunit M1ribonucleotide reductase M1 polypeptideribonucleotide reductase, R1 subunit
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000320316, ENST00000571362, 
ENST00000576955, ENST00000454255, 
ENST00000570753, 		ENST00000300738, 
ENST00000423050, ENST00000534285, 
ENST00000537197, ENST00000528470, 
Fusion gene scores* DoF score2 X 2 X 2=87 X 6 X 4=168
# samples 27
** MAII scorelog2(2/8*10)=1.32192809488736log2(7/168*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PHF23 [Title/Abstract] AND RRM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPHF23(7139380)-RRM1(4144413), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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 PHF23 (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 RRM1 (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
ChiTaRS5.0N/AAU125246PHF23chr17

7139380

-RRM1chr11

4144413

+


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Fusion Gene ORF analysis for PHF23-RRM1

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-3CDSENST00000320316ENST00000300738PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000320316ENST00000423050PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000320316ENST00000534285PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000320316ENST00000537197PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3UTRENST00000320316ENST00000528470PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000571362ENST00000300738PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000571362ENST00000423050PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000571362ENST00000534285PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000571362ENST00000537197PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3UTRENST00000571362ENST00000528470PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000576955ENST00000300738PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000576955ENST00000423050PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000576955ENST00000534285PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000576955ENST00000537197PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3UTRENST00000576955ENST00000528470PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000454255ENST00000300738PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000454255ENST00000423050PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000454255ENST00000534285PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000454255ENST00000537197PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3UTRENST00000454255ENST00000528470PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000570753ENST00000300738PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000570753ENST00000423050PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000570753ENST00000534285PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3CDSENST00000570753ENST00000537197PHF23chr17

7139380

-RRM1chr11

4144413

+
intron-3UTRENST00000570753ENST00000528470PHF23chr17

7139380

-RRM1chr11

4144413

+

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 PHF23-RRM1


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)

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 PHF23-RRM1


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 PHF23-RRM1


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 PHF23-RRM1


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 PHF23-RRM1


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 PHF23-RRM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneRRM1C0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneRRM1C0011999Diastematomyelia1CTD_human
TgeneRRM1C0027794Neural Tube Defects1CTD_human
TgeneRRM1C0027806Neurenteric Cyst1CTD_human
TgeneRRM1C0080218Tethered Cord Syndrome1CTD_human
TgeneRRM1C0152013Adenocarcinoma of lung (disorder)1CTD_human
TgeneRRM1C0152234Iniencephaly1CTD_human
TgeneRRM1C0152426Craniorachischisis1CTD_human
TgeneRRM1C0206686Adrenocortical carcinoma1CTD_human
TgeneRRM1C0235874Disease Exacerbation1CTD_human
TgeneRRM1C0266453Exencephaly1CTD_human
TgeneRRM1C0344479Spinal Cord Myelodysplasia1CTD_human
TgeneRRM1C0702169Acrania1CTD_human
TgeneRRM1C2239176Liver carcinoma1CTD_human