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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:JMJD7-RTF1 (FusionGDB2 ID:HG100137047TG23168)

Fusion Gene Summary for JMJD7-RTF1

check button Fusion gene summary
Fusion gene informationFusion gene name: JMJD7-RTF1
Fusion gene ID: hg100137047tg23168
HgeneTgene
Gene symbol

JMJD7

RTF1

Gene ID

100137047

23168

Gene namejumonji domain containing 7RTF1 homolog, Paf1/RNA polymerase II complex component
Synonyms-GTL7|KIAA0252
Cytomap('JMJD7')('RTF1')

15q15.1

15q15.1

Type of geneprotein-codingprotein-coding
Descriptionbifunctional peptidase and (3S)-lysyl hydroxylase JMJD7L-lysine (3S)-hydroxylase JMJD7jmjC domain-containing protein 7jumonji domain-containing protein 7RNA polymerase-associated protein RTF1 homologRtf1, Paf1/RNA polymerase II complex component, homologortholog of mouse gene trap locus 7
Modification date2020031320200313
UniProtAcc

P0C870

.
Ensembl transtripts involved in fusion geneENST00000405106, ENST00000397299, 
ENST00000408047, 
ENST00000397299, 
ENST00000405106, ENST00000408047, 
Fusion gene scores* DoF score3 X 2 X 3=1814 X 10 X 5=700
# samples 315
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(15/700*10)=-2.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: JMJD7 [Title/Abstract] AND RTF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointJMJD7(42120386)-RTF1(41745099), # samples:2
Anticipated loss of major functional domain due to fusion event.JMJD7-RTF1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
RTF1-JMJD7 seems lost the major protein functional domain in Hgene 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
HgeneJMJD7

GO:0018126

protein hydroxylation

29915238

TgeneRTF1

GO:0019827

stem cell population maintenance

19345177

TgeneRTF1

GO:0032968

positive regulation of transcription elongation from RNA polymerase II promoter

20178742

TgeneRTF1

GO:0045944

positive regulation of transcription by RNA polymerase II

20178742



check button Fusion gene information
* 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-25-1320-01AJMJD7chr15

42120386

+RTF1chr15

41745099

+


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Fusion Gene ORF analysis for JMJD7-RTF1

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
3UTR-3CDSENST00000405106ENST00000389629JMJD7chr15

42120386

+RTF1chr15

41745099

+
3UTR-3UTRENST00000405106ENST00000462276JMJD7chr15

42120386

+RTF1chr15

41745099

+
5CDS-3UTRENST00000397299ENST00000462276JMJD7chr15

42120386

+RTF1chr15

41745099

+
5UTR-3CDSENST00000408047ENST00000389629JMJD7chr15

42120386

+RTF1chr15

41745099

+
5UTR-3UTRENST00000408047ENST00000462276JMJD7chr15

42120386

+RTF1chr15

41745099

+
Frame-shiftENST00000397299ENST00000389629JMJD7chr15

42120386

+RTF1chr15

41745099

+

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 JMJD7-RTF1


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)
JMJD7chr1542120386+RTF1chr1541745098+0.0005360280.999464
JMJD7chr1542120386+RTF1chr1541745098+0.0005360280.999464


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.
genomic feature of top 1%

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Fusion Protein Features for JMJD7-RTF1


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/:42120386/:41745099)
- 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
JMJD7

P0C870

.
FUNCTION: Bifunctional enzyme that acts both as an endopeptidase and 2-oxoglutarate-dependent monoxygenase (PubMed:28847961, PubMed:29915238). Endopeptidase that cleaves histones N-terminal tails at the carboxyl side of methylated arginine or lysine residues, to generate 'tailless nucleosomes', which may trigger transcription elongation (PubMed:28847961). Preferentially recognizes and cleaves monomethylated and dimethylated arginine residues of histones H2, H3 and H4 (PubMed:28847961). After initial cleavage, continues to digest histones tails via its aminopeptidase activity (PubMed:28847961). Additionally, may play a role in protein biosynthesis by modifying the translation machinery (PubMed:29915238). Acts as Fe(2+) and 2-oxoglutarate-dependent monoxygenase, catalyzing (S)-stereospecific hydroxylation at C-3 of 'Lys-22' of DRG1 and 'Lys-21' of DRG2 translation factors (TRAFAC), promoting their interaction with ribonucleic acids (RNA) (PubMed:29915238). {ECO:0000269|PubMed:28847961, ECO:0000269|PubMed:29915238}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 JMJD7-RTF1


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 JMJD7-RTF1


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 JMJD7-RTF1


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 JMJD7-RTF1


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