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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:SEPT9-JMJD6 (FusionGDB2 ID:91)

Fusion Gene Summary for SEPT9-JMJD6

check button Fusion gene summary
Fusion gene informationFusion gene name: SEPT9-JMJD6
Fusion gene ID: 91
HgeneTgene
Gene symbol

SEPT9

JMJD6

Gene ID

10801

23210

Gene nameseptin 9jumonji domain containing 6, arginine demethylase and lysine hydroxylase
SynonymsAF17q25|MSF|MSF1|NAPB|PNUTL4|SEPT9|SINT1|SeptD1PSR|PTDSR|PTDSR1
Cytomap

17q25.3

17q25.1

Type of geneprotein-codingprotein-coding
Descriptionseptin-9MLL septin-like fusion protein MSF-AOv/Br septinovarian/breast septinseptin D1bifunctional arginine demethylase and lysyl-hydroxylase JMJD6arginine demethylase and lysine hydroxylasehistone arginine demethylase JMJD6jmjC domain-containing protein 6jumonji domain containing 6jumonji domain-containing protein 6lysyl-hydroxylase
Modification date2020032820200313
UniProtAcc.

Q6NYC1

Ensembl transtripts involved in fusion geneENST00000427177, ENST00000591198, 
ENST00000449803, ENST00000431235, 
ENST00000329047, ENST00000590294, 
ENST00000588690, ENST00000423034, 
ENST00000427674, ENST00000592420, 
ENST00000585930, ENST00000541152, 
ENST00000592481, ENST00000591088, 
ENST00000592951, ENST00000590917, 
ENST00000427180, 		ENST00000445478, 
ENST00000397625, ENST00000585429, 
Fusion gene scores* DoF score31 X 14 X 18=78127 X 6 X 2=84
# samples 417
** MAII scorelog2(41/7812*10)=-4.25199613438135
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/84*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SEPT9 [Title/Abstract] AND JMJD6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSEPT9(75277636)-JMJD6(74721937), # samples:4
Anticipated loss of major functional domain due to fusion event.SEPT9-JMJD6 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SEPT9-JMJD6 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
SEPT9-JMJD6 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor 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
TgeneJMJD6

GO:0006482

protein demethylation

24498420

TgeneJMJD6

GO:0018395

peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine

19574390|22189873

TgeneJMJD6

GO:0035513

oxidative RNA demethylation

24360279

TgeneJMJD6

GO:0045944

positive regulation of transcription by RNA polymerase II

24360279

TgeneJMJD6

GO:0051260

protein homooligomerization

22189873|24360279

TgeneJMJD6

GO:0070078

histone H3-R2 demethylation

17947579

TgeneJMJD6

GO:0070078

histone H3-R2 demethylation

22189873

TgeneJMJD6

GO:0070079

histone H4-R3 demethylation

17947579|24360279|24498420

TgeneJMJD6

GO:0070079

histone H4-R3 demethylation

22189873


check buttonFusion gene breakpoints across SEPT9 (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 JMJD6 (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
ChimerDB4BRCATCGA-A7-A2KD-01ASEPT9chr17

75277636

+JMJD6chr17

74721937

-
ChimerDB4BRCATCGA-A7-A2KDSEPT9chr17

75277636

+JMJD6chr17

74721937

-
ChimerDB4BRCATCGA-A7-A2KD-01ASEPT9chr17

75277636

+JMJD6chr17

74721937

-
ChimerDB4BRCATCGA-A7-A2KD-01ASEPT9chr17

75277636

-JMJD6chr17

74721937

-


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Fusion Gene ORF analysis for SEPT9-JMJD6

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-shiftENST00000427177ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
Frame-shiftENST00000427177ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
Frame-shiftENST00000427177ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
Frame-shiftENST00000591198ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
Frame-shiftENST00000591198ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
Frame-shiftENST00000591198ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000449803ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000449803ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000449803ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000431235ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000431235ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000431235ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000329047ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000329047ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000329047ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000590294ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000590294ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000590294ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000588690ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000588690ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000588690ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000423034ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000423034ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000423034ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000427674ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000427674ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000427674ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000592420ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000592420ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000592420ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000585930ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000585930ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000585930ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000541152ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000541152ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000541152ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000592481ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000592481ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000592481ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000591088ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000591088ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000591088ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000592951ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000592951ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000592951ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000590917ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000590917ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000590917ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000427180ENST00000445478SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000427180ENST00000397625SEPT9chr17

75277636

+JMJD6chr17

74721937

-
intron-3CDSENST00000427180ENST00000585429SEPT9chr17

75277636

+JMJD6chr17

74721937

-

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 SEPT9-JMJD6


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 SEPT9-JMJD6


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
.JMJD6

Q6NYC1

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: Dioxygenase that can both act as a arginine demethylase and a lysyl-hydroxylase (PubMed:24498420, PubMed:17947579, PubMed:20684070, PubMed:21060799, PubMed:22189873). Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Regulates RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65 (PubMed:19574390). Hydroxylates its own N-terminus, which is required for homooligomerization (PubMed:22189873). In addition to peptidyl-lysine 5-dioxygenase activity, may act as an RNA hydroxylase, as suggested by its ability to bind single strand RNA (PubMed:20679243, PubMed:29176719). Also acts as an arginine demethylase which preferentially demethylates asymmetric dimethylation (PubMed:17947579, PubMed:24498420, PubMed:24360279). Demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), including mono-, symmetric di- and asymmetric dimethylated forms, thereby playing a role in histone code (PubMed:17947579, PubMed:24360279). However, histone arginine demethylation may not constitute the primary activity in vivo (PubMed:17947579, PubMed:21060799, PubMed:22189873). In collaboration with BRD4, interacts with the positive transcription elongation factor b (P-TEFb) complex in its active form to regulate polymerase II promoter-proximal pause release for transcriptional activation of a large cohort of genes. On distal enhancers, so called anti-pause enhancers, demethylates both histone H4R3me2 and the methyl cap of 7SKsnRNA leading to the dismissal of the 7SKsnRNA:HEXIM1 inhibitor complex. After removal of repressive marks, the complex BRD4:JMJD6 attract and retain the P-TEFb complex on chromatin, leading to its activation, promoter-proximal polymerase II pause release, and transcriptional activation (PubMed:24360279). Demethylates other arginine methylated-proteins such as ESR1 (PubMed:24498420). Has no histone lysine demethylase activity (PubMed:21060799). Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65 (By similarity). Seems to be necessary for the regulation of macrophage cytokine responses (PubMed:15622002). {ECO:0000250|UniProtKB:Q9ERI5, ECO:0000269|PubMed:15622002, ECO:0000269|PubMed:17947579, ECO:0000269|PubMed:19574390, ECO:0000269|PubMed:20679243, ECO:0000269|PubMed:20684070, ECO:0000269|PubMed:21060799, ECO:0000269|PubMed:22189873, ECO:0000269|PubMed:24360279, ECO:0000269|PubMed:24498420, ECO:0000269|PubMed:29176719}.

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 SEPT9-JMJD6


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 SEPT9-JMJD6


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 SEPT9-JMJD6


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 SEPT9-JMJD6


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneJMJD6C0006142Malignant neoplasm of breast1CTD_human
TgeneJMJD6C0025202melanoma1CTD_human
TgeneJMJD6C0025500Mesothelioma1CTD_human
TgeneJMJD6C0033578Prostatic Neoplasms1CTD_human
TgeneJMJD6C0151779Cutaneous Melanoma1CTD_human
TgeneJMJD6C0220633Uveal melanoma1CTD_human
TgeneJMJD6C0376358Malignant neoplasm of prostate1CTD_human
TgeneJMJD6C0678222Breast Carcinoma1CTD_human
TgeneJMJD6C0919267ovarian neoplasm1CTD_human
TgeneJMJD6C1140680Malignant neoplasm of ovary1CTD_human
TgeneJMJD6C1257931Mammary Neoplasms, Human1CTD_human
TgeneJMJD6C1458155Mammary Neoplasms1CTD_human
TgeneJMJD6C4704874Mammary Carcinoma, Human1CTD_human