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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:JMJD1C-COPS7A (FusionGDB2 ID:40963)

Fusion Gene Summary for JMJD1C-COPS7A

check button Fusion gene summary
Fusion gene informationFusion gene name: JMJD1C-COPS7A
Fusion gene ID: 40963
HgeneTgene
Gene symbol

JMJD1C

COPS7A

Gene ID

221037

50813

Gene namejumonji domain containing 1CCOP9 signalosome subunit 7A
SynonymsKDM3C|TRIP-8|TRIP8CSN7|CSN7A|SGN7a
Cytomap

10q21.3

12p13.31

Type of geneprotein-codingprotein-coding
Descriptionprobable JmjC domain-containing histone demethylation protein 2CTR-interacting protein 8thyroid hormone receptor interactor 8thyroid receptor-interacting protein 8COP9 signalosome complex subunit 7aCOP9 complex subunit 7aCOP9 constitutive photomorphogenic homolog subunit 7AJAB1-containing signalosome subunit 7adermal papilla-derived protein 10
Modification date2020031320200313
UniProtAcc

Q15652

Q9UBW8

Ensembl transtripts involved in fusion geneENST00000399251, ENST00000399262, 
ENST00000402544, ENST00000489372, 
ENST00000542921, 		ENST00000229251, 
ENST00000534877, ENST00000534947, 
ENST00000538410, ENST00000539735, 
ENST00000543155, ENST00000542150, 
Fusion gene scores* DoF score29 X 18 X 10=52203 X 3 X 1=9
# samples 313
** MAII scorelog2(31/5220*10)=-4.07370968618301
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: JMJD1C [Title/Abstract] AND COPS7A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointJMJD1C(65280261)-COPS7A(6840406), # 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
TgeneCOPS7A

GO:0000338

protein deneddylation

19141280


check buttonFusion gene breakpoints across JMJD1C (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 COPS7A (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/ACB050419JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+


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Fusion Gene ORF analysis for JMJD1C-COPS7A

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-3UTRENST00000399251ENST00000229251JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399251ENST00000534877JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399251ENST00000534947JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399251ENST00000538410JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399251ENST00000539735JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399251ENST00000543155JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399262ENST00000229251JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399262ENST00000534877JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399262ENST00000534947JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399262ENST00000538410JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399262ENST00000539735JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000399262ENST00000543155JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000402544ENST00000229251JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000402544ENST00000534877JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000402544ENST00000534947JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000402544ENST00000538410JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000402544ENST00000539735JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000402544ENST00000543155JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000489372ENST00000229251JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000489372ENST00000534877JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000489372ENST00000534947JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000489372ENST00000538410JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000489372ENST00000539735JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000489372ENST00000543155JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000542921ENST00000229251JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000542921ENST00000534877JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000542921ENST00000534947JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000542921ENST00000538410JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000542921ENST00000539735JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-3UTRENST00000542921ENST00000543155JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-intronENST00000399251ENST00000542150JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-intronENST00000399262ENST00000542150JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-intronENST00000402544ENST00000542150JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-intronENST00000489372ENST00000542150JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+
intron-intronENST00000542921ENST00000542150JMJD1Cchr10

65280261

-COPS7Achr12

6840406

+

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 JMJD1C-COPS7A


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 JMJD1C-COPS7A


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/:65280261/:6840406)
- 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
JMJD1C

Q15652

COPS7A

Q9UBW8

FUNCTION: Probable histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May be involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes (By similarity). {ECO:0000250}.FUNCTION: Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively. {ECO:0000269|PubMed:11285227, ECO:0000269|PubMed:11337588, ECO:0000269|PubMed:12628923, ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:9535219}.

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 JMJD1C-COPS7A


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 JMJD1C-COPS7A


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 JMJD1C-COPS7A


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 JMJD1C-COPS7A


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