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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:JMJD1C-GABPB1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: JMJD1C-GABPB1
FusionPDB ID: 40967
FusionGDB2.0 ID: 40967
HgeneTgene
Gene symbol

JMJD1C

GABPB1

Gene ID

221037

2553

Gene namejumonji domain containing 1CGA binding protein transcription factor subunit beta 1
SynonymsKDM3C|TRIP-8|TRIP8BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4TF1B|GABPB|GABPB-1|GABPB2|NRF2B1|NRF2B2
Cytomap

10q21.3

15q21.2

Type of geneprotein-codingprotein-coding
Descriptionprobable JmjC domain-containing histone demethylation protein 2CTR-interacting protein 8thyroid hormone receptor interactor 8thyroid receptor-interacting protein 8GA-binding protein subunit beta-1GA binding protein transcription factor beta subunit 1 transcript variant gamma-2GABP subunit beta-2nuclear respiratory factor 2transcription factor E4TF1-47transcription factor E4TF1-53
Modification date2020031320200313
UniProtAcc

Q15652

Q06547

Ensembl transtripts involved in fusion geneENST idsENST00000399262, ENST00000399251, 
ENST00000402544, ENST00000489372, 
ENST00000542921, 		ENST00000359031, 
ENST00000396464, ENST00000429662, 
ENST00000543881, ENST00000560825, 
ENST00000220429, ENST00000380877, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score29 X 18 X 10=52205 X 5 X 2=50
# samples 315
** MAII scorelog2(31/5220*10)=-4.07370968618301
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/50*10)=0
Context (manual curation of fusion genes in FusionPDB)

PubMed: JMJD1C [Title/Abstract] AND GABPB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)JMJD1C(65225255)-GABPB1(50601995), # samples:1
Anticipated loss of major functional domain due to fusion event.JMJD1C-GABPB1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
JMJD1C-GABPB1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
JMJD1C-GABPB1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
JMJD1C-GABPB1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
TgeneGABPB1

GO:0045944

positive regulation of transcription by RNA polymerase II

9857059


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.
all structure

check buttonFusion gene breakpoints across GABPB1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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-AO-A03P-01AJMJD1Cchr10

65225255

-GABPB1chr15

50601995

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000399262JMJD1Cchr1065225255-ENST00000380877GABPB1chr1550601995-29793871831538451
ENST00000399262JMJD1Cchr1065225255-ENST00000220429GABPB1chr1550601995-29443871831574463

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
ENST00000399262ENST00000380877JMJD1Cchr1065225255-GABPB1chr1550601995-0.0003449170.9996551
ENST00000399262ENST00000220429JMJD1Cchr1065225255-GABPB1chr1550601995-0.0004265870.9995734

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>40967_40967_1_JMJD1C-GABPB1_JMJD1C_chr10_65225255_ENST00000399262_GABPB1_chr15_50601995_ENST00000220429_length(amino acids)=463AA_BP=68
MEEAAAASAATAMAVETRAELVGKRFLCVAVGDEARSERWESGRGWRSWRAGVIRAVSHRDSRNPDLAMSLVDLGKKLLEAARAGQDDEV
RILMANGAPFTTDWLGTSPLHLAAQYGHYSTTEVLLRAGVSRDARTKVDRTPLHMAASEGHASIVEVLLKHGADVNAKDMLKMTALHWAT
EHNHQEVVELLIKYGADVHTQSKFCKTAFDISIDNGNEDLAEILQIAMQNQINTNPESPDTVTIHAATPQFIIGPGGVVNLTGLVSSENS
SKATDETGVSAVQFGNSSTSVLATLAALAEASAPLSNSSETPVVATEEVVTAESVDGAIQQVVSSGGQQVITIVTDGIQLGNLHSIPTSG
IGQPIIVTMPDGQQVLTVPATDIAEETVISEEPPAKRQCIEIIENRVESAEIEEREALQKQLDEANREAQKYRQQLLKKEQEAEAYRQKL

--------------------------------------------------------------

>40967_40967_2_JMJD1C-GABPB1_JMJD1C_chr10_65225255_ENST00000399262_GABPB1_chr15_50601995_ENST00000380877_length(amino acids)=451AA_BP=68
MEEAAAASAATAMAVETRAELVGKRFLCVAVGDEARSERWESGRGWRSWRAGVIRAVSHRDSRNPDLAMSLVDLGKKLLEAARAGQDDEV
RILMANGAPFTTDWLGTSPLHLAAQYGHYSTTEVLLRAGVSRDARTKVDRTPLHMAASEGHASIVEVLLKHGADVNAKDMLKMTALHWAT
EHNHQEVVELLIKYGADVHTQSKFCKTAFDISIDNGNEDLAEILQIAMQNQINTNPESPDTVTIHAATPQFIIGPGGVVNLTDETGVSAV
QFGNSSTSVLATLAALAEASAPLSNSSETPVVATEEVVTAESVDGAIQQVVSSGGQQVITIVTDGIQLGNLHSIPTSGIGQPIIVTMPDG
QQVLTVPATDIAEETVISEEPPAKRQCIEIIENRVESAEIEEREALQKQLDEANREAQKYRQQLLKKEQEAEAYRQKLEAMTRLQTNKEA

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Fusion Protein Functional Features


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/chr10:65225255/chr15:50601995)
- 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

GABPB1

Q06547

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: Transcription factor capable of interacting with purine rich repeats (GA repeats) (PubMed:8441384, PubMed:10675337, PubMed:8816484). Acts as a a master regulator of nuclear-encoded mitochondrial genes (By similarity). {ECO:0000250|UniProtKB:Q00420, ECO:0000269|PubMed:10675337, ECO:0000269|PubMed:8441384, ECO:0000269|PubMed:8816484}.; FUNCTION: (Microbial infection) Necessary for the expression of the Adenovirus E4 gene. {ECO:0000269|PubMed:8441384}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneGABPB1chr10:65225255chr15:50601995ENST0000022042909103_1320.0396.0RepeatNote=ANK 4
TgeneGABPB1chr10:65225255chr15:50601995ENST0000022042909136_1660.0396.0RepeatNote=ANK 5
TgeneGABPB1chr10:65225255chr15:50601995ENST000002204290937_660.0396.0RepeatNote=ANK 2
TgeneGABPB1chr10:65225255chr15:50601995ENST00000220429095_340.0396.0RepeatNote=ANK 1
TgeneGABPB1chr10:65225255chr15:50601995ENST000002204290970_990.0396.0RepeatNote=ANK 3
TgeneGABPB1chr10:65225255chr15:50601995ENST0000035903119103_1320.0349.0RepeatNote=ANK 4
TgeneGABPB1chr10:65225255chr15:50601995ENST0000035903119136_1660.0349.0RepeatNote=ANK 5
TgeneGABPB1chr10:65225255chr15:50601995ENST000003590311937_660.0349.0RepeatNote=ANK 2
TgeneGABPB1chr10:65225255chr15:50601995ENST00000359031195_340.0349.0RepeatNote=ANK 1
TgeneGABPB1chr10:65225255chr15:50601995ENST000003590311970_990.0349.0RepeatNote=ANK 3
TgeneGABPB1chr10:65225255chr15:50601995ENST0000038087709103_1320.0384.0RepeatNote=ANK 4
TgeneGABPB1chr10:65225255chr15:50601995ENST0000038087709136_1660.0384.0RepeatNote=ANK 5
TgeneGABPB1chr10:65225255chr15:50601995ENST000003808770937_660.0384.0RepeatNote=ANK 2
TgeneGABPB1chr10:65225255chr15:50601995ENST00000380877095_340.0384.0RepeatNote=ANK 1
TgeneGABPB1chr10:65225255chr15:50601995ENST000003808770970_990.0384.0RepeatNote=ANK 3
TgeneGABPB1chr10:65225255chr15:50601995ENST0000039646408103_1320.0349.0RepeatNote=ANK 4
TgeneGABPB1chr10:65225255chr15:50601995ENST0000039646408136_1660.0349.0RepeatNote=ANK 5
TgeneGABPB1chr10:65225255chr15:50601995ENST000003964640837_660.0349.0RepeatNote=ANK 2
TgeneGABPB1chr10:65225255chr15:50601995ENST00000396464085_340.0349.0RepeatNote=ANK 1
TgeneGABPB1chr10:65225255chr15:50601995ENST000003964640870_990.0349.0RepeatNote=ANK 3
TgeneGABPB1chr10:65225255chr15:50601995ENST0000042966208103_1320.0361.0RepeatNote=ANK 4
TgeneGABPB1chr10:65225255chr15:50601995ENST0000042966208136_1660.0361.0RepeatNote=ANK 5
TgeneGABPB1chr10:65225255chr15:50601995ENST000004296620837_660.0361.0RepeatNote=ANK 2
TgeneGABPB1chr10:65225255chr15:50601995ENST00000429662085_340.0361.0RepeatNote=ANK 1
TgeneGABPB1chr10:65225255chr15:50601995ENST000004296620870_990.0361.0RepeatNote=ANK 3

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneJMJD1Cchr10:65225255chr15:50601995ENST00000399251-1252274_24980477.0DomainJmjC
HgeneJMJD1Cchr10:65225255chr15:50601995ENST00000399262-1262274_249856.02541.0DomainJmjC
HgeneJMJD1Cchr10:65225255chr15:50601995ENST00000542921-1252274_249802359.0DomainJmjC
HgeneJMJD1Cchr10:65225255chr15:50601995ENST00000399251-1252066_20700477.0MotifNote=LXXLL motif
HgeneJMJD1Cchr10:65225255chr15:50601995ENST00000399262-1262066_207056.02541.0MotifNote=LXXLL motif
HgeneJMJD1Cchr10:65225255chr15:50601995ENST00000542921-1252066_207002359.0MotifNote=LXXLL motif
HgeneJMJD1Cchr10:65225255chr15:50601995ENST00000399251-1251846_18710477.0Zinc fingerC6-type
HgeneJMJD1Cchr10:65225255chr15:50601995ENST00000399262-1261846_187156.02541.0Zinc fingerC6-type
HgeneJMJD1Cchr10:65225255chr15:50601995ENST00000542921-1251846_187102359.0Zinc fingerC6-type


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors
JMJD1CVHL, Thrb, ESR2, PPARG, NUDT21, TK1, GADD45A, AR, RNF8, RNF168, MT2A, PSMC1, SRPK2, RBPJ, NR3C1, TXNIP, HNRNPL, EGLN3, CBFA2T3, RNF4, SOX2, Nav2, HIST1H3A, GOLGA2, TP53BP1, KIAA1429, MYC, HDAC2, XRCC6, FBXO38, HIST1H4A, RHBDD1, HCVgp1, SMC2, MYOM2, ALG13, CNOT2, RQCD1, PARN, SMG7, SUPT5H, RPN1, vpr, TRIM37, QPRT, CCNF, BCOR, KLF3, NKX2-5,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
JMJD1Call structure
GABPB1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to JMJD1C-GABPB1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to JMJD1C-GABPB1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneJMJD1CC0004352Autistic Disorder1CTD_human
HgeneJMJD1CC0010606Adenoid Cystic Carcinoma1CTD_human
HgeneJMJD1CC0012236DiGeorge Syndrome1ORPHANET
HgeneJMJD1CC0087031Juvenile-Onset Still Disease1CTD_human
HgeneJMJD1CC0220704Shprintzen syndrome1ORPHANET
HgeneJMJD1CC0431406Asymmetric crying face association1ORPHANET
HgeneJMJD1CC0795907CONOTRUNCAL ANOMALY FACE SYNDROME1ORPHANET
HgeneJMJD1CC1333813Central Nervous System Germinoma1ORPHANET
HgeneJMJD1CC293634622q11 Deletion Syndrome1ORPHANET
HgeneJMJD1CC326610122q11 partial monosomy syndrome1ORPHANET
HgeneJMJD1CC3495559Juvenile arthritis1CTD_human
HgeneJMJD1CC3714758Juvenile psoriatic arthritis1CTD_human
HgeneJMJD1CC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneJMJD1CC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human