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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 37553

FusionGeneSummary for TCF12_NR4A3

check button Fusion gene summary
Fusion gene informationFusion gene name: TCF12_NR4A3
Fusion gene ID: 37553
HgeneTgene
Gene symbol

TCF12

NR4A3

Gene ID

6938

8013

Gene nametranscription factor 12nuclear receptor subfamily 4 group A member 3
SynonymsCRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64CHN|CSMF|MINOR|NOR1|TEC
Cytomap

15q21.3

9q31.1

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor 12DNA-binding protein HTF4E-box-binding proteinclass B basic helix-loop-helix protein 20helix-loop-helix transcription factor 4transcription factor HTF-4nuclear receptor subfamily 4 group A member 3chondrosarcoma, extraskeletal myxoid, fused to EWSmitogen-induced nuclear orphan receptorneuron-derived orphan receptor 1nuclear hormone receptor NOR-1translocated in extraskeletal chondrosarcoma
Modification date2018052320180527
UniProtAcc

Q99081

Q92570

Ensembl transtripts involved in fusion geneENST00000438423, ENST00000267811, 
ENST00000452095, ENST00000333725, 
ENST00000557843, ENST00000560764, 
ENST00000543579, ENST00000537840, 
ENST00000343827, ENST00000559710, 
ENST00000559703, 
ENST00000338488, 
ENST00000395097, ENST00000330847, 
Fusion gene scores* DoF score22 X 12 X 9=23766 X 6 X 4=144
# samples 2210
** MAII scorelog2(22/2376*10)=-3.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/144*10)=-0.526068811667588
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TCF12 [Title/Abstract] AND NR4A3 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneTCF12

GO:0045944

positive regulation of transcription by RNA polymerase II

11802795

TgeneNR4A3

GO:0010828

positive regulation of glucose transmembrane transport

24022864

TgeneNR4A3

GO:0045944

positive regulation of transcription by RNA polymerase II

20558821

TgeneNR4A3

GO:0048008

platelet-derived growth factor receptor signaling pathway

23554459

TgeneNR4A3

GO:0048660

regulation of smooth muscle cell proliferation

25852083


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1AF289510TCF12chr15

57384089

+NR4A3chr9

102590322

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
5CDS-5UTRENST00000438423ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000438423ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000438423ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000267811ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000267811ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000267811ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000452095ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000452095ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000452095ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000333725ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000333725ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000333725ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000557843ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000557843ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
5CDS-5UTRENST00000557843ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000560764ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000560764ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000560764ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000543579ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000543579ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000543579ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000537840ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000537840ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000537840ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000343827ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000343827ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000343827ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000559710ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000559710ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000559710ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000559703ENST00000338488TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000559703ENST00000395097TCF12chr15

57384089

+NR4A3chr9

102590322

+
intron-5UTRENST00000559703ENST00000330847TCF12chr15

57384089

+NR4A3chr9

102590322

+

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FusionProtFeatures for TCF12_NR4A3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
TCF12

Q99081

NR4A3

Q92570

Transcriptional regulator. Involved in the initiation ofneuronal differentiation. Activates transcription by binding tothe E box (5'-CANNTG-3').

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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FusionGeneSequence for TCF12_NR4A3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for TCF12_NR4A3


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
TCF12ID2, ASCL4, TCF23, OLIG3, PRSS23, TAL1, ID1, ID3, TAL2, RUNX1T1, CREBBP, EP300, TAF4, TBP, RUNX1, TRIM33, ELAVL1, SMAD2, SMAD3, TCF3, FOXH1, NOTCH1, MYC, SOX2, TCF21, BMF, DGCR6, CDKN2C, MLLT6, PSMA1, QARS, RNASEL, SRI, STAT5A, TSNAX, STK16, MAPKBP1, ARMC8, EDRF1, CRCP, OSGIN1, NEUROG3, VPS28, SPG21, C1orf109, NAGK, HOPX, C16orf45, TWIST2, MORN4, HEXIM2, C6orf165, LYSMD1, TRIM72, SHMT2, MOV10, NXF1, MYOG, CCDC101, NEUROD1, MESP2, NTRK1, TCF12, FRMD6, MYF6, XPO1, ZWINT, STRN3, TCF4, NFATC2, ATOH1, FERD3L, TRIM25NR4A3SIX3, KDM5B, TRIM28, COPS5


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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RelatedDrugs for TCF12_NR4A3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneNR4A3Q92570DB01254DasatinibNuclear receptor subfamily 4 group A member 3small moleculeapproved|investigational

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RelatedDiseases for TCF12_NR4A3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTCF12C3715051CRANIOSYNOSTOSIS 32UNIPROT
HgeneTCF12C0010278Craniosynostosis1CTD_human;HPO
TgeneNR4A3C0003873Rheumatoid Arthritis1CTD_human
TgeneNR4A3C0020443Hypercholesterolemia1CTD_human
TgeneNR4A3C0021655Insulin Resistance1CTD_human
TgeneNR4A3C3495559Juvenile arthritis1CTD_human