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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: 21469

FusionGeneSummary for MED13_DDX42

check button Fusion gene summary
Fusion gene informationFusion gene name: MED13_DDX42
Fusion gene ID: 21469
HgeneTgene
Gene symbol

MED13

DDX42

Gene ID

9969

11325

Gene namemediator complex subunit 13DEAD-box helicase 42
SynonymsARC250|DRIP250|HSPC221|THRAP1|TRAP240DDX42P|RHELP|RNAHP|SF3B8|SF3b125
Cytomap

17q23.2

17q23.3

Type of geneprotein-codingprotein-coding
Descriptionmediator of RNA polymerase II transcription subunit 13activator-recruited cofactor 250 kDa componentmediator of RNA polymerase II transcription, subunit 13 homologthyroid hormone receptor-associated protein 1thyroid hormone receptor-associated proteinATP-dependent RNA helicase DDX42DEAD (Asp-Glu-Ala-Asp) box helicase 42DEAD (Asp-Glu-Ala-Asp) box polypeptide 42SF3b DEAD box proteinsplicing factor 3B-associated 125 kDa proteinsplicing factor 3b, subunit 8
Modification date2018052320180519
UniProtAcc

Q9UHV7

Q86XP3

Ensembl transtripts involved in fusion geneENST00000397786, ENST00000580896, 
ENST00000578681, ENST00000583590, 
ENST00000359353, ENST00000389924, 
ENST00000457800, ENST00000582985, 
Fusion gene scores* DoF score13 X 13 X 6=10147 X 7 X 4=196
# samples 147
** MAII scorelog2(14/1014*10)=-2.85655892005837
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/196*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MED13 [Title/Abstract] AND DDX42 [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
HgeneMED13

GO:0006367

transcription initiation from RNA polymerase II promoter

12218053

HgeneMED13

GO:0030518

intracellular steroid hormone receptor signaling pathway

11867769

HgeneMED13

GO:0030521

androgen receptor signaling pathway

12218053

HgeneMED13

GO:0045893

positive regulation of transcription, DNA-templated

10198638

HgeneMED13

GO:0045944

positive regulation of transcription by RNA polymerase II

12037571

TgeneDDX42

GO:0008104

protein localization

19377511


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
TCGARVLUADTCGA-78-7146-01AMED13chr17

60129898

-DDX42chr17

61886180

+
* 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
Frame-shiftENST00000397786ENST00000578681MED13chr17

60129898

-DDX42chr17

61886180

+
Frame-shiftENST00000397786ENST00000583590MED13chr17

60129898

-DDX42chr17

61886180

+
Frame-shiftENST00000397786ENST00000359353MED13chr17

60129898

-DDX42chr17

61886180

+
Frame-shiftENST00000397786ENST00000389924MED13chr17

60129898

-DDX42chr17

61886180

+
Frame-shiftENST00000397786ENST00000457800MED13chr17

60129898

-DDX42chr17

61886180

+
5CDS-intronENST00000397786ENST00000582985MED13chr17

60129898

-DDX42chr17

61886180

+
intron-3CDSENST00000580896ENST00000578681MED13chr17

60129898

-DDX42chr17

61886180

+
intron-3CDSENST00000580896ENST00000583590MED13chr17

60129898

-DDX42chr17

61886180

+
intron-3CDSENST00000580896ENST00000359353MED13chr17

60129898

-DDX42chr17

61886180

+
intron-3CDSENST00000580896ENST00000389924MED13chr17

60129898

-DDX42chr17

61886180

+
intron-3CDSENST00000580896ENST00000457800MED13chr17

60129898

-DDX42chr17

61886180

+
intron-intronENST00000580896ENST00000582985MED13chr17

60129898

-DDX42chr17

61886180

+

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FusionProtFeatures for MED13_DDX42


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MED13

Q9UHV7

DDX42

Q86XP3

Component of the Mediator complex, a coactivatorinvolved in the regulated transcription of nearly all RNApolymerase II-dependent genes. Mediator functions as a bridge toconvey information from gene-specific regulatory proteins to thebasal RNA polymerase II transcription machinery. Mediator isrecruited to promoters by direct interactions with regulatoryproteins and serves as a scaffold for the assembly of a functionalpreinitiation complex with RNA polymerase II and the generaltranscription factors. {ECO:0000269|PubMed:16595664}. ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondarystructures. Unwinding is promoted in the presence of single-strandbinding proteins. Mediates also RNA duplex formation therebydisplacing the single-strand RNA binding protein. ATP and ADPmodulate its activity: ATP binding and hydrolysis by DDX42triggers RNA strand separation, whereas the ADP-bound form of theprotein triggers annealing of complementary RNA strands. Involvedin the survival of cells by interacting with TP53BP2 and therebycounteracting the apoptosis-stimulating activity of TP53BP2.Relocalizes TP53BP2 to the cytoplasm.{ECO:0000269|PubMed:16397294, ECO:0000269|PubMed:19377511}.

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 MED13_DDX42


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 MED13_DDX42


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
MED13MED10, MED9, MED29, MED19, MED28, MED26, CDK8, VDR, ESR1, MED1, MED18, MED30, TRRAP, SREBF1, SUPT3H, MED12, ZC3H13, TRIP4, OBFC1, QKI, TADA2A, MED25, MED15, MED4, MED24, MED14, MED16, MED21, FBXW7, MED7, CDK19, CCNC, NR1I3, TCL1B, HIF1A, EFTUD2, MED17, PRPF8, MED27, MED6, MED8, RANBP2, MED23, TSC22D2, TRIM25DDX42RECQL5, SF3B1, SF3A2, RUVBL2, RUVBL1, MEPCE, SIRT7, ISG15, APP, TCERG1, SYNCRIP, RPS6KA4, RPL36, PIN4, PHF20, KAL1, NOSIP, EPRS, FOXJ3, SNRPC, SF3A1, SF3B4, DHX15, U2SURP, PRPF19, ITGA4, LMNA, FBXO25, SHFM1, FUS, MOV10, NXF1, CUL7, OBSL1, EED, MAGEA10, NTRK1, LRIF1, SNW1, CDC5L, MDM2, SNRPE, SERPINB2, FOXA1, TRIM25


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 MED13_DDX42


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for MED13_DDX42


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