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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: 21479

FusionGeneSummary for MED13_VMP1

check button Fusion gene summary
Fusion gene informationFusion gene name: MED13_VMP1
Fusion gene ID: 21479
HgeneTgene
Gene symbol

MED13

VMP1

Gene ID

9969

81671

Gene namemediator complex subunit 13vacuole membrane protein 1
SynonymsARC250|DRIP250|HSPC221|THRAP1|TRAP240EPG3|TANGO5|TMEM49
Cytomap

17q23.2

17q23.1

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 proteinvacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homolog
Modification date2018052320180523
UniProtAcc

Q9UHV7

Q96GC9

Ensembl transtripts involved in fusion geneENST00000397786, ENST00000580896, 
ENST00000262291, ENST00000537567, 
ENST00000539763, ENST00000536180, 
ENST00000545362, ENST00000588617, 
Fusion gene scores* DoF score13 X 13 X 6=101424 X 11 X 12=3168
# samples 1427
** MAII scorelog2(14/1014*10)=-2.85655892005837
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(27/3168*10)=-3.55254102302878
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MED13 [Title/Abstract] AND VMP1 [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


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
TCGALDBRCATCGA-AO-A03L-01AMED13chr17

60028186

-VMP1chr17

57915656

+
* 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-shitENST00000397786ENST00000262291MED13chr17

60028186

-VMP1chr17

57915656

+
Frame-shitENST00000397786ENST00000537567MED13chr17

60028186

-VMP1chr17

57915656

+
Frame-shitENST00000397786ENST00000539763MED13chr17

60028186

-VMP1chr17

57915656

+
Frame-shitENST00000397786ENST00000536180MED13chr17

60028186

-VMP1chr17

57915656

+
Frame-shitENST00000397786ENST00000545362MED13chr17

60028186

-VMP1chr17

57915656

+
5CDS-intronENST00000397786ENST00000588617MED13chr17

60028186

-VMP1chr17

57915656

+
intron-3CDSENST00000580896ENST00000262291MED13chr17

60028186

-VMP1chr17

57915656

+
intron-3CDSENST00000580896ENST00000537567MED13chr17

60028186

-VMP1chr17

57915656

+
intron-3CDSENST00000580896ENST00000539763MED13chr17

60028186

-VMP1chr17

57915656

+
intron-3CDSENST00000580896ENST00000536180MED13chr17

60028186

-VMP1chr17

57915656

+
intron-3CDSENST00000580896ENST00000545362MED13chr17

60028186

-VMP1chr17

57915656

+
intron-intronENST00000580896ENST00000588617MED13chr17

60028186

-VMP1chr17

57915656

+

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FusionProtFeatures for MED13_VMP1


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

Q9UHV7

VMP1

Q96GC9

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}. Stress-induced protein that, when overexpressed,promotes formation of intracellular vacuoles followed by celldeath. May be involved in the cytoplasmic vacuolization of acinarcells during the early stage of acute pancreatitis. Plays a rolein the initial stages of the autophagic process through itsinteraction with BECN1 (By similarity). Involved in cell-celladhesion. Plays an essential role in formation of cell junctions.{ECO:0000250, ECO:0000269|PubMed:17724469}.

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_VMP1


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_VMP1


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, TRIM25VMP1HGS, ELAVL1, TJP1, KLK11, LPAR6, ERGIC3, FAF2, KRAS, TCTN2, TCTN3, TMEM216, DPEP1, CDH13, MAS1, LMNA


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_VMP1


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_VMP1


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