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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: 29716

FusionGeneSummary for PVT1_COL6A1

check button Fusion gene summary
Fusion gene informationFusion gene name: PVT1_COL6A1
Fusion gene ID: 29716
HgeneTgene
Gene symbol

PVT1

COL6A1

Gene ID

5820

1291

Gene namePvt1 oncogenecollagen type VI alpha 1 chain
SynonymsLINC00079|MIR1204HG|MYC|NCRNA00079|onco-lncRNA-100BTHLM1|OPLL|UCHMD1
Cytomap

8q24.21

21q22.3

Type of genencRNAprotein-coding
DescriptionCXCR4/PVT1 fusionHIST1H2BD/PVT1 fusionMIR1204, MIR1205, MIR1206 and MIR1207 hostOncogene PVT-1 (MYC activator)PVT1/CASC8 fusionPVT1/CCDC26 fusionPVT1/IFRD1 fusionPVT1/IRF2BP2 fusionPVT1/LINC00824 fusionPVT1/MYC fusionPVT1/NFIL3 fusionPVT1/NSMCEcollagen alpha-1(VI) chainalpha 1 (VI) chain (61 AA)collagen VI, alpha-1 polypeptidecollagen, type VI, alpha 1
Modification date2018052020180523
UniProtAcc

P12109

Ensembl transtripts involved in fusion geneENST00000408388, ENST00000361866, 
ENST00000498614, 
Fusion gene scores* DoF score37 X 12 X 15=666011 X 11 X 5=605
# samples 3921
** MAII scorelog2(39/6660*10)=-4.09397614820901
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(21/605*10)=-1.52654581449583
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PVT1 [Title/Abstract] AND COL6A1 [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

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
ChiTaRS3.1AK128687PVT1chr8

128943398

+COL6A1chr21

47424394

+
* 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
intron-3UTRENST00000408388ENST00000361866PVT1chr8

128943398

+COL6A1chr21

47424394

+
intron-3UTRENST00000408388ENST00000498614PVT1chr8

128943398

+COL6A1chr21

47424394

+

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FusionProtFeatures for PVT1_COL6A1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PVT1

COL6A1

P12109

Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}. Collagen VI acts as a cell-binding protein.

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 PVT1_COL6A1


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 PVT1_COL6A1


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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RelatedDrugs for PVT1_COL6A1


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 PVT1_COL6A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePVT1C0019829Hodgkin Disease1CTD_human
HgenePVT1C0162538Immunoglobulin A deficiency (disorder)1CTD_human
TgeneCOL6A1C1834674Bethlem myopathy5CTD_human;ORPHANET;UNIPROT
TgeneCOL6A1C0410179Scleroatonic muscular dystrophy3CTD_human;ORPHANET;UNIPROT
TgeneCOL6A1C0000786Spontaneous abortion1CTD_human
TgeneCOL6A1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneCOL6A1C0024121Lung Neoplasms1CTD_human
TgeneCOL6A1C0026850Muscular Dystrophy1CTD_human