VISDB Viral Integration Site DataBase

VIS ID

TVIS20005091

Fusion event

HPV-RAP2B integration

Validated

Yes

Detection method

RNA-Seq+RT-PCR

Data source

Curated

Sample type

Disease

Squamous-cell carcinoma (SCC)

Quality evaluation

Good

Reported year

2014

PubMed ID

Virus name

HPV

Subtype

HPV18

Reference genome

Not given

Chromosome

chr3

Cytoband

q25.2

Reference genome

Start

End

152937321/153219532 (Hg38)

Location type

Intronic

Fragile sites / regions

Target gene

miRNAs that regulate target gene

hsa-mir-324-5p ; hsa-mir-378a-5p ; hsa-mir-205-5p ; hsa-mir-1273e ; hsa-mir-4722-5p ; hsa-mir-219b-3p ; hsa-mir-4649-3p ; hsa-mir-6840-3p ; hsa-mir-4768-3p ; hsa-mir-302f ; hsa-mir-4435 ; hsa-mir-203a-3p ; hsa-mir-3190-5p ; hsa-mir-6849-3p ; hsa-mir-3941 ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-3692-3p ; hsa-mir-548t-3p ; hsa-mir-548ap-3p ; hsa-mir-548aa ; hsa-mir-548z ; hsa-mir-548h-3p ; hsa-mir-548d-3p ; hsa-mir-548bb-3p ; hsa-mir-548ac ; hsa-mir-665 ; hsa-mir-887-5p ; hsa-mir-6780a-5p ; hsa-mir-6779-5p ; hsa-mir-3689c ; hsa-mir-3689b-3p ; hsa-mir-3689a-3p ; hsa-mir-30b-3p ; hsa-mir-1273h-5p ; hsa-mir-6788-5p ; hsa-mir-30c-2-3p ; hsa-mir-30c-1-3p ; hsa-mir-6799-5p ; hsa-mir-6883-5p ; hsa-mir-6785-5p ; hsa-mir-4728-5p ; hsa-mir-149-3p ; hsa-mir-7106-5p ; hsa-mir-6774-5p ; hsa-mir-635 ; hsa-mir-4733-5p ; hsa-mir-4789-3p ; hsa-mir-335-3p ; hsa-mir-6833-3p ; hsa-mir-4768-5p ; hsa-mir-6873-3p ; hsa-mir-6867-3p ; hsa-mir-942-5p ; hsa-mir-6845-3p ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-7113-3p ; hsa-mir-4469 ; hsa-mir-4667-3p ; hsa-mir-1470 ; hsa-mir-3121-3p ; hsa-mir-603 ; hsa-mir-4668-5p ; hsa-mir-143-5p ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-6499-3p ; hsa-mir-6776-5p ; hsa-mir-6787-3p ; hsa-mir-5693 ; hsa-mir-8067 ; hsa-mir-6508-5p ; hsa-mir-708-3p ; hsa-mir-337-5p ; hsa-mir-548f-3p ; hsa-mir-548e-3p ; hsa-mir-548az-3p ; hsa-mir-548ar-3p ; hsa-mir-548a-3p ; hsa-mir-6748-5p ; hsa-mir-609 ; hsa-mir-4455 ; hsa-mir-6772-5p ; hsa-mir-18b-3p ; hsa-mir-4485-3p ; hsa-mir-22-3p ; hsa-mir-1292-3p ; hsa-mir-1910-3p ; hsa-mir-2467-3p ; hsa-mir-377-5p ; hsa-mir-4257 ; hsa-mir-4537 ; hsa-mir-455-3p ; hsa-mir-490-3p ; hsa-mir-6086 ; hsa-mir-6511a-5p ; hsa-mir-6516-5p ; hsa-mir-7851-3p

Nearest miRNA

hsa-let-7g/Upstream/1597459; hsa-mir-1224/Downstream/6063114;

Nearest TSS

Nearest CpG islands

None/Target, chr3-CpG: 148/Upstream/157, chr3-CpG: 131/Downstream/901466

Nearby gene

P2RY1 ; C3orf79(+) ;

Upstream sequence

tttagtctgatagaagagacttagtccagcccggccaacatggtgaaaccacgtctttactaaaaatacaaaaattagccaggtgtggaggaatcacttg

Downstream sequence

GTTGAGTATTTACAAAATGTATGAGCACAAAGAAGAAAGAATTGGCTTGACACATGCACCTATAttctaactcatgtttcctcttctacacttgactccc

Target sequence

GAAATGTGGCTCTTTGCAGCATGTACGTTTCTCCCTGATTTTGGTTGATGCATATTTCCCCGTTTAAGTAGCCGTTAGGGCGCAGTATCGGCAGCTTGACACCCACCAAGCAAAAGTTTCAGCCTGGAAAAAAAATGGGGGGGAAGGGTGGATGAAAAGGAGGGAGAGAAGGTGGAAATGGtttttttttttttttttctattttctttctttttttttttttttttttttGGTCAACAGCCGTTTTTCTAGTTC