VISDB Viral Integration Site DataBase

VIS ID

TVIS10013857

Fusion event

HBV-HMGA2 integration

Validated

No

Detection method

NGS

Data source

Curated

Sample type

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2018

PubMed ID

Virus name

HBV

Reference genome

Region type

precore/core protein|Core and e antigen|

Start

2146

Orient

+

Integrated sequence

TCACCTCACCATACTGCACTCAGGCAAGCAATTCTTTGCTGGGGGGAACTAATGACTCTAGCTACCTGGGTGGGTGTTAATTTGGAAGATCCAGCGTCTA| |GAGACCTAGTAGTCAGTTATGTCAACACTAATATGGGCCTAAAGTTCAGGCAACTCTTGTGGTTTCACATTTCTTGTCTCACTTTTGGAAGAGAAACAGT

Chromosome

chr12

Cytoband

q14.3

Reference genome

Start

End

66268556/65874776 (Hg38)

Orient

+

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-26a-5p ; hsa-mir-125b-5p ; hsa-mir-34a-5p ; hsa-let-7d-5p ; hsa-let-7e-5p ; hsa-let-7b-5p ; hsa-let-7g-5p ; hsa-let-7c-5p ; hsa-let-7a-5p ; hsa-mir-98-5p ; hsa-mir-370-3p ; hsa-mir-185-5p ; hsa-mir-29b-3p ; hsa-mir-196a-5p ; hsa-mir-16-5p ; hsa-mir-15a-5p ; hsa-mir-204-5p ; hsa-mir-760 ; hsa-let-7f-5p ; hsa-mir-154-5p ; hsa-mir-3199 ; hsa-mir-8052 ; hsa-mir-25-3p ; hsa-mir-32-5p ; hsa-mir-92a-3p ; hsa-let-7i-5p ; hsa-mir-363-3p ; hsa-mir-367-3p ; hsa-mir-196b-5p ; hsa-mir-491-5p ; hsa-mir-92b-3p ; hsa-mir-1296-3p ; hsa-mir-4257 ; hsa-mir-4458 ; hsa-mir-4461 ; hsa-mir-4500 ; hsa-mir-4727-3p ; hsa-mir-6847-5p ; hsa-mir-6857-5p ; hsa-mir-6869-5p ; hsa-mir-33a-5p ; hsa-mir-33b-5p ; hsa-mir-142-3p ; hsa-let-7c-3p ; hsa-mir-508-3p ; hsa-mir-648 ; hsa-mir-2052 ; hsa-mir-3529-3p ; hsa-mir-365a-5p ; hsa-mir-365b-5p ; hsa-mir-145-5p ; hsa-mir-23b-3p ; hsa-mir-493-5p ; hsa-let-7g-3p ; hsa-let-7a-2-3p ; hsa-mir-19b-2-5p ; hsa-mir-19b-1-5p ; hsa-mir-19a-5p ; hsa-mir-4445-5p ; hsa-mir-1244 ; hsa-mir-219a-5p ; hsa-mir-4782-3p ; hsa-mir-6766-3p ; hsa-mir-3143 ; hsa-mir-4450 ; hsa-mir-4262 ; hsa-mir-181d-5p ; hsa-mir-181c-5p ; hsa-mir-181b-5p ; hsa-mir-181a-5p ; hsa-mir-543 ; hsa-mir-490-3p ; hsa-mir-33b-3p ; hsa-mir-633 ; hsa-mir-495-3p ; hsa-mir-107 ; hsa-mir-485-5p ; hsa-mir-1297 ; hsa-mir-106a-5p ; hsa-mir-10a-3p ; hsa-mir-1245b-3p ; hsa-mir-1252-3p ; hsa-mir-1304-5p ; hsa-mir-16-1-3p ; hsa-mir-17-3p ; hsa-mir-194-5p ; hsa-mir-202-3p ; hsa-mir-222-5p ; hsa-mir-30a-3p ; hsa-mir-30d-3p ; hsa-mir-30e-3p ; hsa-mir-3191-5p ; hsa-mir-326 ; hsa-mir-330-5p ; hsa-mir-335-3p ; hsa-mir-3662 ; hsa-mir-3688-3p ; hsa-mir-3978 ; hsa-mir-4261 ; hsa-mir-4418 ; hsa-mir-4720-3p ; hsa-mir-4738-3p ; hsa-mir-4775 ; hsa-mir-4796-3p ; hsa-mir-4804-3p ; hsa-mir-490-5p ; hsa-mir-5003-3p ; hsa-mir-506-5p ; hsa-mir-509-3-5p ; hsa-mir-509-5p ; hsa-mir-518c-5p ; hsa-mir-548ah-3p ; hsa-mir-548am-3p ; hsa-mir-548ar-3p ; hsa-mir-548o-3p ; hsa-mir-5681b ; hsa-mir-591 ; hsa-mir-627-3p ; hsa-mir-629-3p ; hsa-mir-6502-3p ; hsa-mir-6760-5p ; hsa-mir-6764-3p ; hsa-mir-6824-3p ; hsa-mir-6830-3p ; hsa-mir-6878-5p ; hsa-mir-892c-5p

Nearest miRNA

hsa-let-7i/Upstream/1252171; hsa-mir-1178/Downstream/148844;

Nearest TSS

Nearest CpG islands

None/Target, chr12-CpG: 104/Upstream/48375, chr12-CpG: 30/Downstream/255908

Nearest cancer related gene

HMGA2(OG, No orient, 0)

Upstream sequence

TGGCAAGATATCTTTTTTAAAAAAATAAAGTAATGGATAATCATAGTTCAAACTCATTTGTTTTTCTGTATGTATACATACAGGTAAACATTTTCACAAG

Downstream sequence

TACGCTTAAAAATAGTAGAAGAGTTTAAAGATTTGCCCCAATGGGCTCATCTCTCCCTTTTCCAGTTTGGTGCTCCATCTCAGAAAAAGAGAGTCACATT