VISDB Viral Integration Site DataBase

VIS ID

TVIS10008976

Fusion event

HBV-LGSN 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

X protein|

Start

1758

Orient

-

Integrated sequence

AGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAG| |GTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTC

Chromosome

chr6

Cytoband

q12

Reference genome

Start

End

64180880/63470975 (Hg38)

Orient

-

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-1273e ; hsa-mir-6516-5p ; hsa-mir-455-3p ; hsa-mir-6807-5p ; hsa-mir-486-3p ; hsa-mir-2467-3p ; hsa-mir-6499-3p ; hsa-mir-6086 ; hsa-mir-377-5p ; hsa-mir-6764-5p ; hsa-mir-1915-3p ; hsa-mir-6798-5p ; hsa-mir-4257 ; hsa-mir-6805-5p ; hsa-mir-7856-5p ; hsa-mir-4693-5p ; hsa-mir-1200 ; hsa-mir-1911-5p ; hsa-mir-544b ; hsa-mir-4324 ; hsa-mir-4793-5p ; hsa-mir-1278 ; hsa-mir-892a ; hsa-mir-4318 ; hsa-mir-2114-3p ; hsa-mir-6878-3p ; hsa-mir-6744-3p ; hsa-mir-4757-5p ; hsa-mir-4312 ; hsa-mir-3922-3p ; hsa-mir-6778-3p ; hsa-mir-3176 ; hsa-mir-422a ; hsa-mir-378i ; hsa-mir-378h ; hsa-mir-378f ; hsa-mir-378e ; hsa-mir-378d ; hsa-mir-378c ; hsa-mir-378b ; hsa-mir-378a-3p ; hsa-mir-1976 ; hsa-mir-150-5p ; hsa-mir-371a-5p ; hsa-mir-212-5p ; hsa-mir-8073 ; hsa-mir-221-5p ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-186-3p ; hsa-mir-520h ; hsa-mir-520g-3p ; hsa-mir-512-3p ; hsa-mir-888-5p ; hsa-mir-520e ; hsa-mir-520d-3p ; hsa-mir-520c-3p ; hsa-mir-520b ; hsa-mir-520a-3p ; hsa-mir-373-3p ; hsa-mir-372-3p ; hsa-mir-302e ; hsa-mir-302d-3p ; hsa-mir-302c-3p ; hsa-mir-302b-3p ; hsa-mir-302a-3p ; hsa-mir-93-5p ; hsa-mir-526b-3p ; hsa-mir-519d-3p ; hsa-mir-20b-5p ; hsa-mir-20a-5p ; hsa-mir-17-5p ; hsa-mir-106b-5p ; hsa-mir-106a-5p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-519e-5p ; hsa-mir-515-5p ; hsa-mir-5695 ; hsa-mir-519d-5p ; hsa-mir-1279 ; hsa-mir-6809-3p ; hsa-mir-6833-3p ; hsa-mir-4768-5p ; hsa-mir-6873-3p ; hsa-mir-6845-3p ; hsa-mir-136-5p

Nearest miRNA

hsa-mir-10398/Upstream/6080763; hsa-mir-10524/Downstream/7905985;

Nearest TSS

Nearest CpG islands

None/Target, chr6-CpG: 120/Upstream/1184652, chr6-CpG: 163/Downstream/101271

Nearby gene

LGSN(-150998) ; PTP4A1(+101040) ;

Upstream sequence

tgggtcactttagggattccccacttattaactataagaacatgcaaatatgtaagtctctgagcctcggtttcttttctttcttttttatagagacaag

Downstream sequence

tgttgcccaggctgcagtgcaatggcacaatctcagctcactgcaacttccgcctcccaggttcaagtgattctcctacctcagcctcccaagtagctgg