VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10000113

Fusion event

HBV-LSAMP integration

Validated

Yes

Detection method

invPCR

Data source

Curated

Sample type

Cell line

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Perfect

Reported year

2018

PubMed ID

29437961

Virus Sequence

Virus name

HBV

Reference genome

U95551.1

End

1749

Integrated sequence

TCTTACATAAGAGGACTCTTGGACTCTCTGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGA| |GGAGATTAGATTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTT

Host Sequence

Chromosome

chr3

Cytoband

q13.31

Reference genome

GRCh38.p7

Start

115926653 (Hg38)

End

115926653 (Hg38)

Orient

+

Location type

Intronic

Target gene

LSAMP

miRNAs that regulate target gene

hsa-mir-335-5p ; hsa-mir-26b-5p ; hsa-mir-369-3p ; hsa-mir-5584-3p ; hsa-mir-552-5p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-6833-3p ; hsa-mir-4768-5p ; hsa-mir-5006-3p ; hsa-mir-4755-5p ; hsa-mir-3977 ; hsa-mir-6873-3p ; hsa-mir-211-5p ; hsa-mir-204-5p ; hsa-mir-623 ; hsa-mir-103a-2-5p ; hsa-mir-302d-5p ; hsa-mir-302b-5p ; hsa-mir-942-5p ; hsa-mir-4680-3p ; hsa-mir-6845-3p ; hsa-mir-6832-3p ; hsa-mir-345-3p ; hsa-mir-3162-3p ; hsa-mir-3150b-5p ; hsa-mir-3150a-5p ; hsa-mir-6756-3p ; hsa-mir-4469 ; hsa-mir-4667-3p ; hsa-mir-1470 ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-6818-3p ; hsa-mir-6888-3p ; hsa-mir-593-3p ; hsa-mir-6895-3p ; hsa-mir-630 ; hsa-mir-3120-5p ; hsa-mir-4742-3p ; hsa-mir-6817-3p ; hsa-mir-7110-3p ; hsa-mir-361-3p ; hsa-mir-4778-5p ; hsa-mir-629-3p ; hsa-mir-4279 ; hsa-mir-6867-3p ; hsa-mir-4713-5p ; hsa-mir-6868-3p ; hsa-mir-6763-3p ; hsa-mir-5581-5p ; hsa-mir-4297 ; hsa-mir-3124-3p ; hsa-mir-1976 ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-7113-3p ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-660-3p ; hsa-mir-3127-3p ; hsa-mir-553 ; hsa-mir-4762-3p ; hsa-mir-29b-2-5p ; hsa-mir-4256 ; hsa-mir-6719-3p ; hsa-mir-4526 ; hsa-mir-3660 ; hsa-mir-6730-3p ; hsa-mir-296-3p ; hsa-mir-192-3p ; hsa-mir-342-3p

Nearest miRNA

hsa-let-7g/Upstream/1183128; hsa-mir-12124/Downstream/923624;

Nearest TSS

ENST00000440867/Upstream/74075; ENST00000490351/Downstream/124599;

Nearest CpG islands

None/Target, chr3-CpG: 148/Upstream/141919, chr3-CpG: 75/Downstream/2070064

Nearest cancer related gene

LSAMP(TSG, No orient, 0)

Downstream sequence

TTTGTTTAAGACTGGGAGGAGTTGGGGGA

Junction sequence

ACCTGCATCAGGAGTTGAGAACCACAGTCCTTTGTTTAAGACTGGGAGGAGTTGGGGGA

* Color: Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence

Reference

Tu, T., et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol ,2018,92(11).