VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10000216

Fusion event

HBV-CLIP1 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

1699

Integrated sequence

TGCACGTCGCATGGAGACCACCGTGAACGCCCACCGAATGTTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCTGCAATGTCAACGACCGACCTT| |GAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGATTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGG

Host Sequence

Chromosome

chr12

Cytoband

q24.31

Reference genome

GRCh38.p7

Start

122308283 (Hg38)

End

122308283 (Hg38)

Orient

-

Location type

Intronic

Fragile sites / regions

FRA12E

Target gene

CLIP1

miRNAs that regulate target gene

hsa-mir-130b-3p ; hsa-mir-103a-3p ; hsa-mir-19b-3p ; hsa-mir-205-5p ; hsa-mir-4473 ; hsa-mir-4671-3p ; hsa-mir-200b-5p ; hsa-mir-200a-5p ; hsa-mir-4517 ; hsa-mir-337-5p ; hsa-mir-4485-3p ; hsa-mir-559 ; hsa-mir-548y ; hsa-mir-548w ; hsa-mir-548o-5p ; hsa-mir-548j-5p ; hsa-mir-548i ; hsa-mir-548h-5p ; hsa-mir-548d-5p ; hsa-mir-548c-5p ; hsa-mir-548bb-5p ; hsa-mir-548b-5p ; hsa-mir-548ay-5p ; hsa-mir-548au-5p ; hsa-mir-548as-5p ; hsa-mir-548ar-5p ; hsa-mir-548aq-5p ; hsa-mir-548ap-5p ; hsa-mir-548am-5p ; hsa-mir-548ak ; hsa-mir-548ae-5p ; hsa-mir-548ad-5p ; hsa-mir-548ab ; hsa-mir-548a-5p ; hsa-mir-548n ; hsa-mir-454-3p ; hsa-mir-3666 ; hsa-mir-4295 ; hsa-mir-301b-3p ; hsa-mir-130a-3p ; hsa-mir-301a-3p ; hsa-mir-19a-3p ; hsa-mir-653-5p ; hsa-mir-3175 ; hsa-mir-4509 ; hsa-mir-6889-5p ; hsa-mir-6777-5p ; hsa-mir-6741-5p ; hsa-mir-340-5p ; hsa-mir-6748-5p ; hsa-mir-3944-5p ; hsa-mir-376a-2-5p ; hsa-mir-4286 ; hsa-mir-936 ; hsa-mir-6834-3p ; hsa-mir-3163 ; hsa-mir-140-3p ; hsa-mir-3662 ; hsa-mir-107 ; hsa-mir-5010-3p ; hsa-mir-2113 ; hsa-mir-8070 ; hsa-mir-4477a ; hsa-mir-3689f ; hsa-mir-3689e ; hsa-mir-3689b-5p ; hsa-mir-3689a-5p ; hsa-mir-4668-3p

Nearest miRNA

hsa-let-7i/Upstream/863931; hsa-mir-3612/Downstream/387624;

Nearest TSS

ENST00000382841/Upstream/27405; ENST00000539034/Downstream/35761;

Nearest CpG islands

None/Target, chr12-CpG: 104/Upstream/41602, chr12-CpG: 140/Downstream/113574

Downstream sequence

AGACTCTCTGCAATGTCAACGACCGACCTT

Junction sequence

AGTGGGTTCCATAAATAGGAGGAACTTACAAGACTCTCTGCAATGTCAACGACCGACCTT

* 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).