VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10005100

Fusion event

HBV-SLC35E3 integration

Validated

No

Detection method

PCR and Ultra-deep sequencing

Data source

Curated

Sample type

Nontumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2018

PubMed ID

29861854

Virus Sequence

Virus name

HBV

Reference genome

AP011098

Start

1750

Orient

+

Integrated sequence

TACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGA| |GATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTT

Host Sequence

Chromosome

chr12

Cytoband

q15

Reference genome

GRCh37/hg19

Start

69159584/68765804 (Hg38)

End

69159584/68765804 (Hg38)

Orient

-

Location type

Exon

Target gene

SLC35E3

miRNAs that regulate target gene

hsa-mir-1304-5p ; hsa-mir-1273e ; hsa-mir-6765-5p ; hsa-mir-6807-5p ; hsa-mir-6894-5p ; hsa-mir-7160-5p ; hsa-mir-4722-5p ; hsa-mir-6884-5p ; hsa-mir-485-5p ; hsa-mir-1827 ; hsa-mir-1233-3p ; hsa-mir-1225-3p ; hsa-mir-6840-3p ; hsa-mir-665 ; hsa-mir-4459 ; hsa-mir-4478 ; hsa-mir-4419b ; hsa-mir-3929 ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-6808-5p ; hsa-mir-4695-5p ; hsa-mir-1277-5p ; hsa-mir-188-3p ; hsa-mir-4733-5p ; hsa-mir-7151-5p ; hsa-mir-574-5p ; hsa-mir-297 ; hsa-mir-3924 ; hsa-mir-190a-3p ; hsa-mir-4789-5p ; hsa-mir-466 ; hsa-mir-3941 ; hsa-mir-6867-5p ; hsa-mir-223-5p ; hsa-mir-567 ; hsa-mir-511-3p ; hsa-mir-5011-5p ; hsa-mir-4643 ; hsa-mir-4789-3p ; hsa-mir-603 ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-8485 ; hsa-mir-6514-5p ; hsa-mir-8076 ; hsa-mir-4802-5p ; hsa-mir-744-3p ; hsa-mir-106a-3p ; hsa-mir-4423-5p ; hsa-mir-6501-5p ; hsa-mir-4430 ; hsa-mir-3652 ; hsa-mir-122-5p ; hsa-mir-504-3p ; hsa-mir-3135b ; hsa-mir-5579-5p ; hsa-mir-454-3p ; hsa-mir-4295 ; hsa-mir-3666 ; hsa-mir-301b-3p ; hsa-mir-301a-3p ; hsa-mir-130b-3p ; hsa-mir-130a-3p ; hsa-mir-378a-5p ; hsa-mir-4454 ; hsa-mir-6821-3p ; hsa-mir-6790-3p ; hsa-mir-3922-3p ; hsa-mir-3176 ; hsa-mir-3653-5p ; hsa-mir-6513-3p ; hsa-mir-8079 ; hsa-mir-1245a

Nearest miRNA

hsa-let-7i/Upstream/2514647; hsa-mir-1178/Downstream/507353;

Nearest TSS

ENST00000382841/Upstream/13653; ENST00000399333/Downstream/26608;

Nearest CpG islands

None/Target, chr12-CpG: 104/Upstream/19378, chr12-CpG: 107/Downstream/42038

Junction sequence

AC

* 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).