VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10018268

Fusion event

HBV-chr19 integration

Validated

No

Detection method

RNA-Seq

Data source

Curated

Sample type

Nontumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Good

Reported year

2017

PubMed ID

28622513

Virus Sequence

Virus name

HBV

Reference genome

Not given

Start

361

Host Sequence

Chromosome

chr19

Cytoband

q13.32

Reference genome

GRCh37/hg19

Start

45411016/44907759 (Hg38)

End

45452471/44949214 (Hg38)

Location type

Intronic

Fragile sites / regions

FRA19A

Target gene

APOC1 ; APOC1P1 ; APOC2 ; APOC4 ; APOE ; TOMM40

miRNAs that regulate target gene

hsa-mir-335-5p ; hsa-mir-34a-5p ; hsa-mir-615-3p ; hsa-mir-484 ; hsa-mir-324-3p ; hsa-mir-199a-5p ; hsa-mir-1908-5p ; hsa-mir-199a-3p ; hsa-mir-328-3p ; hsa-mir-7155-3p ; hsa-mir-3136-3p ; hsa-mir-1245b-3p ; hsa-mir-4538 ; hsa-mir-4453 ; hsa-mir-6848-3p ; hsa-mir-6843-3p ; hsa-mir-6878-3p ; hsa-mir-3187-3p ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-519e-5p ; hsa-mir-515-5p ; hsa-mir-6744-3p ; hsa-mir-4757-5p ; hsa-mir-6131 ; hsa-mir-4755-3p ; hsa-mir-3663-5p ; hsa-mir-3922-3p ; hsa-mir-3176 ; hsa-mir-5695 ; hsa-mir-519d-5p ; hsa-mir-1306-3p ; hsa-mir-8073 ; hsa-mir-221-5p ; hsa-mir-1268a ; hsa-mir-1268b ; hsa-mir-1908-5p ; hsa-mir-24-3p ; hsa-mir-3190-3p ; hsa-mir-3202 ; hsa-mir-3610 ; hsa-mir-3926 ; hsa-mir-4316 ; hsa-mir-4437 ; hsa-mir-4459 ; hsa-mir-449b-3p ; hsa-mir-4533 ; hsa-mir-4640-5p ; hsa-mir-4710 ; hsa-mir-4721 ; hsa-mir-4726-5p ; hsa-mir-4738-3p ; hsa-mir-4779 ; hsa-mir-4792 ; hsa-mir-5008-5p ; hsa-mir-5088-5p ; hsa-mir-6089 ; hsa-mir-6125 ; hsa-mir-663a ; hsa-mir-665 ; hsa-mir-6762-5p ; hsa-mir-6787-5p ; hsa-mir-6845-5p ; hsa-mir-7855-5p

Nearest miRNA

hsa-mir-10395/Upstream/149038; hsa-let-7e/Downstream/487440;

Nearest TSS

ENST00000633603/Upstream/1399; ENST00000585961/Downstream/4793;

Nearest CpG islands

chr19-CpG: 90/Target, None/Upstream, None/Downstream

Upstream sequence

aatttttgtatttttagtagagacagggtttcaccacattggctaggctggtcttgaactcctgacctcgtgatctgcccgtctcggcctcccaaagtgc

Downstream sequence

ACCAAGTTCTTTCTGTGCTGAAGGGAGAGGAGTAACAGCCAGACCCCCCATCAGTGGACAAGGGGAGAGTCCCCTACTCCCCTGATCCCCCAGGTTCAGA

Reference

Cancer Genome Atlas Research Network. Electronic address, w. b. e. and N. Cancer Genome Atlas Research . Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell ,2017,169(7): 1327-1341 e13