VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10017661

Fusion event

HBV-AFF1 integration

Validated

No

Detection method

TS

Data source

Curated

Sample type

Nontumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2016

PubMed ID

26867494

Virus Sequence

Virus name

HBV

Subtype

B

Reference genome

DQ089769.1

Region type

X protein;

Start

1793

Integrated sequence

CCTTGAGGCATACTTCAAAGACTGTGTATTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGATTAAAGGTCTTTGTACTGGGAGGCTGTAGGCATAAA| |TTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCCACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCT

Host Sequence

Chromosome

chr4

Cytoband

q21.3

Reference genome

GRCh37/hg19

Start

87927072/87005920 (Hg38)

End

87927072/87005920 (Hg38)

Location type

Intronic

Target gene

AFF1

miRNAs that regulate target gene

hsa-mir-128b ; hsa-mir-877-5p ; hsa-mir-615-3p ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-142-3p ; hsa-mir-6073 ; hsa-mir-1914-5p ; hsa-mir-587 ; hsa-mir-17-5p ; hsa-mir-20a-5p ; hsa-mir-93-5p ; hsa-mir-106b-5p ; hsa-mir-20b-5p ; hsa-mir-519d-3p ; hsa-mir-885-3p ; hsa-mir-5197-5p ; hsa-mir-205-5p ; hsa-mir-1228-3p ; hsa-mir-519e-3p ; hsa-mir-515-3p ; hsa-mir-33b-3p ; hsa-mir-371a-3p ; hsa-mir-371b-3p ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-8485 ; hsa-mir-4279 ; hsa-mir-361-5p ; hsa-mir-889-3p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-1324 ; hsa-mir-2115-3p ; hsa-mir-3074-3p ; hsa-mir-5571-5p ; hsa-mir-7161-5p ; hsa-mir-548u ; hsa-mir-4744 ; hsa-mir-1273h-3p ; hsa-mir-143-5p ; hsa-mir-3944-5p ; hsa-mir-5093 ; hsa-mir-4480 ; hsa-mir-3166 ; hsa-mir-4771 ; hsa-mir-6790-3p ; hsa-mir-3691-3p ; hsa-mir-548an ; hsa-mir-31-5p ; hsa-mir-5684 ; hsa-mir-4511 ; hsa-mir-548b-3p ; hsa-mir-5692b ; hsa-mir-5692c

Nearest miRNA

hsa-mir-12113/Upstream/463368; hsa-mir-1243/Downstream/294575;

Nearest TSS

ENST00000502981/Upstream/69510; ENST00000511722/Downstream/1068;

Nearest CpG islands

None/Target, chr4-CpG: 46/Upstream/69868, chr4-CpG: 76/Downstream/856

Nearest cancer related gene

AFF1(OG, No orient, 0)

Upstream sequence

GCATGAGAAAACGCCAGTAAGTGACAGAGTCACCAAATGCTGCACAGAATCCTTGGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACA

Downstream sequence

atcagtgcaaatgtcagcacagtgaaaagacaatgtctttgtgttattctaaaaatagttctgacctctgagagggtcttggggactcccaggaatctag

Reference

Chiu, Y. T., et al. Novel pre-mRNA splicing of intronically integrated HBV generates oncogenic chimera in hepatocellular carcinoma. J Hepatol ,2016,64(6): 1256-1264.