VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10000007

Fusion event

HBV-PARD3 integration

Validated

Yes

Detection method

PCR and Sanger sequencing

Data source

Curated

Sample type

Tumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Perfect

Reported year

2019

PubMed ID

30535432

Virus Sequence

Virus name

HBV

Reference genome

GU815714.1

Region type

P/S

Start

2360

Integrated sequence

CTTTTGGAGTGTGGATTCGCACTCCTCCTGCATATAGACCACCAAATGCCCCTATCTTATCAACACTTCCGGAAACTACTGTTGTTAGACGAAGAGGCAG| |GTCCCCTAGAAGAAGAACTCCCTCGCCTCGCAGACGAAGGTCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCGGGAATCTCAATGTTAGTATTCCTTG

Host Sequence

Chromosome

chr10

Cytoband

p11.21

Reference genome

GRCh37/hg19

Start

34836578/34547650 (Hg38)

End

34836578/34547650 (Hg38)

Location type

Intronic

Target gene

PARD3

miRNAs that regulate target gene

hsa-mir-483-3p ; hsa-mir-93-3p ; hsa-mir-766-3p ; hsa-mir-218-5p ; hsa-mir-4503 ; hsa-mir-6839-3p ; hsa-mir-6836-3p ; hsa-mir-5001-3p ; hsa-mir-6783-3p ; hsa-mir-1343-3p ; hsa-mir-6792-5p ; hsa-mir-629-5p ; hsa-mir-3194-3p ; hsa-mir-7158-5p ; hsa-mir-6829-3p ; hsa-mir-6791-3p ; hsa-mir-6778-3p ; hsa-mir-6742-3p ; hsa-mir-6852-5p ; hsa-mir-939-3p ; hsa-mir-660-3p ; hsa-mir-6796-3p ; hsa-mir-5089-5p ; hsa-mir-7151-3p ; hsa-mir-5095 ; hsa-mir-2861 ; hsa-mir-5589-5p ; hsa-mir-4731-5p ; hsa-mir-661 ; hsa-mir-3116 ; hsa-mir-1254 ; hsa-mir-6506-5p ; hsa-mir-619-5p ; hsa-mir-150-5p ; hsa-mir-6747-3p ; hsa-mir-186-3p ; hsa-mir-520h ; hsa-mir-520g-3p ; hsa-mir-6504-3p ; hsa-mir-512-3p ; hsa-mir-4438 ; hsa-mir-520e ; hsa-mir-520d-3p ; hsa-mir-520c-3p ; hsa-mir-520b ; hsa-mir-520a-3p ; hsa-mir-373-3p ; hsa-mir-372-3p ; hsa-mir-302e ; hsa-mir-302d-3p ; hsa-mir-302c-3p ; hsa-mir-302b-3p ; hsa-mir-302a-3p ; hsa-mir-93-5p ; hsa-mir-526b-3p ; hsa-mir-519d-3p ; hsa-mir-20b-5p ; hsa-mir-20a-5p ; hsa-mir-17-5p ; hsa-mir-106b-5p ; hsa-mir-106a-5p ; hsa-mir-1261 ; hsa-mir-129-5p ; hsa-mir-3201 ; hsa-mir-4791 ; hsa-mir-5004-3p ; hsa-mir-7850-5p ; hsa-mir-8068

Nearest miRNA

hsa-mir-1265/Upstream/4178985; hsa-mir-107/Downstream/531948;

Nearest TSS

ENST00000439456/Upstream/120919; ENST00000446211/Downstream/267671;

Nearest CpG islands

None/Target, chr10-CpG: 68/Upstream/1210381, chr10-CpG: 188/Downstream/266546

Downstream sequence

GGTCCCCTGAGTGCGCTTTCCTTTTCTTCCCATGCCATGACCTGACATCTATTGACCAAGTGGTGACTCCAATTAAAATGCTATTGCTTAATGATGACAAAAAATGCACTGCACAGATGGAAAAAAGAAAAAAACATATTTCAGGCAATGAT

Junction sequence

GAAGCTCCAAATTCTTTATACGGGTCAATGTCCATGCCCCAAAGCCACCCAAGGCACAGCTTGGAGGCTTGAACAGTAGGACATGAACATGAGATGATTAGGCAGAGGGGAAAAAGTTGTTAGACGAAGAGGCAGGTCCCCTGAGTGCGCTTTCCTTTTCTTCCCATGCCATGACCTGACATCTATTGACCAAGTGGTGACTCCAATTAAAATGCTATTGCTTAATGATGACAAAAAATGCACTGCACAGATGGAAAAAAGAAAAAAACATATTTCAGGCAATGAT

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

Reference

Ruan, P., et al. Different types of viralhost junction found in HBV integration breakpoints in HBVinfected patients. Mol Med Rep ,2019,19(2): 1410-1416.