SRP19 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005531
Fusion event
HBV-SRP19 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
876
Orient
-
Integrated sequence
TCTTGAGTCCCTTTTTACCTCTATTACCAATTTTCTTTTGTCTTTGGGTATACATTTGAACCCTAATAAAACCAAACGTTGGGGCTACTCCCTTAACTTC| |ATGGGATATGTAATTGGAAGTTGGGGTACTTTACCACAGGAACATATTGTACGGAAACTCAAGCAATGTTTTCGAAAACTGCCTGTAAATAGACCTATTG
Host Sequence
Chromosome
chr5
Cytoband
q22.2
Reference genome
GRCh37/hg19
Start
112208492/112872795 (Hg38)
End
112208492/112872795 (Hg38)
Orient
-
Location type
Intron
Target gene
SRP19
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-665 ; hsa-mir-6514-3p ; hsa-mir-5571-3p ; hsa-mir-7977 ; hsa-mir-3162-5p ; hsa-mir-891a-3p ; hsa-mir-6811-3p ; hsa-mir-214-5p ; hsa-mir-5589-3p ; hsa-mir-4267 ; hsa-mir-6736-3p ; hsa-mir-4756-5p ; hsa-mir-4739 ; hsa-mir-1321 ; hsa-mir-6760-5p ; hsa-mir-1-3p ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-564 ; hsa-mir-6847-3p ; hsa-mir-4493 ; hsa-mir-383-3p ; hsa-mir-186-5p ; hsa-mir-3133 ; hsa-mir-10a-5p ; hsa-mir-10b-5p ; hsa-mir-3148 ; hsa-mir-339-5p ; hsa-mir-3688-3p ; hsa-mir-4421 ; hsa-mir-4684-5p ; hsa-mir-4802-3p ; hsa-mir-548ac ; hsa-mir-548as-3p ; hsa-mir-548bb-3p ; hsa-mir-548c-3p ; hsa-mir-548d-3p ; hsa-mir-548h-3p ; hsa-mir-548z ; hsa-mir-5699-3p ; hsa-mir-593-3p ; hsa-mir-6124 ; hsa-mir-6732-3p ; hsa-mir-6818-3p ; hsa-mir-6895-3p
Nearest miRNA
hsa-mir-10397/Upstream/2358880; hsa-mir-103a-1/Downstream/3382948;
Nearest TSS
ENST00000502646/Upstream/8186; ENST00000504961/Downstream/48709;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/11245, chr5-CpG: 93/Downstream/48488
Upstream sequence
TGAGGTTACTTTTTACAGATAAAGACATTAGAAAACTGCTTTTATGAAAAAAATTGTCTAAGTATCTAGAATGCTTCAAATACAGTATAAATAAAATGCA
Downstream sequence
atgttactgctttgttttgtatatcttgttctcaggatcttccccagaaaagtgcaagagaggtaaatgttcttagaccttgcatatttgaaaatttcat
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).
Curate