LRRTM4 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004660
Fusion event
HBV-LRRTM4 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
2044
Orient
-
Integrated sequence
ACTCTCTTTTTTGCCTTCTGACTTCTTTCCTTCTATTCGAGATCTCCTCGACACCGCCTCTGCTCTGTATCGGGAGGCCTTAGAGTCTCCGGAACATTGT| |TCACCTCACCATACAGCACTCAGGCAAGCTATTCTGTGTTGGGGTGAGTTGATGAATCTGGCCACCTGGGTGGGAAGTAATTTGGAAGACCCAGCATCCA
Host Sequence
Chromosome
chr2
Cytoband
p12
Reference genome
GRCh37/hg19
Start
77605176/77378050 (Hg38)
End
77605176/77378050 (Hg38)
Orient
+
Location type
Intron
Fragile sites / regions
FRA2S
Target gene
LRRTM4
miRNAs that regulate target gene
hsa-mir-1305 ; hsa-mir-6868-3p ; hsa-mir-4465 ; hsa-mir-26b-5p ; hsa-mir-26a-5p ; hsa-mir-1297 ; hsa-mir-205-5p
Nearest miRNA
hsa-mir-1285-2/Upstream/2287136; hsa-mir-10b/Downstream/2271244;
Nearest TSS
ENST00000437798/Upstream/392085; ENST00000438443/Downstream/144160;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/1667037, chr2-CpG: 32/Downstream/1615016
Junction sequence
CTAA
* 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).
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