RPGR _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10020365
Fusion event
HBV-RPGR integration
Validated
No
Detection method
VirusScan
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2016
PubMed ID
27339696
Virus Sequence
Virus name
HBV
Reference genome
NC_003977.1
Start
1176
End
2276
Orient
+
Integrated sequence
CAAGTGTTTGCTGACGCAACCCCCACGGGTTGGGGCTTGGCCATAGGCCATCGGCGCATGCGTGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTGTTTTGCTCGCAGCCGGTCTGGAGCGAAACTTATCGGAACCGACAACTCAGTTGTCCTCTCTCGGAAATACACCTCCTTTCCATGGCTGCTAGGCTGTGCTGCCAACTGGATCCTGCGCGGGACGTCCTTTGTCTACGTC
Host Sequence
Chromosome
chrX
Cytoband
p11.4
Reference genome
GRCh37/hg19
Start
38166902/38307649 (Hg38)
End
38167952/38308699 (Hg38)
Orient
+
Location type
Intronic
Target gene
RPGR
miRNAs that regulate target gene
hsa-mir-375
Nearest miRNA
hsa-mir-23c/Upstream/283663; hsa-let-7f-2/Downstream/1352517;
Nearest TSS
ENST00000429181/Upstream/2818; ENST00000488812/Downstream/10291;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/51332, chrX-CpG: 57/Downstream/18470
Upstream sequence
aagcaatggcaacaaaaggcaaaatggacaaatgggatctaattaaacctaagagtttctgcacagcaaaagaaactattatcagaatgaacaggcaacc
Downstream sequence
GAAATTATATAAAATTCACTTTTTCAGCAGGAATTCAAAAACATCTTAAACCTCAGAATTATTTCCAAATTTAGAGTATAAGTTTTGAAAAAAAATTATT
Target sequence
atatactcttcAGGTCCATTTCTTCATCAGCTAGGACTAAATATTTTTAAAATTCTGCCTATACTGTGCTCCAGAACCAGGTTCCTCACCAGGGCTGGCTCATAATAAAGCTCTCACAGGTCCATGGAGAAATGTGAAAAACAGGCAAAGTAGTGAAATTTTCATACATATACATTTATACAGTTTAAGGAGGTGCCCTTTATTATATACAATTAAGAGTTTTTTATTTTGAAAATGTTCCTTATTTTATGATAT
Reference
Cao, S., et al.Divergent viral presentation among human tumors and adjacent normal tissues. Sci Rep,2016, 6: 28294.
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