RALGPS1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10014884
Fusion event
HBV-RALGPS1 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Cell line
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
24582836
Virus Sequence
Virus name
HBV
Reference genome
NC_003977.1
Region type
X / Core
Start
1931
End
2190
Orient
+
Integrated sequence
CTTCTGTGGAGTTACTCTCTTTTTTGCCTTCTGACTTCTTTCCTTCTATTCGAGATCTCCTCGACACCGCCTCTGCTCTGTATCGGGAGGCCTTAGAGTCTCCGGAACATTGTTCACCTCACCATACAGCACTCAGGCAAGCTATTCTGTGTTGGGGTGAGTTGATGAATCTGGCCACCTGGGTGGGAAGTAATTTGGAAGACCCAGCATCCAGGGAATTAGTAGTCAGCTATGTCAATGTTAATATGGGCCTAA
Host Sequence
Chromosome
chr9
Cytoband
q33.3
Reference genome
GRCh37.p10
Start
129734404/126972125 (Hg38)
End
129734483/126972204 (Hg38)
Orient
-
Location type
Intronic
Target gene
RALGPS1
miRNAs that regulate target gene
hsa-mir-377-3p ; hsa-mir-342-3p ; hsa-mir-3120-3p ; hsa-mir-8485
Nearest miRNA
hsa-let-7a-1/Upstream/2278327; hsa-mir-12126/Downstream/718483;
Nearest TSS
ENST00000422679/Upstream/9900; ENST00000477700/Downstream/77852;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/56395, chr9-CpG: 161/Downstream/252081
Upstream sequence
TTTAGGCAAAAACAGCAAATGACATATACAGGAAATGATTAGATTACCATCAGTCTTTTTTGACAGAAACATGTTTTTTCCAAAAGGAAATGGAACTACATAATTAAGGAAAGAAAGAAAAAGTGGGGCAATGGGAGCTTCTTCTACCTAGCTCTTGAGTCCGTTTGCCACAAACCCTCCTATTCCTTGACAGCTTCCTCACTCCAAAAGTGTAGGAT
Target sequence
GTGAGGAAGCTGTCAAGGAATAGGAGGGTTTGTGGCAAACGGACTCAAGAGCTAGGTAGAAGAAGCTCCCATTGCCCCA
Junction sequence
TTTAGGCAAAAACAGCAAATGACATATACAGGAAATGATTAGATTACCATCAGTCTTTTTTGACAGAAACATGTTTTTTCCAAAAGGAAATGGAACTACATAATTAAGGAAAGAAAGAAAAAGTGGGGCAATGGGAGCTTCTTCTACCTAGCTCTTGAGTCCGTTTGCCACAAACCCTCCTATTCCTTGACAGCTTCCTCACTCCAAAAGTGTAGGATGCTGCCTAATCATCTCATGTTCATGTCCTACTATTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGAC
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Lau, C. C., et al. Viral-human chimeric transcript predisposes risk to liver cancer development and progression. Cancer Cell ,2014,25(3): 335-349.
Curate