SCARA3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016368
Fusion event
HBV-SCARA3 integration
Validated
No
Detection method
WGS
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2012
PubMed ID
22267523
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Start
1664
End
1699
Orient
-
Integrated sequence
CTCTTGGACTCTCAGCAATGTCAACGACCGACCTTG
Host Sequence
Chromosome
chr8
Cytoband
p21.1
Reference genome
GRCh37/hg19
Start
27525659/27668142 (Hg38)
End
27525694/27668177 (Hg38)
Orient
-
Location type
Intronic
Target gene
SCARA3
miRNAs that regulate target gene
hsa-mir-26b-5p ; hsa-mir-615-3p ; hsa-mir-338-3p ; hsa-mir-4524a-3p ; hsa-mir-4786-5p ; hsa-mir-5683 ; hsa-mir-576-3p ; hsa-mir-6741-5p ; hsa-mir-769-5p
Nearest miRNA
hsa-mir-124-1/Upstream/57391; hsa-mir-10400/Downstream/33496;
Nearest TSS
ENST00000518652/Upstream/33961; ENST00000521510/Downstream/65161;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/33884, chr8-CpG: 54/Downstream/104059
Nearby gene
CLU(-53332) ; MIR3622B(+33530) ;
Upstream sequence
gttcgagaccagtgtgggcaacatggtgaaaacccatctctacaaaaaaaaaaaaaaaaaTTAGATACTGAGAAGAAGAGGGTAAAGAGGGGAAGAAAAG
Downstream sequence
GGAGCTGGAAGGGGCTGGTCGGGAGGAGGGAGAGTTTTTTCTCCTTTGCTGCTGGCACAGAATCCCTTAGAAATCACAGATAgccgggcgcggtggctca
Target sequence
CTAGGGAAAGACTCCCCAGAGCTTTCCGGGAAAGA
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.
Curate