FN1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10014939
Fusion event
HBV-FN1 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2012
PubMed ID
22634754
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Region type
HBVgp1 Polymerase
Start
1211
End
1315
Orient
-
Integrated sequence
GGCTTGGTCATGGGCCATCAGCGCATGCGTGGAACCTTTTCGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCCGCTTGTTTTGCTCGCAGCAGGTCTGGA
Host Sequence
Chromosome
chr2
Cytoband
q35
Reference genome
GRCh37/hg19
Start
216294237/215429514 (Hg38)
End
216294353/215429630 (Hg38)
Orient
+
Location type
Intronic
Target gene
FN1
miRNAs that regulate target gene
hsa-mir-200c-3p ; hsa-mir-200b-3p ; hsa-mir-1-3p ; hsa-let-7g-5p ; hsa-mir-26b-5p ; hsa-mir-615-3p ; hsa-mir-218-5p ; hsa-mir-140-3p
Nearest miRNA
hsa-mir-10b/Upstream/1671355; hsa-mir-1244-1/Downstream/2470883;
Nearest TSS
ENST00000437798/Upstream/8244; ENST00000412951/Downstream/6437;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/117105, chr2-CpG: 43/Downstream/5914
Upstream sequence
TGAGTATAGAGGATCTGATGTCTTTGTGAATTGGATATTGTTGCAACTCCTGGGTTAGAGAAAAAAAATTAATAGTTGATGTAGGTTCAAACAAATACAC
Downstream sequence
actttcagtatttctgttgaaatctttaatactgtgttttgcagatgataaatatgtataagactttctcatctccctgaccccctaagtactctttgaa
Target sequence
ACCCACATCCATCTACCACAAGAATAGAAGTTTGCATGAAGGTATAATTACTGATTAGAGCTTTttcccaaatccccagcgaaaagtattatcatcccctgaacctccatagcact
Reference
Sung, W. K., et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet,2012, 44(7): 765-769.
Curate