hsa-mir-3143 _LIHC.png
FNDC3A _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004886
Fusion event
HBV-FNDC3A 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
1789
Orient
+
Integrated sequence
CCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCA| |TAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGT
Host Sequence
Chromosome
chr13
Cytoband
q14.2
Reference genome
GRCh37/hg19
Start
49725093/49150957 (Hg38)
End
49725093/49150957 (Hg38)
Orient
-
Location type
Intron
Target gene
FNDC3A
miRNAs that regulate target gene
hsa-let-7b-5p ; hsa-mir-1-3p ; hsa-mir-98-5p ; hsa-mir-877-3p ; hsa-let-7a-5p ; hsa-let-7c-5p ; hsa-let-7d-5p ; hsa-let-7e-5p ; hsa-let-7f-5p ; hsa-let-7g-5p ; hsa-let-7i-5p ; hsa-mir-4458 ; hsa-mir-4500 ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-573 ; hsa-mir-646 ; hsa-mir-3616-5p ; hsa-mir-4635 ; hsa-mir-4670-3p ; hsa-mir-101-3p ; hsa-mir-144-3p ; hsa-let-7a-2-3p ; hsa-let-7g-3p ; hsa-mir-142-3p ; hsa-mir-206 ; hsa-mir-561-3p ; hsa-mir-551b-5p ; hsa-mir-613 ; hsa-mir-1303 ; hsa-mir-544a ; hsa-mir-7850-5p ; hsa-mir-6505-5p ; hsa-mir-202-3p ; hsa-mir-323a-3p ; hsa-mir-4668-3p ; hsa-mir-302c-5p ; hsa-mir-513a-5p ; hsa-mir-3143 ; hsa-mir-3160-5p ; hsa-mir-4711-5p ; hsa-mir-302d-5p ; hsa-mir-302b-5p ; hsa-mir-499b-5p ; hsa-mir-4494 ; hsa-mir-543 ; hsa-mir-27a-3p ; hsa-mir-27b-3p ; hsa-mir-1305 ; hsa-mir-498 ; hsa-mir-129-5p
Nearest miRNA
hsa-mir-2276/Upstream/4954757; hsa-mir-1267/Downstream/845458;
Nearest TSS
ENST00000623511/Upstream/40644; ENST00000497644/Downstream/47253;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/174051, chr13-CpG: 150/Downstream/69293
Upstream sequence
tcgcttgaacctgggagacagaggttgcagtgagccaagatggcaccactgcactccatcctggcaacccagcaagactccgtctcaaaaaaaaaaaaaa
Downstream sequence
aaaaaaattgttgagacctgtattgtgtactgacatatggtctaccctaaagaatgtttcatgtttcatgtgttgtaaagaagaatgtgttttctgtagc
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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