Basic Information
VIS ID
TVIS20003654
Fusion event
HPV-FHIT integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
Disease
Not given
Quality evaluation
Perfect
Reported year
2015
PubMed ID
25581428
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.2
Start
2858
End
2665
Orient
-
Integrated sequence
GTATGAGCTTAATGATAAGAACTGGAAATCCTTTTTCTCAAGGACGTGGTCCAGATTAAGTTTGCACGAGGACGAGGACAAGGAAAACGATGGAGACTCTTTGCCAACGTTTAAATGTGTGTCAGGACAAAATACTAACACATTATGAAAATGATAGTACAGACCTACGTGACCATATAGACTATTGGAAACAC
Host Sequence
Chromosome
chr3
Cytoband
p14.2
Reference genome
GRCh37/hg19
Start
60580179/60594446 (Hg38)
End
60580179/60594446 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA3B
Target gene
FHIT
miRNAs that regulate target gene
hsa-mir-143-3p ; hsa-mir-217 ; hsa-mir-331-3p ; hsa-mir-625-5p
Nearest miRNA
hsa-let-7g/Upstream/4741852; hsa-mir-12124/Downstream/23359;
Nearest TSS
ENST00000440867/Upstream/513606; ENST00000475527/Downstream/656938;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/1544228, chr3-CpG: 48/Downstream/656486
Nearest cancer related gene
FHIT(TSG, No orient, 0)
Upstream sequence
CACTTTGGAACCAAAGAAAGCATTTTGAGTGTTACTTTTAATGTTTCCAGAAAAGTTAACACCTATAAAAATATTGTTTCCAGTTTTCTGTATAGAAGTCACTGAAGGAGGATGTGTGAAAGTCTGTGGAAACAGTACACTGGCAAACTGCCAGCTGGAATCGCACGGAGCTCTGTTGTAACTCAAATCTGGCCAGGCCGCAAGTCAAAGCATGTCCTAAGAAATATAGTACACACATACAGTGAACACAACCAT
Junction sequence
CACTTTGGAACCAAAGAAAGCATTTTGAGTGTTACTTTTAATGTTTCCAGAAAAGTTAACACCTATAAAAATATTGTTTCCAGTTTTCTGTATAGAAGTCACTGAAGGAGGATGTGTGAAAGTCTGTGGAAACAGTACACTGGCAAACTGCCAGCTGGAATCGCACGGAGCTCTGTTGTAACTCAAATCTGGCCAGGCCGCAAGTCAAAGCATGTCCTAAGAAATATAGTACACACATACAGTGAACACAACCAT
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Hu, Z., et al. Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism. Nat Genet,2015, 47(2): 158-163.
Curate