Basic Information
VIS ID
TVIS20003675
Fusion event
HPV-LRP1B 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
1743
End
2703
Orient
-
Integrated sequence
TGTCTAAACTATTATGTGTGTCTCCAATGTGTATGATGATAGAGCCTCCAAAATTGCGTAGTACAGCAGCAGCATTATATTGGTATAAAACAGGTATATCAAATATTAGTGAAGTGTATGGAGACACGCCAGAATGGATACAAAGACAAACAGTATTACAACATAGTTTTAATGATTGTACATTTGAATTATCACAGATGGTACAATGGGCCTACGATAATGACATAGTAGACGATAGTGAAATTGCATATAAAT
Host Sequence
Chromosome
chr2
Cytoband
q22.2
Reference genome
GRCh37/hg19
Start
142277662/141520093 (Hg38)
End
142277662/141520093 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA2S
Target gene
LRP1B
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-26b-5p ; hsa-mir-200c-3p ; hsa-mir-106b-3p ; hsa-mir-5692a
Nearest miRNA
hsa-mir-128-1/Upstream/933408; hsa-mir-10b/Downstream/7810185;
Nearest TSS
ENST00000437798/Upstream/1162025; ENST00000410015/Downstream/290308;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/2739013, chr2-CpG: 58/Downstream/610062
Nearest cancer related gene
LRP1B(TSG, No orient, 0)
Upstream sequence
CCAGACTGAAAGAGCCATGAATGAACTTTTTGTCTGACACCAAATGCACCAGTTTCTTTATTTTCCTT
Junction sequence
CCAGACTGAAAGAGCCATGAATGAACTTTTTGTCTGACACCAAATGCACCAGTTTCTTTATTTTCCTTGTCCTCGTCCTCGTGCAAACTTAATCTGGACCACGTCCTTGAG
* 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.
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