Basic Information
VIS ID
TVIS20003769
Fusion event
HPV-RTN4RL1 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
3129
End
3052
Orient
-
Integrated sequence
AAGTGTATTTAACTGCACCAACAGGATGTATAAAAAAACATGGATATACAGTGGAAGTGCAGTTTGATGGAGACATAT
Host Sequence
Chromosome
chr17
Cytoband
p13.3
Reference genome
GRCh37/hg19
Start
1884090/1980796 (Hg38)
End
1884090/1980796 (Hg38)
Location type
Intronic
Target gene
RTN4RL1
miRNAs that regulate target gene
hsa-mir-6831-5p ; hsa-mir-1277-5p ; hsa-mir-190a-3p ; hsa-mir-4732-5p ; hsa-mir-6832-5p ; hsa-mir-574-5p ; hsa-mir-3668 ; hsa-mir-7852-3p ; hsa-mir-5011-5p ; hsa-mir-5586-3p ; hsa-mir-5010-3p ; hsa-mir-223-5p ; hsa-mir-1257
Nearest miRNA
hsa-mir-22/Upstream/266809; hsa-mir-10226/Downstream/69112;
Nearest TSS
ENST00000595228/Upstream/89146; ENST00000574520/Downstream/14818;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/42881, chr17-CpG: 120/Downstream/17036
Downstream sequence
AGGCTAACCCACCACACTCGGCTGTTTTTGTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGCCAGGCTGGTCTTGAAC
Junction sequence
ATGTCTCCATCAAACTGCACTTCCACTGTATATCCATGTTTTTTTATACATCCTGTTGGTGCAGGTAAATACACTTCAAGGCTAACCCACCACACTCGGCTGTTTTTGTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGCCAGGCTGGTCTTGAAC
* 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