Basic Information
VIS ID
TVIS20003739
Fusion event
HPV-GXYLT1 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
1561
End
1601
Orient
-
Integrated sequence
TTGCGATTGGTGTATTGCTGCATTTGGACTTACACCCAGTA
Host Sequence
Chromosome
chr12
Cytoband
q12
Reference genome
GRCh37/hg19
Start
42486206/42092404 (Hg38)
End
42486206/42092404 (Hg38)
Location type
Intronic
Target gene
GXYLT1
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-124-3p ; hsa-mir-33a-5p ; hsa-mir-99a-5p ; hsa-mir-3180-5p ; hsa-mir-3182 ; hsa-mir-525-5p ; hsa-mir-520a-5p ; hsa-mir-9-3p ; hsa-mir-7162-5p ; hsa-mir-516b-3p ; hsa-mir-2115-5p ; hsa-mir-516a-3p ; hsa-mir-4729 ; hsa-mir-545-5p ; hsa-mir-365b-3p ; hsa-mir-365a-3p ; hsa-mir-320d ; hsa-mir-320c ; hsa-mir-320b ; hsa-mir-4429 ; hsa-mir-320a ; hsa-mir-568 ; hsa-mir-340-5p ; hsa-mir-4756-3p ; hsa-mir-5582-5p ; hsa-mir-4484 ; hsa-mir-6768-3p ; hsa-mir-203a-3p ; hsa-mir-548an ; hsa-mir-6088 ; hsa-mir-4770 ; hsa-mir-143-3p ; hsa-mir-5590-3p ; hsa-mir-142-5p ; hsa-mir-4445-5p ; hsa-mir-508-3p ; hsa-mir-6766-3p ; hsa-mir-548c-3p ; hsa-mir-4782-3p ; hsa-mir-219a-5p ; hsa-mir-7856-5p ; hsa-mir-3658 ; hsa-mir-5701 ; hsa-mir-944 ; hsa-mir-3910 ; hsa-mir-3714 ; hsa-mir-641 ; hsa-mir-3617-5p ; hsa-mir-499a-5p ; hsa-mir-208b-3p ; hsa-mir-208a-3p ; hsa-mir-506-3p ; hsa-mir-885-5p ; hsa-mir-4698 ; hsa-mir-3675-3p ; hsa-mir-4303 ; hsa-mir-4682 ; hsa-mir-32-5p ; hsa-mir-92b-3p ; hsa-mir-92a-3p ; hsa-mir-30e-5p ; hsa-mir-30c-5p ; hsa-mir-30d-5p ; hsa-mir-30b-5p ; hsa-mir-30a-5p ; hsa-mir-193b-3p ; hsa-mir-193a-3p
Nearest miRNA
hsa-mir-1244-3/Upstream/16218325; hsa-let-7i/Downstream/231296;
Nearest TSS
ENST00000382841/Upstream/159812; ENST00000551658/Downstream/52308;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/518731, chr12-CpG: 92/Downstream/51919
Downstream sequence
AGTGATACAGCTTGTTAAGTAACAGCATAAATCCAAACCTCCCCTGGATTTGCCCCAAGTCTTGGTCCTTAACATTCACAGAGATCTGGTTCATGCATCCGCCTAGAG
Junction sequence
CTGGGTGTAAGTCCAAATGCAGCAATACACCAATCGCAACAAGTGATACAGCTTGTTAAGTAACAGCATAAATCCAAACCTCCCCTGGATTTGCCCCAAGTCTTGGTCCTTAACATTCACAGAGATCTGGTTCATGCATCCGCCTAGAG
* 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