Basic Information
VIS ID
TVIS20003773
Fusion event
HPV-CSDE1 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
2746
End
2842
Orient
+
Integrated sequence
GGAAAACGATGGAGACTCTTTGCCAACGTTTAAATGTGTGTCAGGACAAAATACTAACACATTATGAAAATGATAGTACAGACCTACGTGACCATAT
Host Sequence
Chromosome
chr1
Cytoband
p13.2
Reference genome
GRCh37/hg19
Start
115257345/114714724 (Hg38)
End
115257345/114714724 (Hg38)
Location type
Intronic
Target gene
CSDE1
miRNAs that regulate target gene
hsa-mir-340-5p ; hsa-mir-16-5p ; hsa-mir-1229-3p ; hsa-mir-1226-3p ; hsa-mir-423-5p ; hsa-mir-92b-3p ; hsa-mir-326 ; hsa-mir-320a ; hsa-mir-23b-3p ; hsa-mir-204-5p ; hsa-mir-30c-5p ; hsa-mir-92a-3p ; hsa-mir-23a-3p ; hsa-mir-298 ; hsa-mir-1202 ; hsa-mir-1252-3p ; hsa-mir-3646 ; hsa-mir-3972 ; hsa-mir-543 ; hsa-mir-412-3p ; hsa-mir-409-3p ; hsa-mir-376a-5p ; hsa-mir-432-5p ; hsa-mir-6124 ; hsa-mir-891b ; hsa-mir-651-3p ; hsa-mir-186-5p ; hsa-mir-3143 ; hsa-mir-542-3p ; hsa-mir-4504 ; hsa-mir-190b ; hsa-mir-190a-5p ; hsa-mir-5006-5p ; hsa-mir-4451 ; hsa-mir-548ax ; hsa-mir-548ao-5p ; hsa-mir-493-3p ; hsa-mir-410-3p ; hsa-mir-6831-5p ; hsa-mir-3927-3p ; hsa-mir-519c-3p ; hsa-mir-519b-3p ; hsa-mir-519a-3p ; hsa-mir-93-5p ; hsa-mir-526b-3p ; hsa-mir-519d-3p ; hsa-mir-20b-5p ; hsa-mir-20a-5p ; hsa-mir-17-5p ; hsa-mir-106b-5p ; hsa-mir-106a-5p ; hsa-mir-548t-5p ; hsa-mir-548az-5p ; hsa-mir-3180-5p ; hsa-mir-2054 ; hsa-mir-525-5p ; hsa-mir-520a-5p ; hsa-mir-7158-5p ; hsa-mir-488-5p ; hsa-mir-6826-5p ; hsa-mir-7705 ; hsa-mir-6854-5p ; hsa-mir-7978 ; hsa-mir-195-5p ; hsa-mir-15b-5p ; hsa-mir-15a-5p
Nearest miRNA
hsa-mir-101-1/Upstream/1832595; hsa-mir-1182/Downstream/1845300;
Nearest TSS
ENST00000473358/Upstream/19106; ENST00000468191/Downstream/2170;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/44360, chr1-CpG: 35/Downstream/65730
Upstream sequence
TCACACTTGGAGAACTCTCTGGAGTACTGGAAGTGCTCTATACTGTTATCTGGGTGGTAGCTACATGACTATATAGAAACGCAAAA
Junction sequence
TCACACTTGGAGAACTCTCTGGAGTACTGGAAGTGCTCTATACTGTTATCTGGGTGGTAGCTACATGACTATATAGAAACGCAAAAGGAAAACGATGGAGACTCTTTGCCAACGTTTAAATGTGTGTCAGGACAAAATTCTATCACATTATGAAAATGATAGTGCAACCCTACGTGACCAT
* 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