Basic Information
VIS ID
TVIS20003778
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
2955
End
2981
Orient
+
Integrated sequence
AAAGCATTACAAGCAATTGAACTGCAA
Host Sequence
Chromosome
chr1
Cytoband
p13.2
Reference genome
GRCh37/hg19
Start
115257404/114714783 (Hg38)
End
115257404/114714783 (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/1832654; hsa-mir-1182/Downstream/1845241;
Nearest TSS
ENST00000473358/Upstream/19165; ENST00000468191/Downstream/2111;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/44419, chr1-CpG: 35/Downstream/65671
Upstream sequence
AGAAACGCAAAAAGCACTGGGCTGTAGACATAAAATTTATGTATTTTACTTATGTAAATTGCTCAATAAAT
Junction sequence
AGAAACGCAAAAAGCACTGGGCTGTAGACATAAAATTTATGTATTTTACTTATGTAAATTGCTCAATAAATGTTTAATGATAAAGCATTACAAGCAATTGAACTGC
* 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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