Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003820
Fusion event
HPV-RBMS3 integration
Validated
Yes
Fusion type
Insert
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Perfect
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Gene
E1
Start
3216
Integrated sequence
CAGGATG TATAAAAAAACATGGATATACAGTGGAAGTGCAGTTTGATGGAGACATATGCAATACAATGCATTATACA AACTGGACACATATATATATT| |TGTGAAGAAGCATCAGTAACTGTGGTAGAGGGTCAAGTTGACTATTATG GTTTATATTATGTTCATGAAGGAATACGAACATATTTTGTGCAGTTTAAA
Host Sequence
Chromosome
chr3
Cytoband
p24.1
Reference genome
Start
End
29852085/29810594 (Hg38)
Location type
Intron6
Target gene
miRNAs that regulate target gene
hsa-mir-30a-5p ; hsa-mir-16-5p ; hsa-mir-578 ; hsa-mir-526b-5p ; hsa-mir-3190-3p ; hsa-mir-6077 ; hsa-mir-7-5p ; hsa-mir-4282 ; hsa-mir-3674 ; hsa-mir-1238-3p ; hsa-mir-670-3p ; hsa-mir-5706 ; hsa-mir-4782-5p ; hsa-mir-516b-5p ; hsa-mir-1299 ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-4703-3p ; hsa-mir-5093 ; hsa-mir-3182 ; hsa-mir-6128 ; hsa-mir-875-3p ; hsa-mir-877-3p ; hsa-mir-1324
Nearest miRNA
hsa-mir-12127/Upstream/4145655; hsa-let-7g/Downstream/1351110;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/1234115, chr3-CpG: 88/Downstream/795901
Nearby gene
Nearest cancer related gene
RBMS3(TSG, No orient, 0)
Upstream sequence
AAATGAAAAGGAAAATGCCAAAGGAT
Junction sequence
AAATGAAAAGGAAAATGCCAAAGGATAGTCAACTTGACCCTCTACCACAGTTACTGATGCTT
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
Reference
Liu, Y., et al. Genome-wide profiling of the human papillomavirus DNA integration in cervical intraepithelial neoplasia and normal cervical epithelium by HPV capture technology. Sci Rep,2016, 6: 35427.