Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004624
Fusion event
HPV-C6orf89 integration
Validated
Yes
Detection method
FISH, WGS, RNA-seq, qPCR
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Gene
L2
Start
4970
End
5109
Integrated sequence
CCCACTAAACTTATTACATATGATAATCCTGCATATGAAGGTATAGATGTGGATAATACATTATATTTTTCTAGTAATGATAATAGTATTAATATAGCTCCAGATCCTGACTTTTTGGATATAGTTGCTTTACATAGGCC
Host Sequence
Chromosome
chr6
Cytoband
p21.2
Reference genome
Start
End
36878572/36910817 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-mir-3918 ; hsa-mir-4685-5p ; hsa-mir-6837-5p ; hsa-mir-6895-5p ; hsa-mir-7106-3p ; hsa-mir-6741-5p ; hsa-mir-4662a-5p ; hsa-mir-5580-5p ; hsa-mir-6868-5p ; hsa-mir-1245b-3p ; hsa-mir-5096 ; hsa-mir-6855-5p ; hsa-mir-3170 ; hsa-mir-3187-3p ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-6802-3p ; hsa-mir-411-5p ; hsa-mir-6832-5p ; hsa-mir-193b-5p ; hsa-mir-1273f ; hsa-mir-3620-3p ; hsa-mir-6865-3p ; hsa-mir-6890-5p ; hsa-mir-10b-5p ; hsa-mir-10a-5p ; hsa-mir-7113-5p
Nearest miRNA
hsa-mir-1236/Upstream/288284; hsa-mir-10398/Downstream/644548;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/24645, chr6-CpG: 35/Downstream/48335
Target sequence
gggattacaagcatcagccac
Junction sequence
GTGGCTGATGCTTGTAATCCCAGCTAAACTTATTACATATGATAATCCTGCATATGAAGGTATAGATGTGGATAATACATTATATTTTCCTAGTAATGATAATAGTATTAATATAGCTCCAGATCCTGACTTTTTGGATATAGTTGCTTTACATAGGCAGGTAGCCtctgcaggtgttggaggctgcaatacagatgggtcagtgaaagtgggattattatgtgtaa
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
Reference
Akagi, K., et al.Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. Genome Res ,2014,24(2): 185-199.