Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004227
Fusion event
HPV-RBBP8 integration
Validated
No
Detection method
TaME-seq
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Normal
Reported year
2019
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV45
Reference genome
Not given
Gene
L1
Start
7120
Host Sequence
Chromosome
chr18
Cytoband
q11.2
Reference genome
Start
End
23021388/23021388 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-375 ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-4459 ; hsa-mir-6516-5p ; hsa-mir-550b-2-5p ; hsa-mir-455-3p ; hsa-mir-1227-3p ; hsa-mir-25-5p ; hsa-mir-658 ; hsa-mir-6499-3p ; hsa-mir-4765 ; hsa-mir-1236-5p ; hsa-mir-6086 ; hsa-mir-377-5p ; hsa-mir-6087 ; hsa-mir-5186 ; hsa-mir-1247-3p ; hsa-mir-3174 ; hsa-mir-1273e
Nearest miRNA
hsa-mir-1-2/Upstream/87950; hsa-mir-122/Downstream/1300287;
Nearest CpG islands
None/Target, chr18-CpG: 67/Upstream/87494, chr18-CpG: 228/Downstream/113616
Nearest cancer related gene
RBBP8(TSG, No orient, 0)
Upstream sequence
cctatagtcccagctacttgggaagctgaggcaagagaatcacttgaacacaggagtgggaggttgcagtgagccaagatcgtgccactgcaccccagcc
Downstream sequence
tgggtgacagagcaggactctgtctctcaaaaaaaaaGTGATTCTGTCATCTATGTTCTATTAAACCTTAAACTACTGCTTTGTTTTCACTAAGTCTAGG
Reference
Lagstrom, S., et al. TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Sci Rep ,2019,9(1): 524.