Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004213
Fusion event
HPV-ARHGAP42 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
HPV16
Reference genome
Not given
Gene
L1
Start
5762
Host Sequence
Chromosome
chr11
Cytoband
q22.1
Reference genome
End
100771699/100771699 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-221-3p ; hsa-mir-28-5p ; hsa-mir-222-3p ; hsa-mir-138-5p ; hsa-mir-376c-3p ; hsa-mir-708-5p ; hsa-mir-3139 ; hsa-mir-4299 ; hsa-mir-3692-5p ; hsa-mir-4633-3p ; hsa-mir-6071 ; hsa-mir-6500-5p ; hsa-mir-587 ; hsa-mir-6131 ; hsa-mir-3185 ; hsa-mir-133a-5p ; hsa-mir-93-3p ; hsa-mir-885-5p ; hsa-mir-6891-5p ; hsa-mir-3173-3p ; hsa-mir-4428 ; hsa-mir-4511
Nearest miRNA
hsa-mir-10392/Upstream/4430173; hsa-let-7a-2/Downstream/748121;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/84029, chr11-CpG: 170/Downstream/355600
Upstream sequence
ggaatttttttttttttgagacagagtcttgctctgtcgcccaggctggagtgcagtggcacgatctcggctcactgcaccctccgcttcccatgttcaa
Downstream sequence
gcaattctcctgcctcagcctcccaagtagatgggactacaggcacccgccaccatgcctggctaatttttttttgtacttttagtagagacggggtttc
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.