Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004224
Fusion event
HPV-GTF2IRD1 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Perfect
Reported year
2019
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV18
Reference genome
Not given
Gene
E1
Start
1459
End
1561
Host Sequence
Chromosome
chr7
Cytoband
q11.23
Reference genome
Start
End
74525503/74525503 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
Nearest miRNA
hsa-mir-1183/Upstream/334334; hsa-mir-10399/Downstream/70465;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/44848, chr7-CpG: 40/Downstream/80972
Downstream sequence
GCATGCCACCATGCCACGCCCAGTTAATTTTTGTATTTTTGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCTCGAGCTCAAGTGATTCACCTGCCTCGGCCTCCCAAAGTGCA
Target sequence
cactttgggaggccgaggcaggtgaatcacttgagctcgagagttcgagaccagcctggccaacatggtgaaaccccgtctctacaaaaatacaaaaattaactgggcgtggcatggtggcatgc
Junction sequence
TACAAGTGACAATAGCAATATAGAAAATGTAAATCCACAATGTACCATAGCACAATTAAAAGACTTGTTAAAAGTAAACAATAAACAAGGAGCTATGTTAGCATGCCACCATGCCACGCCCAGTTAATTTTTGTATTTTTGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCTCGAGCTCAAGTGATTCACCTGCCTCGGCCTCCCAAAGTGCA
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
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.