Basic Information
VIS ID
TVIS20002854
Fusion event
HPV-SHROOM4 integration
Validated
No
Detection method
HIVID
Data source
Curated
Sample type
Tumor
Disease
Squamous-cell carcinoma (SCC)
Quality evaluation
Normal
Reported year
2015
PubMed ID
25581428
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.2
Host Sequence
Chromosome
chrX
Cytoband
p11.22
Reference genome
GRCh37/hg19
Start
50551313/50808313 (Hg38)
End
50551313/50808313 (Hg38)
Location type
Intronic
Target gene
SHROOM4
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-5096 ; hsa-mir-4662a-5p ; hsa-mir-3152-3p ; hsa-mir-6832-5p ; hsa-mir-296-3p ; hsa-mir-2392 ; hsa-mir-4676-5p ; hsa-mir-575 ; hsa-mir-6858-3p ; hsa-mir-6778-3p ; hsa-mir-4661-5p ; hsa-mir-122-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-4722-3p ; hsa-mir-6727-3p ; hsa-mir-6747-3p ; hsa-mir-6783-3p ; hsa-mir-1343-3p ; hsa-mir-23b-5p ; hsa-mir-23a-5p ; hsa-mir-6742-3p ; hsa-mir-6852-5p ; hsa-mir-939-3p ; hsa-mir-660-3p ; hsa-mir-4279 ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-6891-3p ; hsa-mir-6072 ; hsa-mir-5196-3p ; hsa-mir-6729-3p ; hsa-mir-1306-5p
Nearest miRNA
hsa-mir-1587/Upstream/793630; hsa-let-7f-2/Downstream/1528244;
Nearest TSS
ENST00000429181/Upstream/112376; ENST00000252677/Downstream/5731;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/337329, chrX-CpG: 65/Downstream/4946
Upstream sequence
cccgcctctaccaaaaatacacaaaaaattagccaggtgtggtggcaggtgcctgtagtcccagctacttgggaggctgaggcaggagaatcacttgaac
Downstream sequence
aacagaatggataggcttagaagggaatgagctcccctgtgactactgtagaacaagctcagggacactgcacaggaggctcatgaaatggttaagatta
Reference
Hu, Z., et al. Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism. Nat Genet,2015, 47(2): 158-163.
Curate