Basic Information
VIS ID
TVIS30005102
Fusion event
HIV-FBXO42 integration
Validated
No
Detection method
QiaQuick PCR and Sequencing
Data source
download(RID)
Sample type
Cell line
Disease
HIV-infected disease (HID)
Quality evaluation
Normal
Reported year
2013
PubMed ID
23953889
Virus Sequence
Virus name
HIV
Reference genome
Not given
Host Sequence
Chromosome
chr1
Cytoband
p36.13
Reference genome
GRCh37/hg19
Start
16668253/16341758 (Hg38)
End
16668253/16341758 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA1A
Target gene
FBXO42
miRNAs that regulate target gene
hsa-mir-186-5p ; hsa-mir-1281 ; hsa-mir-6881-3p ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-627-3p ; hsa-mir-877-3p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p
Nearest miRNA
hsa-mir-12136/Upstream/3762735; hsa-mir-101-1/Downstream/517191;
Nearest TSS
ENST00000473358/Upstream/26391; ENST00000475078/Downstream/10696;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/104454, chr1-CpG: 52/Downstream/10321
Upstream sequence
CCCTACTATTTGATATTCTTAAAAGTTCTGggccgggtgcggtggctcatgcctgtaatcccagcgctttggtaggccaaggcgggcggatcacctgagg
Downstream sequence
tcaggagttcgagaccaacctgaccaacatggagaaaaccccgtctctactaaaaatacaaaattagccaggcatagtggcgtctgcctgtaatcccagc
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
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