Basic Information
VIS ID
TVIS30009238
Fusion event
HIV-USP42 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
chr7
Cytoband
p22.1
Reference genome
GRCh37/hg19
Start
6155708/6116077 (Hg38)
End
6155708/6116077 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA7B
Target gene
USP42
miRNAs that regulate target gene
hsa-mir-103a-3p ; hsa-mir-16-5p ; hsa-mir-320a ; hsa-mir-15a-5p ; hsa-mir-107 ; hsa-mir-15b-5p ; hsa-mir-143-3p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-497-5p ; hsa-mir-627-5p ; hsa-mir-4310 ; hsa-mir-3607-3p ; hsa-mir-3686 ; hsa-mir-4503 ; hsa-mir-4708-5p ; hsa-mir-4770 ; hsa-mir-1273f ; hsa-mir-6088 ; hsa-mir-6792-5p ; hsa-mir-6838-5p ; hsa-mir-7157-5p ; hsa-mir-4482-3p ; hsa-mir-924 ; hsa-mir-26a-2-3p ; hsa-mir-26a-1-3p ; hsa-mir-6731-3p
Nearest miRNA
hsa-mir-339/Upstream/404167; hsa-mir-10399/Downstream/950887;
Nearest TSS
ENST00000635602/Upstream/11055; ENST00000426246/Downstream/403;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/10389, chr7-CpG: 123/Downstream/37705
Upstream sequence
ctctagtcccagcatactcaggagggtgagacaggaaggtcacctgagtctggaaggttgagactgcagtgagctgtgatcgcactgctgtacttcagcc
Downstream sequence
tagacaacagaaagagaccctgtctcaaaaaaaaaaaaaaaaaaCGTCTGATGCCAGCAACTTGGGACAGGCGAGGTTAAGAAATCCTGCCTCTCCTGGC
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate