Basic Information
VIS ID
TVIS30002301
Fusion event
HIV-RTF1 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
chr15
Cytoband
q15.1
Reference genome
GRCh37/hg19
Start
41732108/41439910 (Hg38)
End
41732108/41439910 (Hg38)
Orient
-
Location type
Intronic
Target gene
RTF1
miRNAs that regulate target gene
hsa-mir-26b-5p ; hsa-mir-196b-5p ; hsa-mir-26a-5p ; hsa-mir-5096 ; hsa-mir-6855-5p ; hsa-mir-3170 ; hsa-mir-411-5p ; hsa-mir-3152-3p ; hsa-mir-6832-5p ; hsa-mir-193b-5p ; hsa-mir-509-3p ; hsa-mir-1273f ; hsa-mir-10b-3p ; hsa-mir-6890-5p ; hsa-mir-6812-3p ; hsa-mir-4639-3p ; hsa-mir-4789-3p ; hsa-mir-466 ; hsa-mir-4672 ; hsa-mir-3941
Nearest miRNA
hsa-mir-1233-1/Upstream/4467009; hsa-mir-10393/Downstream/251675;
Nearest TSS
ENST00000557528/Upstream/22778; ENST00000473214/Downstream/34677;
Nearest CpG islands
None/Target, chr15-CpG: 55/Upstream/22157, chr15-CpG: 58/Downstream/46285
Upstream sequence
ccggctgatttttgtatttttagtggagacagggttttgccacgttcgccaggctggtctcaaacttccgacctcagatgatccacctgccttggcctcc
Downstream sequence
caaactgctgagattacaggcatgagccattgcacccagccTTTCATTTGATTTAAAGTATTTTCTTCCCCTTAGTAATTACTTGCAGAGAAGCCGGATA
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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